[FeFe]-hydrogenases from green algae

Methods in Enzymology - Tập 613 - Trang 203-230 - 2018
Vera Engelbrecht1, Thomas Happe1
1AG Photobiotechnologie, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße, Bochum, Germany

Tài liệu tham khảo

Abendroth, 2008, Optimized over-expression of [FeFe] hydrogenases with high specific activity in Clostridium acetobutylicum, International Journal of Hydrogen Energy, 33, 6076, 10.1016/j.ijhydene.2008.07.122 Adam, 2017, Sunlight-dependent hydrogen production by photosensitizer/hydrogenase systems, ChemSusChem, 10, 894, 10.1002/cssc.201601523 Adamska, 2012, Identification and characterization of the “super-reduced” state of the H-cluster in [FeFe] hydrogenase: A new building block for the catalytic cycle?, Angewandte Chemie (International Ed. in English), 51, 11458, 10.1002/anie.201204800 Adamska-Venkatesh, 2014, New redox states observed in [FeFe] hydrogenases reveal redox coupling within the H-cluster, Journal of the American Chemical Society, 136, 11339, 10.1021/ja503390c Adamska-Venkatesh, 2015, Artificially maturated [FeFe] hydrogenase from Chlamydomonas reinhardtii: A HYSCORE and ENDOR study of a non-natural H-cluster, Physical Chemistry Chemical Physics, 17, 5421, 10.1039/C4CP05426A Akhtar, 2008, Deletion of iscR stimulates recombinant clostridial Fe–Fe hydrogenase activity and H2-accumulation in Escherichia coli BL21(DE3), Applied Microbiology and Biotechnology, 78, 853, 10.1007/s00253-008-1377-6 Albracht, 2006, The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. I. Light sensitivity and magnetic hyperfine interactions as observed by electron paramagnetic resonance, Journal of Biological Inorganic Chemistry, 11, 88, 10.1007/s00775-005-0039-8 Armstrong, 2016, Guiding principles of hydrogenase catalysis instigated and clarified by protein film electrochemistry, Accounts of Chemical Research, 49, 884, 10.1021/acs.accounts.6b00027 Armstrong, 2018, Protein film electrochemistry of iron–sulfur enzymes, Methods in Enzymology, 599, 387, 10.1016/bs.mie.2017.11.001 Arriola, 2018, Genome sequences of chlorella sorokiniana UTEX 1602 and micractinium conductrix SAG 241.80: Implications to maltose excretion by a green alga, The Plant Journal, 93, 566, 10.1111/tpj.13789 Artz, 2017, Reduction potentials of [FeFe]-hydrogenase accessory iron–sulfur clusters provide insights into the energetics of proton reduction catalysis, Journal of the American Chemical Society, 139, 9544, 10.1021/jacs.7b02099 Berggren, 2013, Biomimetic assembly and activation of [FeFe]-hydrogenases, Nature, 499, 66, 10.1038/nature12239 Blanc, 2010, The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex, Plant Cell, 22, 2943, 10.1105/tpc.110.076406 Chernev, 2014, Hydride binding to the active site of [FeFe]-hydrogenase, Inorganic Chemistry, 53, 12164, 10.1021/ic502047q Chin, 2014, Codon Optimization OnLine (COOL): A web-based multi-objective optimization platform for synthetic gene design, Bioinformatics, 30, 2210, 10.1093/bioinformatics/btu192 Cornish, 2015, Characterization of hydrogen metabolism in the multicellular green alga volvox carteri, PLoS One, 10, 10.1371/journal.pone.0125324 de Marco, 2005, Native folding of aggregation-prone recombinant proteins in Escherichia coli by osmolytes, plasmid- or benzyl alcohol-overexpressed molecular chaperones, Cell Stress & Chaperones, 10, 329, 10.1379/CSC-139R.1 Derman, 1993, Mutations that allow disulfide bond formation in the cytoplasm of Escherichia coli, Science, 262, 1744, 10.1126/science.8259521 Dubini, 2015, Engineering photosynthetic organisms for the production of biohydrogen, Photosynthesis Research, 123, 241, 10.1007/s11120-014-9991-x Eilenberg, 2016, The dual effect of a ferredoxin-hydrogenase fusion protein in vivo: successful divergence of the photosynthetic electron flux towards hydrogen production and elevated oxygen tolerance, Biotechnology for Biofuels, 