F. Alkhalfioui, M. Renard, W. H. Vensel, J. Wong, C. K. Tanaka et al., Thioredoxin-Linked Proteins Are Reduced during Germination of Medicago truncatula Seeds, PLANT PHYSIOLOGY, vol.144, issue.3, pp.1559-1579, 2007.
DOI : 10.1104/pp.107.098103

I. S. Arts, D. Vertommen, F. Baldin, G. Laloux, C. et al., Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control, Molecular & Cellular Proteomics, vol.333, issue.6, pp.2125-2140, 2016.
DOI : 10.1073/pnas.1324240111

L. Avilan, S. Lebreton, and B. Gontero, Chloroplasts, Journal of Biological Chemistry, vol.266, issue.13, pp.9447-9451, 2000.
DOI : 10.1016/0968-0004(91)90083-8
URL : https://hal.archives-ouvertes.fr/hal-00347306

M. A. Ballicora, J. B. Frueauf, Y. Fu, P. Schürmann, and J. Preiss, Activation of the Potato Tuber ADP-glucose Pyrophosphorylase by Thioredoxin, Journal of Biological Chemistry, vol.275, issue.2, pp.1315-1320, 2000.
DOI : 10.1074/jbc.275.2.1315

Y. Balmer, A. Koller, G. Del-val, W. Manieri, P. Schürmann et al., Proteomics gives insight into the regulatory function of chloroplast thioredoxins, Proceedings of the National Academy of Sciences, vol.2, issue.9, pp.370-375, 2003.
DOI : 10.1002/1615-9861(200209)2:9<1090::AID-PROT1090>3.0.CO;2-1

Y. Balmer, A. Koller, G. D. Val, P. Schürmann, and B. B. Buchanan, Proteomics Uncovers Proteins Interacting Electrostatically with Thioredoxin in Chloroplasts, Photosynthesis Research, vol.79, issue.3, pp.275-280, 2004.
DOI : 10.1023/B:PRES.0000017207.88257.d4

Y. Balmer, W. H. Vensel, F. M. Dupont, B. B. Buchanan, and W. J. Hurkman, Proteome of amyloplasts isolated from developing wheat endosperm presents evidence of broad metabolic capability*, Journal of Experimental Botany, vol.45, issue.7, pp.1591-1602, 2006.
DOI : 10.1093/pcp/pch044

Y. Balmer, W. H. Vensel, W. J. Hurkman, and B. B. Buchanan, Thioredoxin Target Proteins in Chloroplast Thylakoid Membranes, Antioxidants & Redox Signaling, vol.8, issue.9-10, pp.1829-1834, 2006.
DOI : 10.1089/ars.2006.8.1829

Y. Balmer, W. H. Vensel, C. K. Tanaka, W. J. Hurkman, E. Gelhaye et al., Thioredoxin links redox to the regulation of fundamental processes of plant mitochondria, Proceedings of the National Academy of Sciences, vol.410, issue.6825, pp.2642-2647, 2004.
DOI : 10.1038/35065626

M. Balsera, E. Uberegui, P. Schurmann, and B. B. Buchanan, Evolutionary Development of Redox Regulation in Chloroplasts, Antioxidants & Redox Signaling, vol.21, issue.9, pp.1327-1355, 2014.
DOI : 10.1089/ars.2013.5817

A. L. Barabasi and Z. N. Oltvai, Network biology: understanding the cell's functional organization, Nature Reviews Genetics, vol.184, issue.2, pp.101-113, 2004.
DOI : 10.1128/JB.184.1.152-164.2002

S. Bartsch, J. Monnet, K. Selbach, F. Quigley, J. Gray et al., Three thioredoxin targets in the inner envelope membrane of chloroplasts function in protein import and chlorophyll metabolism, Proceedings of the National Academy of Sciences, vol.245, issue.5, pp.4933-4938, 2008.
DOI : 10.1007/BF00282224

M. Benhar, Nitric oxide and the thioredoxin system: a complex interplay in redox regulation, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1850, issue.12, pp.2476-2484, 2015.
DOI : 10.1016/j.bbagen.2015.09.010

M. Benhar, J. W. Thompson, M. A. Moseley, and J. S. Stamler, Identification of S-Nitrosylated Targets of Thioredoxin Using a Quantitative Proteomic Approach, Biochemistry, vol.49, issue.32, pp.6963-6969, 2010.
DOI : 10.1021/bi100619k

H. Berger, D. Mia, M. Morisse, S. Marchand, C. H. Lemaire et al., A light switch based on protein S-nitrosylation fine-tunes photosynthetic light-harvesting in the microalga Chlamydomonas reinhardtii, Plant Physiology, vol.171, pp.821-832, 2016.
DOI : 10.1104/pp.15.01878

M. B. Bosco, M. C. Aleanzi, and A. A. Iglesias, Plastidic Phosphoglycerate Kinase from Phaeodactylum tricornutum: On the Critical Role of Cysteine Residues for the Enzyme Function, Protist, vol.163, issue.2, pp.188-203, 2012.
DOI : 10.1016/j.protis.2011.07.001

H. K. Brandes, F. W. Larimer, M. K. Geck, C. D. Stringer, P. Schurmann et al., Direct identification of the primary nucleophile of thioredoxin f, J Biol Chem, vol.268, pp.18411-18414, 1993.

B. B. Buchanan, A. Holmgren, J. P. Jacquot, and R. Scheibe, Fifty years in the thioredoxin field and a bountiful harvest, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1820, issue.11, pp.1822-1829, 2012.
DOI : 10.1016/j.bbagen.2012.07.006

S. Casagrande, V. Bonetto, M. Fratelli, E. Gianazza, I. Eberini et al., Glutathionylation of human thioredoxin: A possible crosstalk between the glutathione and thioredoxin systems, Proceedings of the National Academy of Sciences, vol.17, issue.9, pp.9745-9749, 2002.
DOI : 10.1093/emboj/17.9.2596

M. Chiadmi, A. Navaza, M. Miginiac-maslow, J. P. Jacquot, C. et al., Redox signalling in the chloroplast: structure of oxidized pea fructose-1,6-bisphosphate phosphatase, The EMBO Journal, vol.18, issue.23, pp.6809-6815, 1999.
DOI : 10.1093/emboj/18.23.6809

H. Choi, S. Kim, P. Mukhopadhyay, S. Cho, J. Woo et al., Structural Basis of the Redox Switch in the OxyR Transcription Factor, Cell, vol.105, issue.1, pp.103-113, 2001.
DOI : 10.1016/S0092-8674(01)00300-2

C. Choudhary, B. T. Weinert, Y. Nishida, E. Verdin, and M. Mann, The growing landscape of lysine acetylation links metabolism and cell signalling, Nature Reviews Molecular Cell Biology, vol.13, issue.8, pp.536-550, 2014.
DOI : 10.1002/pmic.201200001

J. Couturier, K. Chibani, J. P. Jacquot, and N. Rouhier, Cysteine???based redox regulation and signaling in plants, Frontiers in Plant Science, vol.4, p.105, 2013.
DOI : 10.3389/fpls.2013.00105
URL : https://hal.archives-ouvertes.fr/hal-01578659

