Anita Sellstedt in the KBC cafeteria

Sellstedt, Anita - Energy Production by Microorganisms

Research

Anita Sellstedt in the KBC cafeteriaPhoto: Fredrik Larsson

The aim of our research is to study energy production in microorganisms. The research covers several projects, of which the three main projects will briefly be presented below.

Hydrogen metabolism of Frankia

Nitrogen fixation occurs in Frankia both in free-living as well as in symbioses and may contribute as much as a quarter of the total yearly biologically fixed nitrogen globally in terrestrial ecosystem.

The most important recent achievement in the Frankia research field is 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 Mb, while Frankia ACN14a had an intermediate size of 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.

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. Some nitrogen-fixing systems have dealt with this problem of energy loss through evolving an extra enzyme, called uptake hydrogenase, which is very common in Frankia.

Round vesicles of the bacterium Frankia are shown on the left side and elongated cells of Chalara parvispora on the right side. Left: Light micrograph of the bacterium Frankia showing vesicles; right: Light micrograph of our isolate of Chalara parvispora

Cyanobacteria in association with boreal mosses

We were able to discover that cyanobacteria live in association with feather mosses in the boreal area. We also discovered that they are able of fixing nitrogen and thereby contributing to the N status of that ecosystem.

Heterotrophic production of lipids by algae

Algae are commonly autotrophic carbon dioxide fixing prokaryotes. They are also able of storing different compounds under a variety of conditions. This year a Thesis from my laboratory revealed that some microalgae are able to use glycerol as a carbon source under growing in heterotrophic conditions. Interestingly, a microalgae isolated in the lab and originating from Umeå area has this trait and also accumulated significant amounts of lipids under this condition.


Key Publications

  • Leul M, Normand P, Sellstedt A (2009). The phylogeny of uptake hydrogenases. Int Microbiol. 12(1): 23-28.
  • Normand et al., (2007). Genome structure reflects host biogeography in three plant symbionts Frankia sp. strains. Genome Research, 17, 7-15.
  • Mohapatra A, Leul M, Mattsson U, Sellstedt A (2004). A hydrogen-evolving enzyme is present in Frankia R43. FEMS Microbiol.Lett.236: 235-240
  • DeLuca TH, O Zackrisson, M-C Nilsson, A Sellstedt (2002). Quantifying nitrogen fixation in feather moss carpets. Nature. 419: 917-920.
  • Nzayisenga JC, Eriksson K, Sellstedt A. 2018. Mixotrophic and heterotrophic production of lipids and carbohydrates by a locally isolated microalga using wastewater as growth medium. Bioresource Technology 257: 260-265.
Nathaniel Street in the UPSC bioinformatics office

Street, Nathaniel - A Systems Genetics Approach to Understanding Natural Variation

Research

Nathaniel Street in the UPSC bioinformatics office Photo: Fredrik Larsson

Our group has a focus on genomics research of aspen, Norway spruce and Scots pine. We perform genome assembly, transcriptome and co-expression network analyses with a focus on understanding the genetic architecture of complex traits such as leaf shape variation, wood development and specialised metabolite production and the role of non-coding RNAs in regulation and genome function.

Through collaboration with Prof. Vaughan Hurry we are also performing metagenomics and metatranscriptomics analyses to understand functional links between tree hosts, their associated microbiome and abiotic factors. The group have a strong interest in applications of new sequencing technologies and develop the PlantGenIE.org web resource to make their genomics data available to the community.

We make extensive use of bioinformatics and computational approaches including machine learning, GWAS, network inference, differential, network analysis and a plethora of genome assembly and comparative genomics analysis tools. These approaches are implemented using genomic DNA, RNA-Seq, ATAC-Seq, DAP-Seq, Hi-C and other high-throughput based sequencing methods.

Five photos of aspen buds showing a closed bud on the left followed by different stages of bud burst towards the right side.Stages of leaf development in aspen. We are performing detailed characterisation of developmental profiles in aspen to support our association mapping project and to further understanding of genes functioning during leaf development.

We are also working to establish wet lab methods for validation of candidate genes and regulatory mechanisms identified from our in-silico work. The group are firm believers in implementing reproducible and transparent analyses through the use of resources such as snakmake/nextflow, git and by developing FAIR compliant tools. We make extensive use of R, python and high performance computing infrastructures.

