Przybyla-Toscano, J.; Boussardon, C.; Law, S.; Rouhier, N.; Keech, O. Gene Atlas of Iron-Containing Proteins in Arabidopsis thaliana. Plant J. 2021, doi:10.1111/tpj.15154.
Zanello, P. Structure and Electrochemistry of Proteins Harboring Iron-Sulfur Clusters of Different Nuclearities. Part IV. Canon-ical, Non-Canonical and Hybrid Iron-Sulfur Proteins. J. Struct. Biol. 2019, 205, 103–120, doi:10.1016/j.jsb.2019.01.003.
Lill, R. Function and Biogenesis of Iron-Sulphur Proteins. Nature 2009, 460, 831–838, doi:10.1038/nature08301.
Przybyla-Toscano, J.; Christ, L.; Keech, O.; Rouhier, N. Iron-Sulfur Proteins in Plant Mitochondria: Roles and Maturation. J. Exp. Bot. 2020, doi:10.1093/jxb/eraa578.
Przybyla-Toscano, J.; Roland, M.; Gaymard, F.; Couturier, J.; Rouhier, N. Roles and Maturation of Iron-Sulfur Proteins in Plas-tids. J. Biol. Inorg. Chem. 2018, 23, 545–566, doi:10.1007/s00775-018-1532-1.
Merchant, S.; Sawaya, M.R. The Light Reactions: A Guide to Recent Acquisitions for the Picture Gallery. Plant Cell 2005, 17, 648– 663, doi:10.1105/tpc.105.030676.
Pan, X.; Cao, D.; Xie, F.; Xu, F.; Su, X.; Mi, H.; Zhang, X.; Li, M. Structural Basis for Electron Transport Mechanism of Complex I-like Photosynthetic Nad(p)h Dehydrogenase. Nat. Commun. 2020, 11, 610, doi:10.1038/s41467-020-14456-0.
Hertle, A.P.; Blunder, T.; Wunder, T.; Pesaresi, P.; Pribil, M.; Armbruster, U.; Leister, D. PGRL1 Is the Elusive Ferredoxin-Plas-toquinone Reductase in Photosynthetic Cyclic Electron Flow. Mol. Cell 2013, 49, 511–523, doi:10.1016/j.molcel.2012.11.030.
Yamori, W.; Shikanai, T. Physiological Functions of Cyclic Electron Transport Around Photosystem I in Sustaining Photosynthesis and Plant Growth. Annu. Rev. Plant Biol. 2016, 67, 81–106, doi:10.1146/annurev-arplant-043015-112002.
Couturier, J.; Touraine, B.; Briat, J.-F.; Gaymard, F.; Rouhier, N. The Iron-Sulfur Cluster Assembly Machineries in Plants: Current Knowledge and Open Questions. Front. Plant Sci. 2013, 4, 259, doi:10.3389/fpls.2013.00259.
Garcia, P.S.; Gribaldo, S.; Py, B.; Barras, F. The SUF System: An ABC ATPase-Dependent Protein Complex with a Role in Fe–S Cluster Biogenesis. Res. Microbiol. 2019, 170, 426–434, doi:10.1016/j.resmic.2019.08.001.
Boyd, E.S.; Thomas, K.M.; Dai, Y.; Boyd, J.M.; Outten, F.W. Interplay between Oxygen and Fe-S Cluster Biogenesis: Insights from the Suf Pathway. Biochemistry 2014, 53, 5834–5847, doi:10.1021/bi500488r.
Bai, Y.; Chen, T.; Happe, T.; Lu, Y.; Sawyer, A. Iron-Sulphur Cluster Biogenesis via the SUF Pathway. Metallomics 2018, 10, 1038– 1052, doi:10.1039/c8mt00150b.
Gao, F. Iron-Sulfur Cluster Biogenesis and Iron Homeostasis in Cyanobacteria. Front. Microbiol. 2020, 11, 165, doi:10.3389/fmicb.2020.00165.
Outten, F.W. Recent Advances in the Suf Fe-S Cluster Biogenesis Pathway: Beyond the Proteobacteria. Biochim. Biophys. Acta 2015, 1853, 1464–1469, doi:10.1016/j.bbamcr.2014.11.001.
Blahut, M.; Sanchez, E.; Fisher, C.E.; Outten, F.W. Fe-S Cluster Biogenesis by the Bacterial Suf Pathway. Biochim. Biophys. Acta Mol. Cell Res. 2020, 1867, 118829, doi:10.1016/j.bbamcr.2020.118829.
Braymer, J.J.; Freibert, S.A.; Rakwalska-Bange, M.; Lill, R. Mechanistic Concepts of Iron-Sulfur Protein Biogenesis in Biology. Biochim. Biophys. Acta Mol. Cell Res. 2020, 118863, doi:10.1016/j.bbamcr.2020.118863.
Loiseau, L.; Ollagnier-de-Choudens, S.; Nachin, L.; Fontecave, M.; Barras, F. Biogenesis of Fe-S Cluster by the Bacterial Suf System: SufS and SufE Form a New Type of Cysteine Desulfurase. J. Biol. Chem. 2003, 278, 38352–38359, doi:10.1074/jbc.M305953200.
Outten, F.W.; Wood, M.J.; Munoz, F.M.; Storz, G. The SufE Protein and the SufBCD Complex Enhance SufS Cysteine Desul-furase Activity as Part of a Sulfur Transfer Pathway for Fe-S Cluster Assembly in Escherichia coli. J. Biol. Chem. 2003, 278, 45713– 45719, doi:10.1074/jbc.M308004200.
Ye, H.; Abdel-Ghany, S.E.; Anderson, T.D.; Pilon-Smits, E.A.H.; Pilon, M. CpSufE Activates the Cysteine Desulfurase CpNifS for Chloroplastic Fe-S Cluster Formation. J. Biol. Chem. 2006, 281, 8958–8969, doi:10.1074/jbc.M512737200.
