J.-d. Rochaix - Academia.edu (original) (raw)

Papers by J.-d. Rochaix

Research paper thumbnail of Structure and Expression of Chloroplast and Nuclear Genes in Chlamydomonas reinhardii

Proceedings in Life Sciences, 1984

Research paper thumbnail of The chloroplast ycf8 open reading frame encodes a photosystem II polypeptide which maintains photosynthetic activity under adverse growth conditions

Research paper thumbnail of Isolation of a psaF-deficient mutant of Chlamydomonas reinhardtii: efficient interaction of plastocyanin with the photosystem I reaction center is mediated by the PsaF subunit

Research paper thumbnail of Determinants for stability of the chloroplast psbD RNA are located within its short leader region in Chlamydomonas reinhardtii

Research paper thumbnail of Lack of the D2 protein in a Chlamydomonas reinhardtii psb D mutant affects photosystem II stability and D1 expression

Research paper thumbnail of The 5' leader of a chloroplast mRNA mediates the translational requirements for two nucleus-encoded functions in Chlamydomonas reinhardtii

Molecular and Cellular Biology, 1994

In the green alga Chlamydomonas reinhardtii, the nuclear mutations F34 and F64 have been previous... more In the green alga Chlamydomonas reinhardtii, the nuclear mutations F34 and F64 have been previously shown to abolish the synthesis of the photosystem II core polypeptide subunit P6, which is encoded by the chloroplast psbC gene. In this report the functions encoded by F34 and F64 are shown to be required for translation of the psbC mRNA, on the basis of the finding that the expression of a heterologous reporter gene fused to the psbC 5' nontranslated leader sequence requires wild-type F34 and F64 alleles in vivo. Moreover, a point mutation in the psbC 5' nontranslated leader sequence suppresses this requirement for wild-type F34 function. In vitro RNA-protein cross-linking studies reveal that chloroplast protein extracts from strains carrying the F64 mutation contain an approximately 46-kDa RNA-binding protein. The absence of the RNA-binding activity of this protein in chloroplast extracts of wild-type strains suggests that it is related to the role of the F64-encoded functi...

Research paper thumbnail of Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

The Plant cell, Jan 30, 2014

Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in... more Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in environmental conditions. Proteases and molecular chaperones involved in plastid protein quality control are encoded by the nucleus except for the catalytic subunit of ClpP, an evolutionarily conserved serine protease. Unlike its Escherichia coli ortholog, this chloroplast protease is essential for cell viability. To study its function, we used a recently developed system of repressible chloroplast gene expression in the alga Chlamydomonas reinhardtii. Using this repressible system, we have shown that a selective gradual depletion of ClpP leads to alteration of chloroplast morphology, causes formation of vesicles, and induces extensive cytoplasmic vacuolization that is reminiscent of autophagy. Analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein level, but not at the RNA level. These proteins may comprise some...

Research paper thumbnail of Functional Studies of Ycf3: Its Role in Assembly of Photosystem I and Interactions with Some of Its Subunits

THE PLANT CELL ONLINE, 2001

Research paper thumbnail of Phosphorylation of Photosystem II Controls Functional Macroscopic Folding of Photosynthetic Membranes in Arabidopsis      

The Plant Cell, 2009

Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in ph... more Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in photosystem II, which uses light energy to oxidize water and produce oxygen. The sunlight also causes quantitative phosphorylation of major photosystem II proteins. Analysis of the Arabidopsis thaliana stn7xstn8 double mutant deficient in thylakoid protein kinases STN7 and STN8 revealed light-independent phosphorylation of PsbH protein and greatly reduced N-terminal phosphorylation of D2 protein. The stn7xstn8 and stn8 mutants deficient in light-induced phosphorylation of photosystem II had increased thylakoid membrane folding compared with wild-type and stn7 plants. Significant enhancement in the size of stacked thylakoid membranes in stn7xstn8 and stn8 accelerated gravity-driven sedimentation of isolated thylakoids and was observed directly in plant leaves by transmission electron microscopy. Increased membrane folding, caused by the loss of light-induced protein phosphorylation, obstruc...

