1
|
Ellenbogen JB, Borton MA, McGivern BB, Cronin DR, Hoyt DW, Freire-Zapata V, McCalley CK, Varner RK, Crill PM, Wehr RA, Chanton JP, Woodcroft BJ, Tfaily MM, Tyson GW, Rich VI, Wrighton KC. Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems 2024; 9:e0069823. [PMID: 38063415 PMCID: PMC10805028 DOI: 10.1128/msystems.00698-23] [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: 07/06/2023] [Accepted: 10/24/2023] [Indexed: 01/24/2024] Open
Abstract
While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.
Collapse
Affiliation(s)
- Jared B. Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Mikayla A. Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Bridget B. McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Dylan R. Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Carmody K. McCalley
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Ruth K. Varner
- Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, New Hampshire, USA
| | - Patrick M. Crill
- Department of Geological Sciences, Bolin Center for Climate Research, Stockholm University, Stockholm, Sweden
| | - Richard A. Wehr
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jeffrey P. Chanton
- Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, Florida, USA
| | - Ben J. Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Malak M. Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
2
|
Lynes MM, Jay ZJ, Kohtz AJ, Hatzenpichler R. Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring. THE ISME JOURNAL 2024; 18:wrae026. [PMID: 38452205 PMCID: PMC10945360 DOI: 10.1093/ismejo/wrae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70°C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.
Collapse
Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| |
Collapse
|
3
|
Kountz DJ, Balskus EP. A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551370. [PMID: 37577662 PMCID: PMC10418091 DOI: 10.1101/2023.07.31.551370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Analyses of microbial genomes have revealed unexpectedly wide distributions of enzymes from specialized metabolism, including methanogenesis, providing exciting opportunities for discovery. Here, we identify a family of gene clusters (the type 1 mlp gene clusters (MGCs)) that encodes homologs of the soluble coenzyme M methyltransferases (SCMTs) involved in methylotrophic methanogenesis and is widespread in bacteria and archaea. Type 1 MGCs are expressed and regulated in medically, environmentally, and industrially important organisms, making them likely to be physiologically relevant. Enzyme annotation, analysis of genomic context, and biochemical experiments suggests these gene clusters play a role in methyl-sulfur and/or methyl-selenide metabolism in numerous anoxic environments, including the human gut microbiome, potentially impacting sulfur and selenium cycling in diverse, anoxic environments.
Collapse
Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
4
|
Li Z, Ren L, Wang X, Chen M, Wang T, Dai R, Wang Z. Anaerobic hydrolysis of recalcitrant tetramethylammonium from semiconductor wastewater: Performance and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132239. [PMID: 37567140 DOI: 10.1016/j.jhazmat.2023.132239] [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: 05/23/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The treatment of tetramethylammonium hydroxide (TMAH)-bearing wastewater, generated in the electronic and semiconductor industries, raises significant concerns due to the neurotoxic, recalcitrant, and bio-inhibiting effects of TMAH. In this study, we proposed the use of an anaerobic hydrolysis bioreactor (AHBR) for TMAH removal, achieving a high removal efficiency of approximately 85%, which greatly surpassed the performance of widely-used advanced oxidation processes (AOPs). Density functional theory calculations indicated that the unexpectedly poor efficiency (5.8-8.0%) of selected AOPs can be attributed to the electrostatic repulsion between oxidants and the tightly bound electrons of TMAH. Metagenomic analyses of the AHBR revealed that Proteobacteria and Euryarchaeota played a dominant role in the transformation of TMAH through processes such as methyl transfer, methanogenesis, and acetyl-coenzyme A synthesis, utilizing methyl-tetrahydromethanopterin as a substrate. Moreover, several potential functional genes (e.g., mprF, basS, bcrB, sugE) related to TMAH resistance have been identified. Molecular docking studies between five selected proteins and tetramethylammonium further provided evidence supporting the roles of these potential functional genes. This study demonstrates the superiority of AHBR as a pretreatment technology compared to several widely-researched AOPs, paving the way for the proper design of treatment processes to abate TMAH in semiconductor wastewater.
Collapse
Affiliation(s)
- Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lehui Ren
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xueye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tianlin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| |
Collapse
|
5
|
Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
Collapse
Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
6
|
QM/MM study of the [4Fe-4S]-dependent (R)-2-hydroxyisocaproyl-CoA dehydratase: Dehydration via a redox pathway with an α-carbonyl radical intermediate. J Catal 2023. [DOI: 10.1016/j.jcat.2023.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
7
|
Li J, Kang PT, Jiang R, Lee JY, Soares JA, Krzycki JA, Chan MK. Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex. Commun Biol 2023; 6:54. [PMID: 36646841 PMCID: PMC9842639 DOI: 10.1038/s42003-022-04397-3] [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: 05/02/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.
Collapse
Affiliation(s)
- Jiaxin Li
- grid.10784.3a0000 0004 1937 0482School of Life Sciences, and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Patrick T. Kang
- grid.261103.70000 0004 0459 7529Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272 USA ,grid.261331.40000 0001 2285 7943Ohio State University Biochemistry Program, Columbus, OH 43210 USA
| | - Ruisheng Jiang
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Jodie Y. Lee
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,grid.422834.b0000 0004 0387 4571TechLab, Inc., Blacksburg, VA 24060 USA
| | - Jitesh A. Soares
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,grid.286879.a0000 0001 1090 0879Division of Scientific Advancement, American Chemical Society, Washington, DC 20036 USA
| | - Joseph A. Krzycki
- grid.261331.40000 0001 2285 7943Ohio State University Biochemistry Program, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Michael K. Chan
- grid.10784.3a0000 0004 1937 0482School of Life Sciences, and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China ,grid.261331.40000 0001 2285 7943Ohio State University Biochemistry Program, Columbus, OH 43210 USA
| |
Collapse
|
8
|
Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [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: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
Collapse
Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia,Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,*Correspondence: Matthew Lee,
| |
Collapse
|
9
|
Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein. Proc Natl Acad Sci U S A 2022; 119:e2203576119. [PMID: 35905315 PMCID: PMC9351452 DOI: 10.1073/pnas.2203576119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Electron transfers coupled to the hydrolysis of ATP allow various metalloenzymes to catalyze reductions at very negative reduction potentials. The double-cubane cluster protein (DCCP) catalyzes the reduction of small molecules, such as acetylene and hydrazine, with electrons provided by its cognate ATP-hydrolyzing reductase (DCCP-R). How ATP-driven electron transfer occurs is not known. To resolve the structural basis for ATP-driven electron transfer, we solved the structures of the DCCP:DCCP-R complex in three different states. The structures show that the DCCP-R homodimer is covalently bridged by a [4Fe4S] cluster that is aligned with the twofold axis of the DCCP homodimer, positioning the [4Fe4S] cluster to enable electron transfer to both double-cubane clusters in the DCCP dimer. DCCP and DCCP-R form stable complexes independent of oxidation state or nucleotides present, and electron transfer requires the hydrolysis of ATP. Electron transfer appears to be additionally driven by modulating the angle between the helices binding the [4Fe4S] cluster. We observed hydrogen bond networks running from the ATP binding site via the [4Fe4S] cluster in DCCP-R to the double-cubane cluster in DCCP, allowing the propagation of conformational changes. Remarkable similarities between the DCCP:DCCP-R complex and the nonhomologous nitrogenases suggest a convergent evolution of catalytic strategies to achieve ATP-driven electron transfers between iron-sulfur clusters.
