Research Groups at UPSC
Benedicte Riber Albrectsen - Populus Resistance to Biotic Stress
Plants have evolved numerous ways to escape damage by antagonists. With changing growing conditions, mainly caused by invasive species and effects of global warming, our forests may be increasingly challenged by biotic stresses.
I am interested in all aspects of plant resistance that may help us understand how the risk of biotic stress may be reduced, including chemical and mechanical defence traits, tolerance, phenology displacement and ecological interactions that rescue plants from attack by antagonists. Currently, in my lab, we concentrate on studies of Populus sp. from four points of view.
Trait association studies and large scale patterns in Populus We relate a number of phenotypic traits measured on Populus tremula genotypes in the field to assess heritability and resistance to herbivores and pathogens. The biobanks SwAsp (116 clones) and UmeAsp (450 clones) are important for these studies. Since 2004, damage to the SwAsp collection has been followed in the field in a G by E setup. We ask if geographical origin matters for resistance properties in clones. Extreme clones (with intensive growth, early bud set, heavy damage by certain antagonists etc.) have been identified for later experimentation in bioassay and plant response studies in the laboratory.Chemical profiling
We characterise secondary and primary metabolites in Populus leaves from the SwAsp biobank to determine palatability to insect herbivores and susceptibility to pathogens. We are interested in how genotypes may change under different environmental stresses and we ask how this plasticity and ability to acclimate may affect susceptibility to antagonists. We particularly focus on the phenylpropanoid pathway. For these traits too, we search for extreme clone behaviour (for example, high levels of certain phenolics, sugars or amino acids) and relate them to association studies in the field.Studies on induced responses in aspen
We challenge extreme clones by introducing antagonists in whole plant assays or on detached leaves. We have mainly worked with the aphid Quitophorous populetii, the beetle Phratora vitellinae, simulated damage and the disease Melampsora magnusiana. The aim with these studies is to compare clone-specific responses in the metabolome to different types of damage, to test theories about clone and antagonist-specific induction in Populus.
Bioassays with bioagents
|Some typical arthropods encountered in our common gardens: 1. Harmandia tremula a leaf-galling mite, 2. Bycticus sp. a leaf rolling weevil, 3. Chrysomela populi a leaf beetle that oviposits and chews on leaves, 4. Phyllocnistis labyrintella a leaf mining butterfly.
Primary and secondary chemical compounds are extracted from aspen leaves to assess their value as feeding attractants and repellents. We use simple colorimetric analyses as well as advanced mass spectrometric separation techniques to study compounds of interest.
We have cultured the leaf beetle Phratora vitellinae and three aphid species of the Quitophorous genus to perform bioassays in the lab. We use choice and no-choice tests to describe preferences and performance of the insects when fed on extreme genotypes.Svensk sammanfattning...
Albrectsen BR, Björkén L, Varad A, Hagner Å, Wedin M, Karlsson J and Jansson S
Endophytic fungi in european Aspen (Populus tremula) leaves – diversity, detection, and a suggested correlation with herbivory resistance. Fungal Diversity.Albrectsen BR, Witzell J, Robinson K, Wulff S, Luquez VMC, Ågren R and Jansson S
(2009) Large scale geographic clines of parasite damage to Populus tremula L. Ecography.Crutsinger G, Sanders NJ, Albrectsen BR, Abreu IN and Wardle DA
(2008) Ecosystem retrogression leads to increased insect abundance and herbivory across an island chrono sequence. Functional Ecology.Luquez Virginia, Hall D, Albrectsen BR, Karlsson J, Ingvarsson P and Jansson S
(2008) Natural phenological variation in aspen (Populus tremula): the SwAsp collection. Tree Genetics & Genomes.Albrectsen BR, Guiterrez L, Fritz RS, Fritz RD, Orians CM
(2007) Does the differential seedling mortality caused by slugs alter the foliar traits and subsequent susceptibility of hybrid willows to a generalist herbivore? Ecological Entomology.Fritz Robert S, Hochwender CG, Albrectsen BR, Czesak ME
(2006) Fitness and genetic architecture of parent and hybrid willows in common gardens. Evolution 60 (6): 1215-1227.Expand List of publications...
Lazlo Bakó - Control of Plant Cell Division and Differentiation
The aim of the project is to understand the molecular mechanism that drives and controls the switch between cell division and differentiation in plant cells. Due to its multiple repression activities the retinoblastoma related protein, RBR, is a crucial regulator of cell division and in mammals the corresponding protein pRB coordinates proliferation and cellular differentiation. Whether the RBR protein has a similar role in plant cell differentiation and the E2F/RBR pathway mediate the switch between cell division and differentiation is not yet known. We address these questions by studying the initiation of lateral root formation.
Unlike most plant organs, lateral roots do not originate from meristems but from an already differentiated tissue, the pericycle. Pericycle cells that will form a new lateral root first dedifferentiate and regain cell division activity then later differentiate into distinct cell types. The plant hormone auxin plays a key role in this process. Pericycle cells are believed to be in the G1 phase of the cell cycle until local auxin accumulation triggers them to proceed with the G1-S transition and start the cell division cycle, thereby initiating growth of a new lateral root. Treatment of Arabidopsis seedlings with the synthetic auxin 1-naphtylacetic acid (NAA) results in nearly synchronous initiation and growth of lateral roots. Conversely, while another synthetic auxin, 2,4-Dichlorophenoxyacetic acid (2,4-D), triggers cell division and primordium formation, further lateral root develop- ment is inhibited. To investigate the underlying molecular mechanisms by which theses auxins act, we studied the auxin response of the Arabidopsis retinoblastoma related protein.
We have shown that auxin-induced lateral root initiation is accompanied by a substantial increase of RBR protein level in the root. Arabidopsis plants expressing RBR fused to the Red Fluorescent Protein also indicates strong induction of RBR protein abundance in the root by exogenous auxin treatments. In 2,4-D treated roots the accumulated RBR was found in complex with transcription factors E2FA/B. By contrast, neither free E2F factors nor RBR/E2F complexes could be detected in roots treated with NAA. Further analysis of RBR status in root exposed to NAA indicated chromatin association of RBR, suggesting that repressor function of RBR independent from E2F interactions might be required. These results imply that the newly synthesized RBR protein plays auxin dependent and distinct roles.
One possibility is that auxin-induced emergence of dividing cells needs more regulator function i.e. higher RBR protein level to maintain proper cell division control. This seems to be the case when lateral roots are induced by 2,4-D. However, the lack of E2F binding and chromatin association suggests that a different regulatory mechanism acts when laterals are induced by NAA.
|Expression of RBR-RFP fusion protein in Arabidopsis root after treatment with 2,4-D (left) or NAA (right).
The Arabidopsis RBR protein interacts with histone deacetylases and polycomb group proteins (e.g. FIE) as well as binding a set of MSI proteins of the WD-40 group to form multiprotein complexes that repress gene transcription. Such repressor complexes are implicated in the regulation of seed development, flowering time, vernalization responses and possibly in other developmental processes that require rapid reprogramming of gene expression patterns. Whether RBR has similar role during lateral root formation is not yet known. We examined the sequence of proteins with known function in lateral root formation and found that some of them contain RBR interaction motif. This suggests that RBR might form distinct chromatin remodeling complexes that modify gene expression during different stages of lateral root formation. We will test this model by co-immunoprecipitation assays to confirm predicted in- teractions. By applying ChIP-chip/ChIP-seq technologies, our further aim is to identify genomic regions repressed by distinct complexes and establish relationships between subunit structure, gene expression pattern and distinct stages of lateral root formation.Svensk sammanfattning...
Bakó L, Umeda M, Tiburcio AF, Schell J and Koncz, C.
(2003) The VirD2 pilot protein of Agrobacterium-transferred DNA interacts with the TATA box-binding protein and a nuclear protein kinase in plants. Proc. Natl. Acad. Sci. USA. 100:10108-10113.Espinoza-Ruiz A, Saxena S, Schmidt J, Mellerowitz E, Miskolczi P, Bakó L, and Bhalerao R.P.
(2004) Differential stage-specific regulation of cyclin-dependent kinases during cambial dormancy in hybrid aspen. Plant Journal 38:603-615.Fülöp K, Pettkó-Szandtner A, Magyar Z, Miskolczi P, Kondorosi E, Dudits D, Bakó L
(2005) The Medicago CDKC;1-CYCLINT;1 kinase complex phosphorylates the carboxy-terminal domain of RNA polymerase II and promotes transcription. Plant Journal 42: 810-820.Magyar Z, De Veylder L, Atanassova A, Bakó L, Inzé D, Bögre L
(2005) The Role of the Arabidopsis E2FB Transcription Fac- tor in Regulating Auxin-Dependent Cell Division. The Plant Cell 17:2527-2542.Horváth BM, Magyar M, Zhang Y, Hamburger AW, Bakó L, Visser RGF, Bachem CWB and Bögre L.
(2006) EBP1 regulates organ size through cell growth and proliferation in plants. The EMBO Journal 25: 4909–4920.Expand Publications list
Catherine Bellini - Control of Adventitious Root Initiation and Phloem Function
My group is conducting research in two different areas using the plant model system Arabidopsis thaliana. The first project is tackling the regulation of adventitious root initiation, which is a key limiting step during vegetative propagation of economically important tree species. Nothing is known about the molecular mechanisms involved and a better understanding will allow the optimization of conditions for vegetative propagation. The second project is aimed at understanding the function of genes expressed in the phloem, the vascular compartment involved in the distribution of photosynthetic products produced in the leaves.
Since malfunction of the phloem has a considerable impact on crop yield, production of biomass, fruits, seeds, and on wood development, it is important to get better insights into the regulatory mechanisms involved in phloem function.
Control of adventitious root initiation
Poplar in vitro propagation. Top left: microcutting in vitro. Bottom left: microcutting unable to develop adventitious roots and make a callus instead. Top right: the microcutting developed proper adventitious roots that will allow future transfer to soil (bottom right).
The root system of a plant is composed of the primary, lateral and adventitious roots. Lateral roots always develop from roots, whereas adventitious roots form from stem or leaf-derived cells. Many species, including strawberries and blackberries, mainly propagate vegetatively from stolons or stems from which adventitious roots regenerate to anchor the new plants to the ground. The adventitious rooting process is also crucial for the propagation of valuable plants or plants for which final yield, whether fruit or dry matter, is influenced by the proper development of adventitious roots, such as maize, wheat or rice.
Over the years, cloning has become an intrinsic step in breeding programmes for the production and propagation of elite genotypes of horticultural and woody species. It is used extensively by horticultural and forest industries, which can lose millions of dollars every year because of difficult-to-root genotypes.
In the last few years we have identified, through the characterization of Arabidopsis mutants altered in their aptitude to produce adventitious roots, several genes that control adventitious root initiation. Some of these genes are supposed to act in the crosstalk of the phytohormone auxin and light signalling pathways. Ongoing experiments aim to better understand the respective contribution of these genes in the control of adventitious rooting. We also expect to understand how auxin and light interact in this developmental process. In addition, poplar orthologues have been identified and transgenic poplar plants altered in their expression could be produced to check their role in adventitious rooting in a tree species. In the future, we expect our results to help in the development of new methods for rooting of difficult-to-root genotypes.Functional characterisation of phloem expressed genes
The complexity of phloem functions at different structural and physiological levels has begun to be recognized. Nevertheless, despite playing key roles in plant life and adaptation, genes controlling phloem differentiation and its functions are poorly known. Recently, analysis of phloem-enriched fractions of plant tissues hasve enabled the establishment of libraries of genes preferentially expressed in the phloem and potentially involved in specific functions. We address the mechanisms controlling phloem functions through a functional genomic approach. From several available transcriptome databases, we selected genes showing high expression in the phloem compartment, encoding transcription factors or membrane proteins. Through an integrative approach combining modern genetics, molecular biology and cell biology, we are now gaining further insights into their role in regulating phloem functioning.Svensk sammanfattning
Barlier I, Kovalczyk M, Marchant A, Ljung K, Bhalearo RP, Bennett M, Sandberg G and Bellini C
(2000) The SUPER-ROOT2 gene of Arabidopsis thaliana, encodes the Cytochrome P450 CYP83B1 - a modulator of auxin homeostasis. Proc. Natl. Acad. Sci. USA, 97, 14819-14824Sorin C, Bussell JD, Camus I, Ljung K, Kowalczyk M, Geiss G, McKhann H, Garcion C, Vaucheret H, Sandberg G, Bellini, C
(2005) Light- an auxin control of adventitious rooting in Arabidopsis involves ARGONAUTE1. Plant Cell 17, 5, 1343-59Sorin C, Negroni L, Balliau T, Corti H, Jacquemot MP, Daventure M, Sandberg G, Zivy M, Bellini C
(2006) Proteomic analysis of different mutant genotypes of Arabidopsis thaliana led to the identification of eleven proteins correlating with adventitious root development. Plant Physiol. 40, 349-364Le Hir R, Beneteau J, Bellini C, Vilaine F, Dinant S
(2008) Gene expression profiling: keys for investigating phloem functions. Trends Plant Sci. 13, 273-280.Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C
(2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by a complex regulation of AUXIN RESPONSE FACTOR transcripts and MicroRNA abundance. Plant Cell 21, 10, 3119-3132 Expand Publications list
Rishikesh P. Bhalerao - Seasonal Control of Growth in Perennial Plants and Regulation of Cell Elongation
Survival of perennial plants, including long-lived trees, depends on their ability to adapt to seasonal changes in environmental conditions. These plants have developed sophisticated mechanisms to sense changes in environmental conditions and modulate their growth and development accordingly. The first project in my lab focuses on understanding how perennial plants sense the changing environmental conditions, by analysing the molecular basis of short-day-induced growth cessation and dormancy in hybrid aspen. The second project is focused on understanding how cell elongation is regulated in plants.
Cell elongation in plant cells presents a unique problem, as plant cells are enclosed in a rigid cell wall that needs to be remodelled in order for cell elongation to occur. The research in my group aims to identify the key components that are involved in regulation of cell elongation and cell wall remodelling in the model plant Arabidopsis.Molecular basis of growth cessation and dormancy in perennial plants
Perennial plants need to undergo growth cessation and establish dormancy prior to the onset of winter, in order to survive low temperatures. These plants anticipate the approach of winter by sensing the reduction in day length. Reduction in day length (short day signal) induces growth cessation that is apparent in the form of bud formation at the apex and eventually the establishment of dormancy. Once dormancy is established, prolonged exposure to chilling temperatures is essential for release from dormancy. Once release from dormancy has occurred, warm temperatures can reinitiate new growth. In my group, we are investigating the molecular basis of short-day-induced growth cessation and dormancy. In particular we are addressing the following questions:1. What are the signal transduction components mediating short day regulated growth cessation?
2. How is dormancy established and what is the molecular mechanism regulating the release from dormancy?
To address these questions, we are applying a combination of genomics, genetics and biochemical approaches with a model perennial plant, hybrid aspen. Using full genome microarrays and metabolic profiling, we have outlined the transcriptional and metabolic networks underlying the distinct stages of induction of growth cessation, establishment and release from dormancy. Using the information from transcriptional and metabolic profiling, we have identified a set of candidate genes that could be key regulators of growth cessation and dormancy acting downstream of the environmental and hormonal signals. We are now analyzing the role of these candidate genes in hybrid aspen by using RNAi and microRNAs to down-regulate their expression, as well as by overexpressing and misexpressing these genes and investigating the effects of modulating their expression on growth cessation and dormancy.Elucidating the control of cell elongation in Arabidopsis thaliana
The final size of plants and their constituent organs is determined by cell division and cell expansion. While cell division serves to increase the number of cells, cell expansion serves to increase the cell size. Mechanistically, cell expansion in plants poses a unique problem compared with animal animal cells. Unilike animal cells, plant cells are surrounded by a rigid cell wall that encompasses the plasma membrane. For cell expansion to occur, the cell wall structure must be remodelled. The process of cell wall remodelling involves loosening of the cell wall by alteration of the interactions between the three major components of the primary plant cell wall, namely cellulose, hemicellulose (of which xyloglucans are the major components) and pectins. This process involves the breakdown of linkages between the various cell wall components, accompanied by the addition of newly synthesized components to growing cell walls as cell size increases. Importantly, at the cellular level cell expansion can be polar. This is the case in root hair formation where cell wall loosening and eventual elongation is localised to the basal end of trichoblast cells. Here the cell wall components and the proteins needed for cell wall remodeling need to be delivered to the specific locations where cell wall expansion will take place. Thus, to understand how cell expansion is regulated, an important question that needs to be answered is:How do cells regulate the delivery of various cell wall components and the proteins involved in cell wall remodelling to their site of action during cell expansion?