Research paper thumbnail of A Nuclear-Encoded Function Essential for Translation of the Chloroplast psaB mRNA in Chlamydomonas

Research paper thumbnail of Molecular and biophysical analysis of herbicide-resistant mutants of Chlamydomonas reinhardtii: structure-function relationship of the photosystem II D1 polypeptide

Research paper thumbnail of Low Density Membranes Are Associated with RNA-binding Proteins and Thylakoids in the Chloroplast of Chlamydomonas reinhardtii

The Journal of Cell Biology, 1998

Chloroplast subfractions were tested with a UV cross-linking assay for proteins that bind to the ... more Chloroplast subfractions were tested with a UV cross-linking assay for proteins that bind to the 5′ untranslated region of the chloroplast psbC mRNA of the green alga Chlamydomonas reinhardtii. These analyses revealed that RNA-binding proteins of 30–32, 46, 47, 60, and 80 kD are associated with chloroplast membranes. The buoyant density and the acyl lipid composition of these membranes are compatible with their origin being the inner chloroplast envelope membrane. However, unlike previously characterized inner envelope membranes, these membranes are associated with thylakoids. One of the membrane-associated RNA-binding proteins appears to be RB47, which has been reported to be a specific activator of psbA mRNA translation. These results suggest that translation of chloroplast mRNAs encoding thylakoid proteins occurs at either a subfraction of the chloroplast inner envelope membrane or a previously uncharacterized intra-chloroplast compartment, which is physically associated with thy...

Research paper thumbnail of Characterization of Tbc2, a nucleus-encoded factor specifically required for translation of the chloroplast psbC mRNA in Chlamydomonas reinhardtii

The Journal of Cell Biology, 2002

Genetic analysis has revealed that the three nucleus-encoded factors Tbc1, Tbc2, and Tbc3 are inv... more Genetic analysis has revealed that the three nucleus-encoded factors Tbc1, Tbc2, and Tbc3 are involved in the translation of the chloroplast psbC mRNA of the eukaryotic green alga Chlamydomonas reinhardtii. In this study we report the isolation and phenotypic characterization of two new tbc2 mutant alleles and their use for cloning and characterizing the Tbc2 gene by genomic complementation. TBC2 encodes a protein of 1,115 residues containing nine copies of a novel degenerate 38–40 amino acid repeat with a quasiconserved PPPEW motif near its COOH-terminal end. The middle part of the Tbc2 protein displays partial amino acid sequence identity with Crp1, a protein from Zea mays that is implicated in the processing and translation of the chloroplast petA and petD RNAs. The Tbc2 protein is enriched in chloroplast stromal subfractions and is associated with a 400-kD protein complex that appears to play a role in the translation of specifically the psbC mRNA.

Research paper thumbnail of Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii

Research paper thumbnail of The PsaC subunit of photosystem I provides an essential lysine residue for fast electron transfer to ferredoxin

Research paper thumbnail of A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii

Research paper thumbnail of Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB / psbT / psbH gene cluster in Chlamydomonas reinhardtii

Proceedings of the National Academy of Sciences, 2000

Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alg... more Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alga Chlamydomonas reinhardtii requires specific nucleus-encoded functions. To gain insight into this process, we have cloned the nuclear gene encoding the Mbb1 factor by genomic rescue of a mutant specifically deficient in the accumulation of the mRNAs of the psbB / psbT / psbH chloroplast transcription unit. Mbb1 is a soluble protein in the stromal phase of the chloroplast. It consists of 662 amino acids with a putative chloroplast-transit peptide at its N-terminal end. A striking feature is the presence of 10 tandemly arranged tetratricopeptide-like repeats that account for half of the protein sequence and are thought to be involved in protein–protein interactions. The Mbb1 protein seems to have a homologue in higher plants and is part of a 300-kDa complex that is associated with RNA. This complex is most likely involved in psbB mRNA processing, stability, and/or translation.

Research paper thumbnail of The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis

Proceedings of the National Academy of Sciences, 2010

The ability of plants to adapt to changing light conditions depends on a protein kinase network i... more The ability of plants to adapt to changing light conditions depends on a protein kinase network in the chloroplast that leads to the reversible phosphorylation of key proteins in the photosynthetic membrane. Phosphorylation regulates, in a process called state transition, a profound reorganization of the electron transfer chain and remodeling of the thylakoid membranes. Phosphorylation governs the association of the mobile part of the light-harvesting antenna LHCII with either photosystem I or photosystem II. Recent work has identified the redox-regulated protein kinase STN7 as a major actor in state transitions, but the nature of the corresponding phosphatases remained unknown. Here we identify a phosphatase of Arabidopsis thaliana , called PPH1, which is specifically required for the dephosphorylation of light-harvesting complex II (LHCII). We show that this single phosphatase is largely responsible for the dephosphorylation of Lhcb1 and Lhcb2 but not of the photosystem II core pr...