Collapse
|
10
|
Kremp F, Müller V. Methanol and methyl group conversion in acetogenic bacteria: biochemistry, physiology and application. FEMS Microbiol Rev 2021; 45:5903270. [PMID: 32901799 DOI: 10.1093/femsre/fuaa040] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/29/2020] [Indexed: 12/24/2022] Open
Abstract
The production of bulk chemicals mostly depends on exhausting petroleum sources and leads to emission of greenhouse gases. Within the last decades the urgent need for alternative sources has increased and the development of bio-based processes received new attention. To avoid the competition between the use of sugars as food or fuel, other feedstocks with high availability and low cost are needed, which brought acetogenic bacteria into focus. This group of anaerobic organisms uses mixtures of CO2, CO and H2 for the production of mostly acetate and ethanol. Also methanol, a cheap and abundant bulk chemical produced from methane, is a suitable substrate for acetogenic bacteria. In methylotrophic acetogens the methyl group is transferred to the Wood-Ljungdahl pathway, a pathway to reduce CO2 to acetate via a series of C1-intermediates bound to tetrahydrofolic acid. Here we describe the biochemistry and bioenergetics of methanol conversion in the biotechnologically interesting group of anaerobic, acetogenic bacteria. Further, the bioenergetics of biochemical production from methanol is discussed.
Collapse
Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| |
Collapse
|
11
|
Kivenson V, Paul BG, Valentine DL. An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria. Front Microbiol 2021; 12:680620. [PMID: 34335502 PMCID: PMC8318568 DOI: 10.3389/fmicb.2021.680620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. Marine sediments in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary strategies. Genetic code expansion is a strategy that increases the structural and functional diversity of proteins in cells, by repurposing stop codons to encode non-canonical amino acids: pyrrolysine (Pyl) and selenocysteine (Sec). Here, we report both a study of the microbiome at a deep sea industrial waste dumpsite and an unanticipated discovery of codon reassignment in its most abundant member, with potential ramifications for interpreting microbial interactions with ocean-dumped wastes. The genomes of abundant Deltaproteobacteria from the sediments of a deep-ocean chemical waste dump site have undergone genetic code expansion. Pyl and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, representing an increased metabolic versatility. The inferred metabolism of these sulfate-reducing bacteria places them in competition with methylotrophic methanogens for TMA, a contention further supported by earlier isotope tracer studies and reanalysis of metatranscriptomic studies. A survey of genomic data further reveals a broad geographic distribution of a niche group of similarly specialized Deltaproteobacteria, including at sulfidic sites in the Atlantic Ocean, Gulf of Mexico, Guaymas Basin, and North Sea, as well as in terrestrial and estuarine environments. These findings reveal an important biogeochemical role for specialized Deltaproteobacteria at the interface of the carbon, nitrogen, selenium, and sulfur cycles, with their niche adaptation and ecological success potentially augmented by genetic code expansion.
Collapse
Affiliation(s)
- Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Blair G. Paul
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| |
Collapse
|
12
|
Neumann F, Dobbek H. ATP Binding and a Second Reduction Enables a Conformationally Gated Uphill Electron Transfer. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felix Neumann
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| |
Collapse
|
13
|
Huening KA, Jiang R, Krzycki JA. Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri. FEMS Microbiol Lett 2020; 367:5896951. [PMID: 32840570 DOI: 10.1093/femsle/fnaa128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/27/2020] [Indexed: 12/30/2022] Open
Abstract
In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.
Collapse
Affiliation(s)
- Katherine A Huening
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ruisheng Jiang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph A Krzycki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
14
|
Channeling C1 Metabolism toward S-Adenosylmethionine-Dependent Conversion of Estrogens to Androgens in Estrogen-Degrading Bacteria. mBio 2020; 11:mBio.01259-20. [PMID: 32843544 PMCID: PMC7448270 DOI: 10.1128/mbio.01259-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Estrogens comprise a group of related hormones occurring in predominantly female vertebrates, with endocrine disrupting and carcinogenic potential. Microbial biodegradation of estrogens is essential for their elimination from surface waters and wastewater. Aerobic bacteria employ oxygenases for the initial cleavage of the aromatic ring A. In contrast, anaerobic degradation of estrogens is initiated by methyl transfer-dependent conversion into androgens involving a putative cobalamin-dependent methyltransferase system. The methyl donor for this unprecedented reaction and its stoichiometric regeneration have remained unknown. With the biomass obtained from large-scale fermentation of an estrogen-degrading denitrifying bacterium, we identified S-adenosyl-methionine (SAM) as the methyl donor for the cobalamin-mediated methyl transfer to estrogens. To continuously supply C1 units to initiate estrogen degradation, genes for SAM regeneration from estradiol-derived catabolites are highly upregulated. Data presented here shed light into biochemical processes involved in the globally important microbial degradation of estrogens. Bacterial degradation of endocrine disrupting and carcinogenic estrogens is essential for their elimination from the environment. Recent studies of the denitrifying, estrogen-degrading Denitratisoma strain DHT3 revealed the conversion of estrogens to androgens by a putative cobalamin-dependent methyltransferase encoded by the emtABCD genes. The methyl donor and its continuous regeneration to initiate estradiol catabolism have remained unknown. Here, large-scale cultivation of the denitrifying bacterium Denitratisoma oestradiolicum with estrogen provided the biomass required for quantitative biochemical analyses. Soluble fractions of extracts from estradiol-grown cells catalyzed the S-adenosyl-l-methionine (SAM)- and Ti(III)-citrate-dependent conversion of 17β-estradiol/estrone to the respective androgens at 0.15 nmol min−1 mg−1. Kinetic studies of 17β-estradiol methylation and reverse 1-dehydrotestosterone demethylation reactions indicated that the exergonic methyl transfer from SAM to the putative cobalamin drives the endergonic methyl transfer from the methylcobalamin intermediate to the phenolic ring A. Based on a high-quality circular genome from D. oestradiolicum, proteogenomic analyses identified a 17β-estradiol-induced gene cluster comprising emtABCD genes together with genes involved in SAM regeneration via l-serine and l-methionine. Consistent with this finding, l-methionine/ATP or l-serine/ATP/tetrahydrofolate/l-homocysteine substituted for SAM as methyl donors, further confirmed by the incorporation of the 13C-methyl-group from 13C-l-methonine into methyl(III)cobalamine and the estrone methylation product androsta-1,4-diene-3-one. This work demonstrates that during bacterial estrogen catabolism, the C1 pool is channeled toward the initiating methyl transfer to ring A. The effective cellular SAM regeneration system may serve as a model for whole-cell SAM-dependent methylation reactions of biotechnological interest.