We are currently addressing this question in the model plant Arabidopsis. We have identified several Arabidopsis mutants altered in cell elongation and these are being characterized using genetic and cell biology techniques. Our results so far indicate a key role for the components of trafficking machinery in the regulation of cell elongation and cell wall remodelling.Svensk samanfattning
Druart N, Johansson A, Baba K, Schrader J, Sjödin A, Bhalerao RR, Resman L, Trygg J, Moritz T, Bhalerao RP
(2007) Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant J 50: 557-573Rohde A, Bhalerao RP
(2007) Plant dormancy in the perennial context. Trends Plant Sci 12: 217-223Ubeda-Thomas S, Swarup R, Coates J., Swarup K, Laplaze L, Beemster G, Hedden P, Bhalerao R and Bennett M
(2008) Root growth in Arabidopsis requires gibberellin/DELLA signaling in endodermis. Nature Cell Biol 10: 625-628Nilsson J, Karlberg A, Antii H, Lopez-Vernaza M, Mellerowicz E, Rechenmann C, Sandberg G and Bhalerao RP
(2008) Dissecting the Molecular Basis of the Regulation of Wood Formation by Auxin in Hybrid Aspen. Plant Cell 20: 843-855Swarup R, Perry P, Hagenbeek D, Van Der Straeten D, Beemster GT, Sandberg G, Bhalerao R, Ljung K, and Bennett MJ
(2007) Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 7: 2186-2196Expand publications list
Ulrika Egertsdotter - Somatic Embryogenesis (SE) in Gymnosperms
A technology for mass propagation of valuable seeds and a powerful research tool
The consumption of wood based products is increasing globally. At the same time, the land base available for production forestry is decreasing. The need to improve the efficiency of production forestry is therefore urgent, especially in the northern hemisphere where growth and yield are low compared to southern hemisphere plantations. The prerequisite for successful plantation forestry is a mass propagation system suitable for sustainable large scale production of selected materials. For spruce, the only available system that meets these demands is Somatic Embryogenesis.
Somatic Embryogenesis (SE) is an in vitro based technology that can be used for propagation of valuable seeds, of commercial value and for conservation purposes. SE is also a valuable tool in fundamental research on embryo development. The fundamental SE process of gymnosperms is summarized below.
Embryo development in the seed (zygotic embryo development) and Somatic Embryogenesis (SE)
My research is focused on the processes that regulate development of gymnosperm embryos, and specifically how signals from the outside of the embryo influences cell specific growth within the embryo. We have identified an aquaglyceroporin with a suggested role in suspensor specific functions. Proteins have been previously identified that are stimulating the formation of the meristematic regions and the protoderm in somatic embryos of Norway spruce. Recently, we have isolated a full length Extracellular Matrix Metalloproteinase (MMP) gene from Loblolly pine involved in ECM modifications, facilitating the cell division and expansion required during seed development, germination completion, and subsequent seedling establishment. We are also interested in the signal transduction from mechanical stimuli to an intracellular response.Svensk sammanfattning
Ciavatta V T, Egertsdotter U, Clapham D, von Arnold S, Cairney J A
. 2002. Promoter from the Loblolly Pine PtNIP1;1 Gene Directs Expression in an Early-Embryogenesis and Suspensor-Specific Fashion. Planta. 215: 694- 698.Egertsdotter U, von Arnold S.
1998. Development of somatic embryos in Norway spruce. J. Exp. Bot. 319:155-162.Kvaalen, H., Dæhlen O.G., Rognstad, A.T., Grønstad, B., Egertsdotter, U.
2005. Somatic embryogenesis for plant production of Abies lasiocarpa. Can. J. For. Res./Rev. Can. Rech. For. 35(5): 1053-1060.Ratnaparkhe S M, Egertsdotter E- M U, Flinn B S.
2009. Identication and characterization of a matrix metalloproteinase (Pta1-MMP) expressed during Loblolly pine (Pinus taeda) seed development, germination completion, and early seedling establishment. Planta. 2009 Jul;230(2):339-54.Sun H, Aidun C K, Egertsdotter E-M U.
2010. Effects from shear stress on morphology and growth of early stages of Norway spruce somatic embryos. Biotechnol Bioeng. 2010 Feb 15;105(3):588-99.Expand publications list
Maria E. Eriksson - Circadian Clock Function and its Importance for the Regulation of Growth
The main focus of our research is to understand the functional aspects of the circadian clock mechanism and how this timing machinery influences the regulation of plant growth. We use both the annual herb Arabidopsis, and the deciduous tree Populus, to address these questions, using forward and reverse genetic approaches and multidisciplinary tools.
To anticipate the diurnal cycle of light and dark, most organisms have developed a molecular time measuring system called a circadian (Lat. circa, diem = about a day) oscillator or clock. It re-sets to local time on a daily basis and synchronizes the organism's cellular and physiological events to its most favourable time of the day. It is also implicated in seasonal events, such as flowering and bud set in trees, in order for them to occur at the most favourable time of year. If we learn more about temporal regulation, there is a great potential for biotechnological application in adapting new plants or re-adapting (in case of climate warming) local plants to local conditions to increase the length of the growth season and to keep winter hardiness.Light and temperature cues set the time
Light is received by multiple photoreceptors in the red, far red and blue spectra and mediates re-setting of the circadian clock, while temperature may be perceived directly by central components of the clock.
An Arabidopsis plant and a simplified model of its circadian clock.
Luciferase imaging of Populus cuttings.
Signs of season. An apex of Populus in active growth (upper left), at bud set (upper right), during dormancy (lower right) and at bud burst (lower left)
The most central clock proteins are TIMING OF CAB1 (TOC1), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and LATE ELONGATED HYPOCOTYLS (LHY), forming a feedback loop in which the transcription factors CCA1 and LHY negatively regulate the expression of the pseudo-response regulator (PRR) TOC1. In addition, this loop is intertwined with at least two additional feedback loops.
Members of the ZEITLUPE (ZTL) gene family, of F-box, Kelch-, and LOV/PAS domain-containing proteins, are thought to be capable of receiving blue light directly. The ZTL family of proteins is directly involved in regulation of the circadian clock and seasonal timing, by targeted destruc- tion of core clock genes and genes controlling photoperiodic flowering.
We use the Arabidopsis clock as a model, which is now being further explored in the perennial Populus tree. In order to find new clock-associated genes, we have obtained mutant Arabidopsis plants. True clock mutants need to be affected in several outputs from the clock, and have to have an effect on genes found close to the central loops. By tracking the movements of leaves or following the expression from clock-controlled genes by reporter gene constructs, like the hands of a mechanical clock, it is possible to tell the pace and features of the inner clock's rhythm and to characterize new clock mutants.
In order to study the clock mechanism and its adaptive value, we use novel Arabidopsis mutants or transgenic trees with altered levels of clock gene expression. Moreover, to investigate clock impact on perennial growth, we monitor elongation growth and seasonal responses, such as flowering, growth cessation, bud set and bud break. Our mutant plants, with an altered timing mechanism, are now helping us to build a better model of the circadian clock, its function and impact on seasonal regulation of growth.
Samanfattning på SvenskaExpand List of Publications
Eriksson ME, Israelsson M, Olsson O, Moritz T (2000) Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length. Nature Biotechnology 18:784-788
Eriksson ME, Hanano S, Southern MM, Hall A, Millar AJ (2003) Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta: 218:159-162
Kozarewa I, Ibáñez C, Johansson M, Ögren E, Mozley D, Nylander E, Chono M, Moritz T, Eriksson ME (2010) Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus. Plant Molecular Biology: 73:143-156
Ibáñez C, Kozarewa I, Johansson M, Ögren E, Rohde A, Eriksson ME (2010) Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees. Plant Physiology: 153:1823-1833
Ashelford K, Eriksson ME, Allen CM, D'Amore L, Johansson M, Gould P, Kay S, Millar AJ, Hall N, Hall A (2011) Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biology: 12:R28, 12 pp
Johansson M, McWatters HG, Bakó L, Takata N, Gyula P, Hall A, Somers DE, Millar AJ, Eriksson ME (2011) Partners in time: EARLY BIRD associates with ZEITLUPE and regulates the speed of the Arabidopsis clock. Plant Physiology: 155:2108-2122
Anders Fries - Genetic Influence on Wood Traits in Scots Pine & Pollination Studies in Seed Orchards
Genetics of wood and fibre traits
One branch of my research is on the genetics of wood and fibre traits in Scots pine, and techniques for measuring and evaluating those traits. The aims are: i) to evaluate techniques and designs for taking wood samples in progeny tests, ii) to evaluate progeny tests for wood and fibre traits, and their relation to growth, iii) to determine the distribution of wood and fibre traits in the stem from ground level to the top, and connect genetic parameters to them for the whole tree, and iv) to develop different techniques for analyzing wood and fibre traits, e.g. X-ray and Kajaani Fiber analyses, and to apply them to progeny testing. Studies in seed orchard
Västerhus seed orchard. The most genetically advanced Scots pine seed orchard is studied for pollen contamination etcetera
Seed orchards are production units for seeds of elite genetic and physiological clones. Production can however be improved, especially with new molecular fingerprinting techniques. I work in a group which studies the following aspects of seed orchards: i) physical development (growth, flowering etc.); ii) the pollination pattern in orchards using molecular techniques, (dominating clones in the pollen cloud, reproductive success, contaminating unselected pollen from surrounding natural stands etc.); iii) the potential of selective seed harvest from individual clones for ingto reach genetic top quality, and iv) the development of a technique for determining parental origins of plants arising from open pollination in seed orchards by molecular fingerprinting, so-called breeding without breeding, as an alternative to progeny testing based on costly controlled crossesparental origin of - as an alternative to progeny testing based on costly controlled crosses.QTLs for wood and fibre traits
Measurement of wood density with X-ray
I work in a group which aims to identify QTLs (Quantitative Trait Loci) for genes that regulate, among others, the following wood and fibre traits in Scots pine:
- wood density, its distribution between earlywood and latewood, and the relation to ring width,
- dimensions of wood fibres
- microfibril angle
Other research areas:
properties of the heartwood and sapwood of Scots pine, e.g. the amount of heartwood and its content of wood extractives, progeny testing in general, gene resources of larch for Sweden, and genetic parameters for production traits. Svensk sammanfattning
Fries A, Ericsson T
2006. Estimating genetic parameters for wood density of Scots pine (Pinus sylvestris L.). Silvae Genet. 55, 84-92.Fries A, Ericsson T
2009. Genetic parameters for earlywood and latewood densities and development by increasing age in Scots pine. Ann. For. Res. 66, 404.Torimaru T, Wang X-R, Fries A, Andersson B, Lindgren D
2008. Evaluation of pollen contamination in an advanced Scots pine seed orchard. Silvae Genet. In print.Expand publications list
Ulrika Ganeteg - Molecular Physiology of Plant Nitrogen Nutrition
The aim of our research is to understand the molecular processes of plant nitrogen nutrition, with a focus on amino acid transport. We seek to understand how transport of amino acids contributes to nitrogen use efficiency and to optimization of plant growth. To accomplish this, we use a methodologically integrative approach, ranging from cell and molecular biology to ecophysiology.
Nitrogen availability is considered a bottleneck for plant biomass production in terrestrial ecosystems. In addition, the demand for nitrogen in different parts of the plant varies during different stages of plant growth and development. Therefore, the ability to appropriately allocate and subsequently re-use nitrogen, together with nitrogen uptake, are the major determinants of nitrogen use efficiency, and hence for optimized plant growth. Being the major form of trans- ported nitrogen, amino acids are the currency of nitrogen within plants. There is therefore a complex network of transport of amino acids during plant growth and development, implying a demand for an intricate and well-orchestrated transport system. How this network is regulated to optimize nitrogen use efficiency in response to developmental and environmental cues during plant growth is at present not very well known. Besides being a key determinant for plant growth, nitrogen is also regarded as a major pollutant, resulting for example in changes in biodiversity. In addition, human perturbation of the global nitrogen cycle is the second largest driver of global climate change. Plant uptake of nitrogen from the soil and internal nitrogen fluxes are key processes in the global nitrogen cycle. Therefore, the molecular dissection of amino acid transport in plants has broad significance for our understanding of how nitrogen fluxes contribute to the overall plant nitrogen budget. This knowledge is also important from a more applied perspective, opening up new avenues to optimize nitrogen fertilization in both agriculture and forestry.
|Arabidopsis plants deficient in the amino acid transporter LHT1
||Arabidopsis plants deficient in the amino acid transporter AAP5 (upper left corner) are insensitive to toxic concentrations of arginine.
We have identified two candidate Arabidopsis amino acid transporters, LHT1 and AAP5, for involvement in root uptake of amino acids from the soil solution. The process of amino acid uptake in plants has been demonstrated both in laboratory and field settings, and has thus been well established. However, the ecological significance of organic Nitrogen uptake for plant nitrogen nutrition is still a matter of intense debate. One of our projects aims to resolve the molecular mechanisms and ecological significance of root amino acid uptake. To accomplish this we use a collection of transgenic Arabidopsis and Populus with different amino acid uptake profiles in our studies.
We also want to understand how the processes of nitrogen allocation and remobilization contribute to nitrogen use efficiency in plants. This work focuses on how amino acid transporters are orchestrated to allocate and redistribute nitrogen in response to developmental and environmental cues. Being mediated by a gene family comprised of 50 genes or more, the investigation of amino acid transport is a complex task (at least 53 and 90 genes have been annotated as putative amino acid/auxin permeases in the Arabidopsis and Populus genomes, respectively). It is believed that amino acid transporters are functionally separated by their substrate specificity and their temporal and spatial expression patterns. However, many amino acid transporters have been shown to have multiple functions in plants. Similarly, LHT1 has been identified as being involved in redistribution of amino acids in leaf mesophyll cells, besides its function in root amino acid uptake. We are investigating the role of LHT1 and a number of other key amino acid transporters in the allocation and remobilization of amino acids. Wild type and transgenic Populus are being analyzed with respect to, for example, gene expression, nutrient uptake, growth and nitrogen allocation, in response to developmental and environmental cues under controlled conditions and in the field.Svensk sammanfattning
Svennerstam H, Ganeteg U, Bellini C, Näsholm T
(2007) Comprehensive screening of Arabidopsis mutants suggests the Lysine Histidine Transporter 1 to be involved in plant uptake of amino acids. Plant Physiology 143: 1853-1860.Forsum O, Svennerstam H, Ganeteg U, Näsholm T
(2008) Capacities and constraints of amino acid utilization in Arabidopsis. New Phytologist 179: 1058-1069.Svennerstam H, Ganeteg U, Näsholm T
(2008) Uptake of cationic amino acids in Arabidopsis depends on functional expression of amino acid permease 5. New Phytologist 180: 620-630Näsholm T, Kielland K, Ganeteg U
(2009) Uptake of organic nitrogen by plants. New Phytologist, 182: 31-48Expand Full Publications List
María Rosario García-Gil - Forest Tree Genetics and Breeding
The research of my group focuses on traits with economic value (e.g. growth, wood formation, wood calorimetric content, frost hardiness and pest resistance) and traits with clear adaptive value (e.g. timing of budset). These traits are very complex and called "quantitative trais" because they are controlled by a large number of genes and gene interactions.
Molecular tools to assist tree breeding
The main contribution of molecular tools to conventional tree breeding is the possibility they provide of early selection to shorten the breeding cycle.
The Quantitative Trait Loci (QTL)-Candidate Gene co-location approach prevents the loss of desired QTLs during recurrent selection, and its high resolution allows breeders to break up undesired trait correlations. We are building a genetic map on a Scots pine (Pinus sylvestris) full sib family of 500 offspring based on AFLP, SSR and SNP markers. We search for co-location of genes (SNPs) with QTLs for growth, spiral grain, timing of budset, frost hardiness and Heterobasidion resistance.
Association Mapping (AM) is another genetic strategy to unravel the genetics behind complex traits. This is a candidate gene-based method which tests for association between candidate genes and phenotypic variation at a population level. With this approach, we intend to identify genes underlying wood formation in Norway spruce and wood calorimetric content in Scots pine.
Genome Wide Selection (GWS) to detect genomic regions harbouring sequence variants that affect complex traits requires the development of arrays scanning for single molecule changes in the genome (SNP). Conceptually, this method is simple and opens the possibility to incorporate high-throughput genomic tools into operative tree breeding. In my group, we are developing a dense SNP array in Scots pine for its application in an advanced Scots pine breeding pedigree.