Black, K.A.; Dos Santos, P.C. Shared-Intermediates in the Biosynthesis of Thio-Cofactors: Mechanism and Functions of Cysteine Desulfurases and Sulfur Acceptors. Biochim. Biophys. Acta 2015, 1853, 1470–1480, doi:10.1016/j.bbamcr.2014.10.018.
Singh, H.; Dai, Y.; Outten, F.W.; Busenlehner, L.S. Escherichia coli SufE Sulfur Transfer Protein Modulates the SufS Cysteine Desulfurase through Allosteric Conformational Dynamics. J. Biol. Chem. 2013, 288, 36189–36200, doi:10.1074/jbc.M113.525709.
Layer, G.; Gaddam, S.A.; Ayala-Castro, C.N.; Ollagnier-de Choudens, S.; Lascoux, D.; Fontecave, M.; Outten, F.W. SufE Trans-fers Sulfur from SufS to SufB for Iron-Sulfur Cluster Assembly. J. Biol. Chem. 2007, 282, 13342–13350, doi:10.1074/jbc.M608555200.
Hirabayashi, K.; Yuda, E.; Tanaka, N.; Katayama, S.; Iwasaki, K.; Matsumoto, T.; Kurisu, G.; Outten, F.W.; Fukuyama, K.; Takahashi, Y.; et al. Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-Binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis. J. Biol. Chem. 2015, 290, 29717–29731, doi:10.1074/jbc.M115.680934.
Yuda, E.; Tanaka, N.; Fujishiro, T.; Yokoyama, N.; Hirabayashi, K.; Fukuyama, K.; Wada, K.; Takahashi, Y. Mapping the Key Residues of SufB and SufD Essential for Biosynthesis of Iron-Sulfur Clusters. Sci. Rep. 2017, 7, 9387, doi:10.1038/s41598-017-09846-2.
Saini, A.; Mapolelo, D.T.; Chahal, H.K.; Johnson, M.K.; Outten, F.W. SufD and SufC ATPase Activity Are Required for Iron Acquisition during in Vivo Fe-S Cluster Formation on SufB. Biochemistry 2010, 49, 9402–9412, doi:10.1021/bi1011546.
Blanc, B.; Clémancey, M.; Latour, J.-M.; Fontecave, M.; Ollagnier de Choudens, S. Molecular Investigation of Iron-Sulfur Cluster Assembly Scaffolds under Stress. Biochemistry 2014, 53, 7867–7869, doi:10.1021/bi5012496.
Wollers, S.; Layer, G.; Garcia-Serres, R.; Signor, L.; Clemancey, M.; Latour, J.-M.; Fontecave, M.; Ollagnier de Choudens, S. Iron-Sulfur (Fe-S) Cluster Assembly: The SufBCD Complex Is a New Type of Fe-S Scaffold with a Flavin Redox Cofactor. J. Biol. Chem. 2010, 285, 23331–23341, doi:10.1074/jbc.M110.127449.
Zheng, C.; Guo, S.; Tennant, W.G.; Pradhan, P.K.; Black, K.A.; Dos Santos, P.C. The Thioredoxin System Reduces Protein Per-sulfide Intermediates Formed during the Synthesis of Thio-Cofactors in Bacillus subtilis. Biochemistry 2019, 58, 1892–1904, doi:10.1021/acs.biochem.9b00045.
Parent, A.; Elduque, X.; Cornu, D.; Belot, L.; Le Caer, J.-P.; Grandas, A.; Toledano, M.B.; D’Autréaux, B. Mammalian Frataxin Directly Enhances Sulfur Transfer of NFS1 Persulfide to Both ISCU and Free Thiols. Nat. Commun. 2015, 6, 5686, doi:10.1038/ncomms6686.
Gervason, S.; Larkem, D.; Mansour, A.B.; Botzanowski, T.; Müller, C.S.; Pecqueur, L.; Le Pavec, G.; Delaunay-Moisan, A.; Brun, O.; Agramunt, J.; et al. Physiologically Relevant Reconstitution of Iron-Sulfur Cluster Biosynthesis Uncovers Persulfide-Pro-cessing Functions of Ferredoxin-2 and Frataxin. Nat. Commun. 2019, 10, 3566, doi:10.1038/s41467-019-11470-9.
Blauenburg, B.; Mielcarek, A.; Altegoer, F.; Fage, C.D.; Linne, U.; Bange, G.; Marahiel, M.A. Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU. PLoS ONE 2016, 11, e0158749, doi:10.1371/journal.pone.0158749.
Turowski, V.R.; Aknin, C.; Maliandi, M.V.; Buchensky, C.; Leaden, L.; Peralta, D.A.; Busi, M.V.; Araya, A.; Gomez-Casati, D.F. Frataxin Is Localized to Both the Chloroplast and Mitochondrion and Is Involved in Chloroplast Fe-S Protein Function in Ara-bidopsis. PLoS ONE 2015, 10, e0141443, doi:10.1371/journal.pone.0141443.
Roret, T.; Tsan, P.; Couturier, J.; Zhang, B.; Johnson, M.K.; Rouhier, N.; Didierjean, C. Structural and Spectroscopic Insights into Bola-Glutaredoxin Complexes. J. Biol. Chem. 2014, 289, 24588–24598, doi:10.1074/jbc.M114.572701.
Vinella, D.; Brochier-Armanet, C.; Loiseau, L.; Talla, E.; Barras, F. Iron-Sulfur (Fe/S) Protein Biogenesis: Phylogenomic and Ge-netic Studies of A-Type Carriers. PLoS Genet. 2009, 5, e1000497, doi:10.1371/journal.pgen.1000497.