Research paper thumbnail of Expression of the nuclear gene encoding oxygen-evolving enhancer protein 2 is required for high levels of photosynthetic oxygen evolution in Chlamydomonas reinhardtii

Proceedings of the National Academy of Sciences, 1987

We have cloned a cDNA encoding a 20-kDa polypeptide, oxygen-evolving enhancer protein 2 (OEE2), i... more We have cloned a cDNA encoding a 20-kDa polypeptide, oxygen-evolving enhancer protein 2 (OEE2), in Chlamydomonas reinhardtii. This polypeptide has been implicated in photosynthetic oxygen evolution, and it is associated with the photosystem II complex, the site of oxygen evolution in all higher plants and algae. The sequence of OEE2 cDNA, the deduced amino acid sequence of the preprotein, the N-terminal protein sequence of mature OEE2 protein, and the coding regions of the single OEE2 gene are presented. The protein is synthesized with a 57-amino acid N-terminal transit peptide that directs the transport of this polypeptide across three cellular membranes. A nuclear mutant of C. reinhardtii, deficient in oxygen-evolving activity, is shown to be specifically missing OEE2 polypeptides. This mutation, which results in the complete absence of all OEE2 mRNA and protein, does not affect the accumulation of other photosystem II polypeptides or their mRNAs.

Research paper thumbnail of Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Proceedings of the National Academy of Sciences, 2011

Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled ... more Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled by protein phosphorylation. Two thylakoid-associated kinases, STN7 and STN8, have distinct roles in short- and long-term photosynthetic acclimation to changes in light quality and quantity. Although some substrates of STN7 and STN8 are known, the complexity of this regulatory kinase system implies that currently unknown substrates connect photosynthetic performance with the regulation of metabolic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with Arabidopsis WT and stn8 mutant plants to identify unique STN8 targets. The phosphorylation status of STN7 was not affected in stn8 , indicating that kinases other than STN8 phosphorylate STN7 under standard growth conditions. Among several putative STN8 substrates, PGRL1-A is of particular importance because of its possible role in the modulation of cyclic electron transfer. The STN8 phosphorylation site on PGRL...

Research paper thumbnail of Structure and Expression of Chloroplast and Nuclear Genes in Chlamydomonas reinhardii

Proceedings in Life Sciences, 1984

Research paper thumbnail of The chloroplast ycf8 open reading frame encodes a photosystem II polypeptide which maintains photosynthetic activity under adverse growth conditions

Research paper thumbnail of Isolation of a psaF-deficient mutant of Chlamydomonas reinhardtii: efficient interaction of plastocyanin with the photosystem I reaction center is mediated by the PsaF subunit

Research paper thumbnail of Determinants for stability of the chloroplast psbD RNA are located within its short leader region in Chlamydomonas reinhardtii

Research paper thumbnail of Lack of the D2 protein in a Chlamydomonas reinhardtii psb D mutant affects photosystem II stability and D1 expression

Research paper thumbnail of The 5' leader of a chloroplast mRNA mediates the translational requirements for two nucleus-encoded functions in Chlamydomonas reinhardtii

Molecular and Cellular Biology, 1994

In the green alga Chlamydomonas reinhardtii, the nuclear mutations F34 and F64 have been previous... more In the green alga Chlamydomonas reinhardtii, the nuclear mutations F34 and F64 have been previously shown to abolish the synthesis of the photosystem II core polypeptide subunit P6, which is encoded by the chloroplast psbC gene. In this report the functions encoded by F34 and F64 are shown to be required for translation of the psbC mRNA, on the basis of the finding that the expression of a heterologous reporter gene fused to the psbC 5' nontranslated leader sequence requires wild-type F34 and F64 alleles in vivo. Moreover, a point mutation in the psbC 5' nontranslated leader sequence suppresses this requirement for wild-type F34 function. In vitro RNA-protein cross-linking studies reveal that chloroplast protein extracts from strains carrying the F64 mutation contain an approximately 46-kDa RNA-binding protein. The absence of the RNA-binding activity of this protein in chloroplast extracts of wild-type strains suggests that it is related to the role of the F64-encoded functi...

