@article{hussain_progression_2026,
	title = {The progression of leaf senescence is gated by the cytosolic arginine pool},
	volume = {12},
	copyright = {2026 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-026-02328-2},
	doi = {10.1038/s41477-026-02328-2},
	abstract = {Leaf senescence aims to degrade cellular components to recover valuable nutrients and reallocate them to other organs1. Once this remobilization is complete, cells undergo a vacuolar-type of programmed cell death2, ultimately leading to the death of the entire organ. But how do cells from a senescing leaf ‘know’ when to die? If the cell death process per se is initiated too early, remobilization may not be completed, rendering it futile. This suggests the presence of a ‘sensing’ mechanism that coordinates the remobilization phase with the onset of cell death during leaf senescence. Here, using Arabidopsis thaliana functional stay-green mutants, we show that senescing cells are wired to metabolically dissipate the cytosolic arginine pool, which otherwise represses the progression of leaf senescence. We propose a model in which a senescing cell uses this pool as a proxy for the completion of nitrogen remobilization and to accurately time the subsequent induction of cell death.},
	language = {en},
	number = {7},
	urldate = {2026-07-24},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Hussain, Shah and Boussardon, Clément and Keech, Olivier},
	month = jul,
	year = {2026},
	keywords = {Abiotic, Cell fate},
	pages = {1325--1333},
}

Leaf senescence aims to degrade cellular components to recover valuable nutrients and reallocate them to other organs1. Once this remobilization is complete, cells undergo a vacuolar-type of programmed cell death2, ultimately leading to the death of the entire organ. But how do cells from a senescing leaf ‘know’ when to die? If the cell death process per se is initiated too early, remobilization may not be completed, rendering it futile. This suggests the presence of a ‘sensing’ mechanism that coordinates the remobilization phase with the onset of cell death during leaf senescence. Here, using Arabidopsis thaliana functional stay-green mutants, we show that senescing cells are wired to metabolically dissipate the cytosolic arginine pool, which otherwise represses the progression of leaf senescence. We propose a model in which a senescing cell uses this pool as a proxy for the completion of nitrogen remobilization and to accurately time the subsequent induction of cell death.

@article{boussardon_comparative_2025,
	title = {Comparative {Study} of the {Mitochondrial} {Proteome} {From} {Mesophyll}, {Vascular}, and {Guard} {Cells} in {Response} to {Carbon} {Starvation}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70465},
	doi = {10.1111/ppl.70465},
	abstract = {A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Boussardon, Clément and Hussain, Shah and Keech, Olivier},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70465},
	keywords = {cell-specific, glutamate, mitochondria, proteome, translation},
	pages = {e70465},
}

A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.

@article{meyer_expanded_2025,
	title = {The {Expanded} {LYR} {Motif}-{Containing} {Protein} {Family} in {Archaeplastida}},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70482},
	doi = {10.1111/ppl.70482},
	abstract = {The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Meyer, Etienne H. and Lopez-Lopez, Alicia and Keech, Olivier and Rouhier, Nicolas},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70482},
	keywords = {Archaeplastida, LYR-motif containing proteins, classification, mitochondria},
	pages = {e70482},
}

The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.

@article{boussardon_atypical_2025,
	title = {The atypical proteome of mitochondria from mature pollen grains},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982224017056},
	doi = {10.1016/j.cub.2024.12.037},
	abstract = {To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.},
	number = {4},
	urldate = {2025-02-28},
	journal = {Current Biology},
	author = {Boussardon, Clément and Simon, Matthieu and Carrie, Chris and Fuszard, Matthew and Meyer, Etienne H. and Budar, Françoise and Keech, Olivier},
	month = feb,
	year = {2025},
	pages = {776--787.e5},
}

To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.

@article{fuchs_plant_2024,
	title = {{PLANT} {UNCOUPLING} {MITOCHONDRIAL} {PROTEIN} 2 localizes to the {Golgi}},
	volume = {194},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad540},
	doi = {10.1093/plphys/kiad540},
	abstract = {Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72\% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.},
	number = {2},
	urldate = {2024-02-02},
	journal = {Plant Physiology},
	author = {Fuchs, Philippe and Feixes-Prats, Elisenda and Arruda, Paulo and Feitosa-Araújo, Elias and Fernie, Alisdair R and Grefen, Christopher and Lichtenauer, Sophie and Linka, Nicole and de Godoy Maia, Ivan and Meyer, Andreas J and Schilasky, Sören and Sweetlove, Lee J and Wege, Stefanie and Weber, Andreas P M and Millar, A Harvey and Keech, Olivier and Florez-Sarasa, Igor and Barreto, Pedro and Schwarzländer, Markus},
	month = feb,
	year = {2024},
	pages = {623--628},
}

Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.

@article{boussardon_comparison_2023,
	title = {Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad133},
	doi = {10.1093/jxb/erad133},
	abstract = {Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92\% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.},
	number = {14},
	urldate = {2023-08-31},
	journal = {Journal of Experimental Botany},
	author = {Boussardon, Clément and Carrie, Chris and Keech, Olivier},
	month = aug,
	year = {2023},
	pages = {4110--4124},
}

Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.