Py, B.; Gerez, C.; Angelini, S.; Planel, R.; Vinella, D.; Loiseau, L.; Talla, E.; Brochier-Armanet, C.; Garcia Serres, R.; Latour, J.-M.; et al. Molecular Organization, Biochemical Function, Cellular Role and Evolution of NfuA, an Atypical Fe-S Carrier. Mol. Mi-crobiol. 2012, 86, 155–171, doi:10.1111/j.1365-2958.2012.08181.x.
Lezhneva, L.; Amann, K.; Meurer, J. The Universally Conserved HCF101 Protein Is Involved in Assembly of [4Fe-4S]-Cluster-Containing Complexes in Arabidopsis thaliana Chloroplasts. Plant J. 2004, 37, 174–185, doi:10.1046/j.1365-313x.2003.01952.x.
Abdel-Ghany, S.E.; Ye, H.; Garifullina, G.F.; Zhang, L.; Pilon-Smits, E.A.H.; Pilon, M. Iron-Sulfur Cluster Biogenesis in Chloro-plasts. Involvement of the Scaffold Protein Cpisca. Plant Physiol. 2005, 138, 161–172, doi:10.1104/pp.104.058602.
Rey, P.; Becuwe, N.; Tourrette, S.; Rouhier, N. Involvement of Arabidopsis Glutaredoxin S14 in the Maintenance of Chlorophyll Content. Plant Cell Environ. 2017, 40, 2319–2332, doi:10.1111/pce.13036.
Touraine, B.; Vignols, F.; Przybyla-Toscano, J.; Ischebeck, T.; Dhalleine, T.; Wu, H.-C.; Magno, C.; Berger, N.; Couturier, J.; Du-bos, C.; et al. Iron-Sulfur Protein NFU2 Is Required for Branched-Chain Amino Acid Synthesis in Arabidopsis Roots. J. Exp. Bot. 2019, 70, 1875–1889, doi:10.1093/jxb/erz050.
Berger, N.; Vignols, F.; Przybyla-Toscano, J.; Roland, M.; Rofidal, V.; Touraine, B.; Zienkiewicz, K.; Couturier, J.; Feussner, I.; Santoni, V.; et al. Identification of Client Iron-Sulfur Proteins of the Chloroplastic NFU2 Transfer Protein in Arabidopsis thaliana. J. Exp. Bot. 2020, doi:10.1093/jxb/eraa166.
Berger, N.; Vignols, F.; Touraine, B.; Taupin-Broggini, M.; Rofidal, V.; Demolombe, V.; Santoni, V.; Rouhier, N.; Gaymard, F.; Dubos, C. A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3. Int. J. Mol. Sci. 2020, 21, doi:10.3390/ijms21218121.
Gao, H.; Subramanian, S.; Couturier, J.; Naik, S.G.; Kim, S.-K.; Leustek, T.; Knaff, D.B.; Wu, H.-C.; Vignols, F.; Huynh, B.H.; et al. Arabidopsis thaliana Nfu2 Accommodates [2Fe-2S] or [4Fe-4S] Clusters and Is Competent for in Vitro Maturation of Chloro-plast [2Fe-2S] and [4Fe-4S] Cluster-Containing Proteins. Biochemistry 2013, 52, 6633–6645, doi:10.1021/bi4007622.
Gao, H.; Azam, T.; Randeniya, S.; Couturier, J.; Rouhier, N.; Johnson, M.K. Function and Maturation of the Fe-S Center in Di-hydroxyacid Dehydratase from Arabidopsis. J. Biol. Chem. 2018, 293, 4422–4433, doi:10.1074/jbc.RA117.001592.
Wang, L.; Ouyang, B.; Li, Y.; Feng, Y.; Jacquot, J.-P.; Rouhier, N.; Xia, B. Glutathione Regulates the Transfer of Iron-Sulfur Cluster from Monothiol and Dithiol Glutaredoxins to Apo Ferredoxin. Protein Cell 2012, 3, 714–721, doi:10.1007/s13238-012-2051-4.
Bandyopadhyay, S.; Gama, F.; Molina-Navarro, M.M.; Gualberto, J.M.; Claxton, R.; Naik, S.G.; Huynh, B.H.; Herrero, E.; Jacquot, J.P.; Johnson, M.K.; et al. Chloroplast Monothiol Glutaredoxins as Scaffold Proteins for the Assembly and Delivery of [2Fe-2S] Clusters. EMBO J. 2008, 27, 1122–1133, doi:10.1038/emboj.2008.50.
Janouškovec, J.; Horák, A.; Oborník, M.; Lukeš, J.; Keeling, P.J. A Common Red Algal Origin of the Apicomplexan, Dinoflagel-late, and Heterokont Plastids. Proc. Natl. Acad. Sci. USA 2010, 107, 10949–10954, doi:10.1073/pnas.1003335107.
Godman, J.; Balk, J. Genome Analysis of Chlamydomonas reinhardtii Reveals the Existence of Multiple, Compartmentalized Iron-Sulfur Protein Assembly Machineries of Different Evolutionary Origins. Genetics 2008, 179, 59–68, doi:10.1534/genet-ics.107.086033.
Terashima, M.; Specht, M.; Naumann, B.; Hippler, M. Characterizing the Anaerobic Response of Chlamydomonas reinhardtii by Quantitative Proteomics. Mol. Cell. Proteom. 2010, 9, 1514–1532, doi:10.1074/mcp.M900421-MCP200.
Murthy, N.U.; Ollagnier-de-Choudens, S.; Sanakis, Y.; Abdel-Ghany, S.E.; Rousset, C.; Ye, H.; Fontecave, M.; Pilon-Smits, E.A.H.; Pilon, M. Characterization of Arabidopsis thaliana SufE2 and SufE3: Functions in Chloroplast Iron-Sulfur Cluster Assembly and Nad Synthesis. J. Biol. Chem. 2007, 282, 18254–18264, doi:10.1074/jbc.M701428200.