Collection of differently formed leavesRepresentative leaf shapes from the Swedish Aspen collection, a collection of natural aspen genotypes from across Sweden that is grown in a common garden experiment near Umeå You can find out more about us at the group web site
Annika Nordin in a winter forest

Nordin, Annika - Forests in the changing climate

Research

Annika Nordin in a winter forestPhoto: Malin Grönborg

Forests are key to CO2 sequestration and how forests are managed influence their potential benefits for mitigating climate change, alongside with their numerous other benefits for people. In my research group we study both forests and forest management visions and decisions by people with different stakes in the forests. Our background is in forest ecophysiology, but we have long experience in interdisciplinary science and successful collaborations with colleagues in social and human sciences.

Our current focus areas are (1) carbon and nitrogen interactions in trees, understory vegetation and soils and how they influence forest growth, (2) new methods for forest regeneration, and (3) local stakeholders’ adaption of forest management to the changing climate.

The left photo shows a close-up of the moss Hylocomium splendens; in the middle, seedlings on a clear-cut site are shown; on the right, a group of people meeting for a presentation in a forest is seen. A) The moss, Hylocomium splendens, has a key role in the forest influencing litter decomposition and soil carbon accumulation as well as the nitrogen supply as it associates to N2-fixing cyanobacteria. We use ecophysiological approaches to study how interactions between the forest’s carbon and nitrogen cycles determine tree growth, understorey species composition and soil carbon accumulation. (Photo: Sverker Johansson) B) Seedlings on a clear-cut are subjected to harsh environmental conditions and large fluctuations in water and nutrient supply. Innovative methods based on new ecophysiological findings on how various nitrogen sources contribute to the seedlings’ successful establishment and growth direct our research activities in forest regeneration. (Photo: Bodil Häggström) C) Forests adaptation to the changing climate depend also on people’s visions on how forests should be managed. In an interdisciplinary project we focus on how stakeholders locally in northern and southern Sweden envision their future forests. (Photo: Lars Klingström)
Stéphanie Robert next to a microscope

Robert, Stéphanie - Regulation of plant cell shape acquisition

Research

Stéphanie Robert next to a microscopePhoto: Erik Abel

The aim of our research is to elucidate the molecular mechanisms underlying the regulation of plant morphogenesis via understanding the process of cell shape acquisition and its associated signaling pathways. We are particularly focusing our studies on auxin transport and signaling and cell wall function in cell shape acquisition. Most of our work is established on the model plant Arabidopsis thaliana but we also work on poplar and lupin. Have also a look on our external group homepage: https://srobertgroup.com

Understanding how various cell types precisely emerge in optimal forms at the right time and location is one of the most importamt questions in developmental biology. This process serves as the foundation of morphogenesis in multicellular organisms. Plants, in particular, exhibit remarkable adaptability, enabling them to adjust their developmental patterns to swiftly changing environments. This adaptability is facilitated by a series of morphological modifications governing the growth of organs like leaves, roots, and stems. Achieving proper morphogenesis is based on the synchronised orchestration of cell expansion, shape acquisition, and fate determination within individual cells.

Using cell biology, classical genetics and chemical genomics approaches we aim to elucidate the molecular mechanisms underlying the regulation of plant morphogenesis via understanding the process of cell shape acquisition and its associated signaling pathways. We are particularly focusing our studies on auxin transport and signaling, endomembrane trafficking and cell wall/cuticle function in cell shape acquisition.


Collage of four photos showing a 24-well plate with one seedling growing in every well is shown on the left, a microscope image of an Arabidopsis root on the second left, a microscope image of an apical hook on the second right and jigsaw-puzzle-shaped leaf pavement cells on the right. Figure legend: A) Chemical screening in a 24-well plate. The chemical genomics approach uses small molecules for rapid dissection of biological mechanisms and gene networks in ways not feasible with mutation-based approaches (picture: Siamsa Doyle).; B) Confocal microscopy image of Arabidopsis thaliana root- Immunostain labeling of PIN-FORMED 1 (purple) and 2 (blue) (picture: Siamsa Doyle); C) Confocal microscopy image of Arabidopsis thaliana apical hook - Propidium iodide staining (white) highlights the plasma membrane of epidermal cells (picture: Sara Raggi); D) Confocal microscopy image of Arabidopsis thaliana leaf pavement cells - The Arabidopsis line imaged expresses an auxin response marker in the nucleus (blue to green/yellow). The plasma membrane is stained with propidium iodide (red) (picture: Zahra Rahneshan).

