@article{hernandez-verdeja_genomes_2022,
	title = {{GENOMES} {UNCOUPLED1} plays a key role during the de-etiolation process in {Arabidopsis}},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18115},
	doi = {10.1111/nph.18115},
	abstract = {One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Hernández-Verdeja, Tamara and Vuorijoki, Linda and Jin, Xu and Vergara, Alexander and Dubreuil, Carole and Strand, Åsa},
	year = {2022},
	keywords = {GUN1, chloroplast, greening, light signalling, plastid retrograde signalling, transcriptional regulation},
	pages = {188--203},
}

One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.

@article{ji_fully_2021,
	title = {A fully assembled plastid‐encoded {\textless}span style="font-variant:small-caps;"{\textgreater}{RNA}{\textless}/span{\textgreater} polymerase complex detected in etioplasts and proplastids in {Arabidopsis}},
	volume = {171},
	issn = {0031-9317, 1399-3054},
	shorttitle = {A fully assembled plastid‐encoded {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13256},
	doi = {10.1111/ppl.13256},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Ji, Yan and Lehotai, Nóra and Zan, Yanjun and Dubreuil, Carole and Díaz, Manuel Guinea and Strand, Åsa},
	month = mar,
	year = {2021},
	pages = {435--446},
}

@article{calderon_how_2021,
	series = {Cell signaling and gene regulation},
	title = {How retrograde signaling is intertwined with the evolution of photosynthetic eukaryotes},
	volume = {63},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526621000935},
	doi = {10/gmkx8p},
	abstract = {Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.},
	language = {en},
	urldate = {2021-11-12},
	journal = {Current Opinion in Plant Biology},
	author = {Calderon, Robert H. and Strand, Åsa},
	month = oct,
	year = {2021},
	keywords = {Cyanobacteria, Endosymbiosis event, Mitochondria, Plastids, Retrograde signals, Stress, lncRNA.},
	pages = {102093},
}

Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.

@article{hernandezverdeja_emerging_2020,
	title = {Emerging from the darkness: interplay between light and plastid signaling during chloroplast biogenesis},
	volume = {169},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Emerging from the darkness},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13100},
	doi = {10.1111/ppl.13100},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Hernández‐Verdeja, Tamara and Vuorijoki, Linda and Strand, Åsa},
	month = jul,
	year = {2020},
	pages = {397--406},
}

@article{crawford_specific_2020,
	title = {Specific functions for {Mediator} complex subunits from different modules in the transcriptional response of {Arabidopsis} thaliana to abiotic stress},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-61758-w},
	doi = {10.1038/s41598-020-61758-w},
	abstract = {Abstract
            
              Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of
              Arabidopsis thaliana
              to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Crawford, Tim and Karamat, Fazeelat and Lehotai, Nóra and Rentoft, Matilda and Blomberg, Jeanette and Strand, Åsa and Björklund, Stefan},
	month = dec,
	year = {2020},
	pages = {5073},
}

Abstract Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.

@article{yang_two_2020,
	title = {Two dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-019-13954-0},
	doi = {10.1038/s41467-019-13954-0},
	abstract = {Abstract
            
              Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine (
              Pinus sylvestris L
              .) and Norway spruce
              (Picea abies
              ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO
              2
              assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO
              2
              assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Yang, Qi and Blanco, Nicolás E. and Hermida-Carrera, Carmen and Lehotai, Nóra and Hurry, Vaughan and Strand, Åsa},
	month = dec,
	year = {2020},
	pages = {128},
}

Abstract Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine ( Pinus sylvestris L .) and Norway spruce (Picea abies ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO 2 assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO 2 assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.

@article{blanco_dual_2019,
	title = {Dual and dynamic intracellular localization of {Arabidopsis} thaliana {SnRK1}.1},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/8/2325/5308885},
	doi = {10.1093/jxb/erz023},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Blanco, Nicolás E and Liebsch, Daniela and Guinea Díaz, Manuel and Strand, Åsa and Whelan, James},
	month = apr,
	year = {2019},
	pages = {2325--2338},
}

@article{dubreuil_establishment_2018,
	title = {Establishment of {Photosynthesis} through {Chloroplast} {Development} {Is} {Controlled} by {Two} {Distinct} {Regulatory} {Phases}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/2/1199-1214/6117139},
	doi = {10/gb2hj6},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dubreuil, Carole and Jin, Xu and Barajas-López, Juan de Dios and Hewitt, Timothy C. and Tanz, Sandra K. and Dobrenel, Thomas and Schröder, Wolfgang P. and Hanson, Johannes and Pesquet, Edouard and Grönlund, Andreas and Small, Ian and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {1199--1214},
}

@article{diaz_redox_2018,
	title = {Redox regulation of {PEP} activity during seedling establishment in {Arabidopsis} thaliana},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-017-02468-2},
	doi = {10/gcthqp},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Díaz, Manuel Guinea and Hernández-Verdeja, Tamara and Kremnev, Dmitry and Crawford, Tim and Dubreuil, Carole and Strand, Åsa},
	month = dec,
	year = {2018},
	pages = {50},
}