Couturier, J.; Jacquot, J.-P.; Rouhier, N. Evolution and Diversity of Glutaredoxins in Photosynthetic Organisms. Cell. Mol. Life Sci. 2009, 66, 2539–2557, doi:10.1007/s00018-009-0054-y.
Waller, J.C.; Ellens, K.W.; Alvarez, S.; Loizeau, K.; Ravanel, S.; Hanson, A.D. Mitochondrial and Plastidial COG0354 Proteins Have Folate-Dependent Functions in Iron-Sulphur Cluster Metabolism. J. Exp. Bot. 2012, 63, 403–411, doi:10.1093/jxb/err286.
Yang, W.; Wittkopp, T.M.; Li, X.; Warakanont, J.; Dubini, A.; Catalanotti, C.; Kim, R.G.; Nowack, E.C.M.; Mackinder, L.C.M.; Aksoy, M.; et al. Critical Role of Chlamydomonas reinhardtii Ferredoxin-5 in Maintaining Membrane Structure and Dark Metab-olism. Proc. Natl. Acad. Sci. USA 2015, 112, 14978–14983, doi:10.1073/pnas.1515240112.
Sawyer, A.; Winkler, M. Evolution of Chlamydomonas reinhardtii Ferredoxins and Their Interactions with [FeFe]-Hydrogenases. Photosynth. Res. 2017, 134, 307–316, doi:10.1007/s11120-017-0409-4.
Goh, F.Q.Y.; Jeyakani, J.; Tipthara, P.; Cazenave-Gassiot, A.; Ghosh, R.; Bogard, N.; Yeo, Z.; Wong, G.K.S.; Melkonian, M.; Wenk, M.R.; et al. Gains and Losses of Metabolic Function Inferred from a Phylotranscriptomic Analysis of Algae. Sci. Rep. 2019, 9, 10482, doi:10.1038/s41598-019-46869-3.
Lichtenthaler, H.K. The 1-Deoxy-d-Xylulose-5-Phosphate Pathway of Isoprenoid Biosynthesis in Plants. Annu. Rev. Plant Biol. 1999, 50, 47–65, doi:10.1146/annurev.arplant.50.1.47.
Lohr, M.; Schwender, J.; Polle, J.E.W. Isoprenoid Biosynthesis in Eukaryotic Phototrophs: A Spotlight on Algae. Plant Sci. 2012, 186, 9–22, doi:10.1016/j.plantsci.2011.07.018.
Ebenezer, T.E.; Zoltner, M.; Burrell, A.; Nenarokova, A.; Novák Vanclová, A.M.G.; Prasad, B.; Soukal, P.; Santana-Molina, C.; O’Neill, E.; Nankissoor, N.N.; et al. Transcriptome, Proteome and Draft Genome of Euglena gracilis. BMC Biol. 2019, 17, 11, doi:10.1186/s12915-019-0626-8.
Lu, Y.; Zhou, W.; Wei, L.; Li, J.; Jia, J.; Li, F.; Smith, S.M.; Xu, J. Regulation of the Cholesterol Biosynthetic Pathway and Its Integration with Fatty Acid Biosynthesis in the Oleaginous Microalga Nannochloropsis oceanica. Biotechnol. Biofuels 2014, 7, 81, doi:10.1186/1754-6834-7-81.
Bentlage, B.; Rogers, T.S.; Bachvaroff, T.R.; Delwiche, C.F. Complex Ancestries of Isoprenoid Synthesis in Dinoflagellates. J. Eukaryot. Microbiol. 2016, 63, 123–137, doi:10.1111/jeu.12261.
Schoefs, B.; Franck, F. Protochlorophyllide Reduction: Mechanisms and Evolution. Photochem. Photobiol. 2003, 78, 543–557, doi:10.1562/0031-8655(2003)078<0543:prmae>2.0.co;2.
Schneidewind, J.; Krause, F.; Bocola, M.; Stadler, A.M.; Davari, M.D.; Schwaneberg, U.; Jaeger, K.E.; Krauss, U. Consensus Model of a Cyanobacterial Light-Dependent Protochlorophyllide Oxidoreductase in Its Pigment-Free Apo-Form and Photoactive Ter-nary Complex. Commun. Biol. 2019, 2, 351, doi:10.1038/s42003-019-0590-4.
Moser, J.; Lange, C.; Krausze, J.; Rebelein, J.; Schubert, W.-D.; Ribbe, M.W.; Heinz, D.W.; Jahn, D. Structure of ADP-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex. Proc. Natl. Acad. Sci. USA 2013, 110, 2094–2098, doi:10.1073/pnas.1218303110.
Cheng, Q.; Day, A.; Dowson-Day, M.; Shen, G.F.; Dixon, R. The Klebsiella pneumoniae Nitrogenase Fe Protein Gene (NifH) Func-tionally Substitutes for the ChlL Gene in Chlamydomonas reinhardtii. Biochem. Biophys. Res. Commun. 2005, 329, 966–975, doi:10.1016/j.bbrc.2005.02.064.
Li, J.; Goldschmidt-Clermont, M.; Timko, M.P. Chloroplast-Encoded ChlB Is Required for Light-Independent Protochlorophyl-lide Reductase Activity in Chlamydomonas reinhardtii. Plant Cell 1993, 5, 1817–1829, doi:10.1105/tpc.5.12.1817.
Cahoon, A.B.; Timko, M.P. Yellow-in-the-Dark Mutants of Chlamydomonas Lack the CHLL Subunit of Light-Independent Pro-tochlorophyllide Reductase. Plant Cell 2000, 12, 559–568, doi:10.1105/tpc.12.4.559.
