1
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Oyamada Y, Ogawa S, Fujishiro T. Nickel-chelatase activity of SirB variants mimicking the His arrangement in the naturally occurring nickel-chelatase CfbA. FEBS Open Bio 2024. [PMID: 38923868 DOI: 10.1002/2211-5463.13849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Metal-tetrapyrrole cofactors are involved in multiple cellular functions, and chelatases are key enzymes for the biosynthesis of these cofactors. CfbA is an ancestral, homodimeric-type class II chelatase which is able to use not only Ni2+ as a physiological metal substrate, but also Co2+ as a nonphysiological substrate with higher activity than for Ni2+. The Ni/Co-chelatase function found in CfbA is also observed in SirB, a descendant, monomeric-type class II chelatase. This is despite the distinct active site structure of CfbA and SirB; specifically, CfbA shows a unique four His residue arrangement, unlike other monomeric class II chelatases such as SirB. Herein, we studied the Ni-chelatase activity of SirB variants R134H, L200H, and R134H/L200H, the latter of which mimics the His alignment of CfbA. Our results showed that the SirB R134H variant exhibited the highest Ni-chelatase activity among the SirB enzymes, which in turn suggests that the position of His134 could be more important for the Ni-chelatase activity than that of His200. The SirB R134H/L200H variant showed lower activity than R134H, despite the four His residues found in SirB R134H/L200H. CD spectroscopy showed secondary structure denaturation and a slight difficulty in Ni-binding of SirB R134H/L200H, which may be related to its lower activity. Finally, a docking simulation suggested that the His134 of the SirB R134H variant could function as a base catalyst for the Ni-chelatase reaction in a class II chelatase architecture.
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Affiliation(s)
- Yuuma Oyamada
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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2
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Li X, Jia T, Zhu H, Cai L, Lu Y, Wang J, Tao H, Li P. Bioelectricity facilitates carbon dioxide fixation by Alcaligenes faecalis ZS-1 in a biocathodic microbial fuel cell (MFC). BIORESOURCE TECHNOLOGY 2024; 399:130555. [PMID: 38460556 DOI: 10.1016/j.biortech.2024.130555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
The CO2 fixation mechanism by Alcaligenes faecalis ZS-1 in a biocathode microbial fuel cell (MFC) was investigated. The closed-circuit MFC (CM) exhibited a significantly higher CO2 fixation rate (10.7%) compared to the open-circuit MFC (OC) (2.0%), indicating that bioelectricity enhances CO2 capture efficiency. During the inward extracellular electron transfer (EET) process, riboflavin concentration increased in the supernatant while cytochrome levels decreased. Genome sequencing revealed diverse metabolic pathways for CO2 fixation in strain ZS-1, with potential dominance of rTCA and C4 pathways under electrotrophic conditions as evidenced by significant upregulation of the ppc gene. Differential metabolite analysis using LC-MS demonstrated that CM promoted upregulation of various lipid metabolites. These findings collectively highlight that ZS-1 simultaneously generated electricity and fixed CO2 and that the ppc associated with bioelectricity played a critical role in CO2 capture. In conclusion, bioelectricity resulted in a significant enhancement in the efficiency of CO2 fixation and lipid production.
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Affiliation(s)
- Xinyi Li
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Tianbo Jia
- School of Petrochemical Engineering and Environment, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Haiguang Zhu
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Luhan Cai
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Yubiao Lu
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jianxin Wang
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Hengcong Tao
- School of Petrochemical Engineering and Environment, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Peng Li
- School of Ocean Science and Technology, Zhejiang Ocean University, Zhoushan 316022, PR China.