Our work is funded by generous support from:

KAW Logotype enLOGO ERC FLAG FPKempestiftelserna Logo SVcarl tryggers stiftelse logologotyp vetenskapsrådet stående ENG RGB 1000px


Totte Niittylä behind aspen trees

Niittylä, Totte - Carbon Allocation and Metabolism

Research

Totte Niittylä behind aspen treesPhoto: Fredrik Larsson

Carbon allocation is a fundamental physiological process in tree growth. Carbon allocation at tree level cascades across scales to ecosystems and global carbon cycle. In my group we investigate the genetic, biochemical and physiological processes linking metabolism and carbon allocation in trees.

We apply a combination of genomics, metabolomics and fluxomics tools to identify genes, enzymes and pathways which are central in carbon allocation to woody biomass. We use aspen as a model in most of our tree work, while Arabidopsis is used to address fundamental questions linked to metabolism and cell wall biosynthesis. Our Arabidopsis work has recently focused on starch and sucrose metabolism as well as carbohydrate active enzymes involved in the biosynthesis of arabinogalactan proteins (AGPs), and the relationship between AGP glycosylation and cellulose biosynthesis.

Collage of three photos showing wood of plants in different resolutionsA) Light microscopy picture of aspen wood fibers and vessels; B) Cross section of Arabidopsis stem. Lignified cell walls are shown in red and non-lignified in blue; C) Cross section of aspen stem.

In addition to the cell wall and metabolism centric work on carbon allocation, we also explore overlooked fundamental processes in plant growth. One third of the genes in the model plant Arabidopsis remain of unknown function. Our ambition is to push new inroads to this unknown gene space. We are particularly interested in identifying essential genes, which are indispensable in dividing and growing plant cells.

Collage with different microscopic images characterising the newly identified gene OPENERSiliques of wild type Arabidopsis and opnr-1 showing the seed abortion phenotype (left). Elongated zygotes of wild type and opnr-1 (middle). Confocal microscopy images showing the dual localisation of OPNR in nuclear envelope and mitochondria labelled with PHB3-mCherry (right)

Our approach is to investigate evolutionarily-conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. Evolutionarily-conserved single copy genes in flowering plants have been shown to be enriched in essential housekeeping functions. This exploratory project has led us to new areas of cell biology.

Our current focus is on understanding the function of an essential gene we named OPENER (OPNR). opnr mutants show zygotic lethality and endosperm arrest, and intriguingly OPNR localizes to both nuclear envelope and mitochondria pointing to an essential process occurring on both nucleus and mitochondria in dividing plant cells.

Recent Key Publications

  • Wang, W., Mahboubi, A., Zhu, S., Hanson, J., Mateus, A., Niittylä, T. (2025). Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized OPENER complex. Nature Communications, 16(1): 7301. doi.org/10.1038/s41467-025-62652-7   
  • Wang W, Talide L, Viljamaa S, Niittylä T (2022). Aspen growth is not limited by starch reserves. Current Biology, 32(16): 3619-3627 doi.org/10.1016/j.cub.2022.06.056
  • Fünfgeld MMFF, Wang W, Ishihara H, Arrivault S, Feil R, Smith AM, Stitt M, Lunn JE, Niittylä T. (2022). Sucrose synthases are not involved in starch synthesis in Arabidopsis Nature Plants, 8(5): 574–582. doi.org/10.1038/s41477-022-01140-y  
  • Dominquez PG, Evgeniy D, Derba-Maceluch M, Bünder A, Hedenström M, Tomášková I, Mellerowicz EJ, Niittylä T (2021). Sucrose synthase determines carbon allocation in developing wood and alters carbon flow at the whole tree level in aspen. New Phytologist, 229: 186-198. https://doi.org/10.1111/nph.16721
  • Nibbering P, Petersen BL, Mohammed SM, Jørgensen B, Ulvskov P, Niittylä T (2020). Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in Arabidopsis. Journal of Biological Chemistry, 295: 10581-10592. https://doi.org/10.1074/jbc.ra120.013878
  • Wang W, Zhang X, Niittylä T (2019). OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis. Plant Cell, 31:1446-1465. https://doi.org/10.1105/tpc.19.00033
Ove Nilsson with aspen trees at the tree phenotyping platform

Nilsson, Ove - Control of Flowering Time and Tree Phenology

Research

Ove Nilsson with aspen trees at the tree phenotyping platformPhoto: Fredrik Larsson

The research in my group is focused on understanding the regulation of flowering time and tree phenology, with a special interest in comparative biology studies of the genetic pathways that are conserved in controlling the two processes. With this approach we aim to contribute to our understanding of the evolution of annual vs. perennial life strategies.