Spatial Genetic Structure in Scots pine
|Bud formation in one-year-old Scots pine seedlings under greenhouse conditions.
||Scots pine trees
Differences in genetic structure between tree species are due mainly to differences in life form and breeding system. The availability of highly variable molecular markers has facilitated fine-scale genetic structure analysis of natural tree populations. Inbreeding depression is an important issue in forestry, due to the poor performance of inbred trees. We investigate the impact of a common forest management strategy, natural seedling regeneration from seed trees, on fine-scale spatial genetic structure.Genetics underlying forest tree adaptation
Single Nucleotidy Polymorphisms (SNPs) scoring
The southwards transfer of Scots pine leads leads to increased growth, but not sufficient to overcome the competitive advantages of the local southern trees. In other words, temperature is not the only factor limiting the growth potential of northern populations. There is much evidence that day length is another major environmental cue shaping the strong adaptive cline in Scots pine. Less attention has been devoted to the study of light composition (wavelength). We are therefore studying the effect of light quality on three month-old Scots pine seedlings. We aim to use proteomics, chemical analyses and microscopy as tools to identify strong associations with genes involved in local adaptation to light composition.Conifer genome evolution
Gene families control important traits in forest trees, such as frost hardiness, pest resistance, and growth, so tree breeding success depends on a good understanding of the composition and function of those gene families'. Conifers have large genome sizes compared with most animal and plant species. However, how and why conifers have evolved such large genomes is not understood. Based on our work on the phytochrome gene family, we have found that conifer gene families can be very complex and contribute to the enormous size of the conifer genome. In the light of our recent findings, we are investigating the composition and function of another important gene family (LP3) involved in water deficit stress.Svensk samanfattning
Komulainen P, Brown GR, Mikkonen M, Karhu A, García-Gil MR, O'Malley D, Lee B, Neale DB and Savolainen O
(2003). Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor App Genet 107: 667-678García-Gil MR, Mikkonen M, Savolainen O
(2003). Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol. 12: 1195-1206Waldmann P, García-Gil MR, Sillanpaa MJ
(2005). Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris. Heredity 94: 623-629Notivol E, García-Gil MR, Alía R, Savolainen O
(2007). Genetic variation of growth rhythm traits in the limits of a latitudinal cline in Scots pine. Can J For Res 37: 540-551García-Gil MR
(2008) Evolutionary aspects of functional and pseudogene family in Scots pine. J Mol Evol 67(2): 222-232Expand Full Publications List
Per Gardeström - Leaf Mitochondria and Their Roles in Photosynthesis and Senescence
Plants need a flexible metabolism in order to respond to the variable environmental conditions that they experience. We investigate leaf metabolism with the aim of obtaining a better understanding of the metabolic pathways involved, their regulation and compartmentation. We focus in particular on the interactions between mitochondria and chloroplasts. The project has two foci: (1) the interaction of respiratory and photosynthetic metabolic pathways in photosynthetically active cells and (2) the involvement of mitochondria and respiratory metabolism in the process of leaf senescence.Respiration/photorespiration
Mitochondria fulfil essential functions in the energy metabo- lism of all cells. The conclusion from studies during the last few years is that mitochondrial oxidative phosphorylation is important for the supply of ATP to the cytosol of photosynthetic cells. However, mitochondrial activities in the light are closely related to photosynthetic metabolism, and many of the interactions between chloroplasts and mitochondria are coupled to photorespiration. In the light, a major function for leaf mitochondria is oxidation of glycine in the photores- piratory glycolate pathway. The flux through this pathway is considerable and involves redox reactions in chloroplasts, peroxisomes and mitochondria that strongly affect the redox situation of the cell. From estimations of subcellular redox states of NAD(H) and NADP(H) pools and ATP/ADP ratios, it is clear that the functions of leaf mitochondria are different in the light with from those in the dark. The TCA cycle appears to be reorganized in the light, so that it changes from being the main source of energy in the cell to providing a flexible mechanism that enables the cell to sustain optimal photosynthesis. This highlights the fact that the cell functions as a unit. Current studies aim to further explore the contributions of mitochondria to photosynthetic metabolism.Senescence
||Rapid senescence is induced by darkening a few leaves while the rest of the plant remain in light (top right). The yellow leaf at 11 o ́clock was darkened for 6 days. Confocal microscopy pictures of leaf cells from whole darkened plants (top left) and individually darkened leaves (bottom left). Chloroplasts are red and mitochondria green.
Leaf senescence is an active and closely controlled process in which nutrients are reallocated from decaying leaves to other plant organs. Mitochondria and respiratory metabolism can contribute to this process by providing ATP and carbon skeletons. Analyses of ESTs from poplar indicate that respiration is important during the process of autumn leaf senescence. This is further supported by analysis of transcripts during the process, and determination of a detailed cellular timetable of autumn senescence.
We use Arabidopsis as a model to study dark-induced leaf senescence by comparing whole darkened plants (DP) and individually darkened leaves (IDL) (figure top right). In DP, chloroplasts are retained after a 6-day dark treatment and photosynthetic capacity is maintained, while the number of mitochondria and respiration decrease (figure top left). In IDL darkened for the same period of time, the photosynthetic capacity severely decreases aused due to chloroplast degra- dation, while mitochondria become bigger and respiration is maintained (figure bottom left). Based on metabolomic and transcriptomic results, we suggest that leaves from DP enter a stand-by metabolic state of low respiratory activity. In contrast, IDL show high respiratory activity with active mitochondrial contribution to the retrieval of nutrients from senescing leaves. In ongoing experiments we aim to elucidate the metabolic adjustments related to the rapid senescence in IDL.Svensk samanfattning
Hurry VM, Keerberg O, Pärnik T, Öquist G, Gardeström P
(1996) Effect of cold hardening on the components of respiratory decarboxylation in the light and in the dark in leaves of winter rye. Plant Physiol 111:713-719Igamberdiev AU, Gardeström P
(2003) Regulation of NAD- and NADP-dependent isocitrate dehydrogenases by reduction levels of pyridine nucleotides in mitochondria and cytosol of pea leaves. BBA 1606:117-125Bykova NV, Keerberg O, Pärnik T, Bauwe H, Gardeström P
(2005) Interaction between photorespiration and respiration in transgenic plants with antisense reduction in glycine decarboxylase. Planta, 222: 130-140Keskitalo J, Bergkvist G, Gardeström P, Jansson S
(2005) A cellular timetable of autumn senescence. Plant Physiol 139: 1635-1648Keech O, Pesquet, Ahad A, Askne A, Malmberg G, Nordvall D, Vodnala S, Tuominen H, Dizengremel P, Hurry V, Gardeström P
(2007) The different fates of mitochondria and chloroplasts during dark-induced senescence in Arabidopsis leaves, Plant Cell & Env 30: 1523-1534Expand Full Publications List
Markus Grebe - Establishment of Epidermal Cell and Tissue Polarity
Many cells in diverse organisms need to acquire specific shapes in order to fulfil their functions within the organism. Cells commonly become polarised with one end being asymmetrically oriented in a certain direction. Moreover, the polarities of individual cells are often coordinated within the tissue layer. However, the mechanisms underlying the establishment of cell polarity and its coordination in plants are poorly understood. We have introduced the root epidermis of the model plant Arabidopsis thaliana as a system to study cell polarity and its coordination within the plane of the tissue layer (planar polarity). Here, we employ the polar localisation of Rho-of-plant (ROP) proteins to, and the polar outgrowth of root hairs from, near the basal ends of the outer epidermal membrane as polarity markers. Similarly, we use the polar localisation of the PIN2 auxin efflux carrier to apical epidermal membranes as a polarity indicator. By combining forward and reverse genetic, molecular, cell biological and physiological approaches, we have started to unravel mechanisms underlying the coordination and execution of cell polarity in root epidermal cells.
Planar polarity in the Arabidopsis root epidermis We have established the Arabidopsis root epidermis as a system for the functional dissection of planar polarity of root-hair positioning. Our recent work shows that the combinatorial action of three genes (AUXIN RESISTANT1, AUX1, ETHYLENE INSENSITIVE2, EIN2 and GNOM) is required to coordinate root-hair positioning within the epidermal layer. These genes act to establish a concentration gradient of the plant hormone auxin in the root tip. This auxin gradient to some extent instructs the coordinated polar positioning of root hairs by acting prior to or at the level of the polar accumulation of small Rho-of-Plant (ROP) GTPases at the polar site of hair initiation (Fischer et al. 2006). However, the regulation of this gradient, the functional connection to downstream molecules, and the signalling cascade between auxin action and polar ROP or actin recruitment, remain a black box in terms of our understanding. We are currently characterising novel planar polarity mutants and interactions between known genes to elucidate the molecular genetic framework of factors regulating cell and tissue polarity in the root epidermis (Ikeda et al. 2009).
Sterol function in epidermal cell polarity
|The confocal laser scanning microscope
||Left panel, green fluorescence of the PIN2 protein fused to enhanced Green-Fluorescent Protein (PIN2-EGFP). Right panel, overlay with filipin-sterol fluorescence (false colour red). Upper row, arrowheads indicate polar PIN2-EGFP localisation only on the upper (apical) membranes of root epidermal cells. Middle row, epidermal cell during division. Lower row, an epidermal cell just after division. Note, both newly formed membranes show PIN2-EGFP fluorescence (Men et al. 2008)
In a second line of research, we address the role of membrane sterols in the establishment of epidermal cell polarity. The common plant sterol sitosterol is a lipid similar to cholesterol in animals. In collaboration with Ben Scheres's group, we have shown that correct membrane sterol composition is needed for cell polarity (Willemsen et al. 2003). Furthermore, I have established methods for the subcellular visualisation of plant sterols and their endocytic transport in Arabidopsis (Grebe et al. 2003). Recently, my group demonstrated that the correct sterol composition of plant membranes is essential for establishment of the specific polar localisation of the auxin transporter PIN2, just after cell division. During cell division, PIN2 is integrated into cell-plate membranes and is located at both newly formed membranes directly after cell division. In order to acquire its polar apical localisation, PIN2 needs to be removed from one end of the cell by internalisation (endocytosis) from the membrane. This can only occur when the membrane has the correct sterol composition. In a sterol biosynthesis mutant, which contains a large amount of precursor sterols that normally do not accumulate in the membrane, PIN2 is not appropriately removed from one end of the cell and apical PIN2 polarity cannot be established (Men et al. 2008). We are currently addressing the sub-cellular mechanisms underlying this phenomenon, as well as the role of sterols during cell division.Svensk samanfattning
Ikeda Y, Men S, Fischer U, Stepanova AN, Alonso JM, Ljung K & Grebe M
(2009). Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis. Nature Cell Biology 11: 731-738.Men S, Boutté Y, Ikeda Y, Li X, Palme K, Stierhof YD, Hartmann MA, Moritz T & Grebe M
(2008). Sterol-dependent endocytosis mediates post-cytokinetic acquisition of PIN2 auxin efflux carrier polarity. Nature Cell Biology 10: 237-244.Fischer U, Ikeda Y, Ljung K, Serralbo O, Singh M, Heidstra R, Palme K, Scheres B & Grebe M
(2006). Vectorial information for Arabidopsis planar polarity is mediated by combined AUX1, EIN2, and GNOM activity. Current Biology 16: 2143-2149. Grebe M, Xu J, Möbius W, Ueda T, Nakano A, Geuze HJ, Rook MB & Scheres B
(2003). Arabidopsis sterol endocytosis involves actin-mediated trafficking via ARA6-positive early endosomes. Current Biology 13: 1378-1387.Willemsen V, Friml J, Grebe M, van den Toorn A, Palme K & Scheres B
(2003). Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function. Plant Cell 15: 612-625.Grebe M, Friml J, Swarup R, Ljung K, Sandberg G, Terlou M, Palme K, Bennett MJ & Scheres B
(2002). Cell polarity signaling in Arabidopsis involves a BFA-sensitive auxin influx pathway. Current Biology 12: 329-334.Expand publications list
Vaughan Hurry - Plant Adaptation to Sub-Optimal Environments
Our primary research goal is to identify the key adaptive mechanisms that result in short- and long-term acquisition of abiotic stress tolerance. To address this, our research currently has two main themes: 1) how are environmental "signals" sensed and, in turn, converted into a genetic response, and 2) how is primary metabolism modulated
in response to fluctuations in growth temperature. The outcomes from this research are being applied to developing new tools for increased stress tolerance in herbaceous crops and forest plantation species and to studies of how we can incorporate understanding of acclimation of primary metabolism into global circulation models.
One of the key questions on the international research agenda today is how various biotopes, natural and cultivated, will respond to the changes to the environment resulting from human activities. Plant carbon metabolism plays a crucial role in determining the functioning of terrestrial ecosystems, the concentration of CO2 in the atmosphere and the mean annual temperature of the earth's surface. Each year, photosynthetic carbon assimilation removes ca. 120 gigatonnes (Gt) of carbon from the atmosphere, with much of this carbon being used by heterotrophic organisms (i.e. animals, fungi, and bacteria).
Scaling up from laboratory based experiments to ecosystem – level responses can be facilitated by studies in intact systems. The experiment shown is from the CANIFLEX project where the fate of carbon taken up by the forest was tracked through the trees and the soil biota and back to the atmosphere using stable isotopes. The impacts of environmental changes, such as altering nitrogen availability, could then be studied at different trophic levels within the intact forest stand. This large scale, multiyear study was carried out together with colleagues from UPSC (T. Näsholm) and SLU (P. Högberg and S. Linder).
In addition, plants return ca. 60 Gt carbon per year to the atmosphere via respiration when producing the energy and carbon intermediates necessary for biosynthesis and cellular maintenance. This is a very large flux compared with the ca. 8 Gt carbon per year released from the burning of fossil fuels. Thus, fundamental metabolic processes such as photosynthesis and respiration play a critical role in determining a wide range of ecologi- cal phenomena, from the productivity of individual plants, species fitness, particular environments, and the resulting species composition of particular biotopes.
Understanding such processes, and how they respond to environmental perturbations, provides insight into the underlying mechanisms that will drive future phenotypic replacements in response to climate change. Growth temperature is one of the most important climate parameters that impacts on the global fluxes through these C-assimilatory and C-emission pathways.
For example, as part of the thermal acclimation process (i.e. adjustment in the rate of metabolism to compensate for a change in growth temperature), cold-grown leaves exhibit higher transcript and activity levels of photosynthetic and sucrose synthesis enzymes, accompanied by increased capacity of mitochondrial electron transport than their warm-grown counterparts. As a result, sustained exposure to low growth temperatures typically results in an increase in the rate of assimilation and respiration at low temperatures. Given the predicted increase in the annual mean temperature of the Earth's surface, a major challenge for plant ecology and climate-vegetation modelling is identifying whether sustained changes in growth temperature will systematically alter the leaf-trait scaling relationships linking assimilation and respiration to leaf mass to area ratio and nitrogen concentrations.
To answer this challenge, a far better understanding of the responses of organellar functions to fluctuations in environmental inputs (e.g. temperature, water and nutrients) is required. We have shown that incorporating acclimation into the predictive models results in significant regional effects on the prevalence of different functional groups in different biomes. For example, it alters the predictions of the abundance of needle trees in the boreal forest zone relative to broad-leafed trees. Such changes will have very significant consequences for major industries such as Sweden's forest industry and consequently for the national economy. Our future research will develop additional data sets to incorporate acclimation to temperature, variations in response to altered soil nutritional status, rainfall, etc. to improve the predictive capacity of climate modelspredictive capacity of climate models.Svensk sammanfattning
Atkin OK, Atkinson LJ, Fisher RA, Campbell CD, Zaragoza-Castells J, Pitchford JW, Woodward FI, Hurry V
(2008) Using temperature-dependent changes in leaf scaling relationships to quantitatively account for thermal acclimation of respiration in a coupled global climate-vegetation model. Global Change Biology, 14: 2709-2726.Högberg P, Högberg MN, Göttlicher SG, Betson NR, Keel SG, Metcalfe DB, Campbell C, Schindlbacher A, Hurry V, Lund- mark T, Linder S, Näsholm T
(2008) High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms. New Phytologist, 177: 220-228.Campbell C, Atkinson L, Zaragoza-Castells J, Lundmark M, Atkin O, Hurry V
(2007) Acclimation of photosynthesis and respiration in response to changes in growth temperature is asynchronous across plant functional groups. New Phytologist, 176: 375–389.Benedict C, Geisler M, Trygg J, Huner N, Hurry V
(2006) Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis. Plant Physiology, 141: 1219–1232.Lundmark M, Cavaco AM, Trevanion S, Hurry V
(2006) Carbon partitioning and export in transgenic Arabidopsis thaliana with altered capacity for sucrose synthesis grown at low temperature: a role for metabolite transporters. Plant Cell & Environment, 29: 1703–1714.Expand publications list
Torgeir R. Hvidsten - Computational Inference of Regulatory Networks in Trees
Forest trees are a renewable source of raw material not only for paper production, but also for energy. However, to get higher productivity from forests, we need to acquire basic understanding of important processes, such as development and growth. To this end, experimentalists collect huge amounts of molecular data from aspen (Populus tremula) using transcriptomics, proteomics and metabolomics platforms. The goal of this project is to use computers to explain these experimental data in terms of network models that describe interactions between genes, proteins and metabolites, and the underlying regulatory logics hard-wired in the treesí DNA. These models will become important platforms from which experimentalists can obtain understanding, overviews and hints for the direction of future experiments.
We take a systems biology approach to the understanding of important molecular processes in trees. Systems biology aims at integrating high-throughput experimental data and existing biological knowledge to model organisms at a system level. Such models can provide an underlying system-wide explanation of the large amount of information produced by experimental platforms, but can also act
as prediction devices to propose new hypotheses for further experiments. For example, the models can be used to generate hypotheses about which biological processes particular genes take part in and which proteins (transcription factors) regulate those particular processes.
Massive readouts of cell contents in terms of RNA molecules (transcriptomics), proteins (proteomics) and the products of metabolic processes (metabolomics) can be explained by the information hard-wired in the DNA sequence. The same is true for complex phenotypes, such as growth or seasonal responses, although the rate of transcription and translation, the stability of proteins and the molecular dynamics of proteins and their interactions with each other and other molecules also come into play. A basic model of gene regulation must describes where transcription factors bind to initiate transcription and how they combine and cooperate to facilitate complex expression responses to, for example, changes in the environment. An extraordinary example of models describing the hard-wired logics of development in sea urchin embryos was published by Davidson et al (Science 295(5560): 1669-1678, 2002). We aim at describing similar logics in aspens. However, we rely on computational inference of regulatory network models from DNA sequences, highthroughput dynamic data and knowledge obtained by studying other plants (comparative genomics).
A model of the transcriptional network in aspen tree leaves. Regulatory proteins (red triangles) orchestrate the activity of modules of genes (grey circles) by recognizing and binding to certain regulatory switches in the DNA (indicated by red arrows). Regulatory proteins are themselves members of modules as indicated by blue lines. The dynamic behavior of genes during four days in the autumn is illustrated by coloring genes and proteins according to their activity levels in the senescence sub-network (red implies high activity while green implies low activity). Leaf senescence is the process in which trees prepare for winter by storing up nutrients before getting rid of the leaves.