Jain, K.; Krause, K.; Grewe, F.; Nelson, G.F.; Weber, A.P.M.; Christensen, A.C.; Mower, J.P. Extreme Features of the Galdieria sulphuraria Organellar Genomes: A Consequence of Polyextremophily. Genome Biol. Evol. 2014, 7, 367–380, doi:10.1093/gbe/evu290.
Ohta, N.; Matsuzaki, M.; Misumi, O.; ya Miyagishima, S.; Nozaki, H.; Tanaka, K.; Shin-i, T.; Kohara, Y.; Kuroiwa, T. Complete Sequence and Analysis of the Plastid Genome of the Unicellular Red Alga Cyanidioschyzon merolae. DNA Res. 2003, 10, 67–77, doi:10.1093/dnares/10.2.67.
Reith, M.; Munholland, J. Complete Nucleotide Sequence of the Porphyra purpurea Chloroplast Genome. Plant Mol. Biol. Rep. 1995, 13, 333–335, doi:10.1007/BF02669187.
Robbens, S.; Derelle, E.; Ferraz, C.; Wuyts, J.; Moreau, H.; Van De Peer, Y. The Complete Chloroplast and Mitochondrial DNA Sequence of Ostreococcus tauri: Organelle Genomes of the Smallest Eukaryote Are Examples of Compaction. Mol. Biol. Evol. 2007, 24, 956–968, doi:10.1093/molbev/msm012.
Lemieux, C.; Otis, C.; Turmel, M. Six Newly Sequenced Chloroplast Genomes from Prasinophyte Green Algae Provide Insights into the Relationships among Prasinophyte Lineages and the Diversity of Streamlined Genome Architecture in Picoplanktonic Species. BMC Genom. 2014, 15, 857, doi:10.1186/1471-2164-15-857.
Gallaher, S.D.; Fitz-Gibbon, S.T.; Strenkert, D.; Purvine, S.O.; Pellegrini, M.; Merchant, S.S. High-Throughput Sequencing of the Chloroplast and Mitochondrion of Chlamydomonas reinhardtii to Generate Improved de Novo Assemblies, Analyze Expression Patterns and Transcript Speciation, and Evaluate Diversity among Laboratory Strains and Wild Isolates. Plant J. 2018, 93, 545– 565, doi:10.1111/tpj.13788.
Wakasugi, T.; Nagai, T.; Kapoor, M.; Sugita, M.; Ito, M.; Ito, S.; Tsudzuki, J.; Nakashima, K.; Tsudzuki, T.; Suzuki, Y.; et al. Complete Nucleotide Sequence of the Chloroplast Genome from the Green Alga Chlorella vulgaris: The Existence of Genes Possibly Involved in Chloroplast Division. Proc. Natl. Acad. Sci. USA 1997, 94, 5967–5972, doi:10.1073/pnas.94.11.5967.
Civan, P.; Foster, P.G.; Embley, M.T.; Séneca, A.; Cox, C.J. Analyses of Charophyte Chloroplast Genomes Help Characterize The ancestral Chloroplast genome of Land Plants. Genome Biol. Evol. 2014, 6, 897–911, doi:10.1093/gbe/evu061.
Turmel, M.; Otis, C.; Lemieux, C. The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants. Mol. Biol. Evol. 2006, 23, 1324–1338, doi:10.1093/molbev/msk018.
Oudot-Le Secq, M.P.; Grimwood, J.; Shapiro, H.; Armbrust, E.V.; Bowler, C.; Green, B.R. Chloroplast Genomes of the Diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: Comparison with Other Plastid Genomes of the Red Lineage. Mol. Genet. Genom. 2007, 277, 427–439, doi:10.1007/s00438-006-0199-4.
Wei, L.; Xin, Y.; Wang, D.; Jing, X.; Zhou, Q.; Su, X.; Jia, J.; Ning, K.; Chen, F.; Hu, Q.; et al. Nannochloropsis Plastid and Mito-chondrial Phylogenomes Reveal Organelle Diversification Mechanism and Intragenus Phylotyping Strategy in Microalgae. BMC Genom. 2013, 14, 534, doi:10.1186/1471-2164-14-534.
Barbrook, A.C.; Voolstra, C.R.; Howe, C.J. The Chloroplast Genome of a Symbiodinium Sp. Clade C3 Isolate. Protist 2014, 165, 1–13, doi:10.1016/j.protis.2013.09.006.
Rogers, M.B.; Gilson, P.R.; Su, V.; McFadden, G.I.; Keeling, P.J. The Complete Chloroplast Genome of the Chlorarachniophyte Bigelowiella natans: Evidence for Independent Origins of Chlorarachniophyte and Euglenid Secondary Endosymbionts. Mol. Biol. Evol. 2007, 24, 54–62, doi:10.1093/molbev/msl129.
Tanifuji, G.; Onodera, N.T.; Brown, M.W.; Curtis, B.A.; Roger, A.J.; Ka-Shu Wong, G.; Melkonian, M.; Archibald, J.M. Nucleo-morph and Plastid Genome Sequences of the Chlorarachniophyte Lotharella oceanica: Convergent Reductive Evolution and Fre-quent Recombination in Nucleomorph-Bearing Algae. BMC Genom. 2014, 15, 374, doi:10.1186/1471-2164-15-374.
Sanchez Puerta, V.; Bachvaroff, T.R.; Delwiche, C.F. The Complete Plastid Genome Sequence of the Haptophyte Emiliania hux-leyi: A Comparison to Other Plastid Genomes. DNA Res. 2005, 12, 151–156, doi:10.1093/dnares/12.2.151.
Méndez-Leyva, A.B.; Guo, J.; Mudd, E.A.; Wong, J.; Schwartz, J.M.; Day, A. The Chloroplast Genome of the Marine Microalga Tisochrysis lutea. Mitochondrial DNA Part B Resour. 2019, 4, 253–255, doi:10.1080/23802359.2018.1547140.