My group has a special interest in the regulation and function of FT-like genes. We contributed to the first studies of the molecular mechanisms controlling flowering time in trees, showing that FT-like genes, that are central in the regulation of flowering time in annual plants, are functionally conserved in being very potent activators of flowering in trees.

Surprisingly, we could also show that FT-like genes in poplar trees control 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 partly 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. These findings have led to a completely new way of looking at the function of FT-like genes.

Four Poplars in four seasons

Subsequent studies in many different annual plants have now shown that these genes have a much more general role in controlling photoperiodic regulation of plant growth and development than was previously anticipated, based on work in Arabidopsis. We could also show that in sugar beet, only a two amino acid difference is critical in determining the sub-functionalization of two FT paralogs into either activators or repressors of flowering, and that the flowering repressor BvFT1 has a central role in the regulation of the biennial growth strategy in sugar beet.

Folding prediction of BvFT1 and BvFT2. The structures are shown as solid three-dimensional traces with an alignment diversity color setting. Down-regulation of BvFT2 by RNAi of BvFT1 result in bolting repression in sugar beet. 400-day old BvFT2 RNAi annual plant grown under long-day conditions.

We are now extending our comparative biology approach to study the similarities and differences in the regulation of flowering in Arabidopsis and the regulation of flowering and phenology in aspen (poplar) trees. Aspen trees have also two sub-functionalized FT-like genes, and we want to understand how these genes contribute to the regulation of growth cessation and bud set in the fall, as well as to the regulation of bud flush and growth in the spring.

Transgenic hybrid aspen tree forming inflorescences and flowers after 6 months instead of after 10-15 years. Bud burst on an aspen branch - The Nilsson group is studying the genes controlling growth cessation, bud set and bud burst in trees

We have also been involved in work showing that polymorphisms within one of the FT-like genes is the most important association that can be found to natural variation in adaptation to growth at different latitudes in Swedish aspen trees. We are investigating the mechanism for this adaptation in detail by studying the role of upstream regulators in the regulation of FT transcription in trees. We have also a long standing interest in extending this work to gymnosperm trees, like Norway spruce. Here, I have been involved in leading several large projects determining the genome sequences and developing genomic resources of conifers, including the first sequence of a gymnosperm, Norway spruce.

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.


Key publications

  • André, D., Marcon, A., Lee, K. C., Goretti, D., Zhang, B., Delhomme, N., Schmid, M., and Nilsson, O. (2022). FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees. Current Biology 32: 2988-2996. https://doi.org/10.1016/j.cub.2022.05.023
  • Ding, J., Zhang, B., Li, Y., André, D. and Nilsson, O. (2021). Phytochrome B and PHYTOCHROME INTERACTING FACTOR8 modulate seasonal growth in trees. New Phytologist 232: 2339-52. https://doi.org/10.1111/nph.17350
  • Ding, J., Böhlenius, H., Rühl, M., Chen, P., Sane, S., Zambrano, J., Zheng, B., Eriksson, M. and Nilsson, O. (2018). GIGANTEA-like genes control seasonal growth cessation in Populus. New Phytologist 218: 1491-1503. https://doi.org/10.1111/nph.15087
  • Zhang, B., Holmlund, M., Lorrain, S., Norberg, M., Bakó, L., Fankhauser, C. and Nilsson, O. (2017). BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR4 abundance. eLife 6:e26759. https://doi.org/10.7554/elife.26759
  • Nystedt B., Street N. et al. (2013). The Norway spruce genome sequence gives insights into conifer genome evolution. Nature 497: 579-584. (Nilsson O. Corresponding author). https://doi.org/10.1038/nature12211
  • Pin P.A., Benlloch R., Bonnet D., Wremert-Weich E., Kraft T., Gielen J.L., Nilsson O. (2010). An antagonistic pair of FT homologs mediates the control of flowering time in sugar beet. Science 330: 1397-1400. https://doi.org/10.1126/science.1197004
  • Tuskan, G.A. et al. (The Populus Genome Consortium). 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 13: 1596-1604. https://doi.org/10.1126/science.1128691
  • Eriksson, 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: 2172-2181. https://doi.org/10.1105/tpc.106.042317
  • Böhlenius, H., Huang, T., Charbonnel-Campaa, L., Brunner, A.M., Jansson, S., Strauss, S.H., Nilsson, O. 2006. The conserved CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312: 1040-1043 https://doi.org/10.1126/science.1126038
  • 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: 2203-2201. https://doi.org/10.1242/dev.01815
  • Parcy, F., Nilsson, O., Busch, M. A., Lee, I. & Weigel, D. (1998). A genetic framework for floral patterning. Nature 395, 561-566. https://doi.org/10.1038/26903
  • Weigel, D. & Nilsson, O. 1995. A developmental switch sufficient for flower initiation in diverse plants. Nature 377, 495-500. https://doi.org/10.1038/377495a0
Portrait photo of Karin Ljung in an outdoor environment