Collapse
|
15
|
Kountz DJ, Behrman EJ, Zhang L, Krzycki JA. MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase. J Biol Chem 2020; 295:11971-11981. [PMID: 32571881 PMCID: PMC7443480 DOI: 10.1074/jbc.ra120.012934] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/18/2020] [Indexed: 12/22/2022] Open
Abstract
The trimethylamine methyltransferase MttB is the first described member of a superfamily comprising thousands of microbial proteins. Most members of the MttB superfamily are encoded by genes that lack the codon for pyrrolysine characteristic of trimethylamine methyltransferases, raising questions about the activities of these proteins. The superfamily member MtcB is found in the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that can grow by demethylation of l-carnitine. Here, we demonstrate that MtcB catalyzes l-carnitine demethylation. When growing on l-carnitine, E. limosum excreted the unusual biological product norcarnitine as well as acetate, butyrate, and caproate. Cellular extracts of E. limosum grown on l-carnitine, but not lactate, methylated cob-(I)alamin or tetrahydrofolate using l-carnitine as methyl donor. MtcB, along with the corrinoid protein MtqC and the methylcorrinoid:tetrahydrofolate methyltransferase MtqA, were much more abundant in E. limosum cells grown on l-carnitine than on lactate. Recombinant MtcB methylates either cob(I)alamin or Co(I)-MtqC in the presence of l-carnitine and, to a much lesser extent, γ-butyrobetaine. Other quaternary amines were not substrates. Recombinant MtcB, MtqC, and MtqA methylated tetrahydrofolate via l-carnitine, forming a key intermediate in the acetogenic Wood-Ljungdahl pathway. To our knowledge, MtcB methylation of cobalamin or Co(I)-MtqC represents the first described mechanism of biological l-carnitine demethylation. The conversion of l-carnitine and its derivative γ-butyrobetaine to trimethylamine by the gut microbiome has been linked to cardiovascular disease. The activities of MtcB and related proteins in E. limosum might demethylate proatherogenic quaternary amines and contribute to the perceived health benefits of this human gut symbiont.
Collapse
Affiliation(s)
- Duncan J Kountz
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Edward J Behrman
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Liwen Zhang
- Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility, Ohio State University, Columbus, Ohio, USA
| | - Joseph A Krzycki
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA; Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio, USA.
| |
Collapse
|
16
|
Kurth JM, Op den Camp HJM, Welte CU. Several ways one goal-methanogenesis from unconventional substrates. Appl Microbiol Biotechnol 2020; 104:6839-6854. [PMID: 32542472 PMCID: PMC7374477 DOI: 10.1007/s00253-020-10724-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022]
Abstract
Abstract Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H2 and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways. Key points • Newly discovered methanogenic substrates and pathways are reviewed for the first time. • The review provides an in-depth analysis of unusual methanogenesis pathways. • The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.
Collapse
Affiliation(s)
- Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. .,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
17
|
Kißling L, Greiser Y, Dürichen H, Studenik S. Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors. FEBS J 2020; 287:4971-4981. [PMID: 32160390 DOI: 10.1111/febs.15290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/31/2020] [Accepted: 03/10/2020] [Indexed: 12/01/2022]
Abstract
Corrinoid-dependent enzyme systems rely on the super-reduced state of the protein-bound corrinoid cofactor to be functional, for example, in methyl transfer reactions. Due to the low redox potential of the [CoII ]/[CoI ] couple, autoxidation of the corrinoid cofactor occurs and leads to the formation of the inactive [CoII ]-state. For the reactivation, which is an energy-demanding process, electrons have to be transferred from a physiological donor to the corrinoid cofactor by the help of a reductive activator protein. In this study, we identified reduced flavodoxin as electron donor for the ATP-dependent reduction of protein-bound corrinoid cofactors of bacterial O-demethylase enzyme systems. Reduced flavodoxin was generated enzymatically using pyruvate:ferredoxin/flavodoxin oxidoreductase rather than hydrogenase. Two of the four flavodoxins identified in Acetobacterium dehalogenans and Desulfitobacterium hafniense DCB-2 were functional in supplying electrons for corrinoid reduction. They exhibited a midpoint potential of about -400 mV (ESHE , pH 7.5) for the semiquinone/hydroquinone transition. Reduced flavodoxin could be replaced by reduced clostridial ferredoxin. It was shown that the low-potential electrons of reduced flavodoxin are first transferred to the iron-sulfur cluster of the reductive activator and finally to the protein-bound corrinoid cofactor. This study further highlights the importance of reduced flavodoxin, which allows maintaining a variety of enzymatic reaction cycles by delivering low-potential electrons.
Collapse
Affiliation(s)
- Lena Kißling
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Yvonne Greiser
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hendrike Dürichen
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Studenik
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
18
|
Jeoung JH, Martins BM, Dobbek H. Double-Cubane [8Fe9S] Clusters: A Novel Nitrogenase-Related Cofactor in Biology. Chembiochem 2020; 21:1710-1716. [PMID: 32187824 PMCID: PMC7317905 DOI: 10.1002/cbic.202000016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/14/2020] [Indexed: 12/20/2022]
Abstract
Three different types of electron-transferring metallo-ATPases are able to couple ATP hydrolysis to the reduction of low-potential metal sites, thereby energizing an electron. Besides the Fe-protein known from nitrogenase and homologous enzymes, two other kinds of ATPase with different scaffolds and cofactors are used to achieve a unidirectional, energetic, uphill electron transfer to either reduce inactive Co-corrinoid-containing proteins (RACE-type activators) or a second iron-sulfur cluster-containing enzyme of a unique radical enzymes family (archerases). We have found a new cofactor in the latter enzyme family, that is, a double-cubane cluster with two [4Fe4S] subclusters bridged by a sulfido ligand. An enzyme containing this cofactor catalyzes the ATP-dependent reduction of small molecules, including acetylene. Thus, enzymes containing the double-cubane cofactor are analogous in function and share some structural features with nitrogenases.
Collapse
Affiliation(s)
- Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| |
Collapse
|
19
|
Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation. Proc Natl Acad Sci U S A 2019; 117:1395-1403. [PMID: 31848239 DOI: 10.1073/pnas.1914380117] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroid estrogens modulate physiology and development of vertebrates. Conversion of C19 androgens into C18 estrogens is thought to be an irreversible reaction. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster, emtABCD, differentially transcribed under estrogen-fed conditions and predicted to encode a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; an emtA-disrupted DHT3 derivative could catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, suggested the occurrence of a cobalamin-dependent estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell extracts requires methylcobalamin and is inhibited by propyl iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-dependent estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.