@article{rohricht_mitochondrial_2023,
	title = {Mitochondrial ferredoxin-like is essential for forming complex {I}-containing supercomplexes in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad040},
	doi = {10.1093/plphys/kiad040},
	abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.},
	number = {4},
	urldate = {2023-04-11},
	journal = {Plant Physiology},
	author = {Röhricht, Helene and Przybyla-Toscano, Jonathan and Forner, Joachim and Boussardon, Clément and Keech, Olivier and Rouhier, Nicolas and Meyer, Etienne H},
	month = apr,
	year = {2023},
	pages = {2170--2184},
}

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.

@article{boussardon_tissue-specific_2023,
	title = {Tissue-{Specific} {Isolation} of {Tagged} {Arabidopsis} {Plastids}},
	volume = {3},
	issn = {2691-1299},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.673},
	doi = {10.1002/cpz1.673},
	abstract = {Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids},
	language = {en},
	number = {2},
	urldate = {2023-02-22},
	journal = {Current Protocols},
	author = {Boussardon, Clément and Keech, Olivier},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.673},
	keywords = {Arabidopsis, biotin-streptavidin interaction, editable Golden Gate plasmids, plastids, tissue-specific isolation},
	pages = {e673},
}

Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids

@incollection{boussardon_cell_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Cell {Type}–{Specific} {Isolation} of {Mitochondria} in {Arabidopsis}},
	isbn = {978-1-07-161653-6},
	url = {https://doi.org/10.1007/978-1-0716-1653-6_2},
	abstract = {Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.},
	language = {en},
	urldate = {2021-09-23},
	booktitle = {Plant {Mitochondria}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Boussardon, Clément and Keech, Olivier},
	editor = {Van Aken, Olivier and Rasmusson, Allan G.},
	month = jan,
	year = {2022},
	keywords = {Biotin–streptavidin interaction, Editable Golden Gate plasmids, Mitochondria, Tagged outer membrane, Tissue-specific isolation},
	pages = {13--23},
}

Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.

@article{lopez-lopez_maturation_2022,
	title = {Maturation and {Assembly} of {Iron}-{Sulfur} {Cluster}-{Containing} {Subunits} in the {Mitochondrial} {Complex} {I} {From} {Plants}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.916948},
	abstract = {In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.},
	urldate = {2022-06-07},
	journal = {Frontiers in Plant Science},
	author = {López-López, Alicia and Keech, Olivier and Rouhier, Nicolas},
	month = may,
	year = {2022},
	keywords = {⛔ No DOI found},
}

In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.

@article{liebsch_metabolic_2022,
	title = {Metabolic control of arginine and ornithine levels paces the progression of leaf senescence},
	volume = {189},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac244},
	doi = {10.1093/plphys/kiac244},
	abstract = {Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.},
	number = {4},
	urldate = {2022-08-08},
	journal = {Plant Physiology},
	author = {Liebsch, Daniela and Juvany, Marta and Li, Zhonghai and Wang, Hou-Ling and Ziolkowska, Agnieszka and Chrobok, Daria and Boussardon, Clément and Wen, Xing and Law, Simon R and Janečková, Helena and Brouwer, Bastiaan and Lindén, Pernilla and Delhomme, Nicolas and Stenlund, Hans and Moritz, Thomas and Gardeström, Per and Guo, Hongwei and Keech, Olivier},
	month = aug,
	year = {2022},
	pages = {1943--1960},
}

Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.

@article{przybyla-toscano_protein_2022,
	title = {Protein lipoylation in mitochondria requires {Fe}–{S} cluster assembly factors {NFU4} and {NFU5}},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab501},
	doi = {10.1093/plphys/kiab501},
	abstract = {Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.},
	number = {2},
	urldate = {2021-11-04},
	journal = {Plant Physiology},
	author = {Przybyla-Toscano, Jonathan and Maclean, Andrew E and Franceschetti, Marina and Liebsch, Daniela and Vignols, Florence and Keech, Olivier and Rouhier, Nicolas and Balk, Janneke},
	month = feb,
	year = {2022},
	pages = {997--1013},
}

Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.

@article{boussardon_rpn12a_2022,
	title = {The {RPN12a} proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03998-2},
	doi = {10.1038/s42003-022-03998-2},
	abstract = {The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.},
	language = {en},
	number = {1},
	urldate = {2022-10-03},
	journal = {Communications Biology},
	author = {Boussardon, Clément and Bag, Pushan and Juvany, Marta and Šimura, Jan and Ljung, Karin and Jansson, Stefan and Keech, Olivier},
	month = sep,
	year = {2022},
	keywords = {Leaf development, Senescence},
	pages = {1--14},
}

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

@article{przybylatoscano_gene_2021,
	title = {Gene atlas of iron‐containing proteins in {Arabidopsis} thaliana},
	volume = {106},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15154},
	doi = {10/gkcr7c},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Przybyla‐Toscano, Jonathan and Boussardon, Clément and Law, Simon R. and Rouhier, Nicolas and Keech, Olivier},
	month = apr,
	year = {2021},
	pages = {258--274},
}

