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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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2
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Prathiviraj R, Chellapandi P. Modeling a global regulatory network of Methanothermobacter thermautotrophicus strain ∆H. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s13721-020-0223-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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3
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Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes. Biosystems 2018; 167:33-46. [DOI: 10.1016/j.biosystems.2018.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
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4
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Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
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Alvarado A, Montañez-Hernández LE, Palacio-Molina SL, Oropeza-Navarro R, Luévanos-Escareño MP, Balagurusamy N. Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters. Front Microbiol 2014; 5:597. [PMID: 25429286 PMCID: PMC4228917 DOI: 10.3389/fmicb.2014.00597] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/22/2014] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.
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Affiliation(s)
- Alejandra Alvarado
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, MarburgGermany
| | - Lilia E. Montañez-Hernández
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | - Sandra L. Palacio-Molina
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | | | - Miriam P. Luévanos-Escareño
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
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Abstract
The ability of organisms to sense and respond to their environment is essential to their survival. This is no different for members of the third domain of life, the Archaea. Archaea are found in diverse and often extreme habitats. However, their ability to sense and respond to their environment at the level of gene expression has been understudied when compared to bacteria and eukaryotes. Over the last decade, the field has expanded, and a variety of unique and interesting regulatory schemes have been unraveled. In this review, the current state of knowledge of archaeal transcription regulation is explored.
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Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A. MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. J Biotechnol 2012; 167:156-65. [PMID: 23026555 DOI: 10.1016/j.jbiotec.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/21/2012] [Accepted: 09/21/2012] [Indexed: 12/01/2022]
Abstract
Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.
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Affiliation(s)
- Martha Zakrzewski
- Institute for Bioinformatics-IfB, Center for Biotechnology-CeBiTec, Bielefeld University, Bielefeld, Germany
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8
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More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:973848. [PMID: 21559116 PMCID: PMC3087415 DOI: 10.1155/2011/973848] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/07/2010] [Accepted: 02/18/2011] [Indexed: 12/19/2022]
Abstract
The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.
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9
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Correlation of methane production and functional gene transcriptional activity in a peat soil. Appl Environ Microbiol 2009; 75:6679-87. [PMID: 19749064 DOI: 10.1128/aem.01021-09] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase; mcrA) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37 degrees C, and real-time quantitative PCR was applied to quantify the abundances of mcrA genes and transcripts; corresponding transcriptional dynamics were calculated from mcrA transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies, mcrA transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25 degrees C, but changes in abundance and transcription of the mcrA gene showed no correlation with temperature. However, mcrA transcript/gene ratios correlated weakly (regression coefficient = 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold. mcrA transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures. mcrA transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.
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10
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Ferguson JT, Wenger CD, Metcalf WW, Kelleher NL. Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1743-50. [PMID: 19577935 PMCID: PMC2832193 DOI: 10.1016/j.jasms.2009.05.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 04/29/2009] [Accepted: 05/23/2009] [Indexed: 05/12/2023]
Abstract
Using both automated nanospray and online liquid chromatography mass spectrometry LC-MS strategies, 99 proteins have been newly identified by top-down tandem mass spectrometry (MS/MS) in Methanosarcina acetivorans, the methanogen with the largest known genome [5.7 mega base pairs (Mb)] for an Archaeon. Because top-down MS/MS was used, 15 proteins were detected with mispredicted start sites along with an additional five from small open reading frames (SORFs). Beyond characterization of these more common discrepancies in genome annotation, one SORF resulted from a rare start codon (AUA) as the initiation site for translation of this protein. Also, a methylation on a 30S ribosomal protein (MA1259) was localized to Pro59-Val69, contrasting sharply from its homologue in Escherichia coli (rp S12) known to harbor an unusual beta-thiomethylated aspartic acid residue.