Collapse
|
20
|
Creighbaum AJ, Ticak T, Shinde S, Wang X, Ferguson DJ. Examination of the Glycine Betaine-Dependent Methylotrophic Methanogenesis Pathway: Insights Into Anaerobic Quaternary Amine Methylotrophy. Front Microbiol 2019; 10:2572. [PMID: 31787957 PMCID: PMC6855144 DOI: 10.3389/fmicb.2019.02572] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/23/2019] [Indexed: 01/23/2023] Open
Abstract
Recent studies indicate that environmentally abundant quaternary amines (QAs) are a primary source for methanogenesis, yet the catabolic enzymes are unknown. We hypothesized that the methanogenic archaeon Methanolobus vulcani B1d metabolizes glycine betaine (GB) through a corrinoid-dependent GB:coenzyme M (CoM) methyl transfer pathway. The draft genome sequence of M. vulcani B1d revealed a gene encoding a predicted non-pyrrolysine MttB homolog (MV8460) with high sequence similarity to the GB methyltransferase encoded by Desulfitobacterium hafniense Y51. MV8460 catalyzes GB-dependent methylation of free cob(I)alamin indicating it is an authentic MtgB enzyme. Proteomic analysis revealed that MV8460 and a corrinoid binding protein (MV8465) were highly abundant when M. vulcani B1d was grown on GB relative to growth on trimethylamine. The abundance of a corrinoid reductive activation enzyme (MV10335) and a methylcorrinoid:CoM methyltransferase (MV10360) were significantly higher in GB-grown B1d lysates compared to other homologs. The GB:CoM pathway was fully reconstituted in vitro using recombinant MV8460, MV8465, MV10335, and MV10360. Demonstration of the complete GB:CoM pathway expands the knowledge of direct QA-dependent methylotrophy and establishes a model to identify additional ecologically relevant anaerobic quaternary amine pathways.
Collapse
Affiliation(s)
- Adam J Creighbaum
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Tomislav Ticak
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Shrameeta Shinde
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Xin Wang
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Donald J Ferguson
- Department of Microbiology, Miami University, Oxford, OH, United States.,Department of Biological Sciences, Miami University Regionals, Hamilton, OH, United States
| |
Collapse
|
21
|
Dürichen H, Diekert G, Studenik S. Redox potential changes during ATP-dependent corrinoid reduction determined by redox titrations with europium(II)-DTPA. Protein Sci 2019; 28:1902-1908. [PMID: 31359509 PMCID: PMC6739815 DOI: 10.1002/pro.3699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 01/26/2023]
Abstract
Corrinoids are essential cofactors of enzymes involved in the C1 metabolism of anaerobes. The active, super-reduced [CoI ] state of the corrinoid cofactor is highly sensitive to autoxidation. In O-demethylases, the oxidation to inactive [CoII ] is reversed by an ATP-dependent electron transfer catalyzed by the activating enzyme (AE). The redox potential changes of the corrinoid cofactor, which occur during this reaction, were studied by potentiometric titration coupled to UV/visible spectroscopy. By applying europium(II)-diethylenetriaminepentaacetic acid (DTPA) as a reductant, we were able to determine the midpoint potential of the [CoII ]/[CoI ] couple of the protein-bound corrinoid cofactor in the absence and presence of AE and/or ATP. The data revealed that the transfer of electrons from a physiological donor to the corrinoid as the electron-accepting site is achieved by increasing the potential of the corrinoid cofactor from -530 ± 15 mV to -250 ± 10 mV (ESHE , pH 7.5). The first 50 to 100 mV of the shift of the redox potential seem to be caused by the interaction of nucleotide-bound AE with the corrinoid protein or its cofactor. The remaining 150-200 mV had to be overcome by the chemical energy of ATP hydrolysis. The experiments revealed that Eu(II)-DTPA, which was already known as a powerful reducing agent, is a suitable electron donor for titration experiments of low-potential redox centers. Furthermore, the results of this study will contribute to the understanding of thermodynamically unfavorable electron transfer processes driven by the power of ATP hydrolysis.
Collapse
Affiliation(s)
- Hendrike Dürichen
- Institute of Microbiology, Department of Applied and Ecological Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Gabriele Diekert
- Institute of Microbiology, Department of Applied and Ecological Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Studenik
- Institute of Microbiology, Department of Applied and Ecological Microbiology, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
22
|
Picking JW, Behrman EJ, Zhang L, Krzycki JA. MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation. J Biol Chem 2019; 294:13697-13707. [PMID: 31341018 DOI: 10.1074/jbc.ra119.009886] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
The trimethylamine methyltransferase MttB is the founding member of a widely distributed superfamily of microbial proteins. Genes encoding most members of the MttB superfamily lack the codon for pyrrolysine that distinguishes previously characterized trimethylamine methyltransferases, leaving the function(s) of most of the enzymes in this superfamily unknown. Here, investigating the MttB family member MtpB from the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that excretes N-methyl proline during growth on proline betaine, we demonstrate that MtpB catalyzes anoxic demethylation of proline betaine. MtpB along with MtqC (a corrinoid protein) and MtqA (a methylcorrinoid:tetrahydrofolate methyltransferase) was much more abundant in E. limosum cells grown on proline betaine than on lactate. We observed that recombinant MtpB methylates Co(I)-MtqC in the presence of proline betaine and that other quaternary amines are much less preferred substrates. MtpB, MtqC, and MtqA catalyze tetrahydrofolate methylation with proline betaine, thereby forming a key intermediate in the Wood-Ljungdahl acetogenesis pathway. To our knowledge, MtpB methylation of Co(I)-MtqC for the subsequent methylation of tetrahydrofolate represents the first described anoxic mechanism of proline betaine demethylation. The activities of MtpB and associated proteins in acetogens or other anaerobes provide a possible mechanism for the production of N-methyl proline by the gut microbiome. MtpB's activity characterized here strengthens the hypothesis that much of the MttB superfamily comprises quaternary amine-dependent methyltransferases.