@article{hernandez-verdeja_retrograde_2018,
	title = {Retrograde {Signals} {Navigate} the {Path} to {Chloroplast} {Development}},
	volume = {176},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.17.01299},
	doi = {10/gc8tpr},
	abstract = {Light is the main source of energy for life on Earth, and plants and algae are able to convert light energy, through photosynthesis, into chemical energy that can be used by all organisms. The photosynthetic reactions are housed in the chloroplasts, but the chloroplasts also are the site for synthesis of essential compounds like fatty acids, vitamins, amino acids, and tetrapyrroles. Given their essential role, the correct formation and function of chloroplasts is vital for the growth and development of plants and algae, and hence for almost all organisms. Chloroplasts evolved from an endosymbiotic event where a photosynthetic prokaryotic organism was acquired by a proeukaryotic cell. With time, the photosynthetic prokaryote lost or transferred most of its genes to the host genome. As a result, plastid protein complexes, such as the photosynthetic complexes, are encoded by genes of both the nuclear and plastid genomes. This division of genetic information requires a precise coordination between the two genomes to achieve proper plastid development and function. Plastid development and gene expression are under nuclear control, in what is referred to as anterograde control. However, there also is a signaling system originating in the plastids, so-called retrograde signals, transmitting information about the developmental and functional state of the plastids to the nucleus to regulate nuclear gene expression. Retrograde signaling is a complex network of signals that can be divided into “biogenic control,” referring to signals generated by the plastid as it develops from a proplastid or etioplast into a chloroplast, and “operational control” signals, including those generated from a mature chloroplast in response to environmental perturbations (Chan et al., 2016).},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Hernández-Verdeja, Tamara and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {967--976},
}

Light is the main source of energy for life on Earth, and plants and algae are able to convert light energy, through photosynthesis, into chemical energy that can be used by all organisms. The photosynthetic reactions are housed in the chloroplasts, but the chloroplasts also are the site for synthesis of essential compounds like fatty acids, vitamins, amino acids, and tetrapyrroles. Given their essential role, the correct formation and function of chloroplasts is vital for the growth and development of plants and algae, and hence for almost all organisms. Chloroplasts evolved from an endosymbiotic event where a photosynthetic prokaryotic organism was acquired by a proeukaryotic cell. With time, the photosynthetic prokaryote lost or transferred most of its genes to the host genome. As a result, plastid protein complexes, such as the photosynthetic complexes, are encoded by genes of both the nuclear and plastid genomes. This division of genetic information requires a precise coordination between the two genomes to achieve proper plastid development and function. Plastid development and gene expression are under nuclear control, in what is referred to as anterograde control. However, there also is a signaling system originating in the plastids, so-called retrograde signals, transmitting information about the developmental and functional state of the plastids to the nucleus to regulate nuclear gene expression. Retrograde signaling is a complex network of signals that can be divided into “biogenic control,” referring to signals generated by the plastid as it develops from a proplastid or etioplast into a chloroplast, and “operational control” signals, including those generated from a mature chloroplast in response to environmental perturbations (Chan et al., 2016).

@article{crawford_role_2018,
	title = {The role of retrograde signals during plant stress responses},
	volume = {69},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erx481},
	doi = {10.1093/jxb/erx481},
	abstract = {Chloroplast and mitochondria not only provide the energy to the plant cell but due to the sensitivity of organellar processes to perturbations caused by abiotic stress, they are also key cellular sensors of environmental fluctuations. Abiotic stresses result in reduced photosynthetic efficiency and thereby reduced energy supply for cellular processes. Thus, in order to acclimate to stress, plants must re-program gene expression and cellular metabolism to divert energy from growth and developmental processes to stress responses. To restore cellular energy homeostasis following exposure to stress, the activities of the organelles must be tightly co-ordinated with the transcriptional re-programming in the nucleus. Thus, communication between the organelles and the nucleus, so-called retrograde signalling, is essential to direct the energy use correctly during stress exposure. Stress-triggered retrograde signals are mediated by reactive oxygen species and metabolites including β-cyclocitral, MEcPP (2-C-methyl-d-erythritol 2,4-cyclodiphosphate), PAP (3ʹ-phosphoadenosine 5ʹ-phosphate), and intermediates of the tetrapyrrole biosynthesis pathway. However, for the plant cell to respond optimally to environmental stress, these stress-triggered retrograde signalling pathways must be integrated with the cytosolic stress signalling network. We hypothesize that the Mediator transcriptional co-activator complex may play a key role as a regulatory hub in the nucleus, integrating the complex stress signalling networks originating in different cellular compartments.},
	number = {11},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Crawford, Tim and Lehotai, Nóra and Strand, Åsa},
	month = may,
	year = {2018},
	pages = {2783--2795},
}