To infer models from data, we use a technique from computer science called machine learning. Machine learning uses observations with biologically known properties as examples to learn general models that can be used to explain underlying patterns in data and to make predictions for new, uncharacterized observations. There are two conceptually different approaches to the computational step. The most common is that of nearest neighbour(s) approaches, where biological knowledge is transferred from the closest example (e.g. sequence) for which such information is available. The second approach is that of inducing a general model from the available examples and to use this model for prediction. The advantage of the latter approach is that similarities can be found among many otherwise dissimilar examples and these patterns can be used to predict weak similarities (e.g. distant homologues). Another advantage is that models can be inspected and interpreted, and thereby provide insight into the biological system. A critical breakthrough for sys- tems biology methods like this is to reach a level of quality in terms of descriptive and predictive power, so that the models can be helpful in guiding experimentalists in choices related to hypotheses to consider and experiments to do next. The results of these experiments may then be used to iteratively improve the model.Svensk samanfattning
Wabnik K, Hvidsten TR, Kedzierska A, Van Leene J, De Jaeger G, Beemster GTS, Komorowski J and Kuiper MTR
(2008). Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics. 2009 1;25(3):322-30.Strömbergsson H, Daniluk P, Kryshtafovych A, Fidelis K, Wikberg JES, Kleywegt GJ and Hvidsten TR
(2008). An interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space. Journal of Chemical Information and Modeling 48: 2278–2288.Wilczynski B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K
(2006). Using local gene expression similarities to discover regulatory binding site modules. BMC Bioinformatics 7: 505.Hvidsten TR, Wilczynski B, Kryshtafovych A, Tiuryn J, Komorowski J and Fidelis K
(2005). Discovering regulatory binding site modules using rule-based learning. Genome Research 15: 856-66.Lægreid A, Hvidsten TR, Midelfart H, Komorowski J, and Sandvik AK
(2003). Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns. Genome Research 13: 965-979.Expand publications list
Johannes Hanson - Metabolic reprograming
The sessile nature of plants necessitates highly efficient responses to adverse environmental conditions. These adaptive processes are not only important in the acute phase of the stress but are in natural environments discriminative for plant fitness and in agricultural systems determining yield.
Reprogrammed metabolism is an important part of stress adaption. Even small changes in metabolic reactions can cause dramatic changes in levels of key metabolites and vice versa. The long time goal of the group is to understand this highly dynamic network of metabolites, enzymes and most important regulatory molecules. Following limited energy availability plant cells reprogram their metabolism to better fit the new condition. The dramatic change involves hundreds of gene products and metabolites and is highly reproducible – we call this the Low Energy Syndrome, LES. The signaling pathway regulating LES is mastered by the SnRK1 kinase complex which is, in a yet not fully resolved way, able to react to low levels of metabolizable carbon (starvation). This parallels the manner in which all eukaryotes regulate starvation responses (AMPK, mammalian homolog, and snf1, yeast). In plants the SnRK1 kinases regulate gene expression of genes encoding key metabolic enzymes by activating certain bZIP transcription factors. Our focus is on the regulation of these transcription factors.
This nine bZIP transcription factors have the capacity to dramatically decreasing growth by reprogramming metabolism. However, the proteins themselves are regulated at several different levels ranging from transcriptional and translational regulation to activation by protein modification and protein dimerization. We want to understand this intricate mechanism. Technically we are using high throughput expression analysis (micro-arrays, massive sequencing, translatomics) as central analysis tool combined with genetics and transgene based methods. Until now we have only used Arabidopsis plants and cells to study the processes but with the move to UPSC we will start to use tree models as well.
Overexpression of the bZIP transcription factor bZIP11 is dramatically affecting the growth (35S::bZIP11). Here compared with a wild-type Arabidopsis plant of similar age (WT).Regulation of metabolism by dimerizing bZIP factors
bZIP transcription factors bind DNA as dimers. S1-bZips bind DNA preferentially by forming dimers with C-bZIPs. We have shown that the specific dimer combinations are regulating specific genes, which shows that the plant can regulate gene expression in an integrative manner by regulating the levels of a few bZIPs and thereby change the dimer pools dramatically to regulate metabolism. Here we are beginning to decipher the S1-C dimer code. We want to understand the regulatory system to gain further insight into how signaling pathway are integrated and to understand the individual roles of the highly coordinated metabolic changes.Translational control of bZIP transcription factors
S1-bZIP factors are translationally repressed in response to high sucrose levels by a small peptide encoded by an open reading frame located in the 5' leader of the bZIP mRNA. We want to understand how metabolite levels can regulate translation of these specific mRNAs.Global translational control
Our work on translational control of bZip translation has taken us into the research on the ribosome. We have shown the proteome of the ribosome to be highly dynamic in response to environmental factors. The changes correlate to global changes of mRNAs bound to ribosomes (translatomics). The biological consequences of this are not yet investigated and we approach this by proteomics as well as molecular, biochemical and genetic tools.Low energy availability and stress activate signaling cascades in the plant starting from the SnRK1 kinase and ending in changed metabolism and growth. The aspects of this that interests us are indicated. Svensk sammanfattning... Open positions
We currently have open positions in both Umeå and Utrecht (both PhD and PostDoc). However, the group is moving to Umeå and newly recruited persons in Utrecht are expected to join in this move. If you like what we are doing and think that you can contribute,, contact
Bio4Energy network - www.bio4energy.se
Utrecht group - Click here-->
Metabolic Reprograming by induction of transcription - http://theory.bio.uu.nl/MERIT/html/
Hanson, J., Hanssen, M., Wiese, A., Hendriks, M.M., and Smeekens, S
. (2008). The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2. Plant J 53, 935-949..Rahmani F., Hummel M., Schuurmans J., Wiese-Klinkenberg A., Smeekens S. and Hanson J
. Sucrose control of translation mediated by a uORF encoded peptide. (2009) Plant Physiology. 150:1356-67Ma, J., Hanssen, M., Lundgren, K., Hernández, L., Delatte, T., Ehlert, A., Liu, C-M., Schluepmann, H. Dröge-Laser, W., Moritz, T., Smeekens, S. and Hanson J
. (2011) The sucrose regulated Arabidopsis transcription factor bZIP11 reprograms metabolism and regulates trehalose metabolism, New Phytologist in press Expand List of publications...
Maria Israelsson Nordström - Control of stomatal movements
The aim in my research group is to better understand how CO2
is perceived and transduced into stomatal movements and how red light-induced stomatal opening may interact with this pathway using Arabidopsis thaliana
as a model organism. We use forward and reverse genetics approaches together with multidisciplinary tools to address how CO2
and red light control the stomatal aperture.
In plants, stomatal pores on the leaf epidermis enable gas exchange between the plant and the atmosphere. Each stomatal pore is made up of a pair of guard cells and turgor changes in these cells evoke stomatal movements. Many factors control the stomatal pore size including humidity, CO2
concentration, temperature, light quality and quantity. The guard cell is an interesting model system to study with thick cell walls and a lack of functional plasmodesmata (mature GC) where starch synthesis occurs during the night and starch degradation during the day. Furthermore, carbon fixation is mainly performed by PEP carboxylase (to create malate2-
as a counter-ion for K+
needed to drive the turgor pressure) as well as functional but limited photosynthesis. My group is particularly interested in whether guard cell photosynthesis participates in CO2
perception and/or red light-induced stomatal movements. In one project we are investigating the possible link between red light-induced photosynthesis, a drop in Ci
and low CO2
-induced stomatal opening.A guard cell protoplast (GCP) compared to a mesophyll cell protoplast (MCP) in Arabidopsis thaliana
Hu, H.*, Boisson-Dernier, A.*, Israelsson-Nordström, M.*, Böhmer, M., Xue S., Ries, A., Godoski, J., Kuhn, J.M. and Schroeder J.I
. Carbonic anhydrases are upstream regulators of CO2-controlled stomatal movements in guard cells. (2010) Nature Cell Biology 12:87-93.
* Joint first authorsIsraelsson, M., Siegel R.S., Young J., Hashimoto, M., Iba, K. and Schroeder, J.I
. Guard cell ABA and CO2 signaling network updates and Ca2+ sensor priming hypothesis. (2006) Current Opinion in Plant Biology 9:654-663.Young, J., Mehta, S., Israelsson, M., Godoski, J., Grill, E. and Schroeder, J. I
. Carbon dioxide signaling in guard cells via calcium response modulation and CO2 insensitivity of gca2 mutant. (2006) Proceedings of the National Academy of Sciences of the United States of America 103:7506-7511.Hashimoto, M., Negi, J., Young, J., Israelsson, M., Schroeder, J. I., and Iba, K
. Arabidopsis HT1 kinase controls stomatal movements in response to CO2. (2006) Nature Cell Biology 8:391-397.Expand List of publications...
Stefan Jansson - Light, Senescence and Natural Variation
We work on many aspects of plant biology. Populus genomics
The ultimate goal of this project is to learn how to find the genetic differences that make aspens (Populus tremula) different from each other. Autumn senescence
Using these tools, we study how aspens acclimate and adapt to the environment. Photosynthetic light harvesting
We are studying the large family of LHC proteins using biochemical, reverse and forward genetic and molecular biological approaches. Populus genomics
The ultimate goal of this project is to learn how to find the genetic differences that make aspens (Populus tremula) different from each other. Forest trees are, in general, more genetically diverse than most other organisms and aspens are, in this respect, extreme. Gene sequences from two aspens are on average 1 % different; two aspens are about as different genetically as humans are from chimpanzees.
We have been developing infrastructure to enable research on genomics and natural variation in aspen. For example, we have generated Populus ESTs and DNA microarrays, developed microarray analysis protocols and databases, genome databases and have been profiling small RNAs. To study natural variation, we have used both genetic genomics to study gene expression in segregating populations, and have created clone collections (the SwAsp and UmAsp collections) that are phenotyped for many traits and genotyped for variation in candidate genes.Autumn senescence
Using these tools, we study how aspens acclimate and adapt to the environment. Particular attention is paid to the process of autumn senescence, trying to answer the question: How do trees know that it is autumn? We are studying gene expression, photosynthesis, metabolism and ultrastructure of the leaves during autumn senescence. One important tool we use is natural variation. There is a steep cline in autumn senescence; trees from northern latitudes enter senescence much earlier than those from southern latitudes, and by us- ing the complete annotated Populus genome sequence, the collection of aspen clones and genetic tools like association mapping, we hope to understand the genetic basis of this adaptively significant trait. The same strategies are also used to dissect other traits, including herbivory and other biotic interactions.
Our “favourite aspen”, growing on the campus
How does the tree know that it is autumn?
Photosynthetic light harvesting
Field experiment with transgenic Arabidopsis
In the photosynthesis apparatus of green plants, the lightharvesting chlorophyll a/b-binding (LHC) proteins serve as antennae for photosystems I and II. Members of the LHC protein family have three membrane-spanning regions and bind the majority of the photosynthetic pigments (chlorophyll and carotenoids), make the photosynthetic light reaction efficient and regulate the photosynthetic light reaction, for example by dissipating excess light and adjusting the excitation balance between the photosystems. There are a group of proteins that are more distant members of this protein family. This group consists of PsbS, ELIPs (early light-inducible proteins) and several smaller proteins, containing only one or two membrane-spanning regions. PsbS is necessary for a light dissipation process – the qE type of non-photochemical quenching (NPQ) or feedback de-excitation (FDE) - that operates when the plants is exposed to "excess light".
We are studying the large family of LHC proteins using biochemical, reverse and forward genetic and molecular biological approaches. In Arabidopsis, over 30 genes encode proteins of this family and we are systematically producing and analysing plants that lack different LHC proteins (T-DNA knockouts or antisense plants). The photosynthetic performance of these plants helps us understand the function of the individual proteins, the structure of the photosystems and energy transfer in the antenna.Svensk sammanfattning
Li, X-P, Björkman, O, Shih C, Grossman, AR, Rosenquist, M, Jansson, S, Niyogi, KK
(2000) A pigment binding protein essential for regulation of photosynthetic light harvesting. Nature 40: 391-395Damkjær JT, Kereïche S, Johnson MP, Kovacs L, Kiss AZ, Boekema EJ, Ruban AV, Horton P, Jansson S
(2009) The Pho- tosystem II light harvesting protein Lhcb3 affects the macrostructure of photosystem II and the rate of state transitions in Arabidopsis. Plant Cell (in press)Külheim C, Ågren J, Jansson S
(2002) Rapid regulation of light harvesting is crucial for plant fitness in the field. Science 297:91-93Sterky F, Bhalerao RR, Unneberg P, Segerman B, Nilsson P, Brunner AM, Campaa L, Jonsson Lindvall J, Tandre K, Strauss SH, Sundberg B, Gustafsson P, Uhlén M, Bhalerao RP, Nilsson O, Sandberg G, Karlsson J, Lundeberg J, Jansson S
(2004) A Populus EST resource for plant functional genomics. PNAS 101 13951–13956Tuskan GA, DiFazio S, Jansson S, et al.
(2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science 313:1596-1604Expand publications list
Leszek A. Kleczkowski - Regulation of Polysaccharide Formation in Plants
Research in my group is focused on regulation of the formation of nucleotide-sugar precursors to polysaccharides (e.g. sucrose, cellulose) in plants. Particular emphasis is placed on elucidation of mechanisms of enzymatic/metabolic control of the proteins involved and those governing the operation of distinct signal transduction pathways that are involved in regulation of genes for nucleotide-sugars synthesis. Structure/ function properties of key enzymes are elucidated, based on their crystal structure, including oligomerization and posttranslational modification processes. In addition, we use bioinformatics/functional genomics resources to define cis regulatory elements (CREs) responsible for gene regulation by specific factors, especially sugars, and then verify them in vivo using synthetic promoters.
We study the role of ADP-glucose (ADPG) and UDP-glucose (UDPG) producing enzymes in plants. The former is the key precursor of starch synthesis, whereas the latter serves as a direct or indirect precursor to all other polysaccharides, including sucrose, cellulose and hemicelluloses. We have studied both genes and proteins responsible for ADPG and UDPG synthesis, including those for ADPG pyrophosphorylase (AGP, AGPase), UDPG pyrophosphorylase (UGP, UGPase) and sucrose synthase (SUS, SuSy). Although we use Arabidopsis as a main model plant system, we also have interest in the woody plant aspen (Populus), using functional genomics resources for Populus within the UPSC. In aspen, we focus on regulation of the biosynthesis of cellulose and hemicelluloses, the primary determinants of wood quality, from sugar nucleotide precursors.
Function/structure studies on UGPase
We have recently homology-modelled the primary sequence for plant UGPase, to produce a predicted 3D structure. The derived structure was consistent with earlier studies on site- directed mutants of UGPase from a variety of organisms. This structural model is used as a testable blueprint to verify details of UGPase catalysis and substrate binding. We are also studying molecular determinants of post-translational modifications of UGPase, focusing on oligomerization and possible phosphorylation/14:3:3 protein binding. Site- directed mutagenesis studies are under way, using plant UGPases produced in bacteria, to identify critical relevant amino acids and functional domains of the protein.
|Central role of UDP-glucose in primary sugar and polysaccharide metabolism
|| Algorithm for CREs validation (Geisler et al. 2006)
Regulation of gene expression, CREs and synthetic promoters Regulation of genes involved in nucleoside-sugars synthesis is being elucidated using plants with impaired sensing/signalling mechanisms (e.g. with altered levels of hexokinase, altered internal Pi pools, or impaired phytohormone levels), plants transformed with constructs containing a given promoter hooked to a GUS reporter gene, and using inhibitors of protein kinases/phosphatases. Factors studied include sugars, light, osmotica, cold, phosphate deficiency, etc. So far, the results are consistent with the existence of various sensing mechanisms and distinct signal transduction pathways involved in nucleoside sugar production.
Recently, we developed a universal algorithm to test the biological significance of cis-regulatory elements (CREs), by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with gene expression profiles on multiple DNA microarrays. The new algorithm can be rapidly applied to any putative motif. In preliminary studies, synthetic promoters (composed of a minimal 35S promoter and several repeats of a single CRE hooked to a GUS reporter) were successfully used to verify some of the putative CREs discovered by the algorithm.Svensk samanfattning
Siedlecka A, Ciereszko I, Mellerowicz E, Martz F, Chen J, Kleczkowski LA
2003. The small subunit ADP-glucose pyrophosphorylase (ApS) promoter mediates okadaic acid-sensitive uidA expression in starch-synthesizing tissues and cells in Arabidopsis. Planta 217: 184-192Kleczkowski LA, Geisler M, Ciereszko I, Johansson H
2004. UDP-glucose pyrophosphorylase. An old protein with new tricks. Plant Physiology 134: 912-918Geisler M, Kleczkowski LA, Karpinski S
2006. A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; Identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis. Plant Journal 45: 384-398Meng M, Wilczynska M, Kleczkowski LA
2008. Molecular and kinetic characterization of two UDP-glucose pyrophosphorylases, products of distinct genes, from Arabidopsis. Biochimica et Biophysica Acta - Proteins and Proteomics 1784: 967-972Meng M, Geisler M, Johansson H, Harholt J, Scheller HV, Mellerowicz EJ, Kleczkowski LA
2009. UDP-glucose pyrophosphorylase is not rate-limiting, but is essential in Arabidopsis. Plant and Cell Physiology 50: 998-1011Expand publications list
Karin Ljung - Root Development and Shoot-Root Communication
The research in my group is focused on the mechanisms and processes regulating plant growth and development. We are particularly interested in the role of different plant growth regulating substances (plant hormones) in primary and secondary root development. We are also interested in understanding how a plant coordinates the growth of its aerial parts with its root system, and the role that plant hormones play in this.
||Above.Confocal laser scanning picture of the Arabidopsis DR5:GFP line, expressing Green Flourescent Protein in specific cell types of the root apex.