R. Dayer, B. B. Fischer, R. I. Eggen, and S. D. Lemaire, The Peroxiredoxin and Glutathione Peroxidase Families in Chlamydomonas reinhardtii, Genetics, vol.179, issue.1, pp.41-57, 2008.
DOI : 10.1534/genetics.107.086041

V. Delorme-hinoux, S. A. Bangash, A. J. Meyer, R. , and J. P. , Nuclear thiol redox systems in plants, Plant Science, vol.243, pp.84-95, 2016.
DOI : 10.1016/j.plantsci.2015.12.002

K. J. Dietz, Peroxiredoxins in Plants and Cyanobacteria, Antioxidants & Redox Signaling, vol.15, issue.4, pp.1129-1159, 2011.
DOI : 10.1089/ars.2010.3657
URL : http://europepmc.org/articles/pmc3135184?pdf=render

S. Doll and A. L. Burlingame, Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications, ACS Chemical Biology, vol.10, issue.1, pp.63-71, 2015.
DOI : 10.1021/cb500904b

H. Du, S. Kim, K. H. Nam, M. S. Lee, O. Son et al., Identification of uricase as a potential target of plant thioredoxin: Implication in the regulation of nodule development, Biochemical and Biophysical Research Communications, vol.397, issue.1, pp.22-26, 2010.
DOI : 10.1016/j.bbrc.2010.05.040

R. Entus, M. Poling, H. , and K. M. , Redox Regulation of Arabidopsis 3-Deoxy-D-arabino-Heptulosonate 7-Phosphate Synthase, PLANT PHYSIOLOGY, vol.129, issue.4, pp.1866-1871, 2002.
DOI : 10.1104/pp.002626

A. Fares, M. Rossignol, and J. B. Peltier, Proteomics investigation of endogenous S-nitrosylation in Arabidopsis, Biochemical and Biophysical Research Communications, vol.416, issue.3-4, pp.331-336, 2011.
DOI : 10.1016/j.bbrc.2011.11.036

J. Feng, C. Wang, Q. Chen, H. Chen, B. Ren et al., S-nitrosylation of phosphotransfer proteins represses cytokinin signaling, Nature Communications, vol.14, p.1529, 2013.
DOI : 10.1110/ps.041076905

A. Filonova, P. Haemsch, C. Gebauer, W. Weisheit, and V. Wagner, Protein Disulfide Isomerase 2 of Chlamydomonas reinhardtii Is Involved in Circadian Rhythm Regulation, Molecular Plant, vol.6, issue.5, 2013.
DOI : 10.1093/mp/sst048

B. B. Fischer, R. Dayer, Y. Schwarzenbach, S. D. Lemaire, R. Behra et al., Function and regulation of the glutathione peroxidase homologous gene GPXH/GPX5 in Chlamydomonas reinhardtii, Plant Molecular Biology, vol.37, issue.3, pp.569-583, 2009.
DOI : 10.1016/S0167-4781(96)00206-0

C. H. Foyer and G. Noctor, Stress-triggered redox signalling: what's in pROSpect?, Plant, Cell & Environment, vol.57, issue.5, pp.951-964, 2016.
DOI : 10.1111/j.1365-313X.2008.03687.x

F. Matika, D. E. Loake, and G. J. , Redox Regulation in Plant Immune Function, Antioxidants & Redox Signaling, vol.21, issue.9, pp.1373-1388, 2014.
DOI : 10.1089/ars.2013.5679

S. Garcia-santamarina, S. Boronat, A. Domenech, J. Ayte, H. Molina et al., Monitoring in vivo reversible cysteine oxidation in proteins using ICAT and mass spectrometry, Nature Protocols, vol.893, issue.5, pp.1131-1145, 2014.
DOI : 10.1021/pr900721e

P. Geigenberger and A. R. Fernie, Metabolic Control of Redox and Redox Control of Metabolism in Plants, Antioxidants & Redox Signaling, vol.21, issue.9, pp.1389-1421, 2014.
DOI : 10.1089/ars.2014.6018

P. Geigenberger, A. Kolbe, and A. Tiessen, Redox regulation of carbon storage and partitioning in response to light and sugars, Journal of Experimental Botany, vol.56, issue.416, pp.1469-1479, 2005.
DOI : 10.1104/pp.003756

E. Gelhaye, N. Rouhier, N. Navrot, and J. P. Jacquot, The plant thioredoxin system, Cellular and Molecular Life Sciences, vol.62, issue.1, pp.24-35, 2005.
DOI : 10.1007/s00018-004-4296-4

Y. M. Go, J. D. Chandler, and D. P. Jones, The cysteine proteome, Free Radical Biology and Medicine, vol.84, pp.227-245, 2015.
DOI : 10.1016/j.freeradbiomed.2015.03.022

Y. M. Go and D. P. Jones, Redox biology: Interface of the exposome with the proteome, epigenome and genome, Redox Biology, vol.2, pp.358-360, 2014.
DOI : 10.1016/j.redox.2013.12.032

G. Gontero and M. E. Salvucci, Regulation of photosynthetic carbon metabolism in aquatic and terrestrial organisms by Rubisco activase, redox-modulation and CP12, Aquatic Botany, vol.118, pp.14-23, 2014.
DOI : 10.1016/j.aquabot.2014.05.011

N. S. Gould, P. Evans, P. Martinez-acedo, S. M. Marino, V. N. Gladyshev et al., Site-Specific Proteomic Mapping Identifies Selectively Modified Regulatory Cysteine Residues in Functionally Distinct Protein Networks, Chemistry & Biology, vol.22, issue.7, pp.965-975, 2015.
DOI : 10.1016/j.chembiol.2015.06.010

A. Goyer, C. Haslekas, M. Miginiac-maslow, U. Klein, L. Maréchal et al., Isolation and characterization of a thioredoxin-dependent peroxidase from Chlamydomonas reinhardtii, European Journal of Biochemistry, vol.92, issue.1, pp.272-282, 2002.
DOI : 10.1073/pnas.92.22.10237

F. Gross, J. Durner, and F. Gaupels, Nitric oxide, antioxidants and prooxidants in plant defence responses, Frontiers in plant science, vol.4, p.419, 2013.

D. D. Gutle, T. Roret, S. J. Muller, J. Couturier, S. D. Lemaire et al., Chloroplast FBPase and SBPase are thioredoxin-linked enzymes with similar architecture but different evolutionary histories, Proceedings of the National Academy of Sciences, vol.460, issue.3, pp.6779-6784, 2016.
DOI : 10.1107/S0021889800018227

P. Hagglund, J. Bunkenborg, K. Maeda, C. Finnie, and B. Svensson, Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags, Methods in molecular biology, vol.1072, pp.677-685, 2014.
DOI : 10.1007/978-1-62703-631-3_47

P. Hagglund, J. Bunkenborg, K. Maeda, and B. Svensson, Identification of Thioredoxin Disulfide Targets Using a Quantitative Proteomics Approach Based on Isotope-Coded Affinity Tags, Journal of Proteome Research, vol.7, issue.12, pp.5270-5276, 2008.
DOI : 10.1021/pr800633y

P. Hagglund, C. Finnie, H. Yano, A. Shahpiri, B. B. Buchanan et al., Seed thioredoxin h, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1864, issue.8, pp.974-982, 2016.
DOI : 10.1016/j.bbapap.2016.02.014