Chloroplast and mitochondria not only provide the energy to the plant cell but due to the sensitivity of organellar processes to perturbations caused by abiotic stress, they are also key cellular sensors of environmental fluctuations. Abiotic stresses result in reduced photosynthetic efficiency and thereby reduced energy supply for cellular processes. Thus, in order to acclimate to stress, plants must re-program gene expression and cellular metabolism to divert energy from growth and developmental processes to stress responses. To restore cellular energy homeostasis following exposure to stress, the activities of the organelles must be tightly co-ordinated with the transcriptional re-programming in the nucleus. Thus, communication between the organelles and the nucleus, so-called retrograde signalling, is essential to direct the energy use correctly during stress exposure. Stress-triggered retrograde signals are mediated by reactive oxygen species and metabolites including β-cyclocitral, MEcPP (2-C-methyl-d-erythritol 2,4-cyclodiphosphate), PAP (3ʹ-phosphoadenosine 5ʹ-phosphate), and intermediates of the tetrapyrrole biosynthesis pathway. However, for the plant cell to respond optimally to environmental stress, these stress-triggered retrograde signalling pathways must be integrated with the cytosolic stress signalling network. We hypothesize that the Mediator transcriptional co-activator complex may play a key role as a regulatory hub in the nucleus, integrating the complex stress signalling networks originating in different cellular compartments.

@article{dubreuil_quantitative_2017,
	title = {A quantitative model of the phytochrome-{PIF} light signalling initiating chloroplast development},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-13473-2},
	doi = {10/gchdr4},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Dubreuil, Carole and Ji, Yan and Strand, Åsa and Grönlund, Andreas},
	month = dec,
	year = {2017},
	pages = {13884},
}

@article{razzak_differential_2017,
	title = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light: {Scots} pine response to light intensity and shade},
	volume = {40},
	issn = {01407791},
	shorttitle = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light},
	url = {http://doi.wiley.com/10.1111/pce.12921},
	doi = {10.1111/pce.12921},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Razzak, Abdur and Ranade, Sonali Sachin and Strand, Åsa and García-Gil, M. R.},
	month = aug,
	year = {2017},
	pages = {1332--1340},
}

@article{noren_circadian_2016,
	title = {Circadian and {Plastid} {Signaling} {Pathways} {Are} {Integrated} to {Ensure} {Correct} {Expression} of the {CBF} and {COR} {Genes} during {Photoperiodic} {Growth}},
	volume = {171},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.16.00374},
	doi = {10/f3rvjv},
	abstract = {The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Norén, Louise and Kindgren, Peter and Stachula, Paulina and Rühl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Åsa},
	month = jun,
	year = {2016},
	pages = {1392--1406},
}

The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.

@article{blanco_interaction_2014,
	title = {Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status},
	volume = {369},
	issn = {0962-8436, 1471-2970},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0231},
	doi = {10/f226pk},
	abstract = {Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The
              regulator of alternative oxidase
              (
              rao1)
              mutant was isolated as a mutant unable to induce
              AOX1a
              expression in response to the inhibitor of the mitochondrial cytochrome
              c
              reductase (complex III), antimycin A.
              RAO1
              encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the
              rao1
              mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both
              LIGHT HARVESTING COMPLEX B
              (
              LHCB
              ) and
              ALTERNATIVE OXIDASE 1
              (
              AOX1a
              ) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.},
	language = {en},
	number = {1640},
	urldate = {2021-06-08},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Blanco, Nicolás E. and Guinea-Díaz, Manuel and Whelan, James and Strand, Åsa},
	month = apr,
	year = {2014},
	pages = {20130231},
}

Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The regulator of alternative oxidase ( rao1) mutant was isolated as a mutant unable to induce AOX1a expression in response to the inhibitor of the mitochondrial cytochrome c reductase (complex III), antimycin A. RAO1 encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the rao1 mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both LIGHT HARVESTING COMPLEX B ( LHCB ) and ALTERNATIVE OXIDASE 1 ( AOX1a ) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.

@article{ng_cyclin-dependent_2013,
	title = {Cyclin-dependent {Kinase} {E1} ({CDKE1}) {Provides} a {Cellular} {Switch} in {Plants} between {Growth} and {Stress} {Responses}},
	volume = {288},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820464580},
	doi = {10/f2z2ws},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Ng, Sophia and Giraud, Estelle and Duncan, Owen and Law, Simon R. and Wang, Yan and Xu, Lin and Narsai, Reena and Carrie, Chris and Walker, Hayden and Day, David A. and Blanco, Nicolás E. and Strand, Åsa and Whelan, James and Ivanova, Aneta},
	month = feb,
	year = {2013},
	pages = {3449--3459},
}

@article{barajas-lopez_papp5_2013,
	title = {{PAPP5} {Is} {Involved} in the {Tetrapyrrole} {Mediated} {Plastid} {Signalling} during {Chloroplast} {Development}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0060305},
	doi = {10/f223sf},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Barajas-López, Juan de Dios and Kremnev, Dmitry and Shaikhali, Jehad and Piñas-Fernández, Aurora and Strand, Åsa},
	editor = {Pandey, Girdhar Kumar},
	month = mar,
	year = {2013},
	pages = {e60305},
}

@article{barajas-lopez_plastid--nucleus_2013,
	series = {Protein {Import} and {Quality} {Control} in {Mitochondria} and {Plastids}},
	title = {Plastid-to-nucleus communication, signals controlling the running of the plant cell},
	volume = {1833},
	issn = {0167-4889},
	url = {https://www.sciencedirect.com/science/article/pii/S0167488912001772},
	doi = {10/f24h6j},
	abstract = {The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research},
	author = {Barajas-López, Juan de Dios and Blanco, Nicolás E. and Strand, Åsa},
	month = feb,
	year = {2013},
	keywords = {Photosynthesis, Plastids, Redox, Retrograde, Signaling, Stress},
	pages = {425--437},
}