Left. The picture shows the relative auxin distribution in the Arabidopsis root. The highest concentration (dark blue) was observed in the quiescent cen- tre of the root apex (Petersson et al. 2009).
Below. Arabidopsis seedlings growing on agar plates
Auxins and cytokinins are plant hormones that are absolutely essential during the whole of a plant's life cycle. They play important roles in cell division, cell differentiation and cell elongation and are believed to act in a concentration dependent manner. Different regulatory mechanisms (synthesis, degradation, transport) act in concert to maintain optimal hormone concentrations for particular plant growth and development processes. Interactions between different hormone signalling pathways are also important for the regulation of plant development in response to integrated external and internal signals. Auxin, cytokinins and other molecules can be transported between root and shoot tissues to coordinate the growth of the roots with the shoot. Cytokinins are transported via the xylem from the root to the shoot, and auxin is transported via both polar auxin transport and phloem transport from the shoot to the root.
We have previously observed that a leaf-mediated pulse of auxin is important for lateral root development, and we are now studying how light and the circadian clock regulate auxin biosynthesis, metabolism and transport and how this influences the coordinated growth of plants. Very little is known about the metabolic pathways involved, and we are using various biochemical and molecular genetic techniques, such as analysis of gene expression, metabolites and proteins, to elucidate these pathways.
The other main area of enquiry in my group is the unravelling of auxin and cytokinin interactions. These two hormones sometimes act synergistically and sometimes antagonistically during growth and development, and the mechanisms behind these interactions are largely unknown. We are currently studying the regulation of auxin and cytokinin metabolism in Arabidopsis, and we have recently shown that auxin and cytokinins regulate each other's biosynthesis. In root tips and young developing leaves, cytokinins upregulate auxin synthesis, whereas auxin down-regulates cytokinin biosynthesis in Arabidopsis seedlings. We are now investigating the mechanisms behind these interactions, and the importance that they have in developmental processes in plants.
By using sensitive mass spectrometry-based methods for plant hormone analysis, we have also shown the formation of local hormone gradients and maxima in plant tissues, e.g. in the primary root apex. It is believed that the formation of such gradients and maxima are very important for specifying stem cell niches and for the regulation of cell division and differentiation in the root apex. We have also shown that the Arabidopsis root system has auxin biosynthesis capacity, and we are trying to understand which factors are important for the regulation of auxin biosynthesis and metabolism in the root. A better understanding of the basic cellular processes we are studying will be very important in the improvement of crop and tree growth and productivity.Svensk samanfattning
Ljung K, Bhalerao RP, Sandberg G
(2001) Sites and homeostatic control of auxin biosynthesis in Arabidopsis during vegetative growth. Plant Journal 28: 465-474.Ljung K, Hull AK, Celenza J, Yamada M, Estelle M, Normanly J, Sandberg G
(2005) Sites and regulation of auxin biosynthesis in Arabidopsis roots. Plant Cell 17: 1090-1104.Swarup R, Perry P, Hagenbeek D, Van Der Straeten D, Beemster GT, Sandberg G, Bhalerao R, Ljung K, Bennett MJ
(2007) Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 19: 2186-2196.Tao Y, Ferrer JL, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y, Bal- laré CL, Sandberg G, Noel JP, Chory J
(2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell 133: 164-176.Petersson SV, Johansson AI, Kowalczyk K, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G, Ljung K
(2009) An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 21:1659-1668.Expand publications list
Ewa Mellerowicz - Wood Fibre Biosynthesis
Wood cells accumulate the major proportion of terrestrial biomass in their thick cell walls, composed of cellulose, matrix polysaccharides and lignin. By interacting with cellulose and lignin, matrix polysaccharides affect the mechanical and chemical properties of wood, which strongly affect delignification, saccharification, and other types of wood industrial processing. Matrix polysaccharides play a special role during wood cell expansion and wood cell differentiation. Our research is aiming at elucidating these matrix functions in wood cell development.
Matrix properties are controlled by Carbohydrate Active Enzymes (CAZYmes) either secreted to cell walls or residing in the Golgi apparatus where the matrix is synthesized. To set the scene for the wood cell wall matrix studies, we analyzed the genomic complement of CAZYmes in Populus and identified the ones highly expressed in developing wood. These enzymes are being studied using Populus and Arabidopsis as model systems.
|Matrix modification affects wood cell expansion and thus regulates the size and shape of wood cells. Fibers and vessel elements have different ways of expansion. Fibers elongate by intrusive tip growth and radially expand by symplastic growth. In contrast, vessel elements do not elongate, but they radially expand by a combination of radial intrusive and symplastic growth. Accordingly, a highly regulated modification of matrix in developing wood cells is required to achieve these different effects.
||A model of growth stress generation and XET action in maturing fibers. Crystallization of cellulose microfibrils (single beige rods) around xyloglucan (yellow) would generate longitudinal tensional stress within the macrofibril (large beige rods) during fiber maturation. XET enzyme (blue) is present associated with xyloglucan between wall layers. Any displacement between the wall layers driven by the shrinkage of cellulose macrofibrils will be quickly stopped by the XET-mediated transglycosylation to a free xyloglucan acceptor thus creating a cross-link between cell wall layers.
|Activity of XET enzyme in the specific cell wall layers visualized by the incorporation of the fluorescent substrate to the XET transglycosylation product. Such activity could be detected in tension wood fibers years after their initiation, indicating that the matrix is being modified even in dead cells.
||Modification of pectin matrix causes accelerated expansion of leaves in transgenic poplar.
The pectin matrix, which cements wood cells together, is extensively modified during xylogenesis. We discovered that pectin modification is important for wood cell expansion, in particular in the intrusive tip growth of fibres. Pectin methyl esterase removes the methyl side chains of pectins in the cell wall. When the methyl groups are removed completely, wood cell growth is inhibited by the formation of intra-molecular cross-links involving calcium ions that rigidify the walls. When the methyl groups are partly removed, pectin can be depolymerised by pectate lyase and cell expansion is stimulated. Monoclonal antibodies specific to various pectin epitopes can detect distinct developmental patterns of pectin methylesterification, demonstrating complex regulation of pectin matrix in developing wood.
Hemicelluloses make the cross-links between cellulose fibrils, which need to be removed to allow cell expansion. Indeed, the modification of hemicelluloses affects wood cell growth. One class of enzymes acting on hemicelluloses is xyloglucan transglycosylases (XETs). We found that these enzymes not only regulate cell growth, but can also act on cell walls after cell death. Such long-lived enzymatic activity could modify cell wall architecture, regulating the mechanical properties of wood and development of growth stresses in the wood.
Most CAZYme genes belong to large multi-gene families. The individual members of the families might have distinct or overlapping functions, or else be non-functional copies. We are currently investigating functions for different members of the family GT43, which includes key xylan biosynthetic genes. Since xylan is the most important matrix component in secondary walls, elucidating its biosynthesis is one of our priorities.
The role of different matrix components can also be investigated by using microbial enzymes of defined specificity. These enzymes, when targeted to cell walls, modify specific chains of the matrix, revealing intricate interactions among different wall components, the extent of matrix plasticity and its role during wood cell development.Svensk samanfattning
Siedlecka A, Wiklund S, Péronne MA, Micheli F, Leśniewska J, Sethson I, Edlund U, Richard L, Sundberg B, and Mellerowicz EJ
.(2008) Pectin methyl esterase inhibits intrusive and symplastic cell growth in developing wood of Populus trees. Plant Physiology 146: 554-565.Gray-Mitsumune M, Blomquist K, McQueen-Mason S, Teeri TT, Sundberg B and Mellerowicz EJ
(2008) Ectopic expression of a wood-abundant expansin PttEXPA1 promotes cell expansion in primary and secondary tissues in aspen. Plant Biotechnology Journal 6: 62-72.Nishikubo N, Awano T, Banasiak A, Bourquin V, Ibatullin F, Funada R, Brumer H, Teeri TT, Hayashi T, Sundberg B, Mellerowicz EJ
(2007) Xyloglucan endo-transglycosylase (XET) functions in gelatinous layers of tension wood fibers in poplar - a glimpse into the mechanism of the balancing act of trees. Plant and Cell Physiology 48: 843-855.Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunnerås S, Sundberg B, Karpinski S, Teeri TT, Kleczkowski LA, Henrissat B, and Mellerowicz EJ.
( 2006). Poplar Carbohydrate-Active Enzymes (CAZymes). Gene identification and expression analyses. Plant Physiol. 140: 946-962.Bourquin, V, Nishikubo, N, Abe, H., Brumer, H, Denman, S, Eklund, M, Christiernin, M, Teeri TT, Sundberg, B and Mellerowicz, EJ
. (2002). Xyloglucan endotransglycosylases have a function during the formation of secondary cell walls of vascular tissues. Plant Cell 14: 3073-3088.Expand publications list
Thomas Moritz - Hormonal Control of Shoot Elongation and Wood Formation
The aim in my research project is to understand the mechanisms of hormonal control of shoot elongation and wood formation in the model plant Populus. We want to understand how plant hormones are involved in the control of plant development, and how different environmental cues, such as photoperiod, affect the hormonal control of growth and development. In parallel, the metabolic changes in response to hormonal and photoperiodic changes are studied by using a metabolomics approach.
Gibberellins (GAs) are a group of tetracyclic diterpenes, some of which are essential endogenous regulators that influence growth and development events throughout the life cycle of a plant, e.g. shoot elongation, expansion and shape of leaves, flowering and seed germination. Our project is concerned with the role of GAs in plant development, and day length responses, focusing on the tree hybrid aspen (Populus tremula x P. tremuloides) as a model system. Our approach for studying the role of GAs in trees is to study endogenous expression of GA biosynthetic and signalling genes and to transform Populus with genes encoding those genes.
Populus transformed with the AtGA20ox1 under the control of the 35S promoter shows elongated internodes, longer petioles and larger leaves, reduced root formation and increased shoot biomass. In contrast, Populus expressing the AtGA3ox1 gene under the 35S promoter exhibits no major changes in morphology. We have concluded that 20-oxida- tion is the limiting step, rather than 3β-hydroxylation, in the formation of GA1 and GA4 in elongating shoots of hybrid aspen, and that ectopic GA3ox expression alone cannot increase the flux towards bioactive GAs.
Recently, we have also characterized the GA receptor, GID1 in Populus. Four orthologs of GID1 have been identified in Populus tremula x P. tremuloides (PttGID1.1 to 1.4). When PttGID1.1 and PttGID1.3 were overexpressed in Populus with a 35S promoter, overexpressors shared several similar phenotypic traits with previously described 35S:AtGA20ox1 overexpressors, including rapid growth and increased elongation.
We are also studying the role of GAs in wood formation. This is done by both using transgenic Populus with increased levels of GAs and signalling, and by predicting where GAs are formed and perceived during wood formation. For example, we have quantified GAs and analyzed the expression of GA biosynthesis genes and genes with predicted roles in GA signalling in tangential sections across the cambial region of aspen trees (Populus tremula). The results show, for example inter alia, that the bioactive GA1 and GA4 predominantly occur in the zone of expansion of xylem cells. Studies with transgenic Populus overexpressing AtGA20ox1 or PttGID1 with 35S or a xylem-specific promoter, suggest that GAs are required for two distinct processes in wood formation with tissue-specific signalling pathways: xylogenesis, mediated by GA signalling in the cambium;, and fibre elongation in developing xylem.
Many woody species with indeterminate growth show complete cessation of elongation growth after only a few weeks in short photoperiods. Studies in Salix have shown that GA levels are decreased after only a few days in short photo periods. In hybrid aspen transformed with the oat PHYA gene, the dwarf phenotype is correlated with a reduction in GA levels, but in short photo-periods there is no further reduction in GA contents, in marked contrast to the pattern in wild-type plants. These observations imply that GAs have an important role as signals in the photo-periodic regulation of shoot elongation. We have also been studying transgenic GA plants to elucidate how changes in GA levels and signalling affect photoperiodic growth. Studies in PHYA and GA biosynthesis/signalling overexpressors are used with transcriptomic and metabolomic approaches to elucidate the early signalling pathways in short-day induced growth cessation, including identification of new putative signalling compounds.Svensk samanfattning
Eriksson M, Israelsson M, Olsson O, Moritz T
2000. Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fibre length. Nature Biotech. 784-788.Israelsson M, Mellerowicz E, Chono M, Gullberg J, Moritz T
2004 Cloning and overproduction of GA 3-oxidase in hybrid aspen trees: effects on GA homeostasis and development. Plant Physiol. 135: 221-230Jonsson P, Johansson A, Gullberg J, Trygg J, A J, Grung B, Marklund S, Sjöström M, Antti H, Moritz T
2005 High through-put data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses Anal. Chem. 77: 5635-5642.Israelsson M, Sundberg B, Moritz T
2005 Tissue-specific localisation of gibberellins in wood-forming tissues in aspen. Plant J. 44: 494-504.Mauriat M, Moritz T
2009 Analyses of GA20ox- and GID1-overexpressing Populus suggest gibberellins play two distinct roles in wood formation. Plant J. 58: 989-1003.Expand publications list
Totte Niittylä - Cell Wall Biosynthesis and Carbohydrate Metabolism
I am interested in carbohydrate metabolism of plants. In particular I wish to understand how carbohydrate metabolism is coupled to cell wall biosynthesis, especially to the biosynthesis of cellulose. Majority of the biomass accumulation on the planet occurs in the cell walls of non-photosynthetic plant tissues such as the wood of trees. This biomass resource provides the main source of biopolymers in the world and its importance will increase in the future as global demand for renewable materials and fuels increases.
For further information please read a recent popular science artikel about our work in International Innovation, the leading global dissemination resource for the wider scientific, technology and research communities. Download PDF325.53 KB
The work in my group addresses genetic factors contributing to stem biomass and wood density. We focus on the molecular mechanisms responsible for carbon allocation to developing wood of trees. The carbon in wood is mostly found in three main cell wall polymers; cellulose, hemicelluloses and lignin. In most plant species majority of this carbon is derived from sucrose imported from photosynthetic tissues. Therefore understanding of sucrose transport to wood and subsequent production of cell wall polymer precursors is central for understanding factors controlling stem biomass and wood density.
|Electron microscope picture of aspen wood fibers and vessels
Cell expansion defect in cellulose biosynthesis
mutant (right) compared to wild-type (left) Arabidopsis.
|Cross section of Arabidopsis stem. A quater of a cross section
through the Arabidopsis stem. The inner parts of the stem is shown on the left upper corner, the outer part in the bottem right corner.
Xylem is light blue, phloem is marked with red colour, the epidermis cell are coloured in dark blue (from the inside to outside). Should be
Cross section of Arabidopsis stem. Lignified cell walls are shown in red
and non-lignified in blue.
In addition to identifying the components of sucrose to cell wall polymer pathway we are interested in how the process is regulated, especially in relation to sugar availability. To this end we work on the protein phosphorylation and protein trafficking responses communicating information about the sugar status of plant cells and organs, and how this information is translated to the responses at the cellular and whole plant level. Protein phosphorylation–dephosphorylation and protein trafficking are fundamental principles in the regulation of many biological responses in all organisms, including the primary carbohydrate metabolism of plants.
Currently our work is carried out with two model plants: The sugar signaling work is mostly done with the small but powerful Arabidopsis thaliana and the carbon allocation to wood with the fully sequenced tree model poplar. In our research we use molecular biology, biochemistry, genetics, microscopy and mass spectrometry.Svensk sammanfattning
Roach M, Gerber L, Sandquist D, Gorzsas A, Hedenström M, Kumar M, Steinhauser MC,Feil R, Daniel G, Stitt M, Sundberg B and Niittylä T
(2012). Fructokinase is required for carbon partitioning to cellulose in aspen wood. Plant Journal, 70(6), 967 – 977.
Niittylä T, Chauduri B, Sauer U, Frommer WB
(2009). Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics. Methods Mol Biol 553, 355-372.Niittylä T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX
(2007). Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol Cell Proteomics 6, 1711-1726Niittylä T, Comparot-Moss S, Lue W-L, Messerli G, Trevisan M, Seymour MD, Gatehouse JA, Villadsen D, Smith SM, Chen J, Zeeman SC, Smith AM
(2006). Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals. J. Biol. Chem. 281, 11815-11818Niittylä T, Messerli G, Trevisan M, Chen J, Smith AM, Zeeman SC
(2004). A previously unknown maltose transporter essential for starch degradation in leaves. Science 303, 87-89Expand publications list
Ove Nilsson - Control of Flowering Time and Meristem Identity
The research in my group is focused on various aspects of the regulation of meristem identity and flowering time in the two model systems, Arabidopsis and poplar. We want to understand the level of functional conservation of genes regulating flowering time between the two systems and to identify new regulators of this transition. With this approach, we aim to gain more insight into the regulation of flowering in both annuals and perennials. In other projects, we are studying the regulation of plant development in response to light and the regulation of vascular cambium identity.