M. Hall, A. Mata-cabana, H. E. Akerlund, F. J. Florencio, W. P. Schroder et al., Thioredoxin targets of the plant chloroplast lumen and their implications for plastid function, PROTEOMICS, vol.133, pp.987-1001, 2010.
DOI : 10.1002/pmic.200900654

J. T. Hancock, The Role of Redox Mechanisms in Cell Signalling, Molecular Biotechnology, vol.425, issue.2, pp.162-166, 2009.
DOI : 10.1152/physrev.00018.2001

E. M. Hanschmann, J. R. Godoy, C. Berndt, C. Hudemann, and C. H. Lillig, Thioredoxins, Glutaredoxins, and Peroxiredoxins???Molecular Mechanisms and Health Significance: from Cofactors to Antioxidants to Redox Signaling, Antioxidants & Redox Signaling, vol.19, issue.13, pp.1539-1605, 2013.
DOI : 10.1089/ars.2012.4599

S. Hara, K. Motohashi, F. Arisaka, P. G. Romano, N. Hosoya-matsuda et al., 1 Reduces and Reactivates the Oxidized Cytosolic Malate Dehydrogenase Dimer in Higher Plants, Journal of Biological Chemistry, vol.7, issue.43, pp.32065-32071, 2006.
DOI : 10.1016/S0969-2126(99)80058-6

A. Harrison, M. Sakato, H. W. Tedford, S. E. Benashski, R. S. Patel-king et al., Redox-based control of the ? heavy chain ATPase fromChlamydomonas outer arm dynein, Cell Motility and the Cytoskeleton, vol.25, issue.3, pp.131-143, 2002.
DOI : 10.1247/csf.25.263

S. I. Hashemy and A. Holmgren, -Nitrosylation of Cysteine Residues, Journal of Biological Chemistry, vol.271, issue.32, pp.21890-21898, 2008.
DOI : 10.1126/science.1159246

X. He, M. Miginiac-maslow, C. Sigalat, E. Keryer, and F. Haraux, Mechanism of Activation of the Chloroplast ATP Synthase, Journal of Biological Chemistry, vol.193, issue.18, pp.13250-13258, 2000.
DOI : 10.1016/0014-5793(96)00246-3

A. S. Hebert, A. L. Richards, D. J. Bailey, A. Ulbrich, E. E. Coughlin et al., The one hour yeast proteome. Molecular & cellular proteomics, pp.339-347, 2014.

J. M. Held and B. W. Gibson, Regulatory Control or Oxidative Damage? Proteomic Approaches to Interrogate the Role of Cysteine Oxidation Status in Biological Processes, Molecular & Cellular Proteomics, vol.12, issue.4, pp.111-013037, 2012.
DOI : 10.1073/pnas.0809620106

D. T. Hess and J. S. Stamler, -Nitrosylation of Protein Post-translational Modification, Journal of Biological Chemistry, vol.58, issue.7, pp.4411-4418, 2012.
DOI : 10.1074/jbc.M413058200

A. Holmgren, Thioredoxin structure and mechanism: conformational changes on oxidation of the active-site sulfhydryls to a disulfide, Structure, vol.3, issue.3, pp.239-243, 1995.
DOI : 10.1016/S0969-2126(01)00153-8

S. C. Hunter and J. B. Ohlrogge, Regulation of Spinach Chloroplast Acetyl-CoA Carboxylase, Archives of Biochemistry and Biophysics, vol.359, issue.2, pp.170-178, 1998.
DOI : 10.1006/abbi.1998.0900

C. A. Hutchison, R. Y. Chuang, V. N. Noskov, N. Assad-garcia, T. J. Deerinck et al., Design and synthesis of a minimal bacterial genome, Science, vol.181, issue.24, p.6253, 2016.
DOI : 10.1016/S0147-619X(02)00121-X

A. Ikegami, N. Yoshimura, K. Motohashi, S. Takahashi, P. G. Romano et al., Magnesium Chelatase Is a Target Protein of the Chloroplast Thioredoxin, Journal of Biological Chemistry, vol.9, issue.27, pp.19282-19291, 2007.
DOI : 10.1073/pnas.94.22.11857

E. Issakidis, M. Lemaire, P. Decottignies, J. P. Jacquot, and M. Miginiac-maslow, Direct evidence for the different roles of the N- and C-terminal regulatory disulfides of sorghum leaf NADP-malate dehydrogenase in its activation by reduced thioredoxin, FEBS Letters, vol.271, issue.2, pp.121-124, 1996.
DOI : 10.1074/jbc.271.7.3333

J. P. Jacquot, H. Eklund, N. Rouhier, and P. Schurmann, Structural and evolutionary aspects of thioredoxin reductases in photosynthetic organisms, Trends in Plant Science, vol.14, issue.6, pp.336-343, 2009.
DOI : 10.1016/j.tplants.2009.03.005

J. P. Jacquot, J. Lopez-jaramillo, M. Miginiac-maslow, S. Lemaire, J. Cherfils et al., Cysteine-153 is required for redox regulation of pea chloroplast fructose-1,6-bisphosphatase, FEBS Letters, vol.401, issue.2-3, pp.143-147, 1997.
DOI : 10.1016/S0014-5793(96)01459-7

J. P. Jacquot, J. Vidal, P. Gadal, and P. Schurmann, Evidence for the existence of several enzyme-specific thioredoxins in plants, FEBS Letters, vol.11, issue.2, pp.243-246, 1978.
DOI : 10.1016/0304-4211(78)90015-9

R. Kandpal, B. Saviola, F. , and J. , The era of 'omics unlimited, BioTechniques, vol.46, issue.5, pp.351-352, 2009.
DOI : 10.2144/000113137

Z. H. Kang, W. , and G. X. , Redox regulation in the thylakoid lumen, Journal of Plant Physiology, vol.192, pp.28-37, 2016.
DOI : 10.1016/j.jplph.2015.12.012

A. Kaya, B. C. Lee, and V. N. Gladyshev, Regulation of Protein Function by Reversible Methionine Oxidation and the Role of Selenoprotein MsrB1, Antioxidants & Redox Signaling, vol.23, issue.10, pp.814-822, 2015.
DOI : 10.1089/ars.2015.6385

S. O. Kim, K. Merchant, R. Nudelman, W. F. Beyer, . Jr et al., OxyR, Cell, vol.109, issue.3, pp.383-396, 2002.
DOI : 10.1016/S0092-8674(02)00723-7
URL : https://doi.org/10.1016/s0092-8674(02)00723-7

S. Kneeshaw, S. Gelineau, Y. Tada, G. J. Loake, and S. H. Spoel, Selective Protein Denitrosylation Activity of Thioredoxin-h5 Modulates Plant Immunity, Molecular Cell, vol.56, issue.1, pp.153-162, 2014.
DOI : 10.1016/j.molcel.2014.08.003

J. Konig, M. Muthuramalingam, and K. J. Dietz, Mechanisms and dynamics in the thiol/disulfide redox regulatory network: transmitters, sensors and targets, Current Opinion in Plant Biology, vol.15, issue.3, pp.261-268, 2012.
DOI : 10.1016/j.pbi.2011.12.002

A. Kozaki, K. Mayumi, and Y. Sasaki, Thiol-Disulfide Exchange between Nuclear-encoded and Chloroplast-encoded Subunits of Pea Acetyl-CoA Carboxylase, Journal of Biological Chemistry, vol.266, issue.43, pp.39919-39925, 2001.
DOI : 10.1073/pnas.89.5.1519

T. C. Laurent, E. C. Moore, R. , and P. , Enzymatic Synthesis of Deoxyribonucleotides. Iv. Isolation and Characterization of Thioredoxin, the Hydrogen Donor from Escherichia Coli B, J Biol Chem, vol.239, pp.3436-3444, 1964.