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Affiliation(s)
- Jonathan T Ferguson
- Department of Chemistry at University of Illinois at Urbana-Champaign, Urbana, Illinois 6180, USA
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11
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Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol 2009; 9:199. [PMID: 19671178 PMCID: PMC2739858 DOI: 10.1186/1471-2148-9-199] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 08/11/2009] [Indexed: 11/29/2022] Open
Abstract
Background Methanogenesis is the sole means of energy production in methanogenic Archaea. H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens. At least one hmd paralog has been identified in nine of the eleven complete genome sequences of class I hydrogenotrophic methanogens. The products of these paralog genes have thus far eluded any detailed functional characterization. Results Here we present a thorough computational analysis of Hmd enzymes and paralogs that includes state of the art phylogenetic inference, structure prediction, and functional site prediction techniques. We determine that the Hmd enzymes are phylogenetically distinct from Hmd paralogs but share a common overall structure. We predict that the active site of the Hmd enzyme is conserved as a functional site in Hmd paralogs and use this observation to propose possible molecular functions of the paralog that are consistent with previous experimental evidence. We also identify an uncharacterized site in the N-terminal domains of both proteins that is predicted by our methods to directly impart function. Conclusion This study contributes to our understanding of the evolutionary history, structural conservation, and functional roles, of the Hmd enzymes and paralogs. The results of our phylogenetic and structural analysis constitute datasets that will aid in the future study of the Hmd protein family. Our functional site predictions generate several testable hypotheses that will guide further experimental characterization of the Hmd paralog. This work also represents a novel approach to protein function prediction in which multiple computational methods are integrated to achieve a detailed characterization of proteins that are not well understood.
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Affiliation(s)
- Aaron D Goldman
- Department of Microbiology, University of Washington, Seattle, WA, USA.
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12
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Specific DNA binding of a potential transcriptional regulator, inosine 5'-monophosphate dehydrogenase-related protein VII, to the promoter region of a methyl coenzyme m reductase I-encoding operon retrieved from Methanothermobacter thermautotrophicus strain DeltaH. Appl Environ Microbiol 2008; 74:6239-47. [PMID: 18757575 DOI: 10.1128/aem.02155-07] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus DeltaH are expressed in response to H(2) availability. In the present study, cis elements and trans-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from mrt-expressing cultures restricted them to 46- and 41-bp-long mcr and mrt upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine beta-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen.
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13
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Kato S, Kosaka T, Watanabe K. Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environ Microbiol 2007; 10:893-905. [PMID: 18036179 DOI: 10.1111/j.1462-2920.2007.01508.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Methanothermobacter thermautotrophicus strain DeltaH is a model hydrogenotrophic methanogen, for which the complete genome sequence and extensive biochemical information are available. Little is known, however, about how this organism regulates its cellular functions in response to environmental stimuli. In this study, whole-genome oligonucleotide microarrays were constructed for M. thermautotrophicus and used to gain insights into how this organism responds to different environmental stimuli, including hydrogen depletion, shifts in pH and temperature and the occurrence of toxics (hydrogen peroxide and ammonia). Our analysis confirmed that methanogenesis genes (including mtd, mer, frh and mcr) were upregulated under hydrogen-limited conditions, while some of them were affected by other environmental stimuli. Concerning stress responses of this organism, several unique features were revealed. First, there was no universal stress response in this organism. Second, genes for alternative redox enzymes, such as rubrerythrin, were upregulated under the oxidative stress, but those for typical antioxidant enzymes were not. Third, genes relevant to the modification of cell surface structures were differentially expressed under stress conditions. Finally, energy-requiring CO(2) assimilation systems were downregulated under stress conditions. These findings suggest that M. thermautotrophicus has complex transcriptional regulation mechanisms that facilitate it to survive in unstable ecosystems such as an anaerobic digester.
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Affiliation(s)
- Souichiro Kato
- Laboratory of Applied Microbiology, Marine Biotechnology Institute, Kamaishi, Iwate 026-0001, Japan
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14
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Vignais PM, Billoud B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem Rev 2007; 107:4206-72. [PMID: 17927159 DOI: 10.1021/cr050196r] [Citation(s) in RCA: 1034] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
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15
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Cubonová L, Sandman K, Karr EA, Cochran AJ, Reeve JN. Spontaneous trpY mutants and mutational analysis of the TrpY archaeal transcription regulator. J Bacteriol 2007; 189:4338-42. [PMID: 17400746 PMCID: PMC1913389 DOI: 10.1128/jb.00164-07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 03/19/2007] [Indexed: 11/20/2022] Open
Abstract
Over 90% of Methanothermobacter thermautotrophicus mutants isolated as spontaneously resistant to 5-methyl tryptophan had mutations in trpY. Most were single-base-pair substitutions that identified separate DNA- and tryptophan-binding regions in TrpY. In vivo and in vitro studies revealed that DNA binding was sufficient for TrpY repression of trpY transcription but that TrpY must bind DNA and tryptophan to assemble a complex that represses trpEGCFBAD.