Ljung, Karin - Root Development and Shoot-Root Communication

Research

Karin Ljung in an outdoor environmentPhoto: Elisabeth Ohlson Wallin

My research is focused on mechanisms regulating plant growth and development, especially root development, and the roles played by plant growth regulating substances (plant hormones) in the developmental processes that lead to the formation of the root system.

Over the years, my research has continuously been focused on mechanisms that regulate plant growth and development. In particular, I am interested in two key mechanisms: i) The roles played by plant hormones in primary and secondary root development; and ii) The role of plant hormones in the integrative coordination of above and below ground growth. In order to answer fundamental questions, e.g. how lateral roots are initiated, my group is employing Arabidopsis thaliana as a model organism, but we have recently started to translate this research also into trees and crops.

Auxins and cytokinins are plant hormones that are essential throughout the whole life cycle of higher plants. They play pivotal roles in key growth and developmental processes, and they are central to coordinate responses to different environmental variables. Both hormones act in a concentration-dependent manner, and a complex range of regulatory mechanisms act in concert to ensure that the levels of these compounds are optimal for growth and development. We are studying auxin and cytokinin metabolism, transport and signalling, how these processes are regulated by internal and external signals, and how they influence primary and secondary root development. Recently, my team discovered an enzyme responsible for auxin degradation, DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), which opens up the possibility to regulate auxin homeostasis in plants via the auxin degradation pathways. Potentially, this can lead to new ways of modifying the root system architecture.

We have recently developed methods for plant hormone profiling in very small amounts of plant tissues, using liquid chromatography coupled to tandem mass spectrometry analysis (LC-MS/MS). We have also developed techniques for using Fluorescent Activated Cell Sorting (FACS) in combination with mass spectrometry analysis to analyse auxin and cytokinin distribution and metabolism within the Arabidopsis root at cellular and sub-cellular resolution. The formation of local hormone gradients and maxima/minima in developing plant tissues has been shown to be very important for organogenesis, through the coordinated regulation of cell division, cell differentiation and cell elongation.


Schematic overview of the procedure to use isolated protoplasts and cell sorting (FACS) as tool to study metabolites and gene and protein networks
“Isolation of cell‐type specific populations from Arabidopsis thaliana root tissues using protoplasting and FACS-sorting for applications in protoplast regeneration and different omics technologies.” Published in: Fluorescence activated cell sorting - A selective tool for plant cell isolation and analysis. Ioanna Antoniadi, Vladimír Skalický, Guiling Sun, Wen Ma, David W. Galbraith, Ondřej Novák, Karin Ljung. (2022). Cytometry Part A, Volume: 101, Issue: 9, Pages: 725-736.

