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Lemaire ON, Belhamri M, Wagner T. Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front Microbiol 2023; 14:1179204. [PMID: 37250035 PMCID: PMC10210160 DOI: 10.3389/fmicb.2023.1179204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.
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Kalajahi ST, Mofradnia SR, Yazdian F, Rasekh B, Neshati J, Taghavi L, Pourmadadi M, Haghirosadat BF. Inhibition performances of graphene oxide/silver nanostructure for the microbial corrosion: molecular dynamic simulation study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:49884-49897. [PMID: 35220537 DOI: 10.1007/s11356-022-19247-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/11/2022] [Indexed: 05/06/2023]
Abstract
Steel is one of the mainly used materials in the oil and gas industry. However, it is susceptible to the marine corrosion, which 20% of the total marine corrosion is caused by microbiologically influenced corrosion (MIC). The economic and environmental impacts of corrosion are significant, and it is crucial to fight against corrosion in a proper sustainability context and environmental-friendly methods. In this study, the graphene oxide/silver nanostructure (GO-Ag) inhibitory effect on the corrosion of steel in the presence of sulfate reducing bacteria (SRB) was investigated, via weight loss (WL) and Tafel polarization measurements. Moreover, molecular dynamic (MD) simulations were performed to obtain a deep understanding of the corrosion inhibition effect of GO-Ag. GO-Ag showed a significant antibacterial effect at 80 ppm. Moreover, WL and Tafel polarization measurements illustrated a great inhibition efficiency, which reached up to 84% reduction of WL and 98% reduction of corrosion current density (Icorr) after 7 days of incubation with GO-Ag. Based on MD simulations, bonding energy reached to the larger value in the presence of GO-Ag, which indicated the ability of graphene oxide nanosheets to be adsorbed on the steel surface and prevent the access of corrosive agents to the steel surface. The radial distribution function (RDF) results implied distance between corrosive agent (water and SRB) and steel surface (Fe atoms), which indicated protection of the steel surface due to the effective adsorption of GO nanosheets through the active sites of the steel surface. The mean square displacement (MSD) result showed smaller displacement of the corrosive particles on the surface of steel, resulting that the GO-Ag molecules bonded with Fe molecules on the surface of steel.
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Affiliation(s)
- Sara Taghavi Kalajahi
- Department of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, North Kargar Street, 1439957131, Tehran, Iran.
| | - Behnam Rasekh
- Environment and Biotechnology Division, West Blvd. of Azadi Sport Complex, Research Institute of Petroleum Industry (RIPI), P.O. Box 14665-137, Tehran, Iran
| | - Jaber Neshati
- Energy and Environment Research Center, West Blvd. of Azadi Sport Complex, Research Institute of Petroleum Industry (RIPI), P.O. Box 14665-137, Tehran, Iran
| | - Lobat Taghavi
- Department of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehrab Pourmadadi
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Bibi Fatemeh Haghirosadat
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Jeoung J, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold. Angew Chem Int Ed Engl 2022; 61:e202117000. [PMID: 35133707 PMCID: PMC9311411 DOI: 10.1002/anie.202117000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 11/12/2022]
Abstract
Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-VCh . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-VCh catalyzes neither CO oxidation, nor CO2 reduction. The active site of CooS-VCh undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H2 O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-VCh , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.