9, 182, 10.1186/s13068-016-0601-3 Engelbrecht, 2017, The structurally unique photosynthetic Chlorella variabilis NC64A hydrogenase does not interact with plant-type ferredoxins, Biochimica et Biophysica Acta, 1858, 771, 10.1016/j.bbabio.2017.06.004 Esselborn, 2013, Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic, Nature Chemical Biology, 9, 607, 10.1038/nchembio.1311 Esselborn, 2016, A structural view of synthetic cofactor integration into [FeFe]-hydrogenases, Chemical Science, 2, 959, 10.1039/C5SC03397G Evans, 2004, Enhanced photocatalytic hydrogen evolution by covalent attachment of plastocyanin to photosystem I, Nano Letters, 4, 1815, 10.1021/nl0493388 Ferrer, 2004, Expression of a temperature-sensitive esterase in a novel chaperone-based Escherichia coli strain, Applied and Environmental Microbiology, 70, 4499, 10.1128/AEM.70.8.4499-4504.2004 Florin, 2001, A novel type of iron hydrogenase in the green alga Scenedesmus obliquus is linked to the photosynthetic electron transport chain, Journal of Biological Chemistry, 276, 6125, 10.1074/jbc.M008470200 Gaffron, 1939, Reduction of carbon dioxide with molecular hydrogen in green algæ, Nature, 143, 204, 10.1038/143204a0 Gaffron, 1942, The effect of specific poisons upon the photoreduction with hydrogen in green algae, The Journal of General Physiology, 26, 195, 10.1085/jgp.26.2.195 Gaffron, 1942, Fermentative and photochemical production of hydrogen in algae, The Journal of General Physiology, 26, 219, 10.1085/jgp.26.2.219 Galván, 1985, Physicochemical properties of ferredoxin from Chlamydomonas reinhardii, Zeitschrift für Naturforschung, 40, 373, 10.1515/znc-1985-5-615 Gauquelin, 2018, Roles of the F-domain in [FeFe] hydrogenase, Biochimica et Biophysica Acta, 1859, 69, 10.1016/j.bbabio.2017.08.010 Ghirardi, 2000, Microalgae: A green source of renewable H(2), Trends in Biotechnology, 18, 506, 10.1016/S0167-7799(00)01511-0 Gilbert-Wilson, 2015, Spectroscopic investigations of [FeFe] hydrogenase maturated with [(57)Fe2(adt)(CN)2(CO)4](2-), Journal of the American Chemical Society, 137, 8998, 10.1021/jacs.5b03270 Girbal, 2005, Homologous and heterologous overexpression in Clostridium acetobutylicum and characterization of purified clostridial and algal Fe-only hydrogenases with high specific activities, Applied and Environmental Microbiology, 71, 2777, 10.1128/AEM.71.5.2777-2781.2005 Gorman, 1965, Cytochrome f and plastocyanin: Their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardi, Proceedings of the National Academy of Sciences of the United States of America, 54, 1665, 10.1073/pnas.54.6.1665 Gorwa, 1996, Molecular characterization and transcriptional analysis of the putative hydrogenase gene of Clostridium acetobutylicum ATCC 824, Journal of Bacteriology, 178, 2668, 10.1128/jb.178.9.2668-2675.1996 Graumann, 2006, Manufacturing of recombinant therapeutic proteins in microbial systems, Biotechnology Journal, 1, 164, 10.1002/biot.200500051 Grimme, 2009, Maximizing H2 production in photosystem I/dithiol molecular wire/platinum nanoparticle bioconjugates, Dalton Transactions, 45, 10106, 10.1039/b909137h Grote, 2005, JCat: A novel tool to adapt codon usage of a target gene to its potential expression host, Nucleic Acids Research, 33, W526, 10.1093/nar/gki376 Guillard, 1962, Studies of marine planktonic diatoms. I. Cyclotella nana Hustedt, and Detonula confervacea (cleve) Gran, Canadian Journal of Microbiology, 8, 229, 10.1139/m62-029 Guzman, 1995, Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter, Journal of Bacteriology, 177, 4121, 10.1128/jb.177.14.4121-4130.1995 Happe, 2002, Differential regulation of the Fe-hydrogenase during anaerobic adaptation in the green alga Chlamydomonas reinhardtii, European Journal of Biochemistry, 269, 1022, 10.1046/j.0014-2956.2001.02743.x Happe, 1993, Isolation, characterization and N-terminal amino acid sequence of