Tang, X.; Bi, G. The Complete Chloroplast Genome of Guillardia theta Strain CCMP2712. Mitochondrial DNA Part DNA Mapp. Seq. Anal. 2016, 27, 4423–4424, doi:10.3109/19401736.2015.1089554.
Khan, H.; Parks, N.; Kozera, C.; Curtis, B.A.; Parsons, B.J.; Bowman, S.; Archibald, J.M. Plastid Genome Sequence of the Cryp-tophyte Alga Rhodomonas salina CCMP1319: Lateral Transfer of Putative DNA Replication Machinery and a Test of Chromist Plastid Phylogeny. Mol. Biol. Evol. 2007, 24, 1832–1842, doi:10.1093/molbev/msm101.
Kim, J.I.; Moore, C.E.; Archibald, J.M.; Bhattacharya, D.; Yi, G.; Yoon, H.S.; Shin, W. Evolutionary Dynamics of Cryptophyte Plastid Genomes. Genome Biol. Evol. 2017, 9, 1859–1872, doi:10.1093/gbe/evx123.
Dabbagh, N.; Bennett, M.S.; Triemer, R.E.; Preisfeld, A. Chloroplast Genome Expansion by Intron Multiplication in the Basal Psychrophilic Euglenoid Eutreptiella pomquetensis. PeerJ 2017, 5, e3725, doi:10.7717/peerj.3725.
Hunsperger, H.M.; Randhawa, T.; Cattolico, R.A. Extensive Horizontal Gene Transfer, Duplication, and Loss of Chlorophyll Synthesis Genes in the Algae. BMC Evol. Biol. 2015, 15, 16, doi:10.1186/s12862-015-0286-4.
Cvetkovska, M.; Orgnero, S.; Hüner, N.P.A.; Smith, D.R. The Enigmatic Loss of Light-Independent Chlorophyll Biosynthesis from an Antarctic Green Alga in a Light-Limited Environment. New Phytol. 2019, 222, 651–656, doi:10.1111/nph.15623.
Peltier, G.; Aro, E.M.; Shikanai, T. NDH-1 and NDH-2 Plastoquinone Reductases in Oxygenic Photosynthesis. Annu. Rev. Plant Biol. 2016, 67, 55–80, doi:10.1146/annurev-arplant-043014-114752.
Schuller, J.M.; Birrell, J.A.; Tanaka, H.; Konuma, T.; Wulfhorst, H.; Cox, N.; Schuller, S.K.; Thiemann, J.; Lubitz, W.; Sétif, P.; et al. Structural Adaptations of Photosynthetic Complex I Enable Ferredoxin-Dependent Electron Transfer. Science 2019, 363, 257– 260, doi:10.1126/science.aau3613.
Martín, M.; Sabater, B. Plastid Ndh Genes in Plant Evolution. Plant Physiol. Biochem. 2010, 48, 636–645, doi:10.1016/j.plaphy.2010.04.009.
Jans, F.; Mignolet, E.; Houyoux, P.A.; Cardol, P.; Ghysels, B.; Cuiné, S.; Cournac, L.; Peltier, G.; Remacle, C.; Franck, F. A Type Ii Nad(p)h Dehydrogenase Mediates Light-Independent Plastoquinone Reduction in the Chloroplast of Chlamydomonas. Proc. Natl. Acad. Sci. USA 2008, 105, 20546–20551, doi:10.1073/pnas.0806896105.
Desplats, C.; Mus, F.; Cuiné, S.; Billon, E.; Cournac, L.; Peltier, G. Characterization of Nda2, a Plastoquinone-Reducing Type II NAD (P) H Dehydrogenase in Chlamydomonas Chloroplasts. J. Biol. Chem. 2009, 284, 4148–4157, doi:10.1074/jbc.M804546200.
Saroussi, S.; Sanz-Luque, E.; Kim, R.G.; Grossman, A.R. Nutrient Scavenging and Energy Management: Acclimation Responses in Nitrogen and Sulfur Deprived Chlamydomonas. Curr. Opin. Plant Biol. 2017, 39, 114–122, doi:10.1016/j.pbi.2017.06.002.
Baltz, A.; Dang, K.V.; Beyly, A.; Auroy, P.; Richaud, P.; Cournac, L.; Peltier, G. Plastidial Expression of Type II NAD(P)H De-hydrogenase Increases the Reducing State of Plastoquinones and Hydrogen Photoproduction Rate by the Indirect Pathway in Chlamydomonas reinhardtii. Plant Physiol. 2014, 165, 1344–1352, doi:10.1104/pp.114.240432.
Grossman, A.; Sanz-Luque, E.; Yi, H.; Yang, W. Building the Greencut2 Suite of Proteins to Unmask Photosynthetic Function and Regulation. Microbiology 2019, 165, 697–718, doi:10.1099/mic.0.000788.
Fristedt, R.; Herdean, A.; Blaby-Haas, C.E.; Mamedov, F.; Merchant, S.S.; Last, R.L.; Lundin, B. PHOTOSYSTEM II PROTEIN33, a Protein Conserved in the Plastid Lineage, Is Associated with the Chloroplast Thylakoid Membrane and Provides Stability to Photosystem II Supercomplexes in Arabidopsis. Plant Physiol. 2015, 167, 481–492, doi:10.1104/pp.114.253336.
Kato, Y.; Yokono, M.; Akimoto, S.; Takabayashi, A.; Tanaka, A.; Tanaka, R. Deficiency of the Stroma-Lamellar Protein LIL8/PSB33 Affects Energy Transfer Around PSI in Arabidopsis. Plant Cell Physiol. 2017, 58, 2026–2039, doi:10.1093/pcp/pcx124.
Urzica, E.I.; Casero, D.; Yamasaki, H.; Hsieh, S.I.; Adler, L.N.; Karpowicz, S.J.; Blaby-Haas, C.E.; Clarke, S.G.; Loo, J.A.; Pelle-grini, M.; et al. Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage. Plant Cell 2012, 24, 3921–3948, doi:10.1105/tpc.112.102491.