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3
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Gandhi AK, Sun ZYJ, Huang YH, Kim WM, Yang C, Petsko GA, Beauchemin N, Blumberg RS. Structural analysis of human CEACAM1 oligomerization. Commun Biol 2022; 5:1042. [PMID: 36180783 PMCID: PMC9525683 DOI: 10.1038/s42003-022-03996-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
The human (h) CEACAM1 GFCC’ face serves as a binding site for homophilic and heterophilic interactions with various microbial and host ligands. hCEACAM1 has also been observed to form oligomers and micro-clusters on the cell surface which are thought to regulate hCEACAM1-mediated signaling. However, the structural basis for hCEACAM1 higher-order oligomerization is currently unknown. To understand this, we report a hCEACAM1 IgV oligomer crystal structure which shows how GFCC’ face-mediated homodimerization enables highly flexible ABED face interactions to arise. Structural modeling and nuclear magnetic resonance (NMR) studies predict that such oligomerization is not impeded by the presence of carbohydrate side-chain modifications. In addition, using UV spectroscopy and NMR studies, we show that oligomerization is further facilitated by the presence of a conserved metal ion (Zn++ or Ni++) binding site on the G strand of the FG loop. Together these studies provide biophysical insights on how GFCC’ and ABED face interactions together with metal ion binding may facilitate hCEACAM1 oligomerization beyond dimerization. The crystal structure of human CEACAM1 IgV oligomer and structural analyses provide insight into higher-order oligomerization involving GFCC’ face-mediated homodimerization, flexible ABED interfaces, and dynamic metal-ion bridging.
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Affiliation(s)
- Amit K Gandhi
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - Zhen-Yu J Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Yu-Hwa Huang
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Walter M Kim
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Chao Yang
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Gregory A Petsko
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nicole Beauchemin
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Richard S Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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4
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Sorokin DY, Merkel AY, Messina E, Tugui C, Pabst M, Golyshin PN, Yakimov MM. Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes. THE ISME JOURNAL 2022; 16:1534-1546. [PMID: 35132120 PMCID: PMC9123189 DOI: 10.1038/s41396-022-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/03/2022] [Accepted: 01/27/2022] [Indexed: 05/24/2023]
Abstract
Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Enzo Messina
- IRBIM-CNR, Spianata S.Raineri 86, 98122, Messina, Italy
| | - Claudia Tugui
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Gwynedd, LL57 2UW, UK
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5
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Shah JS, Buckmeier BG, Griffith W, Olafson PU, Perez de Leon AA, Renthal R. Odorant-binding protein from the stable fly (Stomoxys calcitrans) has a high-histidine N-terminal extension that binds transition metals. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 141:103707. [PMID: 34979251 DOI: 10.1016/j.ibmb.2021.103707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
The role of odorant- and pheromone-binding proteins (OBPs) in olfactory function is not fully understood. We found an OBP sequence from the stable fly, Stomoxys calcitrans, ScalOBP60, that has a 25 amino acid N-terminal extension with a high content of histidine and acidic amino acids, suggesting a possible metal binding activity. A search of public databases revealed a large number of other fly OBPs with histidine-rich N-terminal extensions, as well as beetle, wasp and ant OBPs with histidine-rich C-terminal extensions. We recombinantly expressed ScalOBP60, as well as a truncated sequence which lacks the histidine-rich N-terminal region, tScalOBP60. Using fluorescence quenching and electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF), we detected two different types of metal-binding sites. Divalent copper, nickel and zinc bind to the N-terminal histidine-rich region, and divalent copper binds to an internal sequence position. Comparison of the ESI-QTOF spectra of ScalOBP60 and tScalOBP60 showed that the histidine-rich sequence is structurally disordered, but it becomes more ordered in the presence of divalent metal. When copper is bound to the internal site, binding of a hydrophobic ligand to ScalOBP60 is inhibited. The internal and N-terminal metal sites interact allosterically, possibly through a conformational equilibrium, suggesting a mechanism for metal regulation of ligand binding to ScalOBP60. Based on our studies of ScalOBP60, we propose several possible olfactory and non-olfactory functions for this OBP.