Research paper thumbnail of Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

The Plant cell, Jan 30, 2014

Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in... more Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in environmental conditions. Proteases and molecular chaperones involved in plastid protein quality control are encoded by the nucleus except for the catalytic subunit of ClpP, an evolutionarily conserved serine protease. Unlike its Escherichia coli ortholog, this chloroplast protease is essential for cell viability. To study its function, we used a recently developed system of repressible chloroplast gene expression in the alga Chlamydomonas reinhardtii. Using this repressible system, we have shown that a selective gradual depletion of ClpP leads to alteration of chloroplast morphology, causes formation of vesicles, and induces extensive cytoplasmic vacuolization that is reminiscent of autophagy. Analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein level, but not at the RNA level. These proteins may comprise some...

Research paper thumbnail of Functional Studies of Ycf3: Its Role in Assembly of Photosystem I and Interactions with Some of Its Subunits

THE PLANT CELL ONLINE, 2001

Research paper thumbnail of Phosphorylation of Photosystem II Controls Functional Macroscopic Folding of Photosynthetic Membranes in Arabidopsis      

The Plant Cell, 2009

Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in ph... more Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in photosystem II, which uses light energy to oxidize water and produce oxygen. The sunlight also causes quantitative phosphorylation of major photosystem II proteins. Analysis of the Arabidopsis thaliana stn7xstn8 double mutant deficient in thylakoid protein kinases STN7 and STN8 revealed light-independent phosphorylation of PsbH protein and greatly reduced N-terminal phosphorylation of D2 protein. The stn7xstn8 and stn8 mutants deficient in light-induced phosphorylation of photosystem II had increased thylakoid membrane folding compared with wild-type and stn7 plants. Significant enhancement in the size of stacked thylakoid membranes in stn7xstn8 and stn8 accelerated gravity-driven sedimentation of isolated thylakoids and was observed directly in plant leaves by transmission electron microscopy. Increased membrane folding, caused by the loss of light-induced protein phosphorylation, obstruc...

Research paper thumbnail of A Nuclear-Encoded Function Essential for Translation of the Chloroplast psaB mRNA in Chlamydomonas

Research paper thumbnail of Molecular and biophysical analysis of herbicide-resistant mutants of Chlamydomonas reinhardtii: structure-function relationship of the photosystem II D1 polypeptide

Research paper thumbnail of Low Density Membranes Are Associated with RNA-binding Proteins and Thylakoids in the Chloroplast of Chlamydomonas reinhardtii

The Journal of Cell Biology, 1998

Chloroplast subfractions were tested with a UV cross-linking assay for proteins that bind to the ... more Chloroplast subfractions were tested with a UV cross-linking assay for proteins that bind to the 5′ untranslated region of the chloroplast psbC mRNA of the green alga Chlamydomonas reinhardtii. These analyses revealed that RNA-binding proteins of 30–32, 46, 47, 60, and 80 kD are associated with chloroplast membranes. The buoyant density and the acyl lipid composition of these membranes are compatible with their origin being the inner chloroplast envelope membrane. However, unlike previously characterized inner envelope membranes, these membranes are associated with thylakoids. One of the membrane-associated RNA-binding proteins appears to be RB47, which has been reported to be a specific activator of psbA mRNA translation. These results suggest that translation of chloroplast mRNAs encoding thylakoid proteins occurs at either a subfraction of the chloroplast inner envelope membrane or a previously uncharacterized intra-chloroplast compartment, which is physically associated with thy...

Research paper thumbnail of Characterization of Tbc2, a nucleus-encoded factor specifically required for translation of the chloroplast psbC mRNA in Chlamydomonas reinhardtii

The Journal of Cell Biology, 2002

Genetic analysis has revealed that the three nucleus-encoded factors Tbc1, Tbc2, and Tbc3 are inv... more Genetic analysis has revealed that the three nucleus-encoded factors Tbc1, Tbc2, and Tbc3 are involved in the translation of the chloroplast psbC mRNA of the eukaryotic green alga Chlamydomonas reinhardtii. In this study we report the isolation and phenotypic characterization of two new tbc2 mutant alleles and their use for cloning and characterizing the Tbc2 gene by genomic complementation. TBC2 encodes a protein of 1,115 residues containing nine copies of a novel degenerate 38–40 amino acid repeat with a quasiconserved PPPEW motif near its COOH-terminal end. The middle part of the Tbc2 protein displays partial amino acid sequence identity with Crp1, a protein from Zea mays that is implicated in the processing and translation of the chloroplast petA and petD RNAs. The Tbc2 protein is enriched in chloroplast stromal subfractions and is associated with a 400-kD protein complex that appears to play a role in the translation of specifically the psbC mRNA.