Ibrahim, I.M.; Wu, H.; Ezhov, R.; Kayanja, G.E.; Zakharov, S.D.; Du, Y.; Tao, W.A.; Pushkar, Y.; Cramer, W.A.; Puthiyaveetil, S. An Evolutionarily Conserved Iron-Sulfur Cluster Underlies Redox Sensory Function of the Chloroplast Sensor Kinase. Commun. Biol. 2020, 3, 13, doi:10.1038/s42003-019-0728-4.
Harris, E.H. The Chlamydomonas Sourcebook; Elsevier Academic Press Inc.: New York, NY, USA, 1989; ISBN 978-0-12-326880-8.
Atteia, A.; Van Lis, R.; Tielens, A.G.M.; Martin, W.F. Anaerobic Energy Metabolism in Unicellular Photosynthetic Eukaryotes. Biochim. Biophys. Acta Bioenerg. 2013, 1827, 210–223, doi:10.1016/j.bbabio.2012.08.002.
Catalanotti, C.; Yang, W.; Posewitz, M.C.; Grossman, A.R. Fermentation Metabolism and Its Evolution in Algae. Front. Plant Sci. 2013, 4, 150, doi:10.3389/fpls.2013.00150.
Yang, W.; Catalanotti, C.; Wittkopp, T.M.; Posewitz, M.C.; Grossman, A.R. Algae after Dark: Mechanisms to Cope with An-oxic/Hypoxic Conditions. Plant J. 2015, 82, 481–503, doi:10.1111/tpj.12823.
Olson, A.C.; Carter, C.J. The Involvement of Hybrid Cluster Protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas rein-hardtii. PLoS ONE 2016, 11, e0149816, doi:10.1371/journal.pone.0149816.
Atteia, A.; van Lis, R.; Gelius-Dietrich, G.; Adrait, A.; Garin, J.; Joyard, J.; Rolland, N.; Martin, W. Pyruvate Formate-Lyase and a Novel Route of Eukaryotic ATP Synthesis in Chlamydomonas Mitochondria. J. Biol. Chem. 2006, 281, 9909–9918, doi:10.1074/jbc.M507862200.
Shisler, K.A.; Hutcheson, R.U.; Horitani, M.; Duschene, K.S.; Crain, A.V.; Byer, A.S.; Shepard, E.M.; Rasmussen, A.; Yang, J.; Broderick, W.E.; et al. Monovalent Cation Activation of the Radical SAM Enzyme Pyruvate Formate-Lyase Activating Enzyme. J. Am. Chem. Soc. 2017, 139, 11803−11813, doi:10.1021/jacs.7b04883.
Wagner, A.F.V.; Frey, M.; Neugebauer, F.A.; Schafer, W.; Knappe, J. The Free Radical in Pyruvate Formate-Lyase Is Located on Glycine-734. Proc. Natl. Acad. Sci. USA 1992, 89, 996–1000, doi:10.1073/pnas.89.3.996.
Catalanotti, C.; Dubini, A.; Subramanian, V.; Yang, W.; Magneschi, L.; Mus, F.; Seibert, M.; Posewitz, M.C.; Grossman, A.R. Altered Fermentative Metabolism in Chlamydomonas reinhardtii Mutants Lacking Pyruvate Formate Lyase and Both Pyruvate Formate Lyase and Alcohol Dehydrogenase. Plant Cell 2012, 24, 692–707, doi:10.1105/tpc.111.093146.
Van Lis, R.; Baffert, C.; Couté, Y.; Nitschke, W.; Atteia, A. Chlamydomonas reinhardtii Chloroplasts Contain a Homodimeric Py-ruvate:Ferredoxin Oxidoreductase That Functions with FDX1. Plant Physiol. 2013, 161, 57–71, doi:10.1104/pp.112.208181.
Noth, J.; Krawietz, D.; Hemschemeier, A.; Happe, T. Pyruvate:Ferredoxin Oxidoreductase Is Coupled to Light-Independent Hydrogen Production in Chlamydomonas reinhardtii. J. Biol. Chem. 2013, 288, 4368–4377, doi:10.1074/jbc.M112.429985.
Fukuda, E.; Kino, H.; Matsuzawa, H.; Wakagi, T. Role of a Highly Conserved YPITP Motif in 2-Oxoacid:Ferredoxin Oxidore-ductase. Eur. J. Biochem. 2001, 268, 5639–5646, doi:10.1046/j.1432-1033.2001.02504.x.
Meuser, J.E.; D’Adamo, S.; Jinkerson, R.E.; Mus, F.; Yang, W.; Ghirardi, M.L.; Seibert, M.; Grossman, A.R.; Posewitz, M.C. Ge-netic Disruption of Both Chlamydomonas reinhardtii [FeFe]-Hydrogenases: Insight into the Role of HYDA2 in H2 Production. Biochem. Biophys. Res. Commun. 2012, 417, 704–709, doi:10.1016/j.bbrc.2011.12.002.
Mulder, D.W.; Boyd, E.S.; Sarma, R.; Lange, R.K.; Endrizzi, J.A.; Broderick, J.B.; Peters, J.W. Stepwise FeFe-Hydrogenase H-Cluster Assembly Revealed in the Structure of HydA ΔeFG. Nature 2010, 465, 248–252, doi:10.1038/nature08993.
Peters, J.W. X-Ray Crystal Structure of the Fe-Only Hydrogenase (CpI) from Clostridium pasteurianum to 1.8 Angstrom Resolu-tion. Science 1998, 282, 1853–1858, doi:10.1126/science.282.5395.1853.