Key publications

  • Antoniadi I, Mateo-Bonmatí E, Pernisová M, Brunoni F, Antoniadi M, Villalonga M, Ament A, Karády M, Turnbull C, Doležal K, Pěnčík A, Ljung K, Novák O. (2022). IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth. Frontiers in Plant Science, 13
  • Casanova-Sáez, R., Mateo-Bonmatí, E., Šimura, J., Pěnčík, A., Novák, O., & Ljung, K. (2022). Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit. New Phytologist, 235(1): 263–275
  • Pařízková, B., Antoniadi, I., Poxson, D. J., Karady, M., Simon, D. T., Zatloukal, M., Strnad, M., Doležal, K., Novák, O., & Ljung, K. (2022) iP & OEIP – Cytokinin Micro Application Modulates Root Development with High Spatial Resolution. Adv. Mat. Techn., 7 (10), 2101664
  • Antoniadi, I., Skalický, V., Sun, G., Ma, W., Galbraith, D. W., Novák, O., & Ljung, K. (2022). Fluorescence activated cell sorting - A selective tool for plant cell isolation and analysis. Cytometry Part A, 101(9): 725–736.
  • Mateo-Bonmatí, E., Casanova-Sáez, R., Šimura, J., & Ljung, K. (2021). Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development. The New Phytologist, 232 (2): 642-654.
  • Brunoni F, Collani S, Casanova-Sáez R, Šimura J, Karady M, Schmid M, Ljung K, Bellini C. (2020). Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. New Phytol., 226(6):1753-1765
  • Antoniadi I, Novák O, Gelová Z, Johnson A, Plíha O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Frim J, Doležal K, Ljung K, Turnbull C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nat Commun, 11(1):4284
  • Pencík A, Casanova-Sáez R, Pilarová V, Žukauskaite A, Pinto R, Luis Micol J, Ljung K, Novák O. (2018). Ultra-Rapid Auxin Metabolite Profiling for High-Throughput Arabidopsis Mutant Screening. J Exp Bot., 69 (10):2569-2579
  • Šimura J, Antoniadi I, Široká J, Tarkowská D, Strnad M, Ljung K, Novák O. (2018). Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics. Plant Physiol. 177: 476-489.
  • Poxson D J, Karady M, Gabrielsson R, Alkattan A Y, Gustavsson A, Doyle S M, Robert S, Ljung K, Grebe M, Simon D T, Berggren M. (2017). Regulating plant physiology with organic electronics. PNAS, 114(18):4597-4602
  • Novák O, Antoniadi I, Ljung K. (2017). High-Resolution Cell-Type Specific Analysis of Cytokinins in Sorted Root Cell Populations of Arabidopsis thaliana. Methods Mol Biol 1497: 231-248.
  • Novák O, Napier R, Ljung K. (2017). Zooming In on Plant Hormone Analysis: Tissue- and Cell-Specific Approaches. Annu Rev Plant Biol 68: 323-348.
  • Porco S, Pěnčík A, Rashed A, Voß U, Casanova-Sáez R, Bishopp A, Golebiowska A, Bhosale R, Swarup R, Swarup K, Peňáková P, Novák O, Staswick P, Hedden P, Phillips AL, Vissenberg K, Bennett MJ, Ljung K. (2016). Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis. Proc Natl Acad Sci U S A 113: 11016-21.
  • Petersson SV, Lindén P, Moritz T, Ljung K. (2015) Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology. Metabolomics 11: 1679-1689.
  • Antoniadi I, Plačková L, Simonovik B, Doležal K, Turnbull C, Ljung K*, Novák O* (2015). Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex. Plant Cell 27:1955-67.
  • Pencík A, Simonovik B, Petersson SV, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zazímalová E, Novák O, Sandberg G and Ljung K (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell 25: 3858-3870
  • Sairanen I, Novák O, Pencík A, Ikeda Y, Jones B, Sandberg G and Ljung K (2012). Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis. Plant Cell 24: 4907-4916.
  • Novák O, Hényková E, Sairanen I, Kowalczyk M, Pospíšil T and Ljung K (2012). Tissue-specific profiling of the Arabidopsis thaliana auxin metabolome. Plant J. 72: 523-536.
  • Jones B, Andersson Gunnerås S, Petersson SV, Tarkowski P, Graham N, May S, Dolezal K, Sandberg G and Ljung K (2010). Cytokinin regulation of auxin synthesis in Arabidopsis involves a homeostatic feedback loop regulated via auxin and cytokinin signal transduction. Plant Cell 22: 2956-2969.
  • Petersson SV, Johansson AI, Kowalczyk K, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G and 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.

Supplemental Resources
 xlsxParizkova_et_al_Data_repository.xlsx1.79 MB20/12/2024, 08:29_

Portrait of Benedicte Riber Albrectsen with a dog cowering next to plant cultivation boxes

Albrectsen, Benedicte Riber - Populus Resistance to Biotic Stress

Research

Portrait of Benedicte Riber Albrectsen with a dog cowering next to plant cultivation boxesPhoto: Mattias Petterson

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 natural habitats may be increasingly challenged. 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 tremula, Salix spp., and Brassica nigra.