S. Lebreton, E. Graciet, and B. Gontero, Modulation, via Protein-Protein Interactions, of Glyceraldehyde-3-phosphate Dehydrogenase Activity through Redox Phosphoribulokinase Regulation, Journal of Biological Chemistry, vol.266, issue.14, pp.12078-12084, 2003.
DOI : 10.1016/S1874-6047(08)60239-5

S. Lee, S. M. Kim, L. , and R. T. , Thioredoxin and Thioredoxin Target Proteins: From Molecular Mechanisms to Functional Significance, Antioxidants & Redox Signaling, vol.18, issue.10, pp.1165-1207, 2013.
DOI : 10.1089/ars.2011.4322
URL : http://europepmc.org/articles/pmc3579385?pdf=render

S. D. Lemaire, V. Collin, E. Keryer, E. Issakidis-bourguet, D. Lavergne et al., Chlamydomonas reinhardtii: a model organism for the study of the thioredoxin family, Plant Physiology and Biochemistry, vol.41, issue.6-7, pp.513-522, 2003.
DOI : 10.1016/S0981-9428(03)00079-2

S. D. Lemaire, B. Guillon, L. Marechal, P. Keryer, E. Miginiac-maslow et al., New thioredoxin targets in the unicellular photosynthetic eukaryote Chlamydomonas reinhardtii, Proceedings of the National Academy of Sciences, vol.21, issue.14, pp.7475-7480, 2004.
DOI : 10.1093/emboj/cdf372

S. D. Lemaire, L. Michelet, M. Zaffagnini, V. Massot, and E. Bourguet, Thioredoxins in chloroplasts, Current Genetics, vol.99, issue.Suppl 1, pp.343-365, 2007.
DOI : 10.1016/S0167-4838(01)00178-9

S. D. Lemaire and M. Miginiac-maslow, The thioredoxin superfamily in Chlamydomonas reinhardtii, Photosynthesis Research, vol.95, issue.3, pp.203-220, 2004.
DOI : 10.1073/pnas.122243399

S. D. Lemaire, A. Quesada, F. Merchan, J. M. Corral, M. I. Igeno et al., NADP-Malate Dehydrogenase from Unicellular Green Alga Chlamydomonas reinhardtii. A First Step toward Redox Regulation?, PLANT PHYSIOLOGY, vol.137, issue.2, pp.514-521, 2005.
DOI : 10.1104/pp.104.052670
URL : http://www.plantphysiol.org/content/plantphysiol/137/2/514.full.pdf

S. E. Leonard, K. G. Reddie, C. , and K. S. , Mining the Thiol Proteome for Sulfenic Acid Modifications Reveals New Targets for Oxidation in Cells, ACS Chemical Biology, vol.4, issue.9, pp.783-799, 2009.
DOI : 10.1021/cb900105q

M. Lindahl, F. , and F. J. , Thioredoxin-linked processes in cyanobacteria are as numerous as in chloroplasts, but targets are different, Proceedings of the National Academy of Sciences, vol.54, issue.383, pp.16107-16112, 2003.
DOI : 10.1093/jxb/erg076

M. Lindahl, A. Mata-cabana, and T. Kieselbach, The Disulfide Proteome and Other Reactive Cysteine Proteomes: Analysis and Functional Significance, Antioxidants & Redox Signaling, vol.14, issue.12, pp.2581-2642, 2011.
DOI : 10.1089/ars.2010.3551

C. Lindermayr, G. Saalbach, and J. Durner, Proteomic Identification of S-Nitrosylated Proteins in Arabidopsis, PLANT PHYSIOLOGY, vol.137, issue.3, pp.921-930, 2005.
DOI : 10.1104/pp.104.058719

P. E. Lopez-calcagno, T. P. Howard, and C. A. Raines, The CP12 protein family: a thioredoxin-mediated metabolic switch?, Frontiers in Plant Science, vol.5, p.9, 2014.
DOI : 10.3389/fpls.2014.00009

J. Lu and A. Holmgren, The thioredoxin antioxidant system, Free Radical Biology and Medicine, vol.66, pp.75-87, 2014.
DOI : 10.1016/j.freeradbiomed.2013.07.036

H. Maeda and N. Dudareva, The Shikimate Pathway and Aromatic Amino Acid Biosynthesis in Plants, Annual Review of Plant Biology, vol.63, issue.1, pp.73-105, 2012.
DOI : 10.1146/annurev-arplant-042811-105439

K. Maeda, C. Finnie, and B. Svensson, Cy5 maleimide labelling for sensitive detection of free thiols in native protein extracts: identification of seed proteins targeted by barley thioredoxin h isoforms, Biochemical Journal, vol.378, issue.2, pp.497-507, 2004.
DOI : 10.1042/bj20031634

K. Maeda, C. Finnie, and B. Svensson, Identification of thioredoxin?h-reducible disulphides in proteomes by differential labelling of cysteines: Insight into recognition and regulation of proteins in barley seeds by thioredoxin?h, PROTEOMICS, vol.207, issue.6, pp.1634-1644, 2005.
DOI : 10.1016/0167-4838(86)90318-3

C. Marchand, L. Marechal, P. Meyer, Y. Decottignies, and P. , Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin, PROTEOMICS, vol.138, issue.1, pp.6528-6537, 2006.
DOI : 10.1002/pmic.200600443
URL : https://hal.archives-ouvertes.fr/hal-00164223

C. Marchand, L. Maréchal, P. Meyer, Y. Miginiac-maslow, M. Issakidis-bourguet et al., New targets of Arabidopsis thioredoxins revealed by proteomic analysis, PROTEOMICS, vol.4, issue.9, pp.2696-2706, 2004.
DOI : 10.1002/pmic.200400805
URL : https://hal.archives-ouvertes.fr/hal-00169106

C. H. Marchand, H. Vanacker, V. Collin, E. Issakidis-bourguet, P. L. Marechal et al., Thioredoxin targets in Arabidopsis roots, PROTEOMICS, vol.278, issue.13, pp.2418-2428, 2010.
DOI : 10.1074/mcp.M600250-MCP200
URL : https://hal.archives-ouvertes.fr/hal-01183616

J. Marin-navarro and J. Moreno, Cysteines 449 and 459 modulate the reduction-oxidation conformational changes of ribulose 1.5-bisphosphate carboxylase/oxygenase and the translocation of the enzyme to membranes during stress, Plant, Cell and Environment, vol.269, issue.5, pp.898-908, 2006.
DOI : 10.1074/jbc.271.31.18494

L. Marri, M. Zaffagnini, V. Collin, E. Issakidis-bourguet, S. D. Lemaire et al., Prompt and Easy Activation by Specific Thioredoxins of Calvin Cycle Enzymes of Arabidopsis thaliana Associated in the GAPDH/CP12/PRK Supramolecular Complex, Molecular Plant, vol.2, issue.2, pp.259-269, 2009.
DOI : 10.1093/mp/ssn061

J. L. Martin, Thioredoxin ???a fold for all reasons, Structure, vol.3, issue.3, pp.245-250, 1995.
DOI : 10.1016/S0969-2126(01)00154-X

C. Marx, J. H. Wong, and B. B. Buchanan, Thioredoxin and germinating barley: targets and protein redox changes, Planta, vol.216, pp.454-460, 2003.