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Affiliation(s)
- L'ubomíra Cubonová
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA
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16
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de Poorter LMI, Geerts WJ, Keltjens JT. Coupling of Methanothermobacter thermautotrophicus methane formation and growth in fed-batch and continuous cultures under different H2 gassing regimens. Appl Environ Microbiol 2007; 73:740-9. [PMID: 17142379 PMCID: PMC1800739 DOI: 10.1128/aem.01885-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 11/16/2006] [Indexed: 11/20/2022] Open
Abstract
In nature, H2- and CO2-utilizing methanogenic archaea have to couple the processes of methanogenesis and autotrophic growth under highly variable conditions with respect to the supply and concentration of their energy source, hydrogen. To study the hydrogen-dependent coupling between methanogenesis and growth, Methanothermobacter thermautotrophicus was cultured in a fed-batch fermentor and in a chemostat under different 80% H(2)-20% CO2 gassing regimens while we continuously monitored the dissolved hydrogen partial pressures (pH2). In the fed-batch system, in which the conditions continuously changed the uptake rates by the growing biomass, the organism displayed a complex and yet defined growth behavior, comprising the consecutive lag, exponential, and linear growth phases. It was found that the in situ hydrogen concentration affected the coupling between methanogenesis and growth in at least two respects. (i) The microorganism could adopt two distinct theoretical maximal growth yields (YCH4 max), notably approximately 3 and 7 g (dry weight) of methane formed mol-1, for growth under low (pH2 < 12 kPa)- and high-hydrogen conditions, respectively. The distinct values can be understood from a theoretical analysis of the process of methanogenesis presented in the supplemental material associated with this study. (ii) The in situ hydrogen concentration affected the "specific maintenance" requirements or, more likely, the degree of proton leakage and proton slippage processes. At low pH2 values, the "specific maintenance" diminished and the specific growth yields approached YCH4 max, indicating that growth and methanogenesis became fully coupled.
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Affiliation(s)
- Linda M I de Poorter
- Department of Microbiology, Faculty of Science, Radboud University of Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
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17
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Luo HW, Zhang H, Suzuki T, Hattori S, Kamagata Y. Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs. Appl Environ Microbiol 2002; 68:1173-9. [PMID: 11872465 PMCID: PMC123741 DOI: 10.1128/aem.68.3.1173-1179.2002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture sufficiently supplied with H(2) plus CO(2) and in a coculture with an acetate-oxidizing hydrogen-producing bacterium, Thermacetogenium phaeum strain PB, in which hydrogen partial pressure was constantly kept very low (20 to 80 Pa). Northern blot analysis indicated that only the mcr gene, which encodes methyl coenzyme M reductase I (MRI), catalyzing the final step of methanogenesis, was expressed in the coculture, whereas mcr and mrt, which encodes methyl coenzyme M reductase II (MRII), the isofunctional enzyme of MRI, were expressed at the early to late stage of growth in the pure culture. In contrast to these two genes, two isofunctional genes (mtd and mth) for N(5),N(10)-methylene-tetrahydromethanopterin dehydrogenase, which catalyzes the fourth step of methanogenesis, and two hydrogenase genes (frh and mvh) were expressed both in a pure culture and in a coculture at the early and late stages of growth. The same expression pattern was observed for Methanothermobacter thermoautotrophicus strain DeltaH cocultured with a thermophilic butyrate-oxidizing syntroph, Syntrophothermus lipocalidus strain TGB-C1. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole proteins of M. thermoautotrophicus strain TM obtained from a pure culture and a coculture with the acetate-oxidizing syntroph and subsequent N-terminal amino acid sequence analysis confirmed that MRI and MRII were produced in the pure culture, while only MRI was produced in the coculture. These results indicate that under syntrophic growth conditions, the methanogen preferentially utilizes MRI but not MRII. Considering that hydrogenotrophic methanogens are strictly dependent for growth on hydrogen-producing fermentative microbes in the natural environment and that the hydrogen supply occurs constantly at very low concentrations compared with the supply in pure cultures in the laboratory, the results suggest that MRI is an enzyme primarily functioning in natural methanogenic ecosystems.