Trait association studies and large-scale patterns in Populus

We relate a number of phenotypic traits measured on aspen (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, biotic and abiotic 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. Extreme clones (with intensive growth, early bud set, heavy damage by certain antagonists etc.) have been identified for later experimentation in bioassays. We also perform network analyses to understand the arthropod associated communities of our aspen genotypes and chemotypes.

Chemical profiling

We profile the metabolome in Populus, Salix and Brassica especially targeting natural products that may shape resistance to biotic stress. We are interested in the genetics of chemotypes within populations of aspen and between Salix species that display differences in resistance properties against arthropod herbivores and various micro-fungi. We are also interested in getting an organismal perspective on allocation responses in plants in response to various stresses including volatile emissions and induction of various metabolic pools. We use GC/MS to evaluate volatile emissions and general chemical profiles and LC/MS for profiling of specialized natural products (mainly phenolics and glucosinolates).

Studies on induced responses in aspen

We challenge genotypes that display extreme phenotypes by introducing antagonists in whole plant assays or on detached leaves. In aspen, we have for example worked with the aphid Quitophorous populetii the Chrysomela beetles, and the disease Melampsora magnusiana. The aim with these studies is to compare genotypic specific responses in the metabolome to different types of damage, and to test theories on resource allocation to growth and defence.
We have cultured the leaf beetle Chrysomela tremulae and three aphid species of the Quitophorous genus to perform these bioassays. We use choice and no-choice tests to describe preferences and performance of the insects when fed on extreme genotypes under various treatments.

Collage of four photos showing on the left red galls on a leaf, on the second left a mettalic green weevil on a leaf, on the second a red leaf beetle sitting on a twig and on the right a leaf with eating traces from a leaf mining butterflySome typical arthropods encountered in our common gardens. Left: Harmandia tremula a leaf-galling mite; second from left: Bycticus sp. a leaf rolling weevil; second from right: Chrysomela populi a leaf beetle that oviposits and chews on leaves; right: Phyllocnistis labyrintella a leaf mining butterfly

Volatile Collection Platform

To study volatile responses to biotic stress and simulated stresses (MeJA, and mechanical damaged plants) we have established a volatile collection platform. This platform is created primary for studies of volatile emission in Brassica nigra, however, it is designed to also be used for other plant species.

Two persons in a lab environment who are placing a sample in a spectrophotometer.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.

Key Publications

  • Keefover-Ring K, Carlsson M, Albrectsen BR (2014). 2′-(Z)-Cinnamoylsalicortin: A novel salicinoid isolated from Populus tremula. Phytochemistry Letters; 7:212–216
  • Bernhardsson C, Robinson KM, Abreu IN, Jansson S, Albrectsen BR, Ingvarsson PK. (2013). Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes. Ecology Letters, 16 (6):791-798.
  • Robinsson KM, Ingvarsson PK, Jansson S, Albrectsen BR. (2012). Both spatial and genetic variation influence plant functional traits, a specialist-rich arthropod community, and their interaction. PLoS ONE 7(5): e37679. doi:10.1371/journal.pone.0037679
  • Abreu, IN, Ahnlund, M, Moritz, T. Albrectsen, BR. (2011). UHPLC-ESI/TOFMS Determination of Salicylate-like Phenolic Gycosides in Populus tremula Leaves. J Chem Ecol. 2011 37(8): 857–870. doi: 10.1007/s10886-011-9991-7.
  • Albrectsen BR, Björkén L, Varad A, Hagner Å, Wedin M, Karlsson J and Jansson S (2010). Endophytic fungi in european Aspen (Populus tremula) leaves – diversity, detection, and a suggested correlation with herbivory resistance.Fungal Diversity 41:17-28
  • Albrectsen BR, Witzell J, Robinson K, Wulff S, Luquez VMC, Ågren R and Jansson S (2010). Large scale geographic clines of parasite damage to Populus tremula L.Ecography 33: 483-493
  • 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 Volume 4, Issue 2 , pp 279-292
Laszlo Bako standing in a lab wearing a white labcoat

Bakó, László - Control of Plant Cell Division and Differentiation

Research

Laszlo Bako standing in a lab wearing a white labcoatPhoto: Mattias Pettersson, Umeå University

In many dicot plants lateral roots arise from a dedicated cell file of the main root called pericycle. Initiation of lateral roots requires the phytohormone auxin that first triggers critical asymmetric cell divisions in the pericycle then acts as an instructive signal for lateral root growth and development.
While recent works have provided a large body of information concerning the role of auxin signaling and identified elements of the signaling pathway, our knowledge of the mechanism acting downstream of the auxin signal is still limited. In particular, we have just begun to understand the mechanism controlling the first critical formative pericycle divisions.