Y. Meyer, C. Belin, V. Delorme-hinoux, J. P. Reichheld, R. et al., Thioredoxin and Glutaredoxin Systems in Plants: Molecular Mechanisms, Crosstalks, and Functional Significance, Antioxidants & Redox Signaling, vol.17, issue.8, pp.1124-1160, 2012.
DOI : 10.1089/ars.2011.4327

Y. Meyer, B. B. Buchanan, F. Vignols, R. , and J. P. , Thioredoxins and Glutaredoxins: Unifying Elements in Redox Biology, Annual Review of Genetics, vol.43, issue.1, pp.335-367, 2009.
DOI : 10.1146/annurev-genet-102108-134201
URL : https://hal.archives-ouvertes.fr/hal-00685724

L. Michelet, M. Zaffagnini, C. Marchand, V. Collin, P. Decottignies et al., Glutathionylation of chloroplast thioredoxin f is a redox signaling mechanism in plants, Proceedings of the National Academy of Sciences, vol.335, issue.1, pp.16478-16483, 2005.
DOI : 10.1006/abbi.1996.0482

L. Michelet, M. Zaffagnini, S. Morisse, F. Sparla, M. E. Perez-perez et al., Redox regulation of the Calvin???Benson cycle: something old, something new, Frontiers in Plant Science, vol.4, p.470, 2013.
DOI : 10.3389/fpls.2013.00470
URL : https://hal.archives-ouvertes.fr/hal-01578991

R. Mikkelsen, K. E. Mutenda, A. Mant, P. Schürmann, and A. Blennow, ??-Glucan, water dikinase (GWD): A plastidic enzyme with redox-regulated and coordinated catalytic activity and binding affinity, Proceedings of the National Academy of Sciences, vol.135, issue.4, pp.1785-1790, 2005.
DOI : 10.1104/pp.104.041301

S. Milanez, R. J. Mural, and F. C. Hartman, Roles of cysteinyl residues of phosphoribulokinase as examined by site-directed mutagenesis, J Biol Chem, vol.266, pp.10694-10699, 1991.

H. P. Mock and K. J. Dietz, Redox proteomics for the assessment of redox-related posttranslational regulation in plants, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1864, issue.8, pp.967-973, 2016.
DOI : 10.1016/j.bbapap.2016.01.005

F. Montrichard, F. Alkhalfioui, H. Yano, W. H. Vensel, W. J. Hurkman et al., Thioredoxin targets in plants: The first 30??years, Journal of Proteomics, vol.72, issue.3, pp.452-474, 2009.
DOI : 10.1016/j.jprot.2008.12.002

J. Moreno, M. J. Garcia-murria, and J. Marin-navarro, Redox modulation of Rubisco conformation and activity through its cysteine residues, Journal of Experimental Botany, vol.59, issue.7, pp.1605-1614, 2008.
DOI : 10.1093/jxb/erm310

J. V. Moroney, C. S. Fullmer, and R. E. Mccarty, Characterization of the cysteinyl-containing peptides of the gamma subunit of coupling factor 1, J Biol Chem, vol.259, pp.7281-7285, 1984.

K. Motohashi, A. Kondoh, M. T. Stumpp, and T. Hisabori, Comprehensive survey of proteins targeted by chloroplast thioredoxin, Proceedings of the National Academy of Sciences, vol.276, issue.32, pp.11224-11229, 2001.
DOI : 10.1074/jbc.M101822200

N. Navrot, V. Collin, J. Gualberto, E. Gelhaye, M. Hirasawa et al., Plant Glutathione Peroxidases Are Functional Peroxiredoxins Distributed in Several Subcellular Compartments and Regulated during Biotic and Abiotic Stresses, PLANT PHYSIOLOGY, vol.142, issue.4, pp.1364-1379, 2006.
DOI : 10.1104/pp.106.089458

G. Nee, M. Aumont-nicaise, M. Zaffagnini, S. Nessler, M. Valerio-lepiniec et al., Redox regulation of chloroplastic G6PDH activity by thioredoxin occurs through structural changes modifying substrate accessibility and cofactor binding, Biochemical Journal, vol.41, issue.1, pp.117-125, 2014.
DOI : 10.1074/jbc.272.43.26985

L. Nikkanen, R. , and E. , Thioredoxin-dependent regulatory networks in chloroplasts under fluctuating light conditions, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.63, issue.1, p.20130224, 2014.
DOI : 10.1093/jxb/err282
URL : http://rstb.royalsocietypublishing.org/content/royptb/369/1640/20130224.full.pdf

G. Noctor, A. C. Arisi, L. Jouanin, and C. H. Foyer, Manipulation of Glutathione and Amino Acid Biosynthesis in the Chloroplast, Plant Physiology, vol.118, issue.2, pp.471-482, 1998.
DOI : 10.1104/pp.118.2.471

J. S. Paige, G. Xu, B. Stancevic, and S. R. Jaffrey, Nitrosothiol Reactivity Profiling Identifies S-Nitrosylated Proteins with Unexpected Stability, Chemistry & Biology, vol.15, issue.12, pp.1307-1316, 2008.
DOI : 10.1016/j.chembiol.2008.10.013
URL : https://doi.org/10.1016/j.chembiol.2008.10.013

R. S. Patel-king, S. E. Benashki, A. Harrison, and S. M. King, Outer Dynein Arm, Journal of Biological Chemistry, vol.1, issue.11, pp.6283-6291, 1996.
DOI : 10.1073/pnas.91.6.2100

C. E. Paulsen, C. , and K. S. , Orchestrating Redox Signaling Networks through Regulatory Cysteine Switches, ACS Chemical Biology, vol.5, issue.1, pp.47-62, 2010.
DOI : 10.1021/cb900258z
URL : http://europepmc.org/articles/pmc4537063?pdf=render

C. E. Paulsen, C. , and K. S. , Cysteine-Mediated Redox Signaling: Chemistry, Biology, and Tools for Discovery, Chemical Reviews, vol.113, issue.7, pp.4633-4679, 2013.
DOI : 10.1021/cr300163e
URL : https://doi.org/10.1021/cr300163e

M. E. Pérez-pérez, F. J. Florencio, and M. Lindahl, Selecting thioredoxins for disulphide proteomics: Target proteomes of three thioredoxins from the cyanobacterium Synechocystis sp. PCC 6803, PROTEOMICS, vol.181, issue.S1, pp.186-195, 2006.
DOI : 10.1128/jb.179.14.4513-4522.1997

M. E. Perez-perez, S. D. Lemaire, and J. L. Crespo, Is Mediated through Redox-Dependent Inactivation of the ATG4 Protease, Plant Physiology, vol.172, issue.4, pp.2219-2234, 2016.
DOI : 10.1104/pp.16.01582