Collapse
Affiliation(s)
- Jonathan W Picking
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210
| | - Edward J Behrman
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Liwen Zhang
- Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility, Ohio State University, Columbus, Ohio 43210
| | - Joseph A Krzycki
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210 .,Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
23
|
Tavares NK, Zayas CL, Escalante-Semerena JC. The Methanosarcina mazei MM2060 Gene Encodes a Bifunctional Kinase/Decarboxylase Enzyme Involved in Cobamide Biosynthesis. Biochemistry 2018; 57:4478-4495. [PMID: 29950091 PMCID: PMC6143143 DOI: 10.1021/acs.biochem.8b00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cobamides (Cbas) are synthesized by many archaea, but some aspects of Cba biosynthesis in these microorganisms remain unclear. Here, we demonstrate that open reading frame MM2060 in the archaeum Methanosarcina mazei strain Gö1 encodes a bifunctional enzyme with l-threonine- O-3-phosphate (l-Thr-P) decarboxylase (EC 4.1.1.81) and l-Thr kinase activities (EC 2.7.1.177). In Salmonella enterica, where Cba biosynthesis has been extensively studied, the activities mentioned above are encoded by separate genes, namely, cobD and pduX, respectively. The activities associated with the MM2060 protein ( MmCobD) were validated in vitro and in vivo. In vitro, MmCobD used ATP and l-Thr as substrates and generated ADP, l-Thr-P, and ( R)-1-aminopropan-2-ol O-phosphate as products. Notably, MmCobD has a 111-amino acid C-terminal extension of unknown function, which contains a putative metal-binding motif. This C-terminal domain alone did not display activity either in vivo or in vitro. Although the C-terminal MmCobD domain was not required for l-Thr-P decarboxylase or l-Thr kinase activities in vivo, its absence negatively affected both activities. In vitro results suggested that this domain may have a regulatory or substrate-gating role. When purified under anoxic conditions, MmCobD displayed Michaelis-Menten kinetics and had a 1000-fold higher affinity for ATP and a catalytic efficiency 1300-fold higher than that of MmCobD purified under oxic conditions. To the best of our knowledge, MmCobD is the first example of a new class of l-Thr-P decarboxylases that also have l-Thr kinase activity. An archaeal protein with l-Thr kinase activity had not been identified prior to this work.
Collapse
Affiliation(s)
- Norbert K. Tavares
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Carmen L. Zayas
- Department of Bacteriology, University of Wisconsin, Madison, 53706, USA
| | | |
Collapse
|
24
|
ATP-dependent substrate reduction at an [Fe 8S 9] double-cubane cluster. Proc Natl Acad Sci U S A 2018; 115:2994-2999. [PMID: 29507223 DOI: 10.1073/pnas.1720489115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemically demanding reductive conversions in biology, such as the reduction of dinitrogen to ammonia or the Birch-type reduction of aromatic compounds, depend on Fe/S-cluster-containing ATPases. These reductions are typically catalyzed by two-component systems, in which an Fe/S-cluster-containing ATPase energizes an electron to reduce a metal site on the acceptor protein that drives the reductive reaction. Here, we show a two-component system featuring a double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2(μ2-S)]. The double-cubane-cluster-containing enzyme is capable of reducing small molecules, such as acetylene (C2H2), azide (N3-), and hydrazine (N2H4). We thus present a class of metalloenzymes akin in fold, metal clusters, and reactivity to nitrogenases.
Collapse
|
25
|
Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet 2018; 14:e1007147. [PMID: 29324779 PMCID: PMC5764234 DOI: 10.1371/journal.pgen.1007147] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/10/2017] [Indexed: 11/18/2022] Open
Abstract
For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes. For a few bacteria, it is well known how they can make all 20 of the standard amino acids (the building blocks of proteins). For many other bacteria, their genome sequence implies that there are gaps in these biosynthetic pathways, so that the bacteria cannot make all of the amino acids and would need to take up some of them from their environment instead. But many bacteria can grow in minimal media (without any amino acids) despite these apparent gaps. We studied 10 bacteria with predicted gaps in amino acid biosynthesis that nevertheless grow in minimal media. Most of these gaps were spurious, but 11 of the gaps were genuine and could not be explained by current knowledge. Using high-throughput genetics, we systematically identified genes that were required for growth in minimal media and identified the biosynthetic genes that fill 9 of the 11 gaps. We hope that this approach can be applied to many more bacteria and will eventually allow us to accurately predict the nutritional requirements of a bacterium from its genome sequence.
Collapse
Affiliation(s)
- Morgan N. Price
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Jennifer V. Kuehl
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ryan A. Melnyk
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
| | - Adam P. Arkin
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
| |
Collapse
|
26
|
Goetzl S, Teutloff C, Werther T, Hennig SE, Jeoung JH, Bittl R, Dobbek H. Protein Dynamics in the Reductive Activation of a B12-Containing Enzyme. Biochemistry 2017; 56:5496-5502. [DOI: 10.1021/acs.biochem.7b00477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Goetzl
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Werther
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra E. Hennig
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robert Bittl
- Fachbereich
Physik, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
27
|
Abstract
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“Candidatus Parcubacteria” and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes. Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.
Collapse
|
28
|
Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation. Appl Environ Microbiol 2015; 81:3205-17. [PMID: 25724962 DOI: 10.1128/aem.00217-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative "cap helix" region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.
Collapse
|
29
|
Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species. J Bacteriol 2015; 197:1515-24. [PMID: 25691524 DOI: 10.1128/jb.02605-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Methanosarcina acetivorans uses a variety of methylated sulfur compounds as carbon and energy sources. Previous studies implicated the mtsD, mtsF, and mtsH genes in catabolism of dimethylsulfide, but the genes required for use of other methylsulfides have yet to be established. Here, we show that a four-gene locus, designated mtpCAP-msrH, is specifically required for growth on methylmercaptopropionate (MMPA). The mtpC, mtpA, and mtpP genes encode a putative corrinoid protein, a coenzyme M (CoM) methyltransferase, and a major facilitator superfamily (MFS) transporter, respectively, while msrH encodes a putative transcriptional regulator. Mutants lacking mtpC or mtpA display a severe growth defect in MMPA medium but are unimpaired during growth on other substrates. The mtpCAP genes comprise a transcriptional unit that is highly and specifically upregulated during growth on MMPA, whereas msrH is monocistronic and constitutively expressed. Mutants lacking msrH fail to transcribe mtpCAP and grow poorly in MMPA medium, consistent with the assignment of its product as a transcriptional activator. The mtpCAP-msrH locus is conserved in numerous marine methanogens, including eight Methanosarcina species that we showed are capable of growth on MMPA. Mutants lacking the mtsD, mtsF, and mtsH genes display a 30% reduction in growth yield when grown on MMPA, suggesting that these genes play an auxiliary role in MMPA catabolism. A quadruple ΔmtpCAP ΔmtsD ΔmtsF ΔmtsH mutant strain was incapable of growth on MMPA. Reanalysis of mtsD, mtsF, and mtsH mutants suggests that the preferred substrate for MtsD is dimethylsulfide, while the preferred substrate for MtsF is methanethiol. IMPORTANCE Methylated sulfur compounds play pivotal roles in the global sulfur and carbon cycles and contribute to global temperature homeostasis. Although the degradation of these molecules by aerobic bacteria has been well studied, relatively little is known regarding their fate in anaerobic ecosystems. In this study, we identify the genetic basis for metabolism of methylmercaptopropionate, dimethylsulfide, and methanethiol by strictly anaerobic methanogens of the genus Methanosarcina. These data will aid the development of predictive sulfur cycle models and enable molecular ecological approaches for the study of methylated sulfur metabolism in anaerobic ecosystems.
