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Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
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Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
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2
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Panwar P, Williams TJ, Allen MA, Cavicchioli R. Population structure of an Antarctic aquatic cyanobacterium. Microbiome 2022; 10:207. [PMID: 36457105 PMCID: PMC9716671 DOI: 10.1186/s40168-022-01404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses. RESULTS A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes). CONCLUSION In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. Video Abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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3
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Darrouzet E, Rinaldi C, Zambelli B, Ciurli S, Cavazza C. Revisiting the CooJ family, a potential chaperone for nickel delivery to [NiFe]‑carbon monoxide dehydrogenase. J Inorg Biochem 2021; 225:111588. [PMID: 34530332 DOI: 10.1016/j.jinorgbio.2021.111588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/21/2022]
Abstract
Nickel insertion into nickel-dependent carbon monoxide dehydrogenase (CODH) represents a key step in the enzyme activation. This is the last step of the biosynthesis of the active site, which contains an atypical heteronuclear NiFe4S4 cluster known as the C-cluster. The enzyme maturation is performed by three accessory proteins, namely CooC, CooT and CooJ. Among them, CooJ from Rhodospirillum rubrum is a histidine-rich protein containing two distinct and spatially separated Ni(II)-binding sites: a N-terminal high affinity site (HAS) and a histidine tail at the C-terminus. In 46 CooJ homologues, the HAS motif was found to be strictly conserved with a H(W/F)XXHXXXH sequence. Here, a proteome database search identified at least 150 CooJ homologues and revealed distinct motifs for HAS, featuring 2, 3 or 4 histidines. The purification and biophysical characterization of three representative members of this protein family showed that they are all homodimers able to bind Ni(II) ions via one or two independent binding sites. Initially thought to be present only in R. rubrum, this study strongly suggests that CooJ could play a significant role in CODH maturation or in nickel homeostasis.
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Affiliation(s)
- Elisabeth Darrouzet
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Clara Rinaldi
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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4
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Contaldo U, Guigliarelli B, Perard J, Rinaldi C, Le Goff A, Cavazza C. Efficient Electrochemical CO 2/CO Interconversion by an Engineered Carbon Monoxide Dehydrogenase on a Gas-Diffusion Carbon Nanotube-Based Bioelectrode. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Umberto Contaldo
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
- University Grenoble Alpes, DCM UMR 5250, BEA, F-38000 Grenoble, France
| | | | - Julien Perard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Clara Rinaldi
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Alan Le Goff
- University Grenoble Alpes, DCM UMR 5250, BEA, F-38000 Grenoble, France
| | - Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
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5
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Alfano M, Cavazza C. Structure, function, and biosynthesis of nickel-dependent enzymes. Protein Sci 2020; 29:1071-1089. [PMID: 32022353 DOI: 10.1002/pro.3836] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
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Affiliation(s)
- Marila Alfano
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
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6
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Alfano M, Veronesi G, Musiani F, Zambelli B, Signor L, Proux O, Rovezzi M, Ciurli S, Cavazza C. A Solvent‐Exposed Cysteine Forms a Peculiar Ni
II
‐Binding Site in the Metallochaperone CooT from
Rhodospirillum rubrum. Chemistry 2019; 25:15351-15360. [DOI: 10.1002/chem.201903492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Marila Alfano
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Giulia Veronesi
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Francesco Musiani
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Luca Signor
- IRIG, IBSUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Olivier Proux
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Mauro Rovezzi
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Christine Cavazza
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
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7
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Wittenborn EC, Cohen SE, Merrouch M, Léger C, Fourmond V, Dementin S, Drennan CL. Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase. J Biol Chem 2019; 294:13017-13026. [PMID: 31296570 DOI: 10.1074/jbc.ra119.009610] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
The nickel-dependent carbon monoxide dehydrogenase (CODH) employs a unique heterometallic nickel-iron-sulfur cluster, termed the C-cluster, to catalyze the interconversion of CO and CO2 Like other complex metalloenzymes, CODH requires dedicated assembly machinery to form the fully intact and functional C-cluster. In particular, nickel incorporation into the C-cluster depends on the maturation factor CooC; however, the mechanism of nickel insertion remains poorly understood. Here, we compare X-ray structures (1.50-2.48 Å resolution) of CODH from Desulfovibrio vulgaris (DvCODH) heterologously expressed in either the absence (DvCODH-CooC) or presence (DvCODH+CooC) of co-expressed CooC. We find that the C-cluster of DvCODH-CooC is fully loaded with iron but does not contain any nickel. Interestingly, the so-called unique iron ion (Feu) occupies both its canonical site (80% occupancy) and the nickel site (20% occupancy), with addition of reductant causing further mismetallation of the nickel site (60% iron occupancy). We also demonstrate that a DvCODH variant that lacks a surface-accessible iron-sulfur cluster (the D-cluster) has a C-cluster that is also replete in iron but lacks nickel, despite co-expression with CooC. In this variant, all Feu is in its canonical location, and the nickel site is empty. This D-cluster-deficient CODH is inactive despite attempts to reconstitute it with nickel. Taken together, these results suggest that an empty nickel site is not sufficient for nickel incorporation. Based on our findings, we propose a model for C-cluster assembly that requires both CooC and a functioning D-cluster, involves precise redox-state control, and includes a two-step nickel-binding process.
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Affiliation(s)
- Elizabeth C Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Steven E Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Mériem Merrouch
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Christophe Léger
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vincent Fourmond
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Sébastien Dementin
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France.
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada.