M. E. Pérez-pérez, E. Martin-figueroa, F. , and F. J. , Photosynthetic Regulation of the Cyanobacterium Synechocystis sp. PCC 6803 Thioredoxin System and Functional Analysis of TrxB (Trx x) and TrxQ (Trx y) Thioredoxins, Molecular Plant, vol.2, issue.2, pp.270-283, 2009.
DOI : 10.1093/mp/ssn070

M. E. Perez-perez, A. Mata-cabana, A. M. Sanchez-riego, M. Lindahl, F. et al., A Comprehensive Analysis of the Peroxiredoxin Reduction System in the Cyanobacterium Synechocystis sp. Strain PCC 6803 Reveals that All Five Peroxiredoxins Are Thioredoxin Dependent, Journal of Bacteriology, vol.191, issue.24, pp.7477-7489, 2009.
DOI : 10.1128/JB.00831-09

M. E. Perez-perez, M. Zaffagnini, C. H. Marchand, J. L. Crespo, and S. D. Lemaire, The yeast autophagy protease Atg4 is regulated by thioredoxin, Autophagy, vol.266, issue.11, pp.1953-1964, 2014.
DOI : 10.1074/jbc.M709567200

E. Pieroni, S. De-la-fuente-van-bentem, G. Mancosu, E. Capobianco, H. Hirt et al., Protein networking: insights into global functional organization of proteomes, PROTEOMICS, vol.13, issue.4, pp.799-816, 2008.
DOI : 10.1074/mcp.M600046-MCP200

L. B. Poole and C. Schoneich, Introduction: What we do and do not know regarding redox processes of thiols in signaling pathways, Free Radical Biology and Medicine, vol.80, pp.145-147, 2015.
DOI : 10.1016/j.freeradbiomed.2015.02.005

M. A. Porter, C. D. Stringer, and F. C. Hartman, Characterization of the regulatory thioredoxin site of phosphoribulokinase, J Biol Chem, vol.263, pp.123-129, 1988.

A. R. Portis and . Jr, Rubisco activase -Rubisco's catalytic chaperone, Photosynthesis Research, vol.75, issue.1, pp.11-27, 2003.
DOI : 10.1023/A:1022458108678

A. R. Portis, . Jr, C. Li, D. Wang, and M. E. Salvucci, Regulation of Rubisco activase and its interaction with Rubisco, Journal of Experimental Botany, vol.59, issue.7, pp.1597-1604, 2008.
DOI : 10.1093/jxb/erm240

B. B. Quimby and M. Dasso, The small GTPase Ran: interpreting the signs, Current Opinion in Cell Biology, vol.15, issue.3, pp.338-344, 2003.
DOI : 10.1016/S0955-0674(03)00046-2

K. G. Reddie, C. , and K. S. , Expanding the functional diversity of proteins through cysteine oxidation, Current Opinion in Chemical Biology, vol.12, issue.6, pp.746-754, 2008.
DOI : 10.1016/j.cbpa.2008.07.028

N. M. Riley, A. S. Hebert, and J. J. Coon, Proteomics Moves into the Fast Lane, Cell Systems, vol.2, issue.3, pp.142-143, 2016.
DOI : 10.1016/j.cels.2016.03.002

S. Rinalducci, C. Marrocco, and L. Zolla, Thiol-based regulation of glyceraldehyde-3-phosphate dehydrogenase in blood bank-stored red blood cells: a strategy to counteract oxidative stress, Transfusion, vol.288, issue.Suppl 3, pp.499-506, 2015.
DOI : 10.1074/jbc.M112.428573

R. Rivera-madrid, D. Mestres, P. Marinho, J. P. Jacquot, P. Decottignies et al., Evidence for five divergent thioredoxin h sequences in Arabidopsis thaliana., Proceedings of the National Academy of Sciences, vol.92, issue.12, pp.5620-5624, 1995.
DOI : 10.1073/pnas.92.12.5620

R. J. Rodriguez-suarez, S. Mora-garcia, and R. A. Wolosiuk, Characterization of cysteine residues involved in the reductive activation and the structural stability of rapeseed (Brassica napus) chloroplast fructose-1,6- bisphosphatase, pp.388-393, 1997.

J. M. Romero and O. A. Bizzozero, Intracellular glutathione mediates the denitrosylation of protein nitrosothiols in the rat spinal cord, Journal of Neuroscience Research, vol.20, issue.3, pp.701-709, 2009.
DOI : 10.1042/bj3150931

S. A. Ross, M. X. Zhang, and B. R. Selman, Coupling Factor 1 ??-Subunit Cysteine Bridge in the Regulation of ATP Synthase, Journal of Biological Chemistry, vol.5, issue.17, pp.9813-9818, 1995.
DOI : 10.1073/pnas.90.19.9199

N. Rouhier, D. Cerveau, J. Couturier, J. P. Reichheld, R. et al., Involvement of thiol-based mechanisms in plant development, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1850, issue.8, pp.1479-1496, 2015.
DOI : 10.1016/j.bbagen.2015.01.023
URL : https://hal.archives-ouvertes.fr/hal-01579585

E. Ruelland, M. Lemaire-chamley, L. Maréchal, P. Issakidis-bourguet, E. Djukic et al., An Internal Cysteine Is Involved in the Thioredoxin-dependent Activation of Sorghum Leaf NADP-malate Dehydrogenase, Journal of Biological Chemistry, vol.275, issue.32, pp.19851-19857, 1997.
DOI : 10.1016/S0014-5793(96)01459-7

E. Sadeghnezhad, M. Sharifi, and H. Zare-maivan, Profiling of acidic (amino and phenolic acids) and phenylpropanoids production in response to methyl jasmonate-induced oxidative stress in Scrophularia striata suspension cells, Planta, vol.23, issue.3, pp.75-85, 2016.
DOI : 10.1016/j.biotechadv.2005.01.003

M. E. Salvucci, A. , and J. C. , Factors Affecting the Activation State and the Level of Total Activity of Ribulose Bisphosphate Carboxylase in Tobacco Protoplasts, PLANT PHYSIOLOGY, vol.85, issue.1, pp.66-71, 1987.
DOI : 10.1104/pp.85.1.66

Y. Sasaki, A. Kozaki, and M. Hatano, Link between light and fatty acid synthesis: Thioredoxin-linked reductive activation of plastidic acetyl-CoA carboxylase, Proceedings of the National Academy of Sciences, vol.37, issue.8, pp.11096-11101, 1997.
DOI : 10.1093/oxfordjournals.pcp.a029073

R. Scheibe, A. , and L. E. , Dark modulation of NADP-dependent malate dehydrogenase and glucose-6-phosphate dehydrogenase in the chloroplast, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.636, issue.1, pp.58-64, 1981.
DOI : 10.1016/0005-2728(81)90075-X

P. Schürmann and B. B. Buchanan, The Ferredoxin/Thioredoxin System of Oxygenic Photosynthesis, Antioxidants & Redox Signaling, vol.10, issue.7, pp.1235-1274, 2008.
DOI : 10.1089/ars.2007.1931

O. Schwarz, P. Schürmann, and H. Strotmann, -ATPase, Journal of Biological Chemistry, vol.257, issue.27, pp.16924-16927, 1997.
DOI : 10.1002/prot.340110103