Collapse
|
30
|
Mingo FS, Studenik S, Diekert G. Conversion of phenyl methyl ethers byDesulfitobacteriumspp. and screening for the genes involved. FEMS Microbiol Ecol 2014; 90:783-90. [DOI: 10.1111/1574-6941.12433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/09/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Felix S. Mingo
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
| | - Sandra Studenik
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
| |
Collapse
|
31
|
Sperfeld M, Diekert G, Studenik S. Kinetic regulation of a corrinoid-reducing metallo-ATPase by its substrates. Mol Microbiol 2014; 92:598-608. [PMID: 24646146 DOI: 10.1111/mmi.12582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2014] [Indexed: 02/06/2023]
Abstract
Corrinoid cofactors play a crucial role as methyl group carriers in the C1 metabolism of anaerobes, e.g. in the cleavage of phenyl methyl ethers by O-demethylases. For the methylation, the protein-bound corrinoid has to be in the super-reduced [Co(I) ]-state, which is highly sensitive to autoxidation. The reduction of inadvertently oxidized corrinoids ([Co(II) ]-state) is catalysed in an ATP-dependent reaction by RACE proteins, the reductive activators of corrinoid-dependent enzymes. In this study, a reductive activator of O-demethylase corrinoid proteins was characterized with respect to its ATPase and corrinoid reduction activity. The reduction of the corrinoid cofactor was dependent on the presence of potassium or ammonium ions. In the absence of the corrinoid protein, a basal slow ATP hydrolysis was observed which was obviously not coupled to corrinoid reduction. ATP hydrolysis was significantly stimulated by the corrinoid protein in the [Co(II) ]-state of the corrinoid cofactor. The stoichiometry of ATP hydrolysed per mol corrinoid reduced was near 1:1. Site-directed mutagenesis was applied to study the impact of a highly conserved region possibly involved in nucleotide binding of RACE proteins, indicating that an aspartate and a glycine residue may play an essential role for the function of the enzyme.
Collapse
Affiliation(s)
- Martin Sperfeld
- Institut für Mikrobiologie, Friedrich-Schiller-Universität Jena, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, Philosophenweg 12, 07743, Jena, Germany
| | | | | |
Collapse
|
32
|
Nguyen HD, Studenik S, Diekert G. Corrinoid activation by a RACE protein: studies on the interaction of the proteins involved. FEMS Microbiol Lett 2013; 345:31-8. [DOI: 10.1111/1574-6968.12178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/17/2013] [Accepted: 05/13/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hai Dang Nguyen
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
| | - Sandra Studenik
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
| | - Gabriele Diekert
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
| |
Collapse
|
33
|
Roselli S, Nadalig T, Vuilleumier S, Bringel F. The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study. PLoS One 2013; 8:e56598. [PMID: 23593113 PMCID: PMC3621897 DOI: 10.1371/journal.pone.0056598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/11/2013] [Indexed: 12/24/2022] Open
Abstract
Chloromethane (CH3Cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. The only known pathway for bacterial chloromethane utilization (cmu) was characterized in Methylobacterium extorquens CM4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. Previous work demonstrated that tetrahydrofolate and vitamin B12 are essential cofactors of cmuA- and cmuB-encoded methyltransferases of chloromethane dehalogenase, and that the pathway for chloromethane utilization is distinct from that for methanol. This work reports genomic and proteomic data demonstrating that cognate cmu genes are located on the 380 kb pCMU01 plasmid, which drives the previously defined pathway for tetrahydrofolate-mediated chloromethane dehalogenation. Comparison of complete genome sequences of strain CM4 and that of four other M. extorquens strains unable to grow with chloromethane showed that plasmid pCMU01 harbors unique genes without homologs in the compared genomes (bluB2, btuB, cobA, cbiD), as well as 13 duplicated genes with homologs of chromosome-borne genes involved in vitamin B12-associated biosynthesis and transport, or in tetrahydrofolate-dependent metabolism (folC2). In addition, the presence of both chromosomal and plasmid-borne genes for corrinoid salvaging pathways may ensure corrinoid coenzyme supply in challenging environments. Proteomes of M. extorquens CM4 grown with one-carbon substrates chloromethane and methanol were compared. Of the 49 proteins with differential abundance identified, only five (CmuA, CmuB, PurU, CobH2 and a PaaE-like uncharacterized putative oxidoreductase) are encoded by the pCMU01 plasmid. The mainly chromosome-encoded response to chloromethane involves gene clusters associated with oxidative stress, production of reducing equivalents (PntAA, Nuo complex), conversion of tetrahydrofolate-bound one-carbon units, and central metabolism. The mosaic organization of plasmid pCMU01 and the clustering of genes coding for dehalogenase enzymes and for biosynthesis of associated cofactors suggests a history of gene acquisition related to chloromethane utilization.
Collapse
Affiliation(s)
- Sandro Roselli
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Thierry Nadalig
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Stéphane Vuilleumier
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Françoise Bringel
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
- * E-mail:
| |
Collapse
|
34
|
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J 2013; 8:1070-9. [PMID: 23420771 DOI: 10.1002/biot.201200266] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/15/2013] [Accepted: 02/13/2013] [Indexed: 11/11/2022]
Abstract
Methanosarcina barkeri is an Archaeon that produces methane anaerobically as the primary byproduct of its metabolism. M. barkeri can utilize several substrates for ATP and biomass production including methanol, acetate, methyl amines, and a combination of hydrogen and carbon dioxide. In 2006, a metabolic reconstruction of M. barkeri, iAF692, was generated based on a draft genome annotation. The iAF692 reconstruction enabled the first genome-Scale simulations for Archaea. Since the publication of the first metabolic reconstruction of M. barkeri, additional genomic, biochemical, and phenotypic data have clarified several metabolic pathways. We have used this newly available data to improve the M. barkeri metabolic reconstruction. Modeling simulations using the updated model, iMG746, have led to increased accuracy in predicting gene knockout phenotypes and simulations of batch growth behavior. We used the model to examine knockout lethality data and make predictions about metabolic regulation under different growth conditions. Thus, the updated metabolic reconstruction of M. barkeri metabolism is a useful tool for predicting cellular behavior, studying the methanogenic lifestyle, guiding experimental studies, and making predictions relevant to metabolic engineering applications.