@article{przybyla-toscano_ironsulfur_2021,
	title = {Iron–sulfur proteins in plant mitochondria: roles and maturation},
	volume = {72},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Iron–sulfur proteins in plant mitochondria},
	url = {https://academic.oup.com/jxb/article/72/6/2014/6029934},
	doi = {10.1093/jxb/eraa578},
	abstract = {Abstract
            Iron–sulfur (Fe–S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe–S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe–S proteins. Several other proteins or complexes present in the matrix require Fe–S clusters as well, or depend either on Fe–S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe–S proteins. In this review, we have listed and discussed the Fe–S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe–S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe–S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Przybyla-Toscano, Jonathan and Christ, Loïck and Keech, Olivier and Rouhier, Nicolas},
	editor = {Dietz, Karl-Josef},
	month = mar,
	year = {2021},
	pages = {2014--2044},
}

Abstract Iron–sulfur (Fe–S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe–S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe–S proteins. Several other proteins or complexes present in the matrix require Fe–S clusters as well, or depend either on Fe–S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe–S proteins. In this review, we have listed and discussed the Fe–S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe–S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe–S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.

@article{law_centralization_2020,
	title = {Centralization {Within} {Sub}-{Experiments} {Enhances} the {Biological} {Relevance} of {Gene} {Co}-expression {Networks}: {A} {Plant} {Mitochondrial} {Case} {Study}},
	volume = {11},
	issn = {1664-462X},
	shorttitle = {Centralization {Within} {Sub}-{Experiments} {Enhances} the {Biological} {Relevance} of {Gene} {Co}-expression {Networks}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00524/full},
	doi = {10.3389/fpls.2020.00524},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Law, Simon R. and Kellgren, Therese G. and Björk, Rafael and Ryden, Patrik and Keech, Olivier},
	month = jun,
	year = {2020},
	pages = {524},
}

@article{putintseva_siberian_2020,
	title = {Siberian larch ({Larix} sibirica {Ledeb}.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07061-4},
	doi = {10.1186/s12864-020-07061-4},
	abstract = {Abstract
            
              Background
              
                Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from {\textasciitilde} 222 Kbp in
                Brassica napus
                to 11.3 Mbp in
                Silene conica
                . To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (
                Larix sibirica
                Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied.
              
            
            
              Results
              Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11\% of the entire Siberian larch mitogenome.
            
            
              Conclusions
              
                Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant
                Silene conica
                (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46\% of the mitogenome sequence.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Putintseva, Yuliya A. and Bondar, Eugeniya I. and Simonov, Evgeniy P. and Sharov, Vadim V. and Oreshkova, Natalya V. and Kuzmin, Dmitry A. and Konstantinov, Yuri M. and Shmakov, Vladimir N. and Belkov, Vadim I. and Sadovsky, Michael G. and Keech, Olivier and Krutovsky, Konstantin V.},
	month = dec,
	year = {2020},
	pages = {654},
}

Abstract Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica . To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch ( Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

@article{sullivan_mitogenome_2020,
	title = {The {Mitogenome} of {Norway} {Spruce} and a {Reappraisal} of {Mitochondrial} {Recombination} in {Plants}},
	volume = {12},
	issn = {1759-6653},
	url = {https://academic.oup.com/gbe/article/12/1/3586/5644343},
	doi = {10.1093/gbe/evz263},
	abstract = {Abstract
            Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology and Evolution},
	author = {Sullivan, Alexis R and Eldfjell, Yrin and Schiffthaler, Bastian and Delhomme, Nicolas and Asp, Torben and Hebelstrup, Kim H and Keech, Olivier and Öberg, Lisa and Møller, Ian Max and Arvestad, Lars and Street, Nathaniel R and Wang, Xiao-Ru},
	editor = {Vision, Todd},
	month = jan,
	year = {2020},
	pages = {3586--3598},
}

Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

@article{boussardon_tissuespecific_2020,
	title = {Tissue‐specific isolation of {Arabidopsis}/plant mitochondria – {IMTACT} (isolation of mitochondria tagged in specific cell types)},
	volume = {103},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14723},
	doi = {10.1111/tpj.14723},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Boussardon, Clément and Przybyla‐Toscano, Jonathan and Carrie, Chris and Keech, Olivier},
	month = jul,
	year = {2020},
	pages = {459--473},
}

@article{sylvestre-gonon_functional_2019,
	title = {Functional, {Structural} and {Biochemical} {Features} of {Plant} {Serinyl}-{Glutathione} {Transferases}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00608/full},
	doi = {10/gjdxch},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Sylvestre-Gonon, Elodie and Law, Simon R. and Schwartz, Mathieu and Robe, Kevin and Keech, Olivier and Didierjean, Claude and Dubos, Christian and Rouhier, Nicolas and Hecker, Arnaud},
	month = may,
	year = {2019},
	pages = {608},
}

@article{law_darkened_2018,
	title = {Darkened {Leaves} {Use} {Different} {Metabolic} {Strategies} for {Senescence} and {Survival}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/1/132-150/6116945},
	doi = {10.1104/pp.18.00062},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Law, Simon R. and Chrobok, Daria and Juvany, Marta and Delhomme, Nicolas and Lindén, Pernilla and Brouwer, Bastiaan and Ahad, Abdul and Moritz, Thomas and Jansson, Stefan and Gardeström, Per and Keech, Olivier},
	month = may,
	year = {2018},
	pages = {132--150},
}