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Affiliation(s)
- Hong-Wei Luo
- Research Institute of Biological Resources, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
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18
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Smith KS, Jakubzick C, Whittam TS, Ferry JG. Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Proc Natl Acad Sci U S A 1999; 96:15184-9. [PMID: 10611359 PMCID: PMC24794 DOI: 10.1073/pnas.96.26.15184] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbonic anhydrases catalyze the reversible hydration of CO(2) and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (gamma class) in a methanoarchaeon and our present finding that the beta class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the beta and gamma classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.
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Affiliation(s)
- K S Smith
- Department of Biochemistry, The Pennsylvania State University, University Park, PA 16802, USA
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19
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Smith KS, Ferry JG. A plant-type (beta-class) carbonic anhydrase in the thermophilic methanoarchaeon Methanobacterium thermoautotrophicum. J Bacteriol 1999; 181:6247-53. [PMID: 10515911 PMCID: PMC103756 DOI: 10.1128/jb.181.20.6247-6253.1999] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbonic anhydrase, a zinc enzyme catalyzing the interconversion of carbon dioxide and bicarbonate, is nearly ubiquitous in the tissues of highly evolved eukaryotes. Here we report on the first known plant-type (beta-class) carbonic anhydrase in the archaea. The Methanobacterium thermoautotrophicum DeltaH cab gene was hyperexpressed in Escherichia coli, and the heterologously produced protein was purified 13-fold to apparent homogeneity. The enzyme, designated Cab, is thermostable at temperatures up to 75 degrees C. No esterase activity was detected with p-phenylacetate as the substrate. The enzyme is an apparent tetramer containing approximately one zinc per subunit, as determined by plasma emission spectroscopy. Cab has a CO(2) hydration activity with a k(cat) of 1.7 x 10(4) s(-1) and K(m) for CO(2) of 2.9 mM at pH 8.5 and 25 degrees C. Western blot analysis indicates that Cab (beta class) is expressed in M. thermoautotrophicum; moreover, a protein cross-reacting to antiserum raised against the gamma carbonic anhydrase from Methanosarcina thermophila was detected. These results show that beta-class carbonic anhydrases extend not only into the Archaea domain but also into the thermophilic prokaryotes.
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Affiliation(s)
- K S Smith
- Department of Biochemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
Methanoarchaea, the largest and most phylogenetically diverse group in the Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. All of the pathways have in common the two-electron reduction of methyl-coenzyme M to methane catalyzed by methyl-coenzyme M reductase but deviate in the source of the methyl group transferred to coenzyme M. Most of the methane produced in nature derives from acetate in a pathway where the activated substrate is cleaved by CO dehydrogenase/acetyl-CoA synthase and the methyl group is transferred to coenzyme M via methyltetrahydromethanopterin or methyltetrahydrosarcinapterin. Electrons for reductive demethylation of the methyl-coenzyme M originate from oxidation of the carbonyl group of acetate to carbon dioxide by the synthase. In the other major pathway, formate or H2 is oxidized to provide electrons for reduction of carbon dioxide to the methyl level and reduction of methyl-coenzyme to methane. Methane is also produced from the methyl groups of methanol and methylamines. In these pathways specialized methyltransferases transfer the methyl groups to coenzyme M. Electrons for reduction of the methyl-coenzyme M are supplied by oxidation of the methyl groups to carbon dioxide by a reversal of the carbon dioxide reduction pathway. Recent progress on the enzymology of one-carbon reactions in these pathways has raised the level of understanding with regard to the physiology and molecular biology of methanogenesis. These advances have also provided a foundation for future studies on the structure/function of these novel enzymes and exploitation of the recently completed sequences for the genomes from the methanoarchaea Methanobacterium thermoautotrophicum and Methanococcus jannaschii.
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Affiliation(s)
- J G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16801, USA.