The transition to flowering is one of the most important events during the life of a plant. Although we know a lot about how this process is regulated in annual plants like Arabidopsis and rice, we still know very little about what controls flowering in perennial trees.
Recently, we have shown that the role of the Arabidopsis gene FT in regulating flowering time is functionally conserved in a plant with a completely different life strategy: the poplar tree. Surprisingly, we could also show that the FT gene in poplar trees controls another important aspect of perennial growth behaviour: the short-day induced growth cessation
and bud set that occurs in the fall. We have shown that the activity of the CO/FT regulon is conserved in the aspen tree and that short days induce a down-regulation of the activity of this regulon, leading to growth cessation and bud set. This study leads to a completely new way of looking at the function of FT. It seems that this gene has a much more general role in controlling photoperiodic regulation of plant growth and development than was previously anticipated, based on work in Arabidopsis. We are taking a comparative biology approach to study the similarities and differences in the regulation of flowering in Arabidopsis and the regulation of flowering and growth cessation in aspen (poplar) trees; two plants with completed genome sequences. This includes analysis of the role of the plant hormone gibberellin and other metabolites that could serve as mobile signals during floral induction. This work will provide us with a better understanding of the genetic pathways responsible for photoperiodic regulation of plant growth and development. It will also allow us to design new ways to enhance the speed of tree breeding through accelerated flowering and to adapt the growing period of trees to new climate zones and to a changing climate.
|Transgenic hybrid aspen tree forming inflorescences and flowers after 6 months instead of after 10-15 years
||The Nilsson group is also studying the genes controlling growth cessation, bud set and bud burst in trees
We have also cloned and characterized the BLADE ON PETIOLE (BOP) genes, which have important roles in controlling the growth and development of lateral organs and appear to be important regulators of plant development in response to light. There is also an interesting interaction with the flower meristem identity-gene LEAFY (LFY) during flower initiation, in which BOP and LFY act together to initiate flower primordia and to suppress the outgrowth of flower-subtending leaves (bracts).
Recently, we identified a poplar homolog of the shoot apical meristem identity gene WUSCHEL (WUS) expressed in the vascular cambium and we have shown that this gene is important for vascular cambium activity and stem secondary growth. This is actually one of the genes that allow a tree to grow as a tree, i.e. to be the tallest plant in the forest. We are now characterizing several genes with a vascular cambium-specific expression pattern that could interact with this WUS-like gene in controlling the activity and identity of the vascular cambium. This knowledge will help to design methods to enhance wood production.Svensk sammanfattning
Weigel D, Nilsson O
1995. A developmental switch sufficient for flower initiation in diverse plants. Nature 377, 495-500.Parcy F, Nilsson O, Busch MA, Lee I, Weigel D
1998. A genetic framework for floral patterning. Nature 395, 561-566.Norberg M, Holmlund M, Nilsson O
(2005) The BLADE ON PETIOLE genes act redundantly to control the growth and development of lateral organs. Development 132: 2203-2213Böhlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O
(2006) CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312: 1040-1043Eriksson S, Böhlenius H, Moritz T, Nilsson O
(2006) GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. Plant Cell 18: 2172-2181Expand publications list
Annika Nordin - Nitrogen Management in Swedish Forests
In boreal forests, nitrogen supply is a limiting factor for plant growth. Fertilizing with nitrogen can double tree biomass, but may interfere with ecosystem functionality, changing plant species composition and soil microbial communities. The research in my group targets nitrogen effects on ecophysiological mechanisms driving nitrogen-induced ecosystem changes. The aim is to increase our knowledge of both positive and negative effects of nitrogen enrichment on important ecosystem services, such as productivity, carbon sequestration, nitrogen retention and biodiversity. Ultimately, we seek ways to wisely manage nitrogen use in forest ecosystems
Nitrogen addition to Swedish forests occurs both passively (via deposition of atmospherically transported nitrogen pol- lutants from agriculture, industry and traffic) and actively (via forest fertilization to increase forest yields). The effects of nitrogen addition on forest ecosystems are both positive (increased productivity and carbon sequestration) and nega- tive (water pollution and decreased biodiversity).
My research group studies nitrogen addition effects on forest ecosystems. We have demonstrated that nitrogen addition may shift the balance between plants and herbivorous organisms. This can lead to vegetation changes. For example, nitrogen addition increases disease incidence of pathogenic fungi on bilberry (Vaccinium myrtillus). This causes premature leaf-shed, which results in increased growth of grass competing with the bilberry shrubs. Nitrogen addition also promotes the abundance of winter-moth larvae feeding on the bilberry shrubs. For lingonberry (Vaccinium vitis-idaea) and heather (Cal- luna vulgaris), nitrogen addition increases leaf infection with snow-blight fungi. Hence, when a forest is subjected to elevated nitrogen input, the dwarf-shrubs decline due to increased disease caused by fungal pathogens and increased competition from grasses and herbs.
|Forest field-layer dominated by Vaccinium myrtillus L
||Vaccinium myrtillus diseased by a fungal leaf pathogen (Valdensia heterodoxa).
Survey of the species composition of forest floor vegetation
Many bryophyte species can be even more sensitive than dwarf-shrubs to nitrogen addition. Particularly sensitive are common forest floor mosses, like stair-step moss (Hylocomium splendens), and many peat-forming mosses (Sphagnum spp). We have studied physiological mechanisms explaining the nitrogen sensitivity of bryophytes. Only in the very long-term (following > 50 years of exposure to continuous high nitrogen input) do mosses have at least a slight capacity to physiologically adjust to high nitrogen input. More often, nitrogen-sensitive bryophytes disappear from ecosystems subjected to high nitrogen input. These studies show that nitrogen addition to a forest may have negative effects on forest biodiversity by decreasing the abundance of important keystone species. Ecosystem functionality can also be affected, since forest understory species composition influences ecosystem carbon sequestration, as well as nitrogen retention. Moreover, nitrogen effects can be very long-lasting. We have demonstrated effects on understory vegetation species composition of forest fertilization in the forest generation following the one fertilized (> 20 years after the fertilization). The effects include increased abundance of nitrogen-favoured grasses and herbs, and decreased (ca. 40 %) abundance of dwarf-shrubs.
Are there ways we can use nitrogen to increase forest yields while avoiding negative effects on forest biodiversity and ecosystem functionality? We think so. Our idea is to find alternative fertilizers and methods of applying fertilizers that cause less severe and long-lasting effects on forest biodiversity, while inducing stronger tree growth responses greaterthan current practices for forest fertilization.Svensk sammanfattning
Wiedermann MM, Gunnarsson U, Ericsson L, Nordin A
2009. Ecophysiological adjustment of two Sphagnum species in response to anthropogenic N deposition. New Phytologist 181: 208 – 217.Strengbom J, Nordin A
2008. Commercial forest fertilization cause long-term residual effects in ground vegetation of boreal forests. Forest, Ecology & Management 256: 2175 – 2181.Wiedermann MM, Nordin A, Gunnarsson U, Nilsson MB, Ericson L
2007. Global change shifts vegetation and plant-parasite interactions in a boreal mire. Ecology 88: 454 – 464.Forsum Å, Dahlman L, Näsholm T, Nordin A
2006. Nitrogen utilization by Hylocomium splendens in a boreal forest fertilization experiment. Functional Ecology 20: 421 – 426.Nordin A, Strengbom J, Witzell J, Näsholm T, Ericson L
2005. Nitrogen deposition and the biodiversity of boreal forests – implications for the nitrogen critical load. Ambio 34: 20 – 24Expand publications list
Torgny Näsholm - Ecophysiology and Molecular Biology of Plant Organic N Nutrition
Plant nitrogen (N) nutrition is a topic that challenges the researcher with a number of problems not encountered in other areas of plant mineral nutrition research. The diversity of N forms present in the soil, their interconversions, their different chemical and physical characteristics and not the least the multitude of adaptations and acclimatisations that plants display to optimize acquisition of various N forms all contribute to the complexity of plant N nutrition.
Thus, plants can use a wide array of chemical N forms, ranging from the simple inorganic N compounds such as NH4+
as well as polymeric N forms such as proteins.
My research deals with plant N physiology, particularly N acquisition and metabolism of forest plants. This research spans from detailed studies of uptake processes to forest fertilization and environmental effects of N. We have studied uptake of various N forms and demonstrated how field-grown plants acquire different organic N compounds.
Tests with arginine based fertilizer in a seedling nursery Rotorua, New Zeeland
Selection on D-amino acids
These studies have stimulated us to characterize the molecular mechanisms underpinning plant organic N nutrition, specifically the specific transporters mediating uptake of various amino acids as well as metabolism of absorbed organic compounds. We have discovered that plants have a well-developed capacity for using the common L-enantiomers of amino acids but a very restricted capacity to metabolise their D-counterparts. We have also shown how transgenic plants expressing genes encoding D-amino acid metabolising enzymes can detoxify and grow on D-amino acids. This finding has formed the basis for the development of a new selectable marker in plant biotechnology, now commercialized under the tradename SELDA. Basic L-amino acids, and in particular L-arginine, are absorbed at high rates by many plants and we have shown that such N forms have specific advantages for cultivation of woody plants such as conifer seedlings. This finding forms the basis for the development of a new fertilizer – arGrow®, which is now commercialized by the company SweTree Technologies.Svensk sammanfattning
Näsholm, T., Ekblad, A., Nordin, A., Giesler, R., Högberg, M. and Högberg, P.
1998. Boreal forest plants take up organic nitrogen. Nature 392, 914-916, 1998.Lipson, D. and Näsholm, T
. 2001. The unexpected versatility of plants: Organic Nitrogen Use and Availability in Terrestrial Ecosystems. Commissioned review. Oecologia 128: 305-316Erikson, O., Hertzberg, M. & Näsholm, T.
2004. A conditional marker gene allowing both positive and negative selection in plants. Nature Biotechnology, 22: 455-458.Svennerstam, H., Ganeteg, U., Bellini, C. & Näsholm, T
. 2007. Comprehensive screening of Arabidopsis mutants suggests the Lysine Histidine Tranporter 1 to be involved in root uptake of amino acids. Plant Physiology 143: 1-8Näsholm, T., Kielland, K. & Ganeteg, U
. 2009. Uptake of organic nitrogen by plants. Tansley Review New Phytologist, 182:31-48.Expand publications list
Edouard Pesquet - Xylem vessel morphogenesis
The evolution of plants from water onto land involved the development of systems for projecting their photosynthetic and reproductive organs up into the atmosphere. Xylem tissue is just such a system for it transports the water up to the leaves and its strength provides essential physical support. Sap is conducted through xylem tracheary elements (TEs) – hollow tubes whose collapse is prevented by patterned thickenings of secondary cell wall.
The aim of my work is to elucidate the molecular mechanism underlying the differentiation processes and more specifically the secondary cell wall formation of xylem vessels of both Arabidopsis (the genetic plant model) and Populus (the genetic tree model). The identification of key regulatory genes modulating xylem vessels cell wall formation will allow transgenic modification of the process to better understand how xylem/wood formation is controlled.
Figure 2: Real-time imaging of tracheary element differentiation. 35S::Histone-2A-GFP transgenic cell lines induced to be tracheary elements are followed for both GFP tagged nucleus presence coupled to brightfield morphology on the left panel and cell wall fluorescent signal using wheat-germ agglutinin coupled to Alexa633 on the right. 1 frame is taken every 10min during 33h allowing to sequentially observe cell elongation [0-350min], secondary cellulose deposition [390-1760min] and programmed cell death [1760-1770min]. Note the extensive cyclosis (cytoplasmic streaming) during the differentiation causing extreme nuclear movement.
|Figure 1: 3D confocal reconstruction of the cell wall of fully differentiated in vitro tracheary element. Reconstruction were made using xyz stack of tracheary element lignin autofluorescent using a Leica SP2 confocal microscope.
Pesquet E, Korolev AV, Calder G, Lloyd CW
The microtubule-associated protein AtMAP70-5 regulates secondary wall patterning in Arabidopsis wood cells. Current Biology: 2010 20:744-749 Endo S, Pesquet E, Tashiro G, Udagawa-Motose M, Kubo M, Fukuda H, Demura T
Identifying new components participating in the secondary cell wall formation of vessel elements in Zinnia and Arabidopsis. The Plant Cell: 2009 21:1155-1165 Endo S, Pesquet E, Tashiro G, Kuriyama H, Goffner D, Fukuda H, Demura T
Transient transformation and RNA silencing in Zinnia tracheary element differentiating cell cultures. The Plant Journal: 2008 53:864-875 Pesquet E, Ranocha P, Legay S, Digonnet C, Barbier O, Pichon M, Goffner D
Novel markers of xylogenesis in Zinnia are differentially regulated by auxin and cytokinin. Plant Physiology: 2005 139:1821-1839 Pesquet E, Barbier O, Ranocha P, Jauneau A, Goffner D
Multiple gene detection by in situ RT-PCR in isolated plant cells and tissues. The Plant Journal: 2004 39:947-959 Expand publications list
Stephanie Robert - Molecular mechanisms of cell elongation
Growth and development of an entire organism depend on coordinated expansion of individual cells. In plant, intracellular turgor pressure is believed to remain the same during growth and, the rate and direction of cell expansion is mainly determined by the surrounded cell wall properties. Our aim is to determine the molecular mechanisms underlying the regulation of cell elongation via understanding the processes regulating cell wall dynamics.
Part of these mechanisms relies on the plant endomembrane system such as synthesis and deposition of new material or trafficking of loosening enzymes (Figure 1).
||Figure 1: Endomembrane trafficking pathways and cell wall biosynthesis.
After their biosynthesis, cell wall components can go through different pathways (1. Delivery of soluble cargo and integral protein to plasma membrane, 2. Recycling of PM material (endocytosis/exocytosis), 3. Degradation of proteins through MVBs). Cellulose synthases (CESAs, light blue rosette) move along the actins filaments (in green) to reach the plasma membrane. Cortical microtubules (in dark-green) that lie beneath the membrane act rather like rails along which the CESA moves. The resulting cellulose aggregates to form fibres. The noncellulosic components are secreted to the cell surface and form a matrix assembled around the cellulose microfibrils. Picture adapted from a figure kindly given by Delphine Gendre (SLU, UPSC). Endoplasmic Reticulum (ER), Trans-Golgi-Network (TGN), Multivesicular Body (MVB).
(Click to enlarge)
However the mechanisms underlying the regulation of the endomembrane trafficking involved in cell wall biosynthesis and modulation remain poorly described. Dissecting rapid processes that target cellular components to their final destination is challenging for classical genetics experiments.Figure 2: Chemical genomics strategy used to study the endomembrane system. (Click to enlarge)
Thus, we decided to employ a chemical genetics strategy by using small molecules to modify or disrupt the function of specific proteins (Figure 2, Robert et al., 2009). The power of this approach is the ability to study protein function with precise control of response via bioactive chemicals.
Drakakaki G, Robert S, Szatmari A, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Y, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR (2011)
. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS: October 17, online publicationKitakura, S., Vanneste, S., Robert, S., Löfke, C., Teichmann, T, Tanaka, H., Friml, J. (2011)
Genetic dissection of the developmental roles of clathrin–mediated endocytosis in Arabidopsis. The Plant Cell, 23: 1920–1931Robert, S., Kleine-Vehn, J., Barbez, E., Sauer, M., Paciorek,T., Baster,P., Vanneste, S., Zhang, J., Simon, S., Covanova, M., Hayashi, H., Dhonukshe, P., Yang, Z., Bednarek, S., Jones, A., Luschnig, C., Aniento,F., Zazımalova, E., and Friml., J. (2010)
ABP1 Mediates Auxin Inhibition of Clathrin-Dependent Endocytosis in Arabidopsis. Cell, 143(1):111-21Robert S, Chary N, Drakakaki G, Yang Z, Raikhel N, Hicks G (2008)
. Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1. Proceedings of the National Academy of Sciences of the United States of America: 2008 105:8464-8469Robert S., Bichet A., Grandjean O., Kierskowski D., Satiat-Jeunmaitre B., Pelletier S., Hauser M-T., Höfte H., Vernhettes S. (2005
). An Arabidopsis endo-1,4-β-D-glucanase involved in cellulose synthesis undergoes regulated cellular cycling. The Plant Cell, 17(12): 3378-89Book chaptersDoyle, S., Robert S. (2012)
. Using mutant studies combined with chemical genetics.
Humana MiMB. In press.Haeger, A., Langowska, M., Robert, S. (2011)
. The use of chemical biology to study plant
cellular processes – subcellular trafficking. John Wiley & Sons Book. In press.Expand publications list
Göran Samuelsson - Photosynthetic Oxidation of Water
The goal of this project is to understand how plants can oxidize water to molecular oxygen, electrons and protons. Plants, green algae and cyanobacteria are unique in that they can use the energy in sunlight to oxidize water. This reaction occurs at a multi protein complex, photosystem II, in the chloroplast and is tightly regulated. If we can fully understand the mechanism of water oxidation and its regulation, we can use that knowledge to create artificial photosynthetic devices to produce clean and renewable energy.
Plants produce oxygen that is released to the atmosphere. Oxygen is important for most living organisms.
Photosystem II (PSII) uses sunlight to split water, an energetically unfavourable reaction in which electrons and protons are extracted from water and oxygen is released as a by-product. Understanding this process is crucial for the future development of clean, renewable and unlimited energy sources.