Esselborn, J.; Muraki, N.; Klein, K.; Engelbrecht, V.; Metzler-Nolte, N.; Apfel, U.P.; Hofmann, E.; Kurisu, G.; Happe, T. A Structural View of Synthetic Cofactor Integration into [Fefe]-Hydrogenases. Chem. Sci. 2016, 7, 959–968, doi:10.1039/c5sc03397g.
Byer, A.S.; Shepard, E.M.; Ratzloff, M.W.; Betz, J.N.; King, P.W.; Broderick, W.E.; Broderick, J.B. H-Cluster Assembly Intermediates Built on HydF by the Radical SAM Enzymes HydE and HydG. J. Biol. Inorg. Chem. 2019, 24, 783–792, doi:10.1007/s00775-019-01709-7.
Sawyer, A.; Bai, Y.; Lu, Y.; Hemschemeier, A.; Happe, T. Compartmentalisation of [FeFe]-Hydrogenase Maturation in Chla-mydomonas reinhardtii. Plant J. 2017, 90, 1134–1143, doi:10.1111/tpj.13535.
Posewitz, M.C.; King, P.W.; Smolinski, S.L.; Zhang, L.; Seibert, M.; Ghirardi, M.L. Discovery of Two Novel Radical S-Adenosyl-methionine Proteins Required for the Assembly of an Active [Fe] Hydrogenase. J. Biol. Chem. 2004, 279, 25711–25720, doi:10.1074/jbc.M403206200.
King, P.W.; Posewitz, M.C.; Ghirardi, M.L.; Seibert, M. Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System. J. Bacteriol. 2006, 188, 2163–2172, doi:10.1128/JB.188.6.2163-2172.2006.
D’Adamo, S.; Jinkerson, R.E.; Boyd, E.S.; Brown, S.L.; Baxter, B.K.; Peters, J.W.; Posewitz, M.C. Evolutionary and Biotechnolog-ical Implications of Robust Hydrogenase Activity in Halophilic Strains of Tetraselmis. PLoS ONE 2014, 9, e85812, doi:10.1371/journal.pone.0085812.
Aragão, D.; Macedo, S.; Mitchell, E.P.; Romão, C.V.; Liu, M.Y.; Frazão, C.; Saraiva, L.M.; Xavier, A.V.; LeGall, J.; Van Dongen, W.M.A.M.; et al. Reduced Hybrid Cluster Proteins (HCP) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-Ray Structures at High Resolution Using Synchrotron Radiation. J. Biol. Inorg. Chem. 2003, 8, 540–548, doi:10.1007/s00775-003-0443-x.
Cooper, S.J.; Garner, C.D.; Hagen, W.R.; Lindley, P.F.; Bailey, S. Hybrid-Cluster Protein (HCP) from Desulfovibrio vulgaris (Hil-denborough) at 1.6 \AA Resolution. Biochemistry 2000, 39, 15044–15054, doi:10.1021/bi001483m.
Arendsen, A.F.; Hadden, J.; Card, G.; McAlpine, A.S.; Bailey, S.; Zaitsev, V.; Duke, E.H.M.; Lindley, P.F.; Kröckel, M.; Trautwein, A.X.; et al. The “prismane” Protein Resolved: X-ray Structure at 1.7 \AA and Multiple Spectroscopy of Two Novel 4Fe Clusters. J. Biol. Inorg. Chem. 1998, 3, 81–95, doi:10.1007/s007750050210.
Van Lis, R.; Brugière, S.; Baffert, C.; Couté, Y.; Nitschke, W.; Atteia, A. Hybrid Cluster Proteins in a Photosynthetic Microalga. FEBS J. 2020, 287, 721–735, doi:10.1111/febs.15025.
Mus, F.; Dubini, A.; Seibert, M.; Posewitz, M.C.; Grossman, A.R. Anaerobic Acclimation in Chlamydomonas reinhardtii: Anoxic Gene Expression, Hydrogenase Induction, and Metabolic Pathways. J. Biol. Chem. 2007, 282, 25475–25486, doi:10.1074/jbc.M701415200.
Jez, J.M. Structural Biology of Plant Sulfur Metabolism: From Sulfate to Glutathione. J. Exp. Bot. 2019, 70, 4089–4013, doi:10.1093/jxb/erz094.
McMinn, A.; Martin, A. Dark Survival in a Warming World. Proc. R. Soc. B Biol. Sci. 2013, 280, 20122909, doi:10.1098/rspb.2012.2909.
Kamp, A.; De Beer, D.; Nitsch, J.L.; Lavik, G.; Stief, P. Diatoms Respire Nitrate to Survive Dark and Anoxic Conditions. Proc. Natl. Acad. Sci. USA 2011, 108, 5649–5654, doi:10.1073/pnas.1015744108.
Kamp, A.; Stief, P.; Knappe, J.; De Beer, D. Response of the Ubiquitous Pelagic Diatom Thalassiosira weissflogii to Darkness and Anoxia. PLoS ONE 2013, 8, e82605, doi:10.1371/journal.pone.0082605.
Kamp, A.; Stief, P.; Bristow, L.A.; Thamdrup, B.; Glud, R.N. Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates. Front. Microbiol. 2016, 7, 1669, doi:10.3389/fmicb.2016.01669.
Kraft, B.; Strous, M.; Tegetmeyer, H.E. Microbial Nitrate Respiration—Genes, Enzymes and Environmental Distribution. J. Bio-technol. 2011, 155, 104–117, doi:10.1016/j.jbiotec.2010.12.025.
Gould, S.B.; Garg, S.G.; Handrich, M.; Nelson-Sathi, S.; Gruenheit, N.; Tielens, A.G.M.; Martin, W.F. Adaptation to Life on Land at High O2 via Transition from Ferredoxin-to NADH-Dependent Redox Balance. Proc. Biol. Sci. 2019, 286, 20191491, doi:10.1098/rspb.2019.1491.