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Affiliation(s)
- Jae‐Hun Jeoung
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Jochen Fesseler
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Lilith Domnik
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Friederike Klemke
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich PhysikArnimallee 1414195BerlinGermany
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich PhysikArnimallee 1414195BerlinGermany
| | - Holger Dobbek
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
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Jeoung J, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. Ein sich umstrukturierender [4Fe‐3S‐nO]‐Cluster in einem Kohlenmonoxid‐Dehydrogenase‐Gerüst. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jae‐Hun Jeoung
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Jochen Fesseler
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Lilith Domnik
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Friederike Klemke
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Holger Dobbek
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
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Fujishiro T, Ooi M, Takaoka K. Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion. FEBS J 2021; 288:6752-6768. [PMID: 34101368 DOI: 10.1111/febs.16062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 01/26/2023]
Abstract
Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Ooi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae. Int J Mol Sci 2021; 22:ijms22063175. [PMID: 33804694 PMCID: PMC8003979 DOI: 10.3390/ijms22063175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023] Open
Abstract
Iron-containing proteins, including iron-sulfur (Fe-S) proteins, are essential for numerous electron transfer and metabolic reactions. They are present in most subcellular compartments. In plastids, in addition to sustaining the linear and cyclic photosynthetic electron transfer chains, Fe-S proteins participate in carbon, nitrogen, and sulfur assimilation, tetrapyrrole and isoprenoid metabolism, and lipoic acid and thiamine synthesis. The synthesis of Fe-S clusters, their trafficking, and their insertion into chloroplastic proteins necessitate the so-called sulfur mobilization (SUF) protein machinery. In the first part, we describe the molecular mechanisms that allow Fe-S cluster synthesis and insertion into acceptor proteins by the SUF machinery and analyze the occurrence of the SUF components in microalgae, focusing in particular on the green alga Chlamydomonas reinhardtii. In the second part, we describe chloroplastic Fe-S protein-dependent pathways that are specific to Chlamydomonas or for which Chlamydomonas presents specificities compared to terrestrial plants, putting notable emphasis on the contribution of Fe-S proteins to chlorophyll synthesis in the dark and to the fermentative metabolism. The occurrence and evolutionary conservation of these enzymes and pathways have been analyzed in all supergroups of microalgae performing oxygenic photosynthesis.
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van Lis R, Couté Y, Brugière S, Tourasse NJ, Laurent B, Nitschke W, Vallon O, Atteia A. Phylogenetic and functional diversity of aldehyde-alcohol dehydrogenases in microalgae. PLANT MOLECULAR BIOLOGY 2021; 105:497-511. [PMID: 33415608 DOI: 10.1007/s11103-020-01105-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol dehydrogenases (ADHEs) are large metalloenzymes that typically perform the two-step reduction of acetyl-CoA into ethanol. These enzymes consist of an N-terminal acetylating aldehyde dehydrogenase domain (ALDH) and a C-terminal alcohol dehydrogenase (ADH) domain. ADHEs are present in various bacterial phyla as well as in some unicellular eukaryotes. Here we focus on ADHEs in microalgae, a diverse and polyphyletic group of plastid-bearing unicellular eukaryotes. Genome survey shows the uneven distribution of the ADHE gene among free-living algae, and the presence of two distinct genes in various species. We show that the non-photosynthetic Chlorophyte alga Polytomella sp. SAG 198.80 harbors two genes for ADHE-like enzymes with divergent C-terminal ADH domains. Immunoblots indicate that both ADHEs accumulate in Polytomella cells growing aerobically on acetate or ethanol. ADHE1 of ~ 105-kDa is found in particulate fractions, whereas ADHE2 of ~ 95-kDa is mostly soluble. The study of the recombinant enzymes revealed that ADHE1 has both the ALDH and ADH activities, while ADHE2 has only the ALDH activity. Phylogeny shows that the divergence occurred close to the root of the Polytomella genus within a clade formed by the majority of the Chlorophyte ADHE sequences, next to the cyanobacterial clade. The potential diversification of function in Polytomella spp. unveiled here likely took place after the loss of photosynthesis. Overall, our study provides a glimpse at the complex evolutionary history of the ADHE in microalgae which includes (i) acquisition via different gene donors, (ii) gene duplication and (iii) independent evolution of one of the two enzymatic domains.
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Affiliation(s)
- Robert van Lis
- Aix Marseille Université, CNRS, BIP UMR 7281, Marseille, France
- LBE, Univ Montpellier, INRAE, Narbonne, France
| | - Yohann Couté
- Univ Grenoble Alpes, CEA, INSERM, IRIG, Grenoble, BGE, France
| | - Sabine Brugière
- Univ Grenoble Alpes, CEA, INSERM, IRIG, Grenoble, BGE, France
| | - Nicolas J Tourasse
- UMR7141 CNRS-Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Benoist Laurent
- FR 550 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | | | - Olivier Vallon
- UMR7141 CNRS-Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Ariane Atteia
- Aix Marseille Université, CNRS, BIP UMR 7281, Marseille, France.
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France.
- MARBEC, Station Ifremer, Avenue Jean Monnet, Sète, France.
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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