R. Sengupta and A. Holmgren, The role of thioredoxin in the regulation of cellular processes by S-nitrosylation, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1820, issue.6, pp.689-700, 2012.
DOI : 10.1016/j.bbagen.2011.08.012

R. Sengupta and A. Holmgren, Thioredoxin and glutaredoxin-mediated redox regulation of ribonucleotide reductase, World Journal of Biological Chemistry, vol.5, issue.1, pp.68-74, 2014.
DOI : 10.4331/wjbc.v5.i1.68

A. J. Serrato, J. Fernandez-trijueque, J. D. Barajas-lopez, A. Chueca, and M. Sahrawy, Plastid thioredoxins: a ???one-for-all??? redox-signaling system in plants, Frontiers in Plant Science, vol.4, p.463, 2013.
DOI : 10.3389/fpls.2013.00463

D. Seth, A. Hausladen, Y. J. Wang, and J. S. Stamler, Endogenous Protein S-Nitrosylation in E. coli: Regulation by OxyR, Science, vol.8, issue.6, pp.470-473, 2012.
DOI : 10.1186/1471-2105-8-133

F. Sevilla, D. Camejo, A. Ortiz-espin, A. Calderon, J. J. Lazaro et al., The thioredoxin/peroxiredoxin/sulfiredoxin system: current overview on its redox function in plants and regulation by reactive oxygen and nitrogen species, Journal of Experimental Botany, vol.183, issue.10, pp.2945-2955, 2015.
DOI : 10.1128/JB.183.15.4562-4570.2001

M. Stein, J. P. Jacquot, E. Jeannette, P. Decottignies, M. Hodges et al., Chlamydomonas reinhardtii thioredoxins: structure of the genes coding for the chloroplastic m and cytosolic h isoforms; expression in Escherichia coli of the recombinant proteins, purification and biochemical properties, Plant Molecular Biology, vol.229, issue.3, pp.487-503, 1995.
DOI : 10.1007/BF00020396

H. Strotmann and S. Sandkötter, Structure, Function, and Regulation of Chloroplast ATPase, Annual Review of Plant Physiology, vol.35, issue.1, pp.97-120, 1984.
DOI : 10.1146/annurev.pp.35.060184.000525

D. Susanti, J. H. Wong, W. H. Vensel, U. Loganathan, R. Desantis et al., Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii, Proceedings of the National Academy of Sciences, vol.35, issue.4, pp.2608-2613, 2014.
DOI : 10.1139/m89-077

M. Tardif, A. Atteia, M. Specht, G. Cogne, N. Rolland et al., PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae, Molecular Biology and Evolution, vol.3, issue.12, pp.3625-3639, 2012.
DOI : 10.1371/journal.pone.0001994
URL : https://hal.archives-ouvertes.fr/hal-00783004

L. Tarrago, E. Laugier, M. Zaffagnini, C. Marchand, L. Marechal et al., Methionine Sulfoxide Reductases B by Glutaredoxins and Thioredoxins, Journal of Biological Chemistry, vol.25, issue.28, pp.18963-18971, 2009.
DOI : 10.1042/BST20051375
URL : http://www.jbc.org/content/284/28/18963.full.pdf

M. C. Terrile, R. Paris, L. I. Calderon-villalobos, M. J. Iglesias, L. Lamattina et al., Nitric oxide influences auxin signaling through S-nitrosylation of the Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 auxin receptor. The Plant journal, pp.492-500, 2012.

G. Thieulin-pardo, T. Remy, S. Lignon, R. Lebrun, and B. Gontero, Phosphoribulokinase from Chlamydomonas reinhardtii: a Benson???Calvin cycle enzyme enslaved to its cysteine residues, Molecular BioSystems, vol.227, issue.186, pp.1134-1145, 2015.
DOI : 10.1038/227680a0
URL : https://hal.archives-ouvertes.fr/hal-01429055

M. B. Toledano, A. Delaunay-moisan, C. E. Outten, and A. Igbaria, Functions and Cellular Compartmentation of the Thioredoxin and Glutathione Pathways in Yeast, Antioxidants & Redox Signaling, vol.18, issue.13, pp.1699-1711, 2013.
DOI : 10.1089/ars.2012.5033

P. Trapet, A. Kulik, O. Lamotte, S. Jeandroz, S. Bourque et al., NO signaling in plant immunity: A tale of messengers, Phytochemistry, vol.112, pp.72-79, 2015.
DOI : 10.1016/j.phytochem.2014.03.015
URL : https://hal.archives-ouvertes.fr/hal-01696276

J. A. Traverso, A. Pulido, M. I. Rodriguez-garcia, and J. D. And-alche, Thiol-based redox regulation in sexual plant reproduction: new insights and perspectives, Frontiers in Plant Science, vol.4, p.465, 2013.
DOI : 10.3389/fpls.2013.00465

P. Trost, S. Fermani, L. Marri, M. Zaffagnini, G. Falini et al., Thioredoxin-dependent regulation of photosynthetic glyceraldehyde-3-phosphate dehydrogenase: autonomous vs. CP12-dependent mechanisms, Photosynthesis Research, vol.65, issue.2-3, pp.263-275, 2006.
DOI : 10.1016/0167-4838(96)00074-X

Y. Tsukamoto, Y. Fukushima, S. Hara, and T. Hisabori, Redox Control of the Activity of Phosphoglycerate Kinase in Synechocystis sp. PCC6803, Plant and Cell Physiology, vol.11, issue.4, pp.484-491, 2013.
DOI : 10.1074/mcp.M111.014142

L. Verdoucq, F. Vignols, J. P. Jacquot, Y. Chartier, M. et al., Characterization of a Thioredoxin h Target Protein Defines a New Peroxiredoxin Family, Journal of Biological Chemistry, vol.10, issue.28, pp.19714-19722, 1999.
DOI : 10.1074/jbc.274.8.4537

C. Vieira-dos-santos, S. Cuine, N. Rouhier, R. , and P. , The Arabidopsis Plastidic Methionine Sulfoxide Reductase B Proteins. Sequence and Activity Characteristics, Comparison of the Expression with Plastidic Methionine Sulfoxide Reductase A, and Induction by Photooxidative Stress, PLANT PHYSIOLOGY, vol.138, issue.2, pp.909-922, 2005.
DOI : 10.1104/pp.105.062430

J. A. Vizcaino, R. G. Cote, A. Csordas, J. A. Dianes, A. Fabregat et al., The Proteomics Identifications (PRIDE) database and associated tools: status in 2013, Nucleic Acids Research, vol.11, issue.D1, pp.1063-1069, 2013.
DOI : 10.1021/pr200824a

O. Voytsekh, S. B. Seitz, D. Iliev, and M. Mittag, Both Subunits of the Circadian RNA-Binding Protein CHLAMY1 Can Integrate Temperature Information, PLANT PHYSIOLOGY, vol.147, issue.4, pp.2179-2193, 2008.
DOI : 10.1104/pp.108.118570

K. Wakabayashi and S. M. King, flagellar motility by redox poise, The Journal of Cell Biology, vol.262, issue.5, pp.743-754, 2006.
DOI : 10.1242/jcs.01297
URL : http://jcb.rupress.org/content/jcb/173/5/743.full.pdf