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Affiliation(s)
- Jaee Shailesh Shah
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | | | - Wendell Griffith
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Pia Untalan Olafson
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Lab, Kerrville, TX, 78028, USA
| | | | - Robert Renthal
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA; Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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6
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Cavazza C, Collin-Faure V, Pérard J, Diemer H, Cianférani S, Rabilloud T, Darrouzet E. Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis. J Proteomics 2022; 250:104389. [PMID: 34601154 DOI: 10.1016/j.jprot.2021.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O → CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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Affiliation(s)
- Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | | | - Julien Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Thierry Rabilloud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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7
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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] [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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8
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ElGamacy M, Hernandez Alvarez B. Expanding the versatility of natural and de novo designed coiled coils and helical bundles. Curr Opin Struct Biol 2021; 68:224-234. [PMID: 33964630 DOI: 10.1016/j.sbi.2021.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Natural helical bundles (HBs) constitute a ubiquitous class of protein folds built of two or more longitudinally arranged α-helices. They adopt topologies that include symmetric, highly regular assemblies all the way to asymmetric, loosely packed domains. The diverse functional spectrum of HBs ranges from structural scaffolds to complex and dynamic effectors as molecular motors, signaling and sensing molecules, enzymes, and molecular switches. Symmetric HBs, particularly coiled coils, offer simple model systems providing an ideal entry point for protein folding and design studies. Herein, we review recent progress unveiling new structural features and functional mechanisms in natural HBs and cover staggering advances in the de novo design of HBs, giving rise to exotic structures and the creation of novel functions.
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Affiliation(s)
- Mohammad ElGamacy
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen, 72076, Germany; Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller-Strasse 10, Tübingen, 72076, Germany; Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany.
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9
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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] [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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10
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Kang S, Song Y, Jin S, Shin J, Bae J, Kim DR, Lee JK, Kim SC, Cho S, Cho BK. Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide. Front Microbiol 2020; 11:402. [PMID: 32218779 PMCID: PMC7079680 DOI: 10.3389/fmicb.2020.00402] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood–Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.
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Affiliation(s)
- Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering, Hanyang University, Seoul, South Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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11
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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: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [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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Anderl A, Kolmar H, Fuchsbauer HL. The metal-binding properties of the long chaplin from Streptomyces mobaraensis: A bioinformatic and biochemical approach. J Inorg Biochem 2019; 202:110878. [PMID: 31698184 DOI: 10.1016/j.jinorgbio.2019.110878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Chaplins are amphiphilic proteins coating the surface of aerial hyphae under formation of amyloid-like rodlet layers in streptomycetes. The long chaplin from Streptomyces mobaraensis, Sm-Chp1, harbors extended histidine-rich stretches allowing protein attachment to metal affinity resins. A comprehensive BLASTP search revealed similarity with many putative metal-binding proteins but the deduced sequence motifs were not shared by histidine-rich domains of well-studied proteins. Biochemical analyses showed affinity of Sm-Chp1 for Ni2+, Cu2+ and Zn2+, a binding capacity of 7-8 metal ions, and dissociation constants in a double digit micromolar range. The occurrence of genes for membrane-bound metal transporters and several intra- and extracellular metalloenzymes in the genome of S. mobaraensis suggests that Sm-Chp1 may be a novel type of translocase shifting metals across the rodlet layer from the environment into the cell wall.
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Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany; Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany.
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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] [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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14
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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] [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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15
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Nickel-Induced Oligomerization of the Histidine-Rich Metallochaperone CooJ from Rhodospirillum Rubrum. INORGANICS 2019. [DOI: 10.3390/inorganics7070084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
[NiFe]-carbon monoxide dehydrogenase reversibly catalyzes the oxidation of CO to CO2. Its active site is a unique NiFe4S4 cluster, known as C-cluster. In Rhodospirillum rubrum, three nickel-dependent proteins, CooC, CooT and CooJ are required for Ni insertion into the active site. Among them, CooJ is a histidine-rich protein, containing two distinct and spatially separated Ni(II)-binding sites: a strictly conserved N-terminal site and a variable histidine tail at the C-terminus. Here, using biophysical techniques, we study the behavior of the protein upon Ni(II) addition. Using circular dichroism and chemical denaturation, we show that the binding of Ni(II) to the protein increases its stability. Moreover, high-order oligomers are formed through nickel–histidine tail interactions, both in vitro and in cellulo, via a dynamical and reversible process.
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