Collapse
Affiliation(s)
- Matthew C Gonnerman
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | | |
Collapse
|
35
|
Chen Z, Yu H, Li L, Hu S, Dong X. The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:633-641. [PMID: 23760934 DOI: 10.1111/j.1758-2229.2012.00389.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 06/30/2012] [Accepted: 08/23/2012] [Indexed: 06/02/2023]
Abstract
We analysed the cold-responsive gene repertoire for a psychrophilic methanogen, Methanolobus psychrophilus R15 through genomic and RNA-seq assayed transcriptomic comparisons for cultures at 18°C (optimal temperature) versus 4°C. The differences found by RNA-seq analysis were verified using quantitative real time-PCR assay. The results showed that as in the Antarctic methanogen, Methanococcoides burtonii, genes for methanogenesis, biosynthesis and protein synthesis were all downregulated by the cold in R15. However, the RNA polymerase complex was upregulated at cold, as well as a gene cluster for a putative exosome complex, suggesting that exosome-mediated RNA decay may be cold-accelerated. Unexpectedly, the chaperonin genes for both thermosome and GroES/EL were all upregulated at 4°C. Strain R15 possessed eight protein families for oxygen detoxification, including both anaerobe-specific superoxide reductase (SOR) and the aerobe-typical superoxide dismutase (SOD)-catalase oxidant-removing system, implying the higher oxidative tolerance. Compared with a mesophilic methanogen, R15 survived in higher paraquat, a redox-cycling drug. Moreover, 71 one-component systems and 50 two-component systems for signal transduction ranked strain R15, together with M. burtonii, as being highly adaptive among archaea. Most of them exhibited cold-enhanced expression, indicating their involvement in cold adaptation. This study has added new perspectives on the cold adaptation of methanogenic archaea.
Collapse
Affiliation(s)
- Zijuan Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing, 100101, China
| | | | | | | | | |
Collapse
|
36
|
Meister W, Hennig SE, Jeoung JH, Lendzian F, Dobbek H, Hildebrandt P. Complex Formation with the Activator RACo Affects the Corrinoid Structure of CoFeSP. Biochemistry 2012; 51:7040-2. [DOI: 10.1021/bi300795n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wiebke Meister
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Sandra E. Hennig
- Humboldt-Universität zu Berlin, Institut für Biologie, Strukturbiologie/Biochemie,
Philippstraße 13, D-10115 Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institut für Biologie, Strukturbiologie/Biochemie,
Philippstraße 13, D-10115 Berlin, Germany
| | - Friedhelm Lendzian
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institut für Biologie, Strukturbiologie/Biochemie,
Philippstraße 13, D-10115 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
37
|
Knauer SH, Buckel W, Dobbek H. On the ATP-dependent activation of the radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase. Biochemistry 2012; 51:6609-22. [PMID: 22827463 DOI: 10.1021/bi300571z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the β,α-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the nonacidic β-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, and has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP, and nucleotide-free states of the reduced activator have been solved at 1.6-3.0 Å resolution, allowing us to define the position of Mg(2+) and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.
Collapse
Affiliation(s)
- Stefan H Knauer
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | | | | |
Collapse
|
38
|
Abstract
Besides acetogenic bacteria, only Desulfitobacterium has been described to utilize and cleave phenyl methyl ethers under anoxic conditions; however, no ether-cleaving O-demethylases from the latter organisms have been identified and investigated so far. In this study, genes of an operon encoding O-demethylase components of Desulfitobacterium hafniense strain DCB-2 were cloned and heterologously expressed in Escherichia coli. Methyltransferases I and II were characterized. Methyltransferase I mediated the ether cleavage and the transfer of the methyl group to the superreduced corrinoid of a corrinoid protein. Desulfitobacterium methyltransferase I had 66% identity (80% similarity) to that of the vanillate-demethylating methyltransferase I (OdmB) of Acetobacterium dehalogenans. The substrate spectrum was also similar to that of the latter enzyme; however, Desulfitobacterium methyltransferase I showed a higher level of activity for guaiacol and used methyl chloride as a substrate. Methyltransferase II catalyzed the transfer of the methyl group from the methylated corrinoid protein to tetrahydrofolate. It also showed a high identity (∼70%) to methyltransferases II of A. dehalogenans. The corrinoid protein was produced in E. coli as cofactor-free apoprotein that could be reconstituted with hydroxocobalamin or methylcobalamin to function in the methyltransferase I and II assays. Six COG3894 proteins, which were assumed to function as activating enzymes mediating the reduction of the corrinoid protein after an inadvertent oxidation of the corrinoid cofactor, were studied with respect to their abilities to reduce the recombinant reconstituted corrinoid protein. Of these six proteins, only one was found to catalyze the reduction of the corrinoid protein.
Collapse
|
39
|
Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein. Proc Natl Acad Sci U S A 2012; 109:5235-40. [PMID: 22431597 DOI: 10.1073/pnas.1117126109] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Movement, cell division, protein biosynthesis, electron transfer against an electrochemical gradient, and many more processes depend on energy conversions coupled to the hydrolysis of ATP. The reduction of metal sites with low reduction potentials (E(0') < -500 mV) is possible by connecting an energetical uphill electron transfer with the hydrolysis of ATP. The corrinoid-iron/sulfur protein (CoFeSP) operates within the reductive acetyl-CoA pathway by transferring a methyl group from methyltetrahydrofolate bound to a methyltransferase to the [Ni-Ni-Fe(4)S(4)] cluster of acetyl-CoA synthase. Methylation of CoFeSP only occurs in the low-potential Co(I) state, which can be sporadically oxidized to the inactive Co(II) state, making its reductive reactivation necessary. Here we show that an open-reading frame proximal to the structural genes of CoFeSP encodes an ATP-dependent reductive activator of CoFeSP. Our biochemical and structural analysis uncovers a unique type of reductive activator distinct from the electron-transferring ATPases found to reduce the MoFe-nitrogenase and 2-hydroxyacyl-CoA dehydratases. The CoFeSP activator contains an ASKHA domain (acetate and sugar kinases, Hsp70, and actin) harboring the ATP-binding site, which is also present in the activator of 2-hydroxyacyl-CoA dehydratases and a ferredoxin-like [2Fe-2S] cluster domain acting as electron donor. Complex formation between CoFeSP and its activator depends on the oxidation state of CoFeSP, which provides evidence for a unique strategy to achieve unidirectional electron transfer between two redox proteins.
Collapse
|
40
|
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. J Bacteriol 2011; 194:855-65. [PMID: 22139506 DOI: 10.1128/jb.06040-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanosarcina acetivorans strain C2A is a marine methanogenic archaeon notable for its substrate utilization, genetic tractability, and novel energy conservation mechanisms. To help probe the phenotypic implications of this organism's unique metabolism, we have constructed and manually curated a genome-scale metabolic model of M. acetivorans, iMB745, which accounts for 745 of the 4,540 predicted protein-coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in peripheral and central metabolism between methanogenic species. Using flux balance analysis, the model quantitatively predicts wild-type phenotypes and is 96% accurate in knockout lethality predictions compared to currently available experimental data. The model was used to probe the mechanisms and energetics of by-product formation and growth on carbon monoxide, as well as the nature of the reaction catalyzed by the soluble heterodisulfide reductase HdrABC in M. acetivorans. The genome-scale model provides quantitative and qualitative hypotheses that can be used to help iteratively guide additional experiments to further the state of knowledge about methanogenesis.