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21
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Thauer RK. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 9):2377-2406. [PMID: 9782487 DOI: 10.1099/00221287-144-9-2377] [Citation(s) in RCA: 622] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Straße, D-35032 Marburg, Germany
In 1933, Stephenson & Stickland (1933a) published that they had isolated from river mud, by the single cell technique, a methanogenic organism capable of growth in an inorganic medium with formate as the sole carbon source.
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Affiliation(s)
- Rudolf K Thauer
- (Delivered at the 140th Ordinary Meeting of the Society for General Microbiology, 31 March 1998)
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Pennings JL, Keltjens JT, Vogels GD. Isolation and characterization of Methanobacterium thermoautotrophicum DeltaH mutants unable to grow under hydrogen-deprived conditions. J Bacteriol 1998; 180:2676-81. [PMID: 9573152 PMCID: PMC107219 DOI: 10.1128/jb.180.10.2676-2681.1998] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
By using random mutagenesis and enrichment by chemostat culturing, we have developed mutants of Methanobacterium thermoautotrophicum that were unable to grow under hydrogen-deprived conditions. Physiological characterization showed that these mutants had poorer growth rates and growth yields than the wild-type strain. The mRNA levels of several key enzymes were lower than those in the wild-type strain. A fed-batch study showed that the expression levels were related to the hydrogen supply. In one mutant strain, expression of both methyl coenzyme M reductase isoenzyme I and coenzyme F420-dependent 5,10-methylenetetrahydromethanopterin dehydrogenase was impaired. The strain was also unable to form factor F390, lending support to the hypothesis that the factor functions in regulation of methanogenesis in response to changes in the availability of hydrogen.
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Affiliation(s)
- J L Pennings
- Department of Microbiology, University of Nijmegen, Nijmegen, The Netherlands.
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23
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Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol 1997; 179:7135-55. [PMID: 9371463 PMCID: PMC179657 DOI: 10.1128/jb.179.22.7135-7155.1997] [Citation(s) in RCA: 840] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative functions based on their similarities to database sequences with assigned functions. A total of 514 (28%) of the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most similar to polypeptide sequences described previously for other organisms in the domain Archaea. Comparisons with the Methanococcus jannaschii genome data underline the extensive divergence that has occurred between these two methanogens; only 352 (19%) of M. thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii polypeptides, and there is little conservation in the relative locations of orthologous genes. When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more similar to eucaryal sequences. The bacterial domain-like gene products include the majority of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the environment. Most proteins predicted to be involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. Gene structure and organization have features that are typical of the Bacteria, including genes that encode polypeptides closely related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are notably absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most of these occur in clusters. Three of the tRNA genes have introns, including the tRNAPro (GGG) gene, which contains a second intron at an unprecedented location. There is no selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or plasmids. The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are members of a family with 18 representatives in the M. jannaschii genome.
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Affiliation(s)
- D R Smith
- Genome Therapeutics Corporation, Collaborative Research Division, Waltham, Massachusetts 02154, USA.
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24
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Vermeij P, Pennings JL, Maassen SM, Keltjens JT, Vogels GD. Cellular levels of factor 390 and methanogenic enzymes during growth of Methanobacterium thermoautotrophicum deltaH. J Bacteriol 1997; 179:6640-8. [PMID: 9352911 PMCID: PMC179590 DOI: 10.1128/jb.179.21.6640-6648.1997] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Methanobacterium thermoautotrophicum deltaH was grown in a fed-batch fermentor and in a chemostat under a variety of 80% hydrogen-20% CO2 gassing regimes. During growth or after the establishment of steady-state conditions, the cells were analyzed for the content of adenylylated coenzyme F420 (factor F390-A) and other methanogenic cofactors. In addition, cells collected from the chemostat were measured for methyl coenzyme M reductase isoenzyme (MCR I and MCR II) content as well as for specific activities of coenzyme F420-dependent and H2-dependent methylenetetrahydromethanopterin dehydrogenase (F420-MDH and H2-MDH, respectively), total (viologen-reducing) and coenzyme F420-reducing hydrogenase (FRH), factor F390 synthetase, and factor F390 hydrolase. The experiments were performed to investigate how the intracellular F390 concentrations changed with the growth conditions used and how the variations were related to changes in levels of enzymes that are known to be differentially expressed. The levels of factor F390 varied in a way that is consistently understood from the biochemical mechanisms underlying its synthesis and degradation. Moreover, a remarkable correlation was observed between expression levels of MCR I and II, F420-MDH, and H2-MDH and the cellular contents of the factor. These results suggest that factor F390 is a reporter compound for hydrogen limitation and may act as a response regulator of methanogenic metabolism.