The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

@article{kindgren_interplay_2012,
	title = {Interplay between {HEAT} {SHOCK} {PROTEIN} 90 and {HY5} {Controls} {PhANG} {Expression} in {Response} to the {GUN5} {Plastid} {Signal}},
	volume = {5},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205214602057},
	doi = {10/fxpbcj},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Molecular Plant},
	author = {Kindgren, Peter and Norén, Louise and Barajas López, Juan de Dios and Shaikhali, Jehad and Strand, Åsa},
	month = jul,
	year = {2012},
	keywords = {abiotic/environmental stress, cell signaling, organelle biogenesis/function},
	pages = {901--913},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.

@article{shaikhali_redox-mediated_2012,
	title = {Redox-mediated {Mechanisms} {Regulate} {DNA} {Binding} {Activity} of the {G}-group of {Basic} {Region} {Leucine} {Zipper} ({bZIP}) {Transcription} {Factors} in {Arabidopsis}},
	volume = {287},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820477762},
	doi = {10/f22pjj},
	language = {en},
	number = {33},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Shaikhali, Jehad and Norén, Louise and de Dios Barajas-López, Juan and Srivastava, Vaibhav and König, Janine and Sauer, Uwe H. and Wingsle, Gunnar and Dietz, Karl-Josef and Strand, Åsa},
	month = aug,
	year = {2012},
	pages = {27510--27525},
}

@article{shaikhali_cryptochrome1-dependent_2012,
	title = {The {CRYPTOCHROME1}-{Dependent} {Response} to {Excess} {Light} {Is} {Mediated} through the {Transcriptional} {Activators} {ZINC} {FINGER} {PROTEIN} {EXPRESSED} {IN} {INFLORESCENCE} {MERISTEM} {LIKE1} and {ZML2} in {Arabidopsis}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/3009-3025/6100855},
	doi = {10/f23c7q},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Shaikhali, Jehad and de Dios Barajas-Lopéz, Juan and Ötvös, Krisztina and Kremnev, Dmitry and Garcia, Ana Sánchez and Srivastava, Vaibhav and Wingsle, Gunnar and Bakó, Laszlo and Strand, Åsa},
	month = jul,
	year = {2012},
	pages = {3009--3025},
}

@article{kindgren_plastid_2012,
	title = {The plastid redox insensitive 2 mutant of {Arabidopsis} is impaired in {PEP} activity and high light-dependent plastid redox signalling to the nucleus},
	volume = {70},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04865.x},
	doi = {10/fzx2j5},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.},
	language = {en},
	number = {2},
	urldate = {2021-09-02},
	journal = {The Plant Journal},
	author = {Kindgren, Peter and Kremnev, Dmitry and Blanco, Nicolás E. and López, Juan de Dios Barajas and Fernández, Aurora Piñas and Tellgren-Roth, Christian and Small, Ian and Strand, Åsa},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2011.04865.x},
	keywords = {LHCB, PEP, chloroplast, photosynthesis, redox, signalling},
	pages = {279--291},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.

@article{kindgren_novel_2011,
	title = {A novel proteomic approach reveals a role for {Mg}-protoporphyrin {IX} in response to oxidative stress},
	volume = {141},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2010.01440.x},
	doi = {10/d2cw82},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Physiologia Plantarum},
	author = {Kindgren, Peter and Eriksson, Mats-Jerry and Benedict, Catherine and Mohapatra, Anasuya and Gough, Simon P. and Hansson, Mats and Kieselbach, Thomas and Strand, Åsa},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01440.x},
	pages = {310--320},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.

@article{fernandez_retrograde_2008,
	title = {Retrograde signaling and plant stress: plastid signals initiate cellular stress responses},
	volume = {11},
	issn = {13695266},
	shorttitle = {Retrograde signaling and plant stress},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526608001052},
	doi = {10/bf6bbr},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Fernández, Aurora Piñas and Strand, Åsa},
	month = oct,
	year = {2008},
	pages = {509--513},
}

@article{kleine_genome-wide_2007,
	title = {Genome-{Wide} {Gene} {Expression} {Analysis} {Reveals} a {Critical} {Role} for {CRYPTOCHROME1} in the {Response} of {Arabidopsis} to {High} {Irradiance}},
	volume = {144},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.107.098293},
	doi = {10/fh8w86},
	abstract = {Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.},
	number = {3},
	urldate = {2021-09-02},
	journal = {Plant Physiology},
	author = {Kleine, Tatjana and Kindgren, Peter and Benedict, Catherine and Hendrickson, Luke and Strand, Åsa},
	month = jul,
	year = {2007},
	pages = {1391--1406},
}

Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.