hydrogenase from the green alga Chlamydomonas reinhardtii, European Journal of Biochemistry, 214, 475, 10.1111/j.1432-1033.1993.tb17944.x Hemschemeier, 2011, Alternative photosynthetic electron transport pathways during anaerobiosis in the green alga Chlamydomonas reinhardtii, Biochimica et Biophysica Acta—Bioenergetics, 1807, 919, 10.1016/j.bbabio.2011.02.010 Hemschemeier, 2009, Analytical approaches to photobiological hydrogen production in unicellular green algae, Photosynthesis Research, 102, 523, 10.1007/s11120-009-9415-5 Iwuchukwu, 2010, Self-organized photosynthetic nanoparticle for cell-free hydrogen production, Nature Nanotechnology, 5, 73, 10.1038/nnano.2009.315 Jacobs, 2009, A novel, anaerobically induced ferredoxin in Chlamydomonas reinhardtii, FEBS Letters, 583, 325, 10.1016/j.febslet.2008.12.018 Jaganaman, 2007, High levels of expression of the iron–sulfur proteins phthalate dioxygenase and phthalate dioxygenase reductase in Escherichia coli, Protein Expression and Purification, 52, 273, 10.1016/j.pep.2006.09.004 Kamp, 2008, Isolation and first EPR characterization of the [FeFe]-hydrogenases from green algae, Biochimica et Biophysica Acta, 1777, 410, 10.1016/j.bbabio.2008.02.002 Kataeva, 2005, Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli, Journal of Proteome Research, 4, 1942, 10.1021/pr050108j Kertess, 2017, Influence of the [4Fe-4S] cluster coordinating cysteines on active site maturation and catalytic properties of C. reinhardtii [FeFe]-hydrogenase, Chemical Science, 8, 8127, 10.1039/C7SC03444J Kertess, 2017, Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity, Dalton Transactions, 46, 16947, 10.1039/C7DT03785F Khanna, 2017, In vivo activation of an [FeFe] hydrogenase using synthetic cofactors, Energy & Environmental Science, 10, 1563, 10.1039/C7EE00135E King, 2006, Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system, Journal of Bacteriology, 188, 2163, 10.1128/JB.188.6.2163-2172.2006 Kuchenreuther, 2010, High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli, PLoS One, 5, 10.1371/journal.pone.0015491 Lambertz, 2011, O2 reactions at the six-iron active site (H-cluster) in [FeFe]-hydrogenase, Journal of Biological Chemistry, 286, 40614, 10.1074/jbc.M111.283648 Lampret, 2017, Interplay between CN(−) ligands and the secondary coordination sphere of the H-cluster in [FeFe]-hydrogenases, Journal of the American Chemical Society, 139, 18222, 10.1021/jacs.7b08735 Lessard, 2013, Chapter eleven—Growth media for E. coli, 533, 181, 10.1016/B978-0-12-420067-8.00011-8 Li, 2002, Iron carbonyl sulfides, formaldehyde, and amines condense to give the proposed azadithiolate cofactor of the Fe-only hydrogenases, Journal of the American Chemical Society, 124, 726, 10.1021/ja016964n Liu, 2014, COStar: A D-star lite-based dynamic search algorithm for codon optimization, Journal of Theoretical Biology, 344, 19, 10.1016/j.jtbi.2013.11.022 Lorimer, 2009, Gene composer: Database software for protein construct design, codon engineering, and gene synthesis, BMC Biotechnology, 9, 36, 10.1186/1472-6750-9-36 Lubitz, 2014, Hydrogenases, Chemical Reviews, 114, 4081, 10.1021/cr4005814 Lubitz, 2007, [nife] and [fefe] hydrogenases studied by advanced magnetic resonance techniques, Chemical Reviews, 107, 4331, 10.1021/cr050186q Lubner, 2011, Solar hydrogen-producing bionanodevice outperforms natural photosynthesis, Proceedings of the National Academy of Sciences of the United States of America, 108, 20988, 10.1073/pnas.1114660108 Martin, 2017, A review of hydrogen production by photosynthetic organisms using whole-cell and cell-free systems, Applied Biochemistry and Biotechnology, 183, 503, 10.1007/s12010-017-2576-3 Mebs, 2018, Hydrogen and oxygen trapping at the H-cluster of [FeFe]-hydrogenase revealed by site-selective spectroscopy and QM/MM calculations, Biochimica et Biophysica Acta, 1859, 28, 10.1016/j.bbabio.2017.09.003 