Plant growth depends on a root system that anchors plant in the soil and functions as an entry site for water and essential nutrients. Development of the root system is a post-embryonic process during which a highly branched network of lateral roots forms.

We have been studying lateral root initiation in the model plant Arabidopsis thaliana and identified a novel molecular mechanism that appears to regulate asymmetric pericycle cell divisions. Main components of this mechanism are the RETINOBLASTOMA-RELATED PROTEIN1 (RBR1) and the ATP-dependent chromatin remodeler PICKLE (PKL) that associates with RBR1. The RBR1-PKL complex negatively regulates expression of certain LDB genes whose activity is required for asymmetric pericycle cell division and lateral root initiation.

We are using biochemical, genetic and cell biology methods to elaborate on this repressor function and better understand the molecular mechanism which directs the RBR1-PKL complex to target loci, to dissect the subunit structure of the holocomplex and to elucidate how auxin signaling dissociate the complex. In ChIP-seq experiments we address the question whether the RBR1-PKL complex plays roles in other plant developmental processes.

Two pictures showing red coloured root cells of Arabidopsis.Expression of RBR-RFP fusion protein in Arabidopsis root after treatment with the auxins 2,4-D (left) or NAA (right).

Key Publications

  • Cruz-Ramírez A, Díaz-Triviño S, Blilou I, Grieneisen VA, Sozzani R, Zamioudis C, Miskolczi P, Nieuwland J, Benjamins R, Dohnuk- se P, Caballero-Pérez J, Horvath B, Long Y, Mähonën AP, Xu J, Murray JA, Benfey PN, Bakó L, Marée AF, Scheres B, (2012). A bis-table circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 150:1002-15.
  • Magyar Z, Horváth B, Khan S, Mohammed B, Henriques R, De Veylder L, Bakó L, Scheres B, Bögre L (2012). Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes. EMBO J. 31:1480-1493.
  • Karlberg A, Bakó L, Bhalerao RP. (2011). Short day-mediated cessation of growth requires the downregulation of AINTEGUMENTALI- KE1 transcription factor in hybrid aspen. PLoS Genet. 7(11):e1002361.
  • Ábrahám E, Miskolczi P, Ayaydin F, Yu P, Kotogány E, Bakó L, Ötvös K, Horváth GV, Dudits D. (2011). Immunodetection of retino- blastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells. J Exp Bot. 62:2155-2168.
Peter Kindgren with aspen trees in the UPSC greenhouse

Kindgren, Peter - Coding versus Non-coding Transcription in Plants

Research

Peter Kindgren with aspen trees in the UPSC greenhousePhoto: Fredrik LarssonThe DNA is the blue-print for how a living organism should develop and respond to different environmental cues. It does so by activating and repressing coding regions of the genome. Surprisingly, most of the DNA in genomes do not encode for proteins but is non-coding. With the development of new sequencing technologies, it is apparent that much of this non-coding DNA is transcribed into RNA. A key question in modern biology is therefore why organisms spend so much energy to transcribe something that is not used as template for protein synthesis.

Increasing evidence shows that transcription of non-coding regions are important players in the response to stress situations and control of organismal development. The challenge is often to detect these non-coding transcripts due to their rapid degradation. Therefore, we are only scratching the surface of the functional role of this hidden layer of transcription. Thus, we need to develop new techniques to fully appreciate the roles and rules of non-coding transcription.

A consequence of wide-spread or pervasive transcription of the genome is that many coding regions have non-coding transcription occurring in proximity. This may lead to transcriptional conflicts when two RNA polymerases meet on the DNA template but also regulate the dynamics of coding transcription.

My research group is interested in the dynamics of active transcription and how conflicts between non-coding and coding transcription regulate and dictate decisions made by the plant for optimal stress response and development. We primarily work with the model plant Arabidopsis thaliana but develop new techniques to study non-coding transcription in trees.

The figure illustrates the research in the Kindgren group.

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