@article{ankele_vivo_2007,
	title = {In {Vivo} {Visualization} of {Mg}-{ProtoporphyrinIX}, a {Coordinator} of {Photosynthetic} {Gene} {Expression} in the {Nucleus} and the {Chloroplast}},
	volume = {19},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.048744},
	doi = {10/cttnp7},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.},
	number = {6},
	urldate = {2021-09-02},
	journal = {The Plant Cell},
	author = {Ankele, Elisabeth and Kindgren, Peter and Pesquet, Edouard and Strand, Åsa},
	month = jun,
	year = {2007},
	pages = {1964--1979},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.

@incollection{strand_plastid--nucleus_2006,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Plastid-to-{Nucleus} {Signaling}},
	isbn = {978-1-4020-4061-0},
	url = {https://doi.org/10.1007/978-1-4020-4061-0_9},
	abstract = {The function of the eukaryotic cell depends on the regulated and reciprocal interaction between its different compartments. This includes not only the exchange of energy equivalents but also information. Most information exchange flows from the nucleus to the organelles, because the large majority of genes encoding proteins with organellar function are encoded in the nucleus.},
	language = {en},
	urldate = {2021-06-11},
	booktitle = {The {Structure} and {Function} of {Plastids}},
	publisher = {Springer Netherlands},
	author = {Strand, Åsa and Kleine, Tatjana and Chory, Joanne},
	editor = {Wise, Robert R. and Hoober, J. Kenneth},
	year = {2006},
	doi = {10.1007/978-1-4020-4061-0_9},
	keywords = {Chloroplast Development, Nuclear Gene Expression, Photosynthetic Gene Expression, Plastid Signal, Tetrapyrrole Biosynthesis},
	pages = {183--197},
}

The function of the eukaryotic cell depends on the regulated and reciprocal interaction between its different compartments. This includes not only the exchange of energy equivalents but also information. Most information exchange flows from the nucleus to the organelles, because the large majority of genes encoding proteins with organellar function are encoded in the nucleus.

@article{strand_plastid--nucleus_2004,
	title = {Plastid-to-nucleus signalling},
	volume = {7},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526604001256},
	doi = {10.1016/j.pbi.2004.09.004},
	abstract = {The function of the eukaryotic cell depends on the reciprocal interaction between its different compartments. Plastids emit signals that regulate nuclear gene expression to ensure the stoichiometric assembly of plastid protein complexes and to initiate macromolecular reorganisation in response to environmental cues. It is now clear that several different plastid processes produce signals that influence the expression of photosynthetic genes in the nucleus. The genome uncoupled (gun) mutants recently revealed one of the plastid signals, the chlorophyll intermediate Mg-protoporphyrinIX.},
	language = {en},
	number = {6},
	urldate = {2021-06-30},
	journal = {Current Opinion in Plant Biology},
	author = {Strand, Åsa},
	month = dec,
	year = {2004},
	pages = {621--625},
}

The function of the eukaryotic cell depends on the reciprocal interaction between its different compartments. Plastids emit signals that regulate nuclear gene expression to ensure the stoichiometric assembly of plastid protein complexes and to initiate macromolecular reorganisation in response to environmental cues. It is now clear that several different plastid processes produce signals that influence the expression of photosynthetic genes in the nucleus. The genome uncoupled (gun) mutants recently revealed one of the plastid signals, the chlorophyll intermediate Mg-protoporphyrinIX.

@incollection{hurry_photosynthesis_2002,
	address = {Boston, MA},
	title = {Photosynthesis at {Low} {Temperatures}},
	isbn = {978-1-4615-0711-6},
	url = {https://doi.org/10.1007/978-1-4615-0711-6_12},
	abstract = {One of the most variable conditions in the field is temperature and relatively severe frost, caused by temperatures below -20°C, can be expected to occur over 42\% of the earth’s surface (Larcher 1995). Low temperature is therefore a major determinant of the geographical distribution and productivity of plant species. Exacerbating this problem, plants from high latitudes and high altitudes are faced with short growing seasons and the need to grow at low temperatures for prolonged periods to extend the growing season. Thus, the capacity for active photosynthesis during prolonged exposure to low growth temperatures is essential in determining their successful site occupancy and subsequent productivity. Despite the importance of low temperatures in determining agricultural productivity and ecological diversity at higher latitudes and altitudes, relatively little is known about either the short-term or long-term effects of cold on the underlying biochemical responses of plant energy metabolism, processes that contribute to plant growth.},
	language = {en},
	urldate = {2021-10-19},
	booktitle = {Plant {Cold} {Hardiness}: {Gene} {Regulation} and {Genetic} {Engineering}},
	publisher = {Springer US},
	author = {Hurry, Vaughan and Druart, Nathalie and Cavaco, Ana and Gardeström, Per and Strand, Åsa},
	editor = {Li, Paul H. and Palva, E. Tapio},
	year = {2002},
	doi = {10.1007/978-1-4615-0711-6_12},
	keywords = {Antisense Line, Calvin Cycle, Cold Acclimation, Freezing Tolerance, Sucrose Synthesis},
	pages = {161--179},
}

One of the most variable conditions in the field is temperature and relatively severe frost, caused by temperatures below -20°C, can be expected to occur over 42% of the earth’s surface (Larcher 1995). Low temperature is therefore a major determinant of the geographical distribution and productivity of plant species. Exacerbating this problem, plants from high latitudes and high altitudes are faced with short growing seasons and the need to grow at low temperatures for prolonged periods to extend the growing season. Thus, the capacity for active photosynthesis during prolonged exposure to low growth temperatures is essential in determining their successful site occupancy and subsequent productivity. Despite the importance of low temperatures in determining agricultural productivity and ecological diversity at higher latitudes and altitudes, relatively little is known about either the short-term or long-term effects of cold on the underlying biochemical responses of plant energy metabolism, processes that contribute to plant growth.