Melis, 2000, Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii, Plant Physiology, 122, 127, 10.1104/pp.122.1.127 Mendoza, 2000, The lower hydrolysis of ATP by the stress protein GroEL is a major factor responsible for the diminished chaperonin activity at low temperature, Cryobiology, 41, 319, 10.1006/cryo.2000.2287 Merchant, 2006, Between a rock and a hard place: Trace element nutrition in chlamydomonas, Biochimica et Biophysica Acta, 1763, 578, 10.1016/j.bbamcr.2006.04.007 Meszaros, 2018, In vivo EPR characterization of semi-synthetic [FeFe] hydrogenases, Angewandte Chemie (International Ed. in English), 57, 2596, 10.1002/anie.201710740 Meuser, 2011, Evolutionary significance of an algal gene encoding an [FeFe]-hydrogenase with F-domain homology and hydrogenase activity in Chlorella variabilis NC64A, Planta, 234, 829, 10.1007/s00425-011-1431-y Mulder, 2017, Identification of a catalytic iron-hydride at the H-cluster of [FeFe]-hydrogenase, Journal of the American Chemical Society, 139, 83, 10.1021/jacs.6b11409 Mulder, 2009, Activation of HydA(DeltaEFG) requires a preformed [4Fe-4S] cluster, Biochemistry, 48, 6240, 10.1021/bi9000563 Mulder, 2013, EPR and FTIR analysis of the mechanism of H2 activation by [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii, Journal of the American Chemical Society, 135, 6921, 10.1021/ja4000257 Nakamura, 1999, Hyperproduction of recombinant ferredoxins in escherichia coli by coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hs cA-fdx-ORF3 gene cluster, Journal of Biochemistry, 126, 10, 10.1093/oxfordjournals.jbchem.a022409 Nelson, 2017, The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization, eLife, 6, 10.7554/eLife.25783 Noth, 2016, [FeFe]-hydrogenase with chalcogenide substitutions at the H-cluster maintains full H2 evolution activity, Angewandte Chemie (International Ed. in English), 55, 8396, 10.1002/anie.201511896 Noth, 2015, Lyophilization protects [FeFe]-hydrogenases against O2-induced H-cluster degradation, Scientific Reports, 5, 10.1038/srep13978 Oey, 2016, Challenges and opportunities for hydrogen production from microalgae, Plant Biotechnology Journal, 14, 1487, 10.1111/pbi.12516 Peters, 1998, X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution, Science, 282, 1853, 10.1126/science.282.5395.1853 Peters, 2015, [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation, Biochimica et Biophysica Acta, 1853, 1350, 10.1016/j.bbamcr.2014.11.021 Posewitz, 2004, Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase, The Journal of Biological Chemistry, 279, 25711, 10.1074/jbc.M403206200 Prochnik, 2010, Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri, Science, 329, 223, 10.1126/science.1188800 Puigbò, 2007, OPTIMIZER: A web server for optimizing the codon usage of DNA sequences, Nucleic Acids Research, 35, W126, 10.1093/nar/gkm219 Ratzloff, 2018, CO-bridged H-cluster intermediates in the catalytic mechanism of [FeFe]-hydrogenase CaI, Journal of the American Chemical Society, 140, 7623, 10.1021/jacs.8b03072 Rosano, 2014, Recombinant protein expression in Escherichia coli: Advances and challenges, Frontiers in Microbiology, 5, 172, 10.3389/fmicb.2014.00172 Roseboom, 2006, The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy, Journal of Biological Inorganic Chemistry, 11, 102, 10.1007/s00775-005-0040-2 Rumpel, 2015, Structural insight into the complex of ferredoxin and [FeFe] hydrogenase from Chlamydomonas reinhardtii, ChemBioChem, 16, 1663, 10.1002/cbic.201500130 Rumpel, 2014, Enhancing hydrogen production of microalgae by redirecting electrons from photosystem I to hydrogenase, Energy & Environmental Science, 7, 3296, 10.1039/C4EE01444H Rumpel, 2018, Direct detection of the terminal hydride intermediate in [FeFe] hydrogenase by NMR spectroscopy, Journal of the American Chemical Society, 140, 3863, 10.1021/jacs.8b00459 Senger, 