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8
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Alfano M, Pérard J, Carpentier P, Basset C, Zambelli B, Timm J, Crouzy S, Ciurli S, Cavazza C. The carbon monoxide dehydrogenase accessory protein CooJ is a histidine-rich multidomain dimer containing an unexpected Ni(II)-binding site. J Biol Chem 2019; 294:7601-7614. [PMID: 30858174 DOI: 10.1074/jbc.ra119.008011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/09/2019] [Indexed: 01/14/2023] Open
Abstract
Activation of nickel enzymes requires specific accessory proteins organized in multiprotein complexes controlling metal transfer to the active site. Histidine-rich clusters are generally present in at least one of the metallochaperones involved in nickel delivery. The maturation of carbon monoxide dehydrogenase in the proteobacterium Rhodospirillum rubrum requires three accessory proteins, CooC, CooT, and CooJ, dedicated to nickel insertion into the active site, a distorted [NiFe3S4] cluster coordinated to an iron site. Previously, CooJ from R. rubrum (RrCooJ) has been described as a nickel chaperone with 16 histidines and 2 cysteines at its C terminus. Here, the X-ray structure of a truncated version of RrCooJ, combined with small-angle X-ray scattering data and a modeling study of the full-length protein, revealed a homodimer comprising a coiled coil with two independent and highly flexible His tails. Using isothermal calorimetry, we characterized several metal-binding sites (four per dimer) involving the His-rich motifs and having similar metal affinity (KD = 1.6 μm). Remarkably, biophysical approaches, site-directed mutagenesis, and X-ray crystallography uncovered an additional nickel-binding site at the dimer interface, which binds Ni(II) with an affinity of 380 nm Although RrCooJ was initially thought to be a unique protein, a proteome database search identified at least 46 bacterial CooJ homologs. These homologs all possess two spatially separated nickel-binding motifs: a variable C-terminal histidine tail and a strictly conserved H(W/F)X 2HX 3H motif, identified in this study, suggesting a dual function for CooJ both as a nickel chaperone and as a nickel storage protein.
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Affiliation(s)
- Marila Alfano
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Julien Pérard
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Philippe Carpentier
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Christian Basset
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Barbara Zambelli
- the Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, I-40127 Bologna, Italy
| | - Jennifer Timm
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Serge Crouzy
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Stefano Ciurli
- the Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, I-40127 Bologna, Italy
| | - Christine Cavazza
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
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9
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Inoue M, Nakamoto I, Omae K, Oguro T, Ogata H, Yoshida T, Sako Y. Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases. Front Microbiol 2019; 9:3353. [PMID: 30705673 PMCID: PMC6344411 DOI: 10.3389/fmicb.2018.03353] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/31/2018] [Indexed: 11/30/2022] Open
Abstract
Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kimiho Omae
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tatsuki Oguro
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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10
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Alfano M, Pérard J, Miras R, Catty P, Cavazza C. Biophysical and structural characterization of the putative nickel chaperone CooT from Carboxydothermus hydrogenoformans. J Biol Inorg Chem 2018; 23:809-817. [PMID: 29882029 DOI: 10.1007/s00775-018-1576-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 06/01/2018] [Indexed: 01/28/2023]
Abstract
Carboxydothermus hydrogenoformans is a model microorganism for the study of [NiFe]-CODH, a key enzyme of carbon cycle in anaerobic microorganisms. The enzyme possesses a unique active site (C-cluster), constituted of a distorted [NiFe3S4] cubane linked to a mononuclear Fe(II) center. Both the biogenesis of the C-cluster and the activation of CODH by nickel insertion remain unclear. Among the three accessory proteins thought to play a role in this latter step (CooC, CooJ, and CooT), CooT is identified as a nickel chaperone involved in CODH maturation in Rhodospirillum rubrum. Here, we structurally and biophysically characterized a putative CooT protein present in C. hydrogenoformans (pChCooT). Despite the low sequence homologies between CooT from R. rubrum (RrCooT) and pChCooT (19% sequence identity), the two proteins share several similarities, such as their overall structure and a solvent-exposed Ni(II)-binding site at the dimer interface. Moreover, the X-ray structure of pChCooT reveals the proximity between the histidine 55, a potential nickel-coordinating residue, and the cysteine 2, a highly conserved key residue in Ni(II)-binding.
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Affiliation(s)
- M Alfano
- University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France
| | - J Pérard
- University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France
| | - R Miras
- University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France
| | - P Catty
- University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France
| | - C Cavazza
- University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France.
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Merrouch M, Benvenuti M, Lorenzi M, Léger C, Fourmond V, Dementin S. Maturation of the [Ni-4Fe-4S] active site of carbon monoxide dehydrogenases. J Biol Inorg Chem 2018; 23:613-20. [PMID: 29445873 DOI: 10.1007/s00775-018-1541-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
Nickel-containing enzymes are diverse in terms of function and active site structure. In many cases, the biosynthesis of the active site depends on accessory proteins which transport and insert the Ni ion. We review and discuss the literature related to the maturation of carbon monoxide dehydrogenases (CODH) which bear a nickel-containing active site consisting of a [Ni–4Fe–4S] center called the C-cluster. The maturation of this center has been much less studied than that of other nickel-containing enzymes such as urease and NiFe hydrogenase. Several proteins present in certain CODH operons, including the nickel-binding proteins CooT and CooJ, still have unclear functions. We question the conception that the maturation of all CODH depends on the accessory protein CooC described as essential for nickel insertion into the active site. The available literature reveals biological variations in CODH active site biosynthesis.
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