@incollection{fernie_vitro_2017,
	address = {New York, NY},
	title = {In {Vitro} {Alkylation} {Methods} for {Assessing} the {Protein} {Redox} {State}},
	volume = {1653},
	isbn = {978-1-4939-7224-1 978-1-4939-7225-8},
	url = {http://link.springer.com/10.1007/978-1-4939-7225-8_4},
	doi = {10.1007/978-1-4939-7225-8_4},
	urldate = {2021-06-07},
	booktitle = {Photorespiration},
	publisher = {Springer New York},
	author = {Zannini, Flavien and Couturier, Jérémy and Keech, Olivier and Rouhier, Nicolas},
	editor = {Fernie, Alisdair R. and Bauwe, Hermann and Weber, Andreas P.M.},
	year = {2017},
	note = {Series Title: Methods in Molecular Biology},
	pages = {51--64},
}

@article{keech_redox_2017,
	title = {The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	shorttitle = {The redox control of photorespiration},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12713},
	doi = {10.1111/pce.12713},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Keech, Olivier and Gardeström, Per and Kleczkowski, Leszek A. and Rouhier, Nicolas},
	month = apr,
	year = {2017},
	pages = {553--569},
}

@article{li_characterization_2016,
	title = {Characterization of a novel β-barrel protein ({AtOM47}) from the mitochondrial outer membrane of \textit{{Arabidopsis} thaliana}},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw366},
	doi = {10/f9c9wf},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Li, Lu and Kubiszewski-Jakubiak, Szymon and Radomiljac, Jordan and Wang, Yan and Law, Simon R. and Keech, Olivier and Narsai, Reena and Berkowitz, Oliver and Duncan, Owen and Murcha, Monika W. and Whelan, James},
	month = nov,
	year = {2016},
	pages = {6061--6075},
}

@article{liebsch_darkinduced_2016,
	title = {Dark‐induced leaf senescence: new insights into a complex light‐dependent regulatory pathway},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Dark‐induced leaf senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14217},
	doi = {10/f3trh7},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Liebsch, Daniela and Keech, Olivier},
	month = nov,
	year = {2016},
	pages = {563--570},
}

@article{chrobok_dissecting_2016,
	title = {Dissecting the {Metabolic} {Role} of {Mitochondria} during {Developmental} {Leaf} {Senescence}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/4/2132-2153/6115841},
	doi = {10/f3vc6g},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Chrobok, Daria and Law, Simon R. and Brouwer, Bastiaan and Lindén, Pernilla and Ziolkowska, Agnieszka and Liebsch, Daniela and Narsai, Reena and Szal, Bozena and Moritz, Thomas and Rouhier, Nicolas and Whelan, James and Gardeström, Per and Keech, Olivier},
	month = dec,
	year = {2016},
	pages = {2132--2153},
}

@article{betti_manipulating_2016,
	title = {Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Manipulating photorespiration to increase plant productivity},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw076},
	doi = {10.1093/jxb/erw076},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Betti, Marco and Bauwe, Hermann and Busch, Florian A. and Fernie, Alisdair R. and Keech, Olivier and Levey, Myles and Ort, Donald R. and Parry, Martin A. J. and Sage, Rowan and Timm, Stefan and Walker, Berkley and Weber, Andreas P. M.},
	month = may,
	year = {2016},
	pages = {2977--2988},
}

@article{dejonghe_mitochondrial_2016,
	title = {Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11710},
	doi = {10/f3r3j2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyáš and Ortiz-Morea, Fausto Andres and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le Son Long and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna-Mária and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian York and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jiří and Verstreken, Patrik and Russinova, Eugenia},
	month = sep,
	year = {2016},
	pages = {11710},
}

@article{hodges_perspectives_2016,
	title = {Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw145},
	doi = {10.1093/jxb/erw145},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Hodges, Michael and Dellero, Younès and Keech, Olivier and Betti, Marco and Raghavendra, Agepati S. and Sage, Rowan and Zhu, Xin-Guang and Allen, Doug K. and Weber, Andreas P.M.},
	month = may,
	year = {2016},
	pages = {3015--3026},
}

@article{linden_reduced_2016,
	title = {Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by $^{\textrm{13}}$ {C} labelling},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw030},
	doi = {10.1093/jxb/erw030},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Lindén, Pernilla and Keech, Olivier and Stenlund, Hans and Gardeström, Per and Moritz, Thomas},
	month = may,
	year = {2016},
	pages = {3123--3135},
}

@article{brouwer_response_2014,
	title = {In response to partial plant shading, the lack of phytochrome {A} does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/eru060},
	doi = {10/f22wjn},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Brouwer, Bastiaan and Gardeström, Per and Keech, Olivier},
	month = jul,
	year = {2014},
	pages = {4037--4049},
}