@article{ganeteg_properties_2001,
	title = {The {Properties} of the {Chlorophyll} a/b-{Binding}  {Proteins} {Lhca2} and {Lhca3} {Studied} in {Vivo} {Using} {Antisense}  {Inhibition}},
	volume = {127},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC117971/},
	abstract = {The specific functions of the light-harvesting proteins Lhca2 and
 Lhca3 were studied in Arabidopsis ecotype Colombia antisense plants in
 which the proteins were individually repressed. The antisense effect
 was specific in each plant, but levels of Lhca proteins other than the
 targeted products were also affected. The contents of Lhca1 and Lhca4
 were unaffected, but Lhca3 (in Lhca2-repressed plants) was almost
 completely depleted, and Lhca2 decreased to about 30\% of wild-type
 levels in Lhca3-repressed plants. This suggests that the Lhca2 and
 Lhca3 proteins are in physical contact with each other and that they
 require each other for stability. Photosystem I fluorescence at 730 nm
 is thought to emanate from pigments bound to Lhca1 and Lhca4. However,
 fluorescence emission and excitation spectra suggest that Lhca2 and
 Lhca3, which fluoresce in vitro at 680 nm, also could contribute to
 far-red fluorescence in vivo. Spectral forms with absorption maxima at
 695 and 715 nm, apparently with emission maxima at 702 and 735 nm,
 respectively, might be associated with Lhca2 and Lhca3.},
	number = {1},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {Ganeteg, Ulrika and Strand, Åsa and Gustafsson, Petter and Jansson, Stefan},
	month = sep,
	year = {2001},
	pmid = {11553743},
	pmcid = {PMC117971},
	pages = {150--158},
}

The specific functions of the light-harvesting proteins Lhca2 and Lhca3 were studied in Arabidopsis ecotype Colombia antisense plants in which the proteins were individually repressed. The antisense effect was specific in each plant, but levels of Lhca proteins other than the targeted products were also affected. The contents of Lhca1 and Lhca4 were unaffected, but Lhca3 (in Lhca2-repressed plants) was almost completely depleted, and Lhca2 decreased to about 30% of wild-type levels in Lhca3-repressed plants. This suggests that the Lhca2 and Lhca3 proteins are in physical contact with each other and that they require each other for stability. Photosystem I fluorescence at 730 nm is thought to emanate from pigments bound to Lhca1 and Lhca4. However, fluorescence emission and excitation spectra suggest that Lhca2 and Lhca3, which fluoresce in vitro at 680 nm, also could contribute to far-red fluorescence in vivo. Spectral forms with absorption maxima at 695 and 715 nm, apparently with emission maxima at 702 and 735 nm, respectively, might be associated with Lhca2 and Lhca3.

@article{strand_decreased_2000,
	title = {Decreased expression of two key enzymes in the sucrose biosynthesis pathway, cytosolic fructose-1,6-bisphosphatase and sucrose phosphate synthase, has remarkably different consequences for photosynthetic carbon metabolism in transgenic {Arabidopsis} thaliana},
	volume = {23},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.2000.00847.x},
	doi = {10/fpq9sb},
	abstract = {Photosynthetic carbon metabolism was investigated in antisense Arabidopsis lines with decreased expression of sucrose phosphate synthase (SPS) and cytosolic fructose-1,6-bisphosphatase (cFBPase). In the light, triose phosphates are exported from the chloroplast and converted to sucrose via cFBPase and SPS. At night, starch is degraded to glucose, exported and converted to sucrose via SPS. cFBPase therefore lies upstream and SPS downstream of the point at which the pathways for sucrose synthesis in the day and night converge. Decreased cFBPase expression led to inhibition of sucrose synthesis; accumulation of phosphorylated intermediates; Pi-limitation of photosynthesis; and stimulation of starch synthesis. The starch was degraded to maintain higher levels of sugars and a higher rate of sucrose export during the night. This resembles the response in other species when expression of enzymes in the upper part of the sucrose biosynthesis pathway is reduced. Decreased expression of SPS inhibited sucrose synthesis, but phosphorylated intermediates did not accumulate and carbon partitioning was not redirected towards starch. Sugar levels and sucrose export was decreased during the night as well as during the day. Although ribulose-1,5-bisphosphate regeneration and photosynthesis were inhibited, the PGA/triose-P ratio remained low and the ATP/ADP ratio high, showing that photosynthesis was not limited by the rate at which Pi was recycled during end-product synthesis. Two novel responses counteracted the decrease in SPS expression and explain why phosphorylated intermediates did not accumulate, and why allocation was not altered in the antisense SPS lines. Firstly, a threefold decrease of PPi and a shift of the UDP-glucose/hexose phosphate ratio favoured sucrose synthesis and prevented the accumulation of phosphorylated intermediates. Secondly, there was no increase of AGPase activity relative to cFBPase activity, which would prevent a shift in carbon allocation towards starch synthesis. These responses are presumably triggered when sucrose synthesis is decreased in the night, as well as by day.},
	language = {en},
	number = {6},
	urldate = {2021-11-08},
	journal = {The Plant Journal},
	author = {Strand, Åsa and Zrenner, Rita and Trevanion, Stephen and Stitt, Mark and Gustafsson, Petter and Gardeström, Per},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.2000.00847.x},
	keywords = {6-bisphosphatase, Arabidopsis, carbon metabolism, cytosolic fructose-1, sucrose phosphate synthase},
	pages = {759--770},
}

