1
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Fenibo EO, Selvarajan R, Wang H, Wang Y, Abia ALK. Untapped talents: insight into the ecological significance of methanotrophs and its prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166145. [PMID: 37579801 DOI: 10.1016/j.scitotenv.2023.166145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023]
Abstract
The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Huiqi Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Yue Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Environmental Research Foundation, Westville 3630, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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2
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Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
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Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
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3
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
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Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
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4
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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5
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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6
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Meneghello M, Uzel A, Broc M, Manuel RR, Magalon A, Léger C, Pereira IAC, Walburger A, Fourmond V. Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202212224. [PMID: 36465058 PMCID: PMC10107981 DOI: 10.1002/anie.202212224] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/28/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO2 . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.
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Affiliation(s)
- Marta Meneghello
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Alexandre Uzel
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Marianne Broc
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Rita R. Manuel
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA)Universidade Nova de LisboaOeirasPortugal
| | - Axel Magalon
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Christophe Léger
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Inês A. C. Pereira
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA)Universidade Nova de LisboaOeirasPortugal
| | - Anne Walburger
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Vincent Fourmond
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
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7
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Kammel M, Pinske C, Sawers RG. FocA and its central role in fine-tuning pH homeostasis of enterobacterial formate metabolism. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36197793 DOI: 10.1099/mic.0.001253] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In Escherichia coli, especially at low pH, formate is then disproportionated to CO2 and H2 by the cytoplasmically oriented, membrane-associated formate hydrogenlyase (FHL) complex. If electron acceptors are available, however, formate is oxidized by periplasmically oriented, respiratory formate dehydrogenases. Formate translocation across the cytoplasmic membrane is controlled by the formate channel, FocA, a member of the formate-nitrite transporter (FNT) family of homopentameric anion channels. This review highlights recent advances in our understanding of how FocA helps to maintain intracellular formate and pH homeostasis during fermentation. Efflux and influx of formate/formic acid are distinct processes performed by FocA and both are controlled through protein interaction between FocA's N-terminal domain with PflB. Formic acid efflux by FocA helps to maintain cytoplasmic pH balance during exponential-phase growth. Uptake of formate against the electrochemical gradient (inside negative) is energetically and mechanistically challenging for a fermenting bacterium unless coupled with proton/cation symport. Translocation of formate/formic acid into the cytoplasm necessitates an active FHL complex, whose synthesis also depends on formate. Thus, FocA, FHL and PflB function together to govern formate homeostasis. We explain how FocA achieves efflux of formic acid and propose mechanisms for pH-dependent uptake of formate both with and without proton symport. We propose that FocA displays both channel- and transporter-like behaviour. Whether this translocation behaviour is shared by other members of the FNT family is also discussed.
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Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Constanze Pinske
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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8
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Oliveira AR, Mota C, Klymanska K, Biaso F, Romão MJ, Guigliarelli B, Pereira IC. Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis. ACS Chem Biol 2022; 17:1901-1909. [PMID: 35766974 PMCID: PMC9774666 DOI: 10.1021/acschembio.2c00336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO2 reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S]1+ clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S]1+ centers range between -250 and -530 mV. Two distinct WV signals were detected, WDV and WFV, which differ in only the g2-value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of WVI/V was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate WV state of FdhAB.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Kateryna Klymanska
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Frédéric Biaso
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France
| | - Maria João Romão
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,
| | - Bruno Guigliarelli
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France,
| | - Inês Cardoso Pereira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal,
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