@article{lallement_still_2014,
	title = {The still mysterious roles of cysteine-containing glutathione transferases in plants},
	volume = {5},
	issn = {1663-9812},
	url = {http://journal.frontiersin.org/article/10.3389/fphar.2014.00192/abstract},
	doi = {10/f3n4qc},
	urldate = {2021-06-08},
	journal = {Frontiers in Pharmacology},
	author = {Lallement, Pierre-Alexandre and Brouwer, Bastiaan and Keech, Olivier and Hecker, Arnaud and Rouhier, Nicolas},
	month = aug,
	year = {2014},
}

@article{peterhansel_engineering_2013,
	title = {Engineering photorespiration: current state and future possibilities},
	volume = {15},
	issn = {14358603},
	shorttitle = {Engineering photorespiration},
	url = {http://doi.wiley.com/10.1111/j.1438-8677.2012.00681.x},
	doi = {10/f22k83},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Biology},
	author = {Peterhansel, C. and Krause, K. and Braun, H.-P. and Espie, G. S. and Fernie, A. R. and Hanson, D. T. and Keech, O. and Maurino, V. G. and Mielewczik, M. and Sage, R. F.},
	month = jul,
	year = {2013},
	pages = {754--758},
}

@article{fernie_perspectives_2013,
	title = {Perspectives on plant photorespiratory metabolism},
	volume = {15},
	issn = {14358603},
	url = {http://doi.wiley.com/10.1111/j.1438-8677.2012.00693.x},
	doi = {10/f2364c},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Biology},
	author = {Fernie, A. R. and Bauwe, H. and Eisenhut, M. and Florian, A. and Hanson, D. T. and Hagemann, M. and Keech, O. and Mielewczik, M. and Nikoloski, Z. and Peterhänsel, C. and Roje, S. and Sage, R. and Timm, S. and von Cammerer, S. and Weber, A. P. M. and Westhoff, P.},
	editor = {Rennenberg, H.},
	month = jul,
	year = {2013},
	pages = {748--753},
}

@article{bussell_requirement_2013,
	title = {Requirement for the plastidial oxidative pentose phosphate pathway for nitrate assimilation in {Arabidopsis}},
	volume = {75},
	copyright = {© 2013 The Authors The Plant Journal © 2013 John Wiley \& Sons Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12222},
	doi = {10/f46xkb},
	abstract = {Sugar metabolism and the oxidative pentose phosphate pathway (OPPP) are strongly implicated in N assimilation, although the relationship between them and the roles of the plastidial and cytosolic OPPP have not been established genetically. We studied a knock-down mutant of the plastid-localized OPPP enzyme 6-phosphogluconolactonase 3 (PGL3). pgl3-1 plants exhibited relatively greater resource allocation to roots but were smaller than the wild type. They had a lower content of amino acids and free in leaves than the wild type, despite exhibiting comparable photosynthetic rates and efficiency, and normal levels of many other primary metabolites. When N-deprived plants were fed via the roots with , pgl3-1 exhibited normal induction of OPPP and nitrate assimilation genes in roots, and amino acids in roots and shoots were labeled with 15N at least as rapidly as in the wild type. However, when N-replete plants were fed via the roots with sucrose, expression of specific OPPP and N assimilation genes in roots increased in the wild type but not in pgl3-1. Thus, sugar-dependent expression of N assimilation genes requires OPPP activity and the specificity of the effect of the pgl3-1 mutation on N assimilation genes establishes that it is not the result of general energy deficiency or accumulation of toxic intermediates. We conclude that expression of specific nitrate assimilation genes in the nucleus of root cells is positively regulated by a signal emanating from OPPP activity in the plastid.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Bussell, John D. and Keech, Olivier and Fenske, Ricarda and Smith, Steven M.},
	year = {2013},
	keywords = {6-phosphogluconolactonase, Arabidopsis thaliana, nitrate, nitrogen assimilation, oxidative pentose phosphate pathway, plastid},
	pages = {578--591},
}

Sugar metabolism and the oxidative pentose phosphate pathway (OPPP) are strongly implicated in N assimilation, although the relationship between them and the roles of the plastidial and cytosolic OPPP have not been established genetically. We studied a knock-down mutant of the plastid-localized OPPP enzyme 6-phosphogluconolactonase 3 (PGL3). pgl3-1 plants exhibited relatively greater resource allocation to roots but were smaller than the wild type. They had a lower content of amino acids and free in leaves than the wild type, despite exhibiting comparable photosynthetic rates and efficiency, and normal levels of many other primary metabolites. When N-deprived plants were fed via the roots with , pgl3-1 exhibited normal induction of OPPP and nitrate assimilation genes in roots, and amino acids in roots and shoots were labeled with 15N at least as rapidly as in the wild type. However, when N-replete plants were fed via the roots with sucrose, expression of specific OPPP and N assimilation genes in roots increased in the wild type but not in pgl3-1. Thus, sugar-dependent expression of N assimilation genes requires OPPP activity and the specificity of the effect of the pgl3-1 mutation on N assimilation genes establishes that it is not the result of general energy deficiency or accumulation of toxic intermediates. We conclude that expression of specific nitrate assimilation genes in the nucleus of root cells is positively regulated by a signal emanating from OPPP activity in the plastid.