Photosynthetic carbon metabolism was investigated in antisense Arabidopsis lines with decreased expression of sucrose phosphate synthase (SPS) and cytosolic fructose-1,6-bisphosphatase (cFBPase). In the light, triose phosphates are exported from the chloroplast and converted to sucrose via cFBPase and SPS. At night, starch is degraded to glucose, exported and converted to sucrose via SPS. cFBPase therefore lies upstream and SPS downstream of the point at which the pathways for sucrose synthesis in the day and night converge. Decreased cFBPase expression led to inhibition of sucrose synthesis; accumulation of phosphorylated intermediates; Pi-limitation of photosynthesis; and stimulation of starch synthesis. The starch was degraded to maintain higher levels of sugars and a higher rate of sucrose export during the night. This resembles the response in other species when expression of enzymes in the upper part of the sucrose biosynthesis pathway is reduced. Decreased expression of SPS inhibited sucrose synthesis, but phosphorylated intermediates did not accumulate and carbon partitioning was not redirected towards starch. Sugar levels and sucrose export was decreased during the night as well as during the day. Although ribulose-1,5-bisphosphate regeneration and photosynthesis were inhibited, the PGA/triose-P ratio remained low and the ATP/ADP ratio high, showing that photosynthesis was not limited by the rate at which Pi was recycled during end-product synthesis. Two novel responses counteracted the decrease in SPS expression and explain why phosphorylated intermediates did not accumulate, and why allocation was not altered in the antisense SPS lines. Firstly, a threefold decrease of PPi and a shift of the UDP-glucose/hexose phosphate ratio favoured sucrose synthesis and prevented the accumulation of phosphorylated intermediates. Secondly, there was no increase of AGPase activity relative to cFBPase activity, which would prevent a shift in carbon allocation towards starch synthesis. These responses are presumably triggered when sucrose synthesis is decreased in the night, as well as by day.

@article{hurry_role_2000,
	title = {The role of inorganic phosphate in the development of freezing tolerance and the acclimatization of photosynthesis to low temperature is revealed by the pho mutants of {Arabidopsis} thaliana},
	volume = {24},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.2000.00888.x},
	doi = {10/c6xzqg},
	abstract = {Low temperature inhibits sucrose synthesis, leading to a phosphate-limitation of photosynthesis. We have used the Arabidopsis pho1-2 and pho2-1 mutants with decreased and increased shoot phosphate, respectively, to investigate whether low phosphate triggers cold acclimatization of photosynthetic carbon metabolism. Wild-type Arabidopsis, pho1-2 and pho2-1 were grown at 23°C and transferred to 5°C to investigate acclimatization in pre-existing leaves and in new leaves developing at 5°C. The development of frost tolerance and the accumulation of proline and sugars was unaltered or improved in pho1-2, and impaired in pho2-1. Sucrose phosphate synthase and cytoplasmic fructose-1,6-bisphosphatase activity and protein increase after transfer to 5°C. This increase was accentuated in pho1-2 and attenuated in pho2-1. RBCS and LHCB2 transcript levels decrease in pre-formed wild-type leaves after transfer to 5°C and recover in new leaves that develop at 5°C. The initial decrease was attenuated in pho1-2, and accentuated in pho2-1, where the recovery in new leaves was also suppressed. Rubisco activity increased in wild-type leaves that developed at 5°C. This increase was accentuated in pho1-2 and absent in pho2-1. NADP-glyceraldehyde-3-phosphate dehydrogenase, plastidic fructose-1,6-bisphosphatase and aldolase activity increase relative to phosphoglycerate kinase, transketolase and phosphoribulokinase in wild-type leaves at 5°C. This shift was accentuated in pho1-2 and reversed in pho2-1. Transcript levels for COR genes increase transiently 1 day after transfer to 5°C but were very low in leaves that developed at 5°C in wild-type Arabidopsis, pho1-2 and pho2-1. We conclude that low phosphate plays an important role in triggering cold acclimatization of leaves, leading in particular to an increase of Rubisco expression, changes in other Calvin cycle enzymes to minimize sequestration of phosphate in metabolites, and increased expression of sucrose biosynthesis enzymes.},
	language = {en},
	number = {3},
	urldate = {2021-11-08},
	journal = {The Plant Journal},
	author = {Hurry, Vaughan and Strand, Åsa and Furbank, Robert and Stitt, Mark},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.2000.00888.x},
	keywords = {Arabidopsis, cold acclimatization, low temperature, phosphate, photosynthesis, sucrose synthesis},
	pages = {383--396},
}