2018, Protonation/reduction dynamics at the [4Fe-4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases, Physical Chemistry Chemical Physics, 20, 3128, 10.1039/C7CP04757F Seyferth, 1981, Di-μ-thiolbis(tricarbonyliron),(μ-HS)2 Fe2(CO)6: An inorganic mimic of organic thiols, Journal of Organometallic Chemistry, 218, C34, 10.1016/S0022-328X(00)86113-6 Siebel, 2015, Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity, Biochemistry, 54, 1474, 10.1021/bi501391d Sivashanmugam, 2009, Practical protocols for production of very high yields of recombinant proteins using Escherichia coli, Protein Science, 18, 936, 10.1002/pro.102 Strocchi, 2006, Low temperature-induced systems failure in Escherichia coli: Insights from rescue by cold-adapted chaperones, Proteomics, 6, 193, 10.1002/pmic.200500031 Tard, 2005, Synthesis of the H-cluster framework of iron-only hydrogenase, Nature, 433, 610, 10.1038/nature03298 Terauchi, 2009, Pattern of expression and substrate specificity of chloroplast ferredoxins from Chlamydomonas reinhardtii, Journal of Biological Chemistry, 284, 25867, 10.1074/jbc.M109.023622 Terpe, 2006, Overview of bacterial expression systems for heterologous protein production: From molecular and biochemical fundamentals to commercial systems, Applied Microbiology and Biotechnology, 72, 211, 10.1007/s00253-006-0465-8 Tian, 2017, Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli, Scientific Reports, 7, 9926, 10.1038/s41598-017-10546-0 Timmins, 2009, Phylogenetic and molecular analysis of hydrogen-producing green algae, Journal of Experimental Botany, 60, 1691, 10.1093/jxb/erp052 Ueno, 1999, Purification and characterization of hydrogenase from the marine green alga, Chlorococcum littorale, FEBS Letters, 443, 144, 10.1016/S0014-5793(98)01699-8 Utschig, 2015, Light-driven hydrogen production from Photosystem I-catalyst hybrids, Current Opinion in Chemical Biology, 25, 1, 10.1016/j.cbpa.2014.11.019 Villalobos, 2006, Gene designer: A synthetic biology tool for constructing artificial DNA segments, BMC Bioinformatics, 7, 285, 10.1186/1471-2105-7-285 Wiegand, 2018, Rational redesign of the ferredoxin-NADP(+)-oxido-reductase/ferredoxin-interaction for photosynthesis-dependent H2-production, Biochimica et Biophysica Acta, 1859, 253, 10.1016/j.bbabio.2018.01.006 Winkler, 2013, Molecular basis of [FeFe]-hydrogenase function an insight into the complex interplay between protein and catalytic cofactor, Biochimica et Biophysica Acta-Bioenergetics, 1827, 974, 10.1016/j.bbabio.2013.03.004 Winkler, 2002, Isolation and molecular characterization of the [Fe]-hydrogenase from the unicellular green alga Chlorella fusca, Biochimica et Biophysica Acta, 1576, 330, 10.1016/S0167-4781(02)00239-7 Winkler, 2009, Characterization of the key step for light-driven hydrogen evolution in green algae, Journal of Biological Chemistry, 284, 36620, 10.1074/jbc.M109.053496 Winkler, 2017, Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases, Nature Communications, 8, 10.1038/ncomms16115 Wykoff, 1998, The regulation of photosynthetic electron transport during nutrient deprivation in Chlamydomonas reinhardtii, Plant Physiology, 117, 129, 10.1104/pp.117.1.129 Yacoby, 2011, Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro, Proceedings of the National Academy of Sciences of the United States of America, 108, 9396, 10.1073/pnas.1103659108 Yacoby, 2012, Optimized expression and purification for high-activity preparations of algal [FeFe]-hydrogenase, PLoS One, 7, 10.1371/journal.pone.0035886 Yan, 2011, Purification and characterization of a hydrogenase from the marine green alga tetraselmis subcordiformis, Process Biochemistry, 46, 1212, 10.1016/j.procbio.2011.02.005 Yano, 1994, Expression of the 25-kilodalton iron-sulfur subunit of the energy-transducing NADH-ubiquinone oxidoreductase of Paracoccus denitrificans, Biochemistry, 33, 494, 10.1021/bi00168a014