Collapse
|
41
|
Gaston MA, Jiang R, Krzycki JA. Functional context, biosynthesis, and genetic encoding of pyrrolysine. Curr Opin Microbiol 2011; 14:342-9. [PMID: 21550296 DOI: 10.1016/j.mib.2011.04.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/01/2011] [Accepted: 04/06/2011] [Indexed: 01/14/2023]
Abstract
In Methanosarcina spp., amber codons in methylamine methyltransferase genes are translated as the 22nd amino acid, pyrrolysine. The responsible pyl genes plus amber-codon containing methyltransferase genes have been identified in four archaeal and five bacterial genera, including one human pathogen. In Escherichia coli, the recombinant pylBCD gene products biosynthesize pyrrolysine from two molecules of lysine and the pylTS gene products direct pyrrolysine incorporation into protein. In the proposed biosynthetic pathway, PylB forms methylornithine from lysine, which is joined to another lysine by PylC, and oxidized to pyrrolysine by PylD. Structures of the catalytic domain of pyrrolysyl-tRNA synthetase (archaeal PylS or bacterial PylSc) revealed binding sites for tRNAPyl and pyrrolysine. PylS and tRNAPyl are now being exploited as an orthogonal pair in recombinant systems for introduction of useful modified amino acids into proteins.
Collapse
Affiliation(s)
- Marsha A Gaston
- Department of Microbiology, 484 West 12th Avenue, The Ohio State University, Columbus, OH 43210, United States
| | | | | |
Collapse
|
42
|
Williams TJ, Lauro FM, Ertan H, Burg DW, Poljak A, Raftery MJ, Cavicchioli R. Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics. Environ Microbiol 2011; 13:2186-203. [PMID: 21443741 DOI: 10.1111/j.1462-2920.2011.02467.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The growth of all microorganisms is limited to a specific temperature range. However, it has not previously been determined to what extent global protein profiles change in response to temperatures that incrementally span the complete growth temperature range of a microorganism. As a result it has remained unclear to what extent cellular processes (inferred from protein abundance profiles) are affected by growth temperature and which, in particular, constrain growth at upper and lower temperature limits. To evaluate this, 8-plex iTRAQ proteomics was performed on the Antarctic microorganism, Methanococcoides burtonii. Methanococcoides burtonii was chosen due to its importance as a model psychrophilic (cold-adapted) member of the Archaea, and the fact that proteomic methods, including subcellular fractionation procedures, have been well developed. Differential abundance patterns were obtained for cells grown at seven different growth temperatures (-2°C, 1°C, 4°C, 10°C, 16°C, 23°C, 28°C) and a principal component analysis (PCA) was performed to identify trends in protein abundances. The multiplex analysis enabled three largely distinct physiological states to be described: cold stress (-2°C), cold adaptation (1°C, 4°C, 10°C and 16°C), and heat stress (23°C and 28°C). A particular feature of the thermal extremes was the synthesis of heat- and cold-specific stress proteins, reflecting the important, yet distinct ways in which temperature-induced stress manifests in the cell. This is the first quantitative proteomic investigation to simultaneously assess the response of a microorganism to numerous growth temperatures, including the upper and lower growth temperatures limits, and has revealed a new level of understanding about cellular adaptive responses.
Collapse
Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | | | | | | | | | | | | |
Collapse
|
43
|
Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. ARCHAEA (VANCOUVER, B.C.) 2010; 2010:690737. [PMID: 21234345 PMCID: PMC3017947 DOI: 10.1155/2010/690737] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/09/2010] [Indexed: 11/17/2022]
Abstract
Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP(T) was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.
Collapse
Affiliation(s)
- Stefan Spring
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Feng Chen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Natalia Ivanova
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Yun-Juan Chang
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Thomas Brettin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Manfred Rohde
- HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Göker
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jim Bristow
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Davis Genome Center, University of California, Davis, CA 95817, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Hans-Peter Klenk
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| |
Collapse
|
44
|
Kung JW, Baumann S, von Bergen M, Müller M, Hagedoorn PL, Hagen WR, Boll M. Reversible biological Birch reduction at an extremely low redox potential. J Am Chem Soc 2010; 132:9850-6. [PMID: 20578740 DOI: 10.1021/ja103448u] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Birch reduction of aromatic rings to cyclohexadiene compounds is widely used in chemical synthesis and requires solvated electrons, the most potent reductants known in organic chemistry. Benzoyl-coenzyme A (CoA) reductases (BCR) are key enzymes in the anaerobic bacterial degradation of aromatic compounds and catalyze an analogous reaction under physiological conditions. Class I BCRs are FeS enzymes and couple the reductive dearomatization of benzoyl-CoA to cyclohexa-1,5-diene-1-carboxyl-CoA (dienoyl-CoA) to a stoichiometric ATP hydrolysis. Here, we report on a tungsten-containing class II BCR from Geobacter metallireducens that catalyzed the fully reversible, ATP-independent dearomatization of benzoyl-CoA to dienoyl-CoA. BCR additionally catalyzed the disproportionation of dienoyl-CoA to benzoyl-CoA/monoenoyl-CoA and the four- and six-electron reduction of benzoyl-CoA in the presence of a reduced low-potential bridged 2,2'-bipyridyl redox dye. Reversible redox titration experiments in the presence of this redox dye revealed a midpoint potential of E(0)' = -622 mV for the benzoyl-CoA/dienoyl-CoA couple, which is far below the values of other known reversible substrate/product redox couples in enzymology. This work demonstrates the efficiency of reversible metalloenzyme catalysis, which in chemical synthesis can only be achieved under essentially irreversible conditions.
Collapse
Affiliation(s)
- Johannes W Kung
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | | | | | | | | | | | | |
Collapse
|
45
|
Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20847933 PMCID: PMC2933860 DOI: 10.1155/2010/453642] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/13/2010] [Indexed: 01/21/2023]
Abstract
Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.
Collapse
|
46
|
Williams TJ, Burg DW, Ertan H, Raftery MJ, Poljak A, Guilhaus M, Cavicchioli R. Global Proteomic Analysis of the Insoluble, Soluble, and Supernatant Fractions of the Psychrophilic Archaeon Methanococcoides burtonii Part II: The Effect of Different Methylated Growth Substrates. J Proteome Res 2009; 9:653-63. [DOI: 10.1021/pr9005102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Dominic W. Burg
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Mark J. Raftery
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Anne Poljak
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Michael Guilhaus
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| |
Collapse
|
47
|
Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crécy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 2009; 10:470. [PMID: 19822009 PMCID: PMC2770081 DOI: 10.1186/1471-2164-10-470] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/12/2009] [Indexed: 11/11/2022] Open
Abstract
Background COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. Results Based on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Conclusion This work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s) might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression of COG0523 and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.
Collapse
Affiliation(s)
- Crysten E Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
| | | | | | | | | | | |
Collapse
|