Low temperature inhibits sucrose synthesis, leading to a phosphate-limitation of photosynthesis. We have used the Arabidopsis pho1-2 and pho2-1 mutants with decreased and increased shoot phosphate, respectively, to investigate whether low phosphate triggers cold acclimatization of photosynthetic carbon metabolism. Wild-type Arabidopsis, pho1-2 and pho2-1 were grown at 23°C and transferred to 5°C to investigate acclimatization in pre-existing leaves and in new leaves developing at 5°C. The development of frost tolerance and the accumulation of proline and sugars was unaltered or improved in pho1-2, and impaired in pho2-1. Sucrose phosphate synthase and cytoplasmic fructose-1,6-bisphosphatase activity and protein increase after transfer to 5°C. This increase was accentuated in pho1-2 and attenuated in pho2-1. RBCS and LHCB2 transcript levels decrease in pre-formed wild-type leaves after transfer to 5°C and recover in new leaves that develop at 5°C. The initial decrease was attenuated in pho1-2, and accentuated in pho2-1, where the recovery in new leaves was also suppressed. Rubisco activity increased in wild-type leaves that developed at 5°C. This increase was accentuated in pho1-2 and absent in pho2-1. NADP-glyceraldehyde-3-phosphate dehydrogenase, plastidic fructose-1,6-bisphosphatase and aldolase activity increase relative to phosphoglycerate kinase, transketolase and phosphoribulokinase in wild-type leaves at 5°C. This shift was accentuated in pho1-2 and reversed in pho2-1. Transcript levels for COR genes increase transiently 1 day after transfer to 5°C but were very low in leaves that developed at 5°C in wild-type Arabidopsis, pho1-2 and pho2-1. We conclude that low phosphate plays an important role in triggering cold acclimatization of leaves, leading in particular to an increase of Rubisco expression, changes in other Calvin cycle enzymes to minimize sequestration of phosphate in metabolites, and increased expression of sucrose biosynthesis enzymes.

@article{strand_acclimation_1999,
	title = {Acclimation of {Arabidopsis} {Leaves} {Developing} at {Low} {Temperatures}. {Increasing} {Cytoplasmic} {Volume} {Accompanies} {Increased} {Activities} of {Enzymes} in the {Calvin} {Cycle} and in the {Sucrose}-{Biosynthesis} {Pathway1}},
	volume = {119},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.119.4.1387},
	doi = {10/fgpkmw},
	abstract = {Photosynthetic and metabolic acclimation to low growth temperatures were studied in Arabidopsis (Heynh.). Plants were grown at 23°C and then shifted to 5°C. We compared the leaves shifted to 5°C for 10 d and the new leaves developed at 5°C with the control leaves on plants that had been left at 23°C. Leaf development at 5°C resulted in the recovery of photosynthesis to rates comparable with those achieved by control leaves at 23°C. There was a shift in the partitioning of carbon from starch and toward sucrose (Suc) in leaves that developed at 5°C. The recovery of photosynthetic capacity and the redirection of carbon to Suc in these leaves were associated with coordinated increases in the activity of several Calvin-cycle enzymes, even larger increases in the activity of key enzymes for Suc biosynthesis, and an increase in the phosphate available for metabolism. Development of leaves at 5°C also led to an increase in cytoplasmic volume and a decrease in vacuolar volume, which may provide an important mechanism for increasing the enzymes and metabolites in cold-acclimated leaves. Understanding the mechanisms underlying such structural changes during leaf development in the cold could result in novel approaches to increasing plant yield.},
	number = {4},
	urldate = {2021-11-08},
	journal = {Plant Physiology},
	author = {Strand, Åsa and Hurry, Vaughan and Henkes, Stefan and Huner, Norman and Gustafsson, Petter and Gardeström, Per and Stitt, Mark},
	month = apr,
	year = {1999},
	pages = {1387--1398},
}

Photosynthetic and metabolic acclimation to low growth temperatures were studied in Arabidopsis (Heynh.). Plants were grown at 23°C and then shifted to 5°C. We compared the leaves shifted to 5°C for 10 d and the new leaves developed at 5°C with the control leaves on plants that had been left at 23°C. Leaf development at 5°C resulted in the recovery of photosynthesis to rates comparable with those achieved by control leaves at 23°C. There was a shift in the partitioning of carbon from starch and toward sucrose (Suc) in leaves that developed at 5°C. The recovery of photosynthetic capacity and the redirection of carbon to Suc in these leaves were associated with coordinated increases in the activity of several Calvin-cycle enzymes, even larger increases in the activity of key enzymes for Suc biosynthesis, and an increase in the phosphate available for metabolism. Development of leaves at 5°C also led to an increase in cytoplasmic volume and a decrease in vacuolar volume, which may provide an important mechanism for increasing the enzymes and metabolites in cold-acclimated leaves. Understanding the mechanisms underlying such structural changes during leaf development in the cold could result in novel approaches to increasing plant yield.