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{keech_genetic_2012,
	title = {The {Genetic} {Dissection} of a {Short}-{Term} {Response} to {Low} {CO2} {Supports} the {Possibility} for {Peroxide}-{Mediated} {Decarboxylation} of {Photorespiratory} {Intermediates} in the {Peroxisome}},
	volume = {5},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214601647},
	doi = {10/gkgdr5},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Keech, Olivier and Zhou, Wenxu and Fenske, Ricarda and Colas-des-Francs-Small, Catherine and Bussell, John D. and Badger, Murray R. and Smith, Steven M.},
	month = nov,
	year = {2012},
	pages = {1413--1416},
}

@article{brouwer_impact_2012,
	title = {The impact of light intensity on shade-induced leaf senescence: {Light}-dependent induction of leaf senescence},
	volume = {35},
	issn = {01407791},
	shorttitle = {The impact of light intensity on shade-induced leaf senescence},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2011.02474.x},
	doi = {10/dthghs},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Brouwer, Bastiaan and Ziolkowska, Agnieszka and Bagard, Matthieu and Keech, Olivier and Gardeström, Per},
	month = jun,
	year = {2012},
	pages = {1084--1098},
}

@article{keech_conserved_2011,
	title = {The conserved mobility of mitochondria during leaf senescence reflects differential regulation of the cytoskeletal components in {Arabidopsis} thaliana},
	volume = {6},
	issn = {null},
	url = {https://doi.org/10.4161/psb.6.1.14307},
	doi = {10/bzzb2q},
	abstract = {Leaf senescence is an organized process, which requires fine tuning between nuclear gene expression, activity of proteases and the maintenance of primary metabolism. Recently, we reported that leaf senescence was accompanied by an early degradation of the microtubule cytoskeleton in Arabidopsis thaliana. As the cytoskeleton is essential for cell stability, vesicle shuttling and organelle mobility, it might be asked how the regulation of these cell functions occurs with such drastic modifications of the cytoskeleton. Based on confocal laser microscopy observations and a micro-array analysis, the following addendum shows that mitochondrial mobility is conserved until the late stages of leaf senescence and provides evidences that the actin-cytoskeleton is maintained longer than the microtubule network. This conservation of actin-filaments is discussed with regards to energy metabolism as well as calcium signaling during programmed cell death.},
	number = {1},
	urldate = {2021-06-10},
	journal = {Plant Signaling \& Behavior},
	author = {Keech, Olivier},
	month = jan,
	year = {2011},
	pages = {147--150},
}

Leaf senescence is an organized process, which requires fine tuning between nuclear gene expression, activity of proteases and the maintenance of primary metabolism. Recently, we reported that leaf senescence was accompanied by an early degradation of the microtubule cytoskeleton in Arabidopsis thaliana. As the cytoskeleton is essential for cell stability, vesicle shuttling and organelle mobility, it might be asked how the regulation of these cell functions occurs with such drastic modifications of the cytoskeleton. Based on confocal laser microscopy observations and a micro-array analysis, the following addendum shows that mitochondrial mobility is conserved until the late stages of leaf senescence and provides evidences that the actin-cytoskeleton is maintained longer than the microtubule network. This conservation of actin-filaments is discussed with regards to energy metabolism as well as calcium signaling during programmed cell death.

@article{pracharoenwattana_arabidopsis_2010,
	title = {Arabidopsis has a cytosolic fumarase required for the massive allocation of photosynthate into fumaric acid and for rapid plant growth on high nitrogen},
	volume = {62},
	copyright = {© 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2010.04189.x},
	doi = {10/bpcb9c},
	abstract = {The Arabidopsis genome has two fumarase genes, one of which encodes a protein with mitochondrial targeting information (FUM1) while the other (FUM2) does not. We show that a FUM1–green fluorescent protein fusion is directed to mitochondria while FUM2–red fluorescent protein remains in the cytosol. While mitochondrial FUM1 is an essential gene, cytosolic FUM2 is not required for plant growth. However FUM2 is required for the massive accumulation of carbon into fumarate that occurs in Arabidopsis leaves during the day. In fum2 knock-out mutants, fumarate levels remain low while malate increases, and these changes can be reversed with a FUM2 transgene. The fum2 mutant has lower levels of many amino acids in leaves during the day compared with the wild type, but higher levels at night, consistent with a link between fumarate and amino acid metabolism. To further test this relationship we grew plants in the absence or presence of nitrogen fertilizer. The amount of fumarate in leaves increased several fold in response to nitrogen in wild-type plants, but not in fum2. Malate increased to a small extent in the wild type but to a greater extent in fum2. Growth of fum2 plants was similar to that of the wild type in low nitrogen but much slower in the presence of high nitrogen. Activities of key enzymes of nitrogen assimilation were similar in both genotypes. We conclude that FUM2 is required for the accumulation of fumarate in leaves, which is in turn required for rapid nitrogen assimilation and growth on high nitrogen.},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Pracharoenwattana, Itsara and Zhou, Wenxu and Keech, Olivier and Francisco, Perigio B. and Udomchalothorn, Thanikan and Tschoep, Hendrik and Stitt, Mark and Gibon, Yves and Smith, Steven M.},
	year = {2010},
	keywords = {Arabidopsis thaliana, fumarase, fumaric acid, nitrogen assimilation, photosynthate allocation, plant growth},
	pages = {785--795},
}