We have been focusing on the role of two lumenal proteins in the water oxidation process, PsbO and Cah3, which are associated with the thylakoid membrane. We have known for many years how electrons are transported in the photosynthetic light reactions, but we have very limited information on how the protons are transported.
Protons must be transported away from the catalytic cen- tre, otherwise the oxidation reaction cannot occur with full efficiency. If water oxidation is hampered, then donor side photoinhibition occurs and the whole photosynthetic machinery will be destroyed. Therefore, one of my tasks is to describe how protons, released in the water oxidation process, are transported away from the catalytic centre and into the lumen. We have recently presented convinc- ing evidence supporting the hypothesis that bicarbonate acts as a proton acceptor in the water-splitting process in PSII. Lumenal carbonic anhydrase, Cah3, identified by us, supplies bicarbonate required for this function. This was shown in one of our photosynthetic model organisms, Chlamydomonas reinhardtii.
Another important constituent of the water-oxidizing complex is the PsbO protein. This protein is conserved in all oxygen-producing organisms and has been studied for at least 20 years, but its function is still unknown. We believe that its role, in addition to stabilizing the Mn4Ca cluster in photosystem II, is to regulate transport of substrate-water to the catalytic centre and and to transport product-protons away from the water oxidation undergoes a pH-dependent conformational change that in turn has influence on its capacity to bind calcium and manganese. We propose that light-induced structural dynamics of the PsbO is of functional relevance for the regulation of proton release and for forming a proton-sensing proton transport pathway. The activities of both proteins may be redoxregulated through their S-S bridges.Protein trafficking
This project is related to protein trafficking in plant cells. Both chloroplasts and mitochondria have small genomes each coding for about 100 proteins,; far less than needed for their functions. This means that the majority of the organellar proteins must be imported from the cytosol. How are these proteins sorted to their correct destinations? The central dogma today is that they are expressed with a N-terminal tag that is recognized by a transporting complex in the chloroplast envelope. Based on experimental evidence, we have launched a theory that a small number of low abundance proteins take a route through the endoplasmic reticulum and the Golgi before entering the chloroplast stroma. We further postulate that these proteins are N-glycosylated. Exactly what signals are required to sort proteins through this pathway are unknown and my ambition is to get a deeper understanding of this.Svensk sammanfattning...
Karlsson J, Clarke AK, Chen* Z, Hugghins SY, Park SI, Husic D, Moroney* JV, Samuelsson G
(1998) A novel a-type carbonic anhydraseassociated with the thylakoid membrane in Chlamydomonas reinhardtii is required for growth at ambient CO2. EMBO J. 17: 1208-1216.Villarejo A, Shutova T, Moskvin O, Forssen M, Klimov VV, Samuelsson G
(2002) A Photosystem II associated Carbonic An- hydrase Regulates the efficiency of Photosynthetic Oxygen Evolution. EMBO J. 21: 1930-1938Shutova T, Nikitina J, Deikus G, Andersson B, Klimov V, Samuelsson G
(2005) Structural dynamics of the manganese-stabilizing protein - Effect of pH, calcium, and manganese. Biochemistry 44, 15182-15192.Villarejo A, Buren S, Larsson S, Dejardin A, Monne M, Rudhe C, Karlsson J, Jansson S, Lerouge P, Rollands N, von Heijne G, Grebe M, Bakó L, Samuelsson G
(2005) Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nature Cell Biology 7, 1124-1131Shutova T, Kenneweg H, Buchta J, Nikitina J, Terentyev V, Chernyshov S, Andersson B, Allakhverdiev S, Klimov VV, Dau H, Junge W, Samuelsson G
(2008) The Photosystem II-associated Cah3 in Chlamydomonas enhances the O2 evolution rate by proton removal. EMBO J. 27: 782–791Expand Publications list
Anita Sellstedt - Energy Production using Microorganisms
The aim of our research is to study energy production in microorganisms. We use an integrative approach with a combination of molecular biology, biochemistry and ecophysiology.Hydrogen metabolism of Frankia
The nitrogen-fixing filamentous actinobacteria of the genus Frankia form root nodules in symbioses with many woody trees and shrubs. Nitrogen fixation by actinorhizal plants may contribute as much as a quarter of the total biologically fixed nitrogen globally in terrestrial ecosystems each year. In addition, actinorhiza are major sources of new soil nitrogen in many different biomes.
The most important recent achievement in the Frankia research field is undoubtedly the sequencing of three Frankia genomes. We were able to show that there are large differences in the genome sizes. Frankia EANpec1 was found to have the largest genome with 9.0 Megabases (Mb), while Frankia ACN14a had an intermediate size (7.5 Mb) and Frankia HFPCcI3 was the smallest at 5.4 Mb. These numbers were correlated with geographical origin, host plant distribution and repeated sequences, such as IS. Our findings open up a new era in Frankia research, yielding possibilities to explore the molecular biology of Frankia and to utilize its traits, e.g. nitrogen fixation.
An inevitable source of energy-inefficiency in the nitrogen-fixation process is the evolution of hydrogen; as much as 25% of the in vitro electron flow through nitrogenase goes to hydrogen evolution, while in vivo these losses are much higher. Some nitrogen-fixing systems have dealt with this problem of energy loss through an enzyme, called uptake hydrogenase, which is very common in Frankia.
|Light micrograph of the bacterium Frankia showing vesicles.
||Light micrograph of our isolate of Chalara parvispora
We are interested in developing ethanol production from cellulose-based biomass. We have shown in a batch fermentation study that a fungal mix could produce 24 gL-1 ethanol using pulp waste as substrate. The fungal mix was able to grow on xylose, hemicellulose and cellulose. In addition, we were able to identify the fungi mix using PCR-amplification of DNA and sequencing as Chalara parvispora and Trametes hirsuta/T. versicolor. In a reconstitution study, the identified fungi were shown to produce equal amounts of ethanol as the fungi mix. In addition, it was shown that C. parvispora could produce ethanol from xylose.
The study shows that refining biomass by ethanol production from pulp waste, a lignocellulose material, can be increased by adding C. parvispora and T. versicolor, which is of great economic significance for energy production.Svensk sammanfattning
DeLuca TH, O Zackrisson, M-C Nilsson, A Sellstedt
2002. Quantifying nitrogen fixation in feather moss carpets. Nature. 419: 917-920.Mohapatra A, Leul M, Mattsson U, Sellstedt A
2004. A hydrogen-evolving enzyme is present in Frankia R43. FEMS Micro- biol. Lett.236: 235-240Leul M, Mattsson U, Sellstedt A
2005. Molecular characterization of uptake hydrogenase in Frankia. Biochem. Soc. Trans. 33: 64-66.Normand, Lapierre, Tisa, Lavire, Alloisio, Cournoyer, Marechal, Pujic, Gogarten,Huang, Mastronunzio, Bickhard, Bassi, Rawnsley, Niemann, Francino, Lapidus, Martinez, Goltsman, Choisne, Schenowitz, Couloux, Demange, Medigue, Cruveiller, Labarre, Rouy, Vallenet, Mullin, Kopp, Wang, Tomkins, Berry, Valverde, Wall, Sellstedt, Tavares Daubi, Benson
2007. Genome structure reflects host biogeography in three plant symbionts Frankia sp. strains. Genome Research, 17, 7-15.Leul M, Normand P, Sellstedt A
2009. The phylogeni of uptake hydrogenases. Int Microbiol. 12(1):23-28.Expand publications list
Eva Selstam - The Role of Lipids in the Plastid Membrane
My research deals with the properties of the chloroplast lipids and how they interact with proteins. One major objective is to understand the reason for the formation of the prolamellar body, a cubic membrane structure formed in etioplasts. Another is to elucidate the functions of the different lipids in the photosynthetic membrane.
Prolamellar body membranes in etioplasts of Arabidopsis.
The chloroplast and etioplast membranes differ in protein composition, but have the same characteristic lipid composition, with a large proportion of galactolipids and minor amounts of phospholipids and a sulpholipid. Approximately 50 % of the lipids are monogalactocyl diacylglycerols (MGDG), which form a reversed hexagonal phase with water, while the other lipids form a lamellar phase. This means that the plastid membranes have a lipid composition that is destabilised by high lateral pressure in the hydrophobic region. My interest is to find out if this physical property has an impact on the structure and function of the plastid membranes.
Recently we found that in a lipid mutant of Arabidopsis, where the content of MGDG has increased to over 60% of wild type level, the photosystem I protein complex was unstable. This instability was due to too high a concentrations of MGDG.
The ‘cubic’ prolamellar body membrane is also dependent on the lipid composition since, in a lipid phase diagram a cubic phase is stable between a lamellar and a reversed hexagonal phase. In light, the prolamellar body is transformed to a normal lamellar chloroplast membrane, the thylakoid. In vitro, we have been able to transform the prolamellar body and then reassemble it again. This means that we now can find out what factors are of vital importance for formation of the prolamellar body.Svensk sammanfattning
Williams, W.P., Selstam, E., Brain, T. Bras, W. & Bennett, P.
1998 X-ray diffraction studies of the struactural organisation of prolamellar bodies isolated from Zea mays. FEBS Lett 422:252-254Selstam E, Schelin J, Brain, T & Williams, WP.
2002. The effects of low pH on the properties of protochlorophyllide oxidoreductase and the organisation of prolamellar bodies of maize (Zea mays). Eur. J. Biochem. 269:2336-2346.Selstam E, Schelin J Williams, WP and Brain, T.
2007. Structural organisation of prolamellar bodies isolated from Zea mays. Parallel TEM, SAX and absorption spectra measurments on samples subjected to freeze-thaw, reduced pH and high-salt perturburation. Biochim. Biophys. Acta1768:2235-2245.Ivanov AG, Hendrickson L, Krol M, Selstam E, Oquist G, Hurry V and Huner NPA
. 2006 Digalactosyl-diacylglycerol deficiency impairs the capacity for photosyntetic intersys- tem electron transport and state transitionsin Arabidopsis thaliana due to photosystem I acceptor-side limitations. Plant Cell Physiol. 47:1146-1157.Hendrickson L,Vlcková A, Selstam E, Huner N, Oquist G and Hurry V.
2006. Cold acclimation of the Arabidopsis dgd1 mutant results in recovery from photosystem I-limited photosynthesis. FEBS Lett 580:4959-4968.Expand publications list
Marianne Sommarin - Molecular Stress Responses
Our research is focused on resolving how some vital processes in the plant cell membrane are regulated at the molecular level when plants are exposed to environmental stress.
Regulation of the plasma membrane proton pump (H+ATPase)
Localization and expression of the 14-3-3 isoform omega at different developmental stages of an Arabidopsis flower as visualized by GUS staining.
Plants have evolved a unique reliance on this pump, its function determines the function of all other transporters and channels in the membrane. Phosphorylation of the penultimate amino acid threonine in the autoinhibitory C terminus allows a 14-3-3 protein to bind which in turn results in activation of the proton pump. More than ten isoforms exist of both proton pumps and 14-3-3 proteins. Our goal is to understand the functional roles of the individual isoforms under different environmental regimes. We have indications that isoform specificity exists on tissue, organ, cell, and subcellular level as well as in the interaction between certain proton pumps and 14-3-3 isoforms.Lipid-derived signalling
In response to a variety of external factors/cues phosphoinositides (PIs; membrane phospholipids) can give rise to several important intracellular signalling molecules that in turn affects Ca2+ levels and the following actions of the cell. We study regulation of PI cycle enzymes such as phosphatidylinositol phosphate kinase (PIPK), an enzyme that produces the signalling molecule PtdIns(4, 5)P2. PIPK knock-out mutants of the moss Physcomitrella patens revealed the importance of PIs in cell type development, rhizoid growth, and sporophyte production.Ca2+ - binding proteins
The sensitivity and responses of the cell to various environmental stresses is often dependent on its ability to sequester and use Ca2+ from internal stores. We focus on the major Ca2+ -binding protein calreticulin, localised in the endoplasmic reticulum, with the aim to understand its detailed regulation and role in these processes as well as in protein folding. Arabidopsis has three isoforms and we have indications that they play complementary but also distinctly different roles, one of them seems to be involved in pathogenesis.Svensk sammanfattning
Alsterfjord M, Sehnke PC, Arkell A. Larsson H, Svennelid F, Rosenquist M, Ferl RJ, Sommarin M, Larsson C
(2004). 14- 3-3 and H+-ATPase isoforms associated with the Arabidopsis leaf plasma membrane. Evidence for isoform specificity in the 14-3-3/H+-ATPase interaction in vivo. Plant Cell Physiol 45: 1202-10Pical C, Westergren T, Dove SK, Larsson C, Sommarin M
(1999). Salinity and hyperosmotic stress induce rapid increases in phosphatidylinositol 4, 5-bisphosphate, diacylglycerol pyrophosphate, and phosphatidylcholine in Arabidopsis thaliana cells. J Biol Chem 274: 38232-38240Christensen A, Svensson K, Persson S, Michalak M, Jung J, Widell S, Sommarin M
(2008). Functional characterization of Arabidopsis Calreticulin1a: a key alleviator of endoplasmic reticulum stress. Plant Cell Physiol 49: 912-924Expand publications list
Åsa Strand - Plastid-to-Nucleus Signalling Pathways
The aim of our research is to dissect and elucidate the signalling pathways between the chloroplast and the nucleus that regulate the expression of nuclear genes encoding chloroplastic proteins. We use an integrative approach with a combination of genetics, molecular biology, cell biology and biochemistry to understand the language of the chloroplasts.
The function of the eukaryotic cell depends on the regulated and reciprocal interaction between its different compartments. This includes not only the exchange of metabolic intermediates and energy equivalents, but also information. The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression from the different genomes. The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast and the expression of these genes is influenced by developmental and environmental cues. In the photosynthetic electron transport complexes of the thylakoid membrane, the core subunits are encoded by the plastidic genome and the peripheral subunits are encoded by the nuclear genome. In the stroma, the large subunit of RUBISCO is encoded by the plastid, whereas the small subunit is nuclear encoded. To ensure that all these photosynthetic complexes are assembled stoichiometrically, and to enable their rapid reorganization in response to a changing environment, the activities of the nuclear and chloroplast genomes must be closely coordinated through intracellular signalling.
|Model of retrograde signalling between the chloroplast and the nucleus. The organelles produce multiple signals at different times of
their development, and in response to changes in the environment, that orchestrate major changes in nuclear gene expression.
|We use Arabidopsis thaliana as a model to understand the role of retrograde communication during plant stress responses
TEMs of Arabidopsis mesophyll cells showing the chloroplast structures
The necessity of a tight coordination of expression by the different genomes has led to the evolution of mechanisms to coordinate nuclear and organellar gene expression. These include both anterograde and retrograde controls. Anterograde mechanisms (nucleus-to-organelle) coordinate gene expression in the plastid, with cellular and environmental cues that are perceived and choreographed by proteins encoded in the nucleus. This type of traffic includes proteins that regulate the transcription and translation of organellar genes. Retrograde (organelle-to-nucleus) signalling, on the other hand, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the plastid and mitochondria through signals emitted from the organelles that regulate nuclear gene expression. It is now clear that several different plastid processes produce these signals and that plastid-to-nucleus communication appears to be of particular importance durng plant stress responses. The plastid signals identified so far can be linked to specific stress conditions, such as: 1) changes of the redox state of the chloroplast, 2) accumula- tion of reactive oxygen species and 3) perturbed flux through tetrapyrrole biosynthesis. The photosynthetic reactions housed in the chloroplasts are extremely sensitive to stress. The chloroplasts therefore act as sensors of environmental changes and complex networks of plastid signals coordinate cellular activities and assist the cell during plant stress responses. Our work suggests that information from both cytosolic and plastid signalling networks must be integrated for the plant cell to respond optimally to environmental stress. In my research group we are taking an integrative approach, using a combination of modern plant genetics, molecular biology, cell biology and biochemistry, to develop a comprehensive model for the plastid-to-nucleus signalling pathways during plant stress response.Svensk sammanfattning
Piñas Fernández A and Strand Å
(2008) Retrograde signaling and plant stress: plastid signals initiate cellular stress response. Curr. Opin. Plant Biol., 11:509-513Ankele E, Pesquet E, Kindgren P and Strand Å
(2007) In vivo visualization of Mg-ProtoporphyrinIX, a coordinator of photosynthetic gene expression in the nucleus and the chloroplast. Plant Cell, 19, 1964-1979.Kleine T, Kindgren P, Benedict C, Hendricksen L and Strand Å
(2007) Genome wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance. Plant Physiol., 144, 1391-1406.Strand Å
(2004). Plastid-to-nucleus signalling. Curr. Opin. Plant Biol., 7(6):621-625Strand Å, Asami T, Alonso J, Ecker JR, and Chory J
(2003) Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature, 421, 79-83.Expand publications list
Nathaniel Street - A Systems Genetics Approach to Understanding Natural Variation
Although we continue to explain the function of many genes individually within a molecular or functional context, we still know very little about how natural variation in complex phenotypes, such as biomass, is determined. QTL studies provide insights into the genetic architecture of complex trait control and tell us that most traits are controlled by a large number of loci and that, in most cases, we can only detect loci that together explain an average of less than half the variation that exists for most traits of interest.