Research paper thumbnail of Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii

Research paper thumbnail of The PsaC subunit of photosystem I provides an essential lysine residue for fast electron transfer to ferredoxin

Research paper thumbnail of A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii

Research paper thumbnail of Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB / psbT / psbH gene cluster in Chlamydomonas reinhardtii

Proceedings of the National Academy of Sciences, 2000

Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alg... more Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alga Chlamydomonas reinhardtii requires specific nucleus-encoded functions. To gain insight into this process, we have cloned the nuclear gene encoding the Mbb1 factor by genomic rescue of a mutant specifically deficient in the accumulation of the mRNAs of the psbB / psbT / psbH chloroplast transcription unit. Mbb1 is a soluble protein in the stromal phase of the chloroplast. It consists of 662 amino acids with a putative chloroplast-transit peptide at its N-terminal end. A striking feature is the presence of 10 tandemly arranged tetratricopeptide-like repeats that account for half of the protein sequence and are thought to be involved in protein–protein interactions. The Mbb1 protein seems to have a homologue in higher plants and is part of a 300-kDa complex that is associated with RNA. This complex is most likely involved in psbB mRNA processing, stability, and/or translation.

Research paper thumbnail of The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis

Proceedings of the National Academy of Sciences, 2010

The ability of plants to adapt to changing light conditions depends on a protein kinase network i... more The ability of plants to adapt to changing light conditions depends on a protein kinase network in the chloroplast that leads to the reversible phosphorylation of key proteins in the photosynthetic membrane. Phosphorylation regulates, in a process called state transition, a profound reorganization of the electron transfer chain and remodeling of the thylakoid membranes. Phosphorylation governs the association of the mobile part of the light-harvesting antenna LHCII with either photosystem I or photosystem II. Recent work has identified the redox-regulated protein kinase STN7 as a major actor in state transitions, but the nature of the corresponding phosphatases remained unknown. Here we identify a phosphatase of Arabidopsis thaliana , called PPH1, which is specifically required for the dephosphorylation of light-harvesting complex II (LHCII). We show that this single phosphatase is largely responsible for the dephosphorylation of Lhcb1 and Lhcb2 but not of the photosystem II core pr...

Research paper thumbnail of Expression of the nuclear gene encoding oxygen-evolving enhancer protein 2 is required for high levels of photosynthetic oxygen evolution in Chlamydomonas reinhardtii

Proceedings of the National Academy of Sciences, 1987

We have cloned a cDNA encoding a 20-kDa polypeptide, oxygen-evolving enhancer protein 2 (OEE2), i... more We have cloned a cDNA encoding a 20-kDa polypeptide, oxygen-evolving enhancer protein 2 (OEE2), in Chlamydomonas reinhardtii. This polypeptide has been implicated in photosynthetic oxygen evolution, and it is associated with the photosystem II complex, the site of oxygen evolution in all higher plants and algae. The sequence of OEE2 cDNA, the deduced amino acid sequence of the preprotein, the N-terminal protein sequence of mature OEE2 protein, and the coding regions of the single OEE2 gene are presented. The protein is synthesized with a 57-amino acid N-terminal transit peptide that directs the transport of this polypeptide across three cellular membranes. A nuclear mutant of C. reinhardtii, deficient in oxygen-evolving activity, is shown to be specifically missing OEE2 polypeptides. This mutation, which results in the complete absence of all OEE2 mRNA and protein, does not affect the accumulation of other photosystem II polypeptides or their mRNAs.

Research paper thumbnail of Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Proceedings of the National Academy of Sciences, 2011

Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled ... more Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled by protein phosphorylation. Two thylakoid-associated kinases, STN7 and STN8, have distinct roles in short- and long-term photosynthetic acclimation to changes in light quality and quantity. Although some substrates of STN7 and STN8 are known, the complexity of this regulatory kinase system implies that currently unknown substrates connect photosynthetic performance with the regulation of metabolic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with Arabidopsis WT and stn8 mutant plants to identify unique STN8 targets. The phosphorylation status of STN7 was not affected in stn8 , indicating that kinases other than STN8 phosphorylate STN7 under standard growth conditions. Among several putative STN8 substrates, PGRL1-A is of particular importance because of its possible role in the modulation of cyclic electron transfer. The STN8 phosphorylation site on PGRL...