The Arabidopsis genome has two fumarase genes, one of which encodes a protein with mitochondrial targeting information (FUM1) while the other (FUM2) does not. We show that a FUM1–green fluorescent protein fusion is directed to mitochondria while FUM2–red fluorescent protein remains in the cytosol. While mitochondrial FUM1 is an essential gene, cytosolic FUM2 is not required for plant growth. However FUM2 is required for the massive accumulation of carbon into fumarate that occurs in Arabidopsis leaves during the day. In fum2 knock-out mutants, fumarate levels remain low while malate increases, and these changes can be reversed with a FUM2 transgene. The fum2 mutant has lower levels of many amino acids in leaves during the day compared with the wild type, but higher levels at night, consistent with a link between fumarate and amino acid metabolism. To further test this relationship we grew plants in the absence or presence of nitrogen fertilizer. The amount of fumarate in leaves increased several fold in response to nitrogen in wild-type plants, but not in fum2. Malate increased to a small extent in the wild type but to a greater extent in fum2. Growth of fum2 plants was similar to that of the wild type in low nitrogen but much slower in the presence of high nitrogen. Activities of key enzymes of nitrogen assimilation were similar in both genotypes. We conclude that FUM2 is required for the accumulation of fumarate in leaves, which is in turn required for rapid nitrogen assimilation and growth on high nitrogen.

@article{keech_leaf_2010,
	title = {Leaf {Senescence} {Is} {Accompanied} by an {Early} {Disruption} of the {Microtubule} {Network} in {Arabidopsis}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/4/1710/6108651},
	doi = {10/cp2qs5},
	abstract = {Abstract
            The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Keech, Olivier and Pesquet, Edouard and Gutierrez, Laurent and Ahad, Abdul and Bellini, Catherine and Smith, Steven M. and Gardeström, Per},
	month = dec,
	year = {2010},
	pages = {1710--1720},
}

Abstract The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.

@article{sani_magicangle_2009,
	title = {Magic‐angle phosphorus {NMR} of functional mitochondria: \textit{in situ} monitoring of lipid response under apoptotic‐like stress},
	volume = {23},
	issn = {0892-6638, 1530-6860},
	shorttitle = {Magic‐angle phosphorus {NMR} of functional mitochondria},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1096/fj.09-134114},
	doi = {10/b8cdxs},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The FASEB Journal},
	author = {Sani, Marc‐Antoine and Keech, Olivier and Gardeström, Per and Dufourc, Erick J. and Gröbner, Gerhard},
	month = sep,
	year = {2009},
	pages = {2872--2878},
}

@article{keech_different_2007,
	title = {The different fates of mitochondria and chloroplasts during dark-induced senescence in {Arabidopsis} leaves},
	volume = {30},
	issn = {0140-7791, 1365-3040},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2007.01724.x},
	doi = {10/bpfzq8},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Plant, Cell \& Environment},
	author = {Keech, Olivier and Pesquet, Edouard and Ahad, Abdul and Askne, Anna and Nordvall, Dag and Vodnala, Sharvani Munender and Tuominen, Hannele and Hurry, Vaughan and Dizengremel, Pierre and Gardeström, Per},
	month = dec,
	year = {2007},
	pages = {1523--1534},
}

@article{gama_mitochondrial_2007,
	title = {The mitochondrial type {II} peroxiredoxin from poplar},
	volume = {129},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2006.00785.x},
	doi = {10/d9wwkk},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Gama, Filipe and Keech, Olivier and Eymery, Françoise and Finkemeier, Iris and Gelhaye, Eric and Gardeström, Per and Dietz, Karl Josef and Rey, Pascal and Jacquot, Jean-Pierre and Rouhier, Nicolas},
	month = jan,
	year = {2007},
	pages = {196--206},
}

@article{keech_adsorption_2005,
	title = {Adsorption of allelopathic compounds by wood-derived charcoal: the role of wood porosity},
	volume = {272},
	issn = {1573-5036},
	shorttitle = {Adsorption of allelopathic compounds by wood-derived charcoal},
	url = {https://doi.org/10.1007/s11104-004-5485-5},
	doi = {10.1007/s11104-004-5485-5},
	abstract = {In Swedish boreal forests, areas dominated by the dwarf shrub Empetrum hermaphroditum Hagerup are known for their poor regeneration of trees and one of the causes of this poor regeneration has been attributed to allelopathy (i.e. chemical interferences) by E. hermaphroditum. Fire-produced charcoal is suggested to play an important role in rejuvenating those ecosystems by adsorbing allelopathic compounds, such as phenols, released by E. hermaphroditum. In this study, we firstly investigated whether the adsorption capacity of charcoal of different plant species varies according to the wood anatomical structures of these, and secondly we tried to relate the adsorption capacity to wood anatomical structure. Charcoal was produced from eight boreal and one temperate woody plant species and the adsorption capacity of charcoal was tested by bioassays technique. Seed germination was used as a measurement of the ability of charcoal to adsorb allelochemicals. The charcoal porosity was estimated and the pore size distribution was then calculated in order to relate the wood anatomical features to the adsorption capacity. The results showed that the adsorption capacity of charcoal was significantly different between plant species and that deciduous trees had a significantly higher adsorption capacity than conifers and ericaceous species. The presence of macro-pores rather than a high porosity appears to be the most important for the adsorption capacity. These results suggest that fire-produced charcoal has different ability to adsorb phenols in boreal forest soil, and therefore may have differing effects on the germination of seeds of establishing tree seedlings.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Plant and Soil},
	author = {Keech, Olivier and Carcaillet, Christopher and Nilsson, Marie-Charlotte},
	month = may,
	year = {2005},
	pages = {291--300},
}