The term missing heritability has been used to refer to the still unexplained 50 % variation. We are interested in identifying the genomic loci involved in controlling natural variation in traits, particularly at the level of gene expression. To do this, we take an approach termed systems genetics where the variation in expression levels, phenotype and genotype within natural populations is utilised in a combinatorial manner to identify polymorphisms underlying key control points, or hubs, within expression networks that result in phenotypic variation.
Gene expression control is highly complex and involves interacting factors such as genome structure, transcription factor binding, epigenetics and short RNAs. As a result we are interested in integrating all levels of information that we can obtain data for. Recently second-generation high throughput sequencing has had a profound influence on the nature and scale of data that can be obtained and much of our current effort involves generating, analysing and disseminating 'NGS' data.
Our current research focuses on using natural variation in Swedish aspen (Populus tremula
) as a model system to explore the control of trait variation. Leaf shape is a particularly suitable trait for study within this species as it is highly heritable and exhibits large-scale variation. We are also interested in using cross-species comparison and exploration of regulatory conservation as a means of identifying novel genes involved in trait control.
To support genome-wide association mapping and expression QTL mapping we are producing a de novo
assembly of the aspen and spruce genomes, including de novo
transcriptome assembly and genome annotation. As an associated activity we develop and maintain PopGenIE
Genome Ingerative Explorer), which is a web resource for the Populus genome and genomics data.
Street NR, Jansson S, Hvidsten TR. (2011)
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. BMC Plant Biology 11:13Klevebring D and Street NR*, Fahlgren N, Carrington JC, Lundeberg J, Jansson S. (2009)
Genome-wide profiling of Populus small RNAs. BMC Genomics 10:620Sjodin A and Street NR*, Sandberg G, Gustafasson P, Jansson S. (2009)
PopGenIE: A new resource for exploring the Populus genome. New Phytologist 182:1013-1025Street NR* and Sjodin A, Bylesjo M, Gustafsson P, Trygg J, Jansson S. (2008)
A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics 9:589
Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR (2008
) LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biology 48: 82Street NR, Ingvarsson PK (2011
) Association genetics of complex traits in plants. New Phytologist 189:909-922Expand List of publications..
Björn Sundberg - Wood Formation
Our research is focused on the developmental and biosynthetic regulation of secondary xylem (wood) formation. Wood biomass, fibre morphology, and ultrastructure and chemistry of cell walls are all industrially important properties determined during the woodforming process. Specific targets of our research are the physiological function and downstream signalling of endogenous ethylene in wood formation, cellulose biosynthesis in wood fibres, and novel tools for wood phenotyping.
Intrinsic control of cambial growth and wood development along the stem assures an appropriate stem form, and regulates the formation of juvenile and mature wood with their different chemical/physical properties. Superimposed on this intrinsic control are environmental factors that also strongly influence wood development. The mechanical and gravitational loads imposed by wind and by leaning stimulate both diameter growth and tension wood (TW) formation in dicotyledonous angiosperms. In addition to a striking increase in cambial cell divisions, TW fibres form an additional inner, cellulose-rich, gelatinous secondary cell-wall layer.
We are using in vitro grown aspen trees as an experimental system to perform pharmacological experiments and for initial screening of wood properties. Picture modified from PNAS 2009 106: 5984-5989
Plant hormones are important signaling molecules by mediating in mediating intrinsic and environmental controls of wood formation and an enduring research interest of the group. Trees respond to mechanical and gravitational load with the production of ethylene, which is followed by stimulation of tension wood formation. We therefore can use tension wood induction to unravel the physiology and downstream signaling associated with endogenous ehtylene production. We have demonstrated that ethylene is an endogenous signal stimulating cambial cell division, and thus diameter growth, in Populus. The same screening system allowed us to unravel the potential role of endogenous ethylene in the regulation of biosynthesis and ultrastructure of cell walls. We found that 20 ethylene response factors (ERFs) in stem tissues. which are induced by ethylene. As part of our exploration of downstream signalling in ethylene responses, we have identified 20 major ethylene response factors (ERFs) induced by applied ethylene in stem tissues. Transgenic Populus plants over- expressing these transcription factors have been phenotyped, using the in vitro system, and candidate genes causing growth and cell wall phenotypes have been selected for in-depth study. We have also demonstrated that ethylene stimulates cambial growth and modifies secondary walls in the Arabidopsis hypocotyls, and are using this model system for genetic analysis of ERF function and hormonal cross-talk.
Tension wood is formed in leaning stems. The fiber cell wall (A) forms a normal S2 layer, but has an inner wall layer of almost pure cellulose (G), without lignin and hemicelluloses. Individual cellulose microfibrils are seen in B. Picture modified from Current Opinion Plant Biology 2008 11: 293-300 was generously provided by Prof. Geoffrey Daniel, SLU Uppsala.
During TW fibre development, the biosynthetic machinery for lignin and hemicellulose is switched off as the cells deposit a new cellulose-enriched inner gelatinous wall layer. We have used the poplar microarray and tangential crysectioning to visualize gene expression across this developmental switch, and thereby differentiate between genes involved in cellulose versus hemicellulose/lignin biosynthesis. Bioinformatic analysis, T-DNA mutant screens in Arabidopsis and previous knowledge were used to find key candidate genes in cellulose biosynthesis.
These genes include PttMAP20, PttCobra-like4, PttAGP-FLAs and unknown proteins, which are now undergoing functional analysis in Arabidopsis and Populus, using genetic, cell biology, biochemical and chemical approaches.
The Sundberg group has been instrumental in establishing the infrastructure for a state-of-the-art carbohydrate/cell wall analysis facility in the UPSC environment to support cell wall research. In addition, this unit is involved in wood chemotyping of the UPSC collection of transgenic trees, as well as spruce and poplar populations for association genetics studies. We are also incorporating additional technologies for wood analysis, including chemical imaging by FT-IR microscopy and GC-MS pyrolysis combined with chemometric tools.Svensk sammanfattning
Uggla C, Moritz T, Sandberg G, Sundberg B
(1996). Auxin as a positional signal in pattern formation in plants.Proc. Natl. Acad. Sci. USA 93: 9282-9286.Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlen M, Teeri T, Lundberg J, Sundberg B, Nilsson P, Sandberg G
. (2001). A transcriptional roadmap to wood formation.Proc. Natl. Acad. Sci. USA 98: 14732-14737.Andersson Gunnerås S, Mellerowicz EJ, Ohmiya Y, Nilsson P, Henrissat B, Love J, Moritz T. and Sundberg B
. (2006). Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J 45: 144-165Rajangam AS, Kumar M, Aspeborg H, Guerriero G, Arvestad L, Pansri P, Brown CJ, Hober S, Blomqvist K, Divne C, Ezcurra I, Mellerowicz E, Sundberg B, Bolone V, Teeri TT
(2008). MAP20, a microtubule-associated protein in the secondary cell walls of Populus tremula L. x tremuloides Michx is a target of the cellulose synthesis inhibitor, 2,6-dichlorobenzonitrile. Plant Physiology 148(3):1283-1294.Love J, Bjorklund S, Vahala J, Hertzberg M, Kangasjärvi J, Sundberg B
(2009). Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus. Proc. Natl. Acad. Sci. USA 106: 5984-5989.Expand publications list
Hannele Tuominen - Xylem Maturation and Wood Properties
The last stage of xylem development is programmed death of the cells, which is followed by complete autolysis of the cell contents. Two cell types predominate in the xylem, the vessel elements and the fibres, and my earlier research in Populus trees has revealed that both of these cell types display programmed cell death (PCD), but in a very different manner. I am interested in why the xylem fibres have to die and the underlying molecular mechanism. From the biotechnological point of view, the fibres should stay alive as long as possible, assince extending the lifetime of the fibres is expected to result in thicker cell walls and therefore higher biomass yields of wood.
Identification of key regulators of xylem cell death should enable modifications in the cell death process using transgenic approaches, in order to test how they affect wood properties. This is especially tractable in xylem fibres, which constitute the main bulk of biomass.
We have taken three different approaches to identify key genes in the regulation of xylem cell death: one is based on knowledge from other PCD processes, mainly in Arabidopsis thaliana; one on sequencing of ESTs from Populus stem tissues undergoing fibre cell death, and the third isone based on microarray analyses of transcripts from various vascular tissues of Populus stems and comparative genom- ics approaches. These analyses have revealed novel putative regulators of xylem PCD, as well as several homologues of known PCD regulators, such as vacuolar processing enzymes, autophagy-related genes, Bcl-2-associated athanogene (BAG) genes and a metacaspase gene. Three candidate genes were selected from these genes for detailed functional and molecular characterisation, encoding: a metacaspase, a bifunctional nuclease, and a polyamine biosynthetic ACL5. The functions of the metacaspase and bifunctional nuclease genes are currently being studied with reverse genetics approaches in both Arabidopsis plants and Populus trees.
|A longitudinal section of Populus wood is shown here after staining with DAPI, which stains nuclear DNA. The contours of the longitudinal xylem fibers and the radially oriented xylem rays are revealed by unspecific staining of the cell walls. The nuclei of the xylem fibers are appressed against the cell wall due to the high pressure from the vacuole in the living cells. When the fibers die, the vacuole bursts and the remaining cellular contents are degraded by hydrolytic enzymes released from the vacuole.
||We have studied xylem maturation in a cell culture system where xylem vessel like structures, called tracheary elements (TEs), differentiate in a semi-synchronous manner after hormonal stimulus. This cell culture system has allowed us to define a critical role for ethylene in xylem maturation by using various pharmacological agents. The figure shows three mature TEs with spiral-type secondary cell wall thickenings.
We have identified a metacaspase gene that is specifically expressed in the xylem elements of both /Populus /and Arabidopsis. The figure shows a confocal microscope image of green fluorescent protein (GFP) expression that is driven by the Arabidopsis /metacaspase 9/ promoter in the Arabidopsis root. The GFP signal is located in the nuclei of the vessel elements that can be recognised by the spiral cell wall thickenings.
The polyamine biosynthetic ACL5 gene has been found to be specifically expressed in the early developing vessels, and a mutation in ACL5 resulted in altered xylem development. Results of xylem morphology analysis and experiments with the xylogenic Zinnia elegans cell culture (see below) lead us to conclude that ACL5 prevents premature death of the developing xylem vessels to allow complete differentiation. This model is supported by the finding that transgenic Arabidopsis plants expressing the DT-A toxin gene under the control of the ACL5 promoter display similar alterations in xylem development to the acl5 mutant.
We have also studied the role of the plant hormone ethylene in xylem differentiation. In an in vitro tracheary element (TE) differentiation system of Zinnia elegans, we showed that ethylene has an important role in the control of lignification and cell death of TEs, since application of ethylene signalling inhibitors blocked both of these processes. We also created suppressive subtractive hybridisation (SSH) libraries in Zinnia elegans, in order to identify genes that were
1) active during the cell death phase of vessel differentiation and 2) that were dependent on the cell-death stimulatory effect of ethylene. One gene fulfilling these criteria was a PIRIN gene that also showed activity during the xylem cell death stage in Populus. There are four PIRIN genes in Arabidopsis, and we have started functional characterisation of this whole gene family.Svensk sammanfattningSee list of publications
Gunnar Wingsle - Regulatory Proteins in the Lignification Process in Wood
Wood is a major source of renewable raw materials that are widely used in the pulp, paper, and timber industries. Poplar has emerged as the model tree for woody species, and molecular tools have been developed that allow breakthrough science in this forest tree. In my research, a major focus has been on proteins that have been shown to play a role in wood development and more specifically in lignin biosynthesis. A major objective has been to develop and use advanced proteomic approaches to study their roles and related biological questions.Reactive oxygen species (ROS)
ROS have recently been suggested to act as signalling molecules in the control of specialized processes, such as plant growth and defence, hormonal signalling, and development. Within the project, my group has explored the possibility to alter wood quality by the regulation of ROS at the plasmalemma/cell wall interface using transgenic methodology. A special type of superoxide dismutase with a high isoelectric point (hipI-SOD) has been mainly considered for this genetic manipulation due to its possible role as a regulator of hydrogen peroxide in the polymerization of lignin. Tthorough characterization of this protein in Poplar
has shown that it exists in two isoforms and in an additional spliced form. We are currently using these plants to study the underlying mechanisms of ROS-mediated regulation of cell wall development.Specific transcription-MYB
Another group of proteins that has been identified as central to the regulation of phenylpropanoid metabolism is the MYB transcription factor family. Each MYB transcription factor contains a conserved DNA-binding domain, located in the N-terminal part of the protein. Some R2R3 MYB proteins bind AC elements in the promoters of several genes of the phenylpropanoid pathway, and thus have been assigned functions in the regulation of phenylpropanoid biosynthesis. For instance, one of these genes, PttMYB21, was found to be much more highly expressed in the secondary cell wall formation zone of xylem and phloem fibres than in other developmental zones. PttMYB21a antisense transgenic plants showed a phenotype with altered growth and elevated levels of total lignin in their vascular tissues. One of the intriguing features of the transgenic plants was the presence of lignin compounds with increased degrees of methoxylation. Moreover, elevated levels of caffeoyl-CoA 3-O-methyltransferase transcripts were found in the transgenic plants, suggesting that PttMYB21a could act as a transcriptional repressor.
General transcription The Mediator
The Mediator and close functional relations between the Mediator modules and other transcriptional regulators (from Oudgenoeg et al. unpulished data)
In all eukaryotes, protein-encoding genes are transcribed by pol II. To perform its most basal functions, pol II requires five general transcription factors (GTFs). It is also now known that a Mediator, a 25 subunit protein complex, functions as a connector between the promoter-bound transcriptional regulators and pol II. The Mediator was first identified in Saccharomyces as an activity required for transcriptional activation in vitro. Later, it was identified as a multiprotein complex that provides an interface for activator and repressor proteins to transmit information from regulatory DNA elements to core promoters. A number of studies have determined that the Mediator is composed of three modules designated as “tail”, “head”, and “middle”. It is important for transcription control, modulating the frequency of initiation in responses to both positive and negative regulatory factors. Surprisingly, prior to our publication (Bäckstrom et al. 2007), there were had been no reports of the Mediator in plants. We are now studying Mediators that seems to play a role in lignin biosynthesis and wood development in Arabidopsis and Poplar.Svensk sammanfattning
Karpinska B, Karlsson M, Srivastava M, Stenberg A, Schrader J, Sterky F, Bhalerao R, Wingsle G
(2004) MYB transcrip- tion factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen. Plant Molecular Biology 56; 255-270.Bäckström S, Elfving N, Nilsson R, Wingsle G, Björklund S
(2007) Purification of mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol Cell 26: 717-729Bylesjö M, Nilsson R, Srivastava V, Grönlund A, Johansson AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J.
(2009) Integrated Analysis of Transcript, Protein and Metabolite Data to Study Lignin Biosynthesis in Hybrid Aspen. J. Prot. Res. 8:199-210.Srivastava V, Srivastav MK, Chibani K, Nilsson R, Melzer M, Wingsle G
(2009) Alternative Splicing Studies of the ROS Gene Network in Populus Reveals Two Isoforms of High Iso-electric point Superoxide Dismutase. Plant Physiol. 149: 1848-1859.Srivastava V, Schinkel H, Witzell J, Hertzberg M, Torp M, Srivastava MK, Karpinska B, Melzer M, Wingsle G
(2007) Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen. Plant J 49: 135-148Expand publications list
Harry Wu - Quantitative genetics and tree breeding
Our group conducts research on forest genetics and tree breeding through understanding and dissecting genetic base of genetic variation for quantitative traits, including tree growth and form traits, wood quality traits, phenology traits, and biotic and abiotic resistance traits. The starting point is to investigate the genetic base of the phenotypic variation we observed between individual trees in forest stands. The first question we ask is how much of this variation between individual trees is due to genetic differences, and how much due to environmental factors. Then we need to find out the number of genes that are responsible for the genetic variation, and how these genes interact to influence the performance of trees in different environments. This basic knowledge can then be used in the design of breeding programmes for increased growth rate and quality of wood products in forest plantations.
To design efficient breeding programmes and to increase genetic gain, we also need to identify the best native tree populations for selection and breeding for a specific forest region. This involves research on genotype by environment interaction and on response curves of existing populations and genotypes, so that we can delineate optimal breeding trees (population) that match the environment (breeding zone). After assembling a breeding population for further improvement, we need to design the best breeding strategy. We not only have to select the individuals that we want to use as a parent, to produce the best progeny, we also need to identify the ideal combinations of parents (mating design). Furthermore, we need to deal with inbreeding depression.
Another important question we need to address is how to deal with improvement of multiple traits that are adversely related, such as wood quantity vs. wood quality. First we need to find out the genetic causes of such correlation, using quantitative and molecular tools. Then we develop a gene model (locus and parametric model) and use simulations to identify the best selection and mating methods for dealing with such adversely correlated multiple traits. We also study the suitability of different mating and selection methods when it comes to avoiding or removing inbreeding depression in advanced breeding programmes.
With the advance of gene sequencing technology, we start to study associations between individual genes or gene complexes with phenotype variation in trees. We study candidate genes or genome-wide approach to increase knowledge about the association between variations in DNA and observable phenotype variation. In addition, we are developing a quantitative genetics tool that integrates DNA sequence-based variation with phenotypic data, in order to improve the efficiency of genetic improvement in trees. This involves the development of advanced methods for breeding value prediction, such as genomic Best Linear Unbiased Prediction (G-BLUP) and Genome-wide Breeding Value (GBV). Expand publications list