P. Wang, Y. Du, Y. J. Hou, Y. Zhao, C. C. Hsu et al., Nitric oxide negatively regulates abscisic acid signaling in guard cells by S-nitrosylation of OST1, Proceedings of the National Academy of Sciences, vol.4, issue.3, pp.613-618, 2015.
DOI : 10.1016/j.cell.2007.02.046

C. Waszczak, S. Akter, S. Jacques, J. Huang, J. Messens et al., Oxidative post-translational modifications of cysteine residues in plant signal transduction, Journal of Experimental Botany, vol.19, issue.10, pp.2923-2934, 2015.
DOI : 10.1105/tpc.107.050666

E. Weerapana, C. Wang, G. M. Simon, F. Richter, S. Khare et al., Quantitative reactivity profiling predicts functional cysteines in proteomes, Nature, vol.319, issue.7325, pp.790-795, 2010.
DOI : 10.1074/mcp.M600381-MCP200
URL : http://europepmc.org/articles/pmc3058684?pdf=render

I. Wenderoth, R. Scheibe, V. Schaewen, and A. , Identification of the Cysteine Residues Involved in Redox Modification of Plant Plastidic Glucose-6-phosphate Dehydrogenase, Journal of Biological Chemistry, vol.269, issue.43, pp.26985-26990, 1997.
DOI : 10.1104/pp.85.2.598

C. C. Winterbourn and M. B. Hampton, Thiol chemistry and specificity in redox signaling, Free Radical Biology and Medicine, vol.45, issue.5, pp.549-561, 2008.
DOI : 10.1016/j.freeradbiomed.2008.05.004

R. A. Wolosiuk and B. B. Buchanan, Thioredoxin and glutathione regulate photosynthesis in chloroplasts, Nature, vol.305, issue.5602, pp.565-567, 1977.
DOI : 10.1038/256668a0

J. H. Wong, N. Cai, Y. Balmer, C. K. Tanaka, W. H. Vensel et al., Thioredoxin targets of developing wheat seeds identified by complementary proteomic approaches, Phytochemistry, vol.65, issue.11, pp.1629-1640, 2004.
DOI : 10.1016/j.phytochem.2004.05.010

C. Wu, M. R. Jain, Q. Li, S. Oka, W. Li et al., Identification of novel nuclear targets of human thioredoxin 1. Molecular & cellular proteomics, pp.3507-3518, 2014.

D. Yamazaki, K. Motohashi, T. Kasama, Y. Hara, and T. Hisabori, Target Proteins of the Cytosolic Thioredoxins in Arabidopsis thaliana, Plant and Cell Physiology, vol.45, issue.1, pp.18-27, 2004.
DOI : 10.1073/pnas.96.16.9438

J. Yang, K. S. Carroll, and D. C. Liebler, The Expanding Landscape of the Thiol Redox Proteome, Molecular & Cellular Proteomics, vol.249, issue.216, pp.1-11, 2016.
DOI : 10.1093/bioinformatics/bts468

H. Yano and M. Kuroda, Disulfide proteome yields a detailed understanding of redox regulations: A model study of thioredoxin-linked reactions in seed germination, PROTEOMICS, vol.101, issue.1, pp.294-300, 2006.
DOI : 10.1002/pmic.200402033

H. Yano, J. H. Wong, Y. M. Lee, M. J. Cho, and B. B. Buchanan, A strategy for the identification of proteins targeted by thioredoxin, Proceedings of the National Academy of Sciences, vol.314, issue.2, pp.4794-4799, 2001.
DOI : 10.1006/abbi.1994.1439

K. Yoshida, K. Noguchi, K. Motohashi, and T. Hisabori, Systematic Exploration of Thioredoxin Target Proteins in Plant Mitochondria, Plant and Cell Physiology, vol.34, issue.6, pp.875-892, 2013.
DOI : 10.1111/j.1365-3040.2010.02267.x

L. M. Yu and B. R. Selman, cDNA sequence and predicted primary structure of the gamma subunit from the ATP synthase from Chlamydomonas reinhardtii, J Biol Chem, vol.263, pp.19342-19345, 1988.

M. Yu, B. W. Yun, S. H. Spoel, and G. J. Loake, A sleigh ride through the SNO: regulation of plant immune function by protein S-nitrosylation, Current Opinion in Plant Biology, vol.15, issue.4, pp.424-430, 2012.
DOI : 10.1016/j.pbi.2012.03.005

M. Zaffagnini, M. Bedhomme, H. Groni, C. H. Marchand, C. Puppo et al., Glutathionylation in the photosynthetic model organism Chlamydomonas reinhardtii: a proteomic survey, Molecular & cellular proteomics : MCP, vol.11, pp.111-014142, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01183584

M. Zaffagnini, M. Bedhomme, S. D. Lemaire, and P. Trost, The emerging roles of protein glutathionylation in chloroplasts. Plant science : an international journal of experimental plant biology, pp.185-18686, 2012.

M. Zaffagnini, M. Bedhomme, C. H. Marchand, S. Morisse, P. Trost et al., Redox Regulation in Photosynthetic Organisms: Focus on Glutathionylation, Antioxidants & Redox Signaling, vol.16, issue.6, pp.567-586, 2012.
DOI : 10.1089/ars.2011.4255

M. Zaffagnini, S. Fermani, A. Costa, S. D. Lemaire, and P. Trost, Plant cytoplasmic GAPDH: redox posttranslational modifications and moonlighting properties, Frontiers in plant science, vol.4, p.450, 2013.
DOI : 10.3389/fpls.2013.00450
URL : https://hal.archives-ouvertes.fr/hal-01579002

M. Zaffagnini, L. Michelet, C. Marchand, F. Sparla, P. Decottignies et al., The thioredoxin-independent isoform of chloroplastic glyceraldehyde-3-phosphate dehydrogenase is selectively regulated by glutathionylation, FEBS Journal, vol.138, issue.1, pp.212-226, 2007.
DOI : 10.1104/pp.105.062117

N. Zhang, A. R. Portis, and . Jr, Mechanism of light regulation of Rubisco: A specific role for the larger Rubisco activase isoform involving reductive activation by thioredoxin-f, Proceedings of the National Academy of Sciences, vol.32, issue.1-2, pp.9438-9443, 1999.
DOI : 10.1007/BF00039375

N. Zhang, P. Schürmann, A. R. Portis, and . Jr, Characterization of the regulatory function of the 46-kDa isoform of Rubisco activase from Arabidopsis, Photosynthesis Research, vol.68, issue.1, pp.29-37, 2001.
DOI : 10.1023/A:1011845506196

T. Zhang, M. Zhu, N. Zhu, J. M. Strul, C. P. Dufresne et al., Identification of thioredoxin targets in guard cell enriched epidermal peels using cysTMT proteomics, Journal of Proteomics, vol.133, pp.48-53, 2016.
DOI : 10.1016/j.jprot.2015.12.008

L. Rubisco, The numbering corresponds to the fulllength sequence. Lines between cysteines indicate confirmed (plain) or suggested (dashed) disulfide bonds in Chlamydomonas enzymes, Cysteines identified as nitrosylated (Morisse et al., 2014b) and glutathionylated (Zaffagnini et al., 2012a) by proteomic approaches in Chlamydomonas are labeled with NO (yellow) and SG (green), respectively