In Swedish boreal forests, areas dominated by the dwarf shrub Empetrum hermaphroditum Hagerup are known for their poor regeneration of trees and one of the causes of this poor regeneration has been attributed to allelopathy (i.e. chemical interferences) by E. hermaphroditum. Fire-produced charcoal is suggested to play an important role in rejuvenating those ecosystems by adsorbing allelopathic compounds, such as phenols, released by E. hermaphroditum. In this study, we firstly investigated whether the adsorption capacity of charcoal of different plant species varies according to the wood anatomical structures of these, and secondly we tried to relate the adsorption capacity to wood anatomical structure. Charcoal was produced from eight boreal and one temperate woody plant species and the adsorption capacity of charcoal was tested by bioassays technique. Seed germination was used as a measurement of the ability of charcoal to adsorb allelochemicals. The charcoal porosity was estimated and the pore size distribution was then calculated in order to relate the wood anatomical features to the adsorption capacity. The results showed that the adsorption capacity of charcoal was significantly different between plant species and that deciduous trees had a significantly higher adsorption capacity than conifers and ericaceous species. The presence of macro-pores rather than a high porosity appears to be the most important for the adsorption capacity. These results suggest that fire-produced charcoal has different ability to adsorb phenols in boreal forest soil, and therefore may have differing effects on the germination of seeds of establishing tree seedlings.

@article{rouhier_identification_2005,
	title = {Identification of {Plant} {Glutaredoxin} {Targets}},
	volume = {7},
	issn = {1523-0864},
	url = {https://www.liebertpub.com/doi/10.1089/ars.2005.7.919},
	doi = {10.1089/ars.2005.7.919},
	abstract = {Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol–disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma β-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.Antioxid. Redox Signal. 7, 919–929.},
	number = {7-8},
	urldate = {2021-06-11},
	journal = {Antioxidants \& Redox Signaling},
	publisher = {Mary Ann Liebert, Inc., publishers},
	author = {Rouhier, Nicolas and Villarejo, Arsenio and Srivastava, Manoj and Gelhaye, Eric and Keech, Olivier and Droux, Michel and Finkemeier, Iris and Samuelsson, Göran and Dietz, Karl Josef and Jacquot, Jean-Pierre and Wingsle, Gunnar},
	month = jul,
	year = {2005},
	pages = {919--929},
}

Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol–disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma β-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.Antioxid. Redox Signal. 7, 919–929.

@article{keech_preparation_2005,
	title = {Preparation of leaf mitochondria from {Arabidopsis} thaliana},
	volume = {124},
	issn = {0031-9317},
	doi = {10/d7jvrz},
	abstract = {Arabidopsis thaliana is, perhaps, the most important model species in modern plant biology. However, the isolation of organelles from leaves of this plant has been difficult. Here, we present two different protocols for the isolation of mitochondria, yielding either highly functional crude mitochondria or highly purified mitochondria. The crude mitochondria were well coupled with the substrates tested (malate + glutamate, glycine and NADH), exhibiting respiratory control ratios of 2.1-3.9. Purified mitochondria with very low levels of chlorophyll contamination were obtained by Percoll gradient centrifugation, yielding 1.2 mg of mitochondrial protein from 50 g of leaves.},
	language = {English},
	number = {4},
	journal = {Physiologia Plantarum},
	publisher = {Wiley},
	author = {Keech, O. and Dizengremel, P. and Gardestrom, P.},
	month = aug,
	year = {2005},
	note = {Place: Hoboken
WOS:000230573300001},
	keywords = {chloroplasts, criteria, dehydrogenase, expression, metabolism, oxidation, photosynthesis, respiration, spinach, tissue},
	pages = {403--409},
}

Arabidopsis thaliana is, perhaps, the most important model species in modern plant biology. However, the isolation of organelles from leaves of this plant has been difficult. Here, we present two different protocols for the isolation of mitochondria, yielding either highly functional crude mitochondria or highly purified mitochondria. The crude mitochondria were well coupled with the substrates tested (malate + glutamate, glycine and NADH), exhibiting respiratory control ratios of 2.1-3.9. Purified mitochondria with very low levels of chlorophyll contamination were obtained by Percoll gradient centrifugation, yielding 1.2 mg of mitochondrial protein from 50 g of leaves.