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Affiliation(s)
- P Vermeij
- Department of Microbiology, Faculty of Science, University of Nijmegen, The Netherlands
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25
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Affiliation(s)
- J N Reeve
- Department of Microbiology, The Ohio State University, Columbus 43210, USA.
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26
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Pennings JL, de Wijs JL, Keltjens JT, van der Drift C. Medium-reductant directed expression of methyl coenzyme M reductase isoenzymes in Methanobacterium thermoautotrophicum (strain deltaH). FEBS Lett 1997; 410:235-7. [PMID: 9237636 DOI: 10.1016/s0014-5793(97)00595-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Methanobacterium thermoautotrophicum was grown in a chemostat under various controlled conditions in the presence of either sodium sulfide or sodium thiosulfate. After establishment of the steady state, cells were taken and examined for expression of the mRNA transcripts coding for the different forms of methyl coenzyme M reductase (MCR) and methylene tetrahydomethanopterin dehydrogenase (MDH). MCR isoenzyme II expression varied most markedly. Expression was found not only to depend on known parameters temperature, pH and gassing rate, but also on the medium composition, especially the reductant present.
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Affiliation(s)
- J L Pennings
- Department of Microbiology, University of Nijmegen, The Netherlands.
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27
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Klein AR, Thauer RK. Overexpression of the coenzyme-F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase gene from the hyperthermophilic Methanopyrus kandleri. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:386-91. [PMID: 9151968 DOI: 10.1111/j.1432-1033.1997.t01-1-00386.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The mtd gene encoding coenzyme-F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase (Mtd) in the hyperthermophilic Methanopyrus kandleri has been cloned, sequenced and functionally overexpressed in Escherichia coli. The overproduced enzyme was purified in a 90% yield to apparent homogeneity by means of only one chromatographic step. Its thermostability properties and most of its catalytic properties were the same as those of the native enzyme purified directly from M. kandleri. Only the dependence of the activity on the concentration of lyotropic salts differed slightly. Northern blot analysis revealed that in M. kandleri the mtd gene is monocistronically transcribed.
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Affiliation(s)
- A R Klein
- Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie des Fachbereichs Biologie der Philipps-Universität,Marburg, Germany
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28
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Tersteegen A, Linder D, Thauer RK, Hedderich R. Structures and functions of four anabolic 2-oxoacid oxidoreductases in Methanobacterium thermoautotrophicum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:862-8. [PMID: 9108258 DOI: 10.1111/j.1432-1033.1997.00862.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Methanobacterium thermoautotrophicum (strain Marburg), which grows autotrophically on H2 and CO2, was found to contain 2-oxoisovalerate oxidoreductase (Vor) and indolepyruvate oxidoreductase (Ior) besides pyruvate oxidoreductase (Por) and 2-oxoglutarate oxidoreductase (Kor). So far, Vor and Ior have only been detected in peptide-utilizing hyperthermophilic Archaea. The four 2-oxoacid oxidoreductases were purified and characterized with respect to their subunit composition, N-terminal amino acid sequences, and catalytic properties. Por and Kor were composed of four different subunits, Vor was composed of three different subunits, and Ior of two different subunits. Comparisons of the N-terminal amino acid sequences revealed that the four enzymes are structurally related to each other and to the respective enzymes from Pyrococcus and Thermococcus sp. Vor from M. thermoautotrophicum differed from Vor from Pyrococcus furiosus in being composed of only three instead of four different subunits. Evidence is presented that in the autotrophic methanogen the four 2-oxoacid oxidoreductases have anabolic functions, Vor and Ior being involved in the biosynthesis of amino acids from fatty acids taken up from the growth medium, as shown by 14C-labelling studies.
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Affiliation(s)
- A Tersteegen
- Max-Planck-Institut für terrestrische Mikrobiologie, Philipps-Universität, Marburg, Germany
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29
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Morgan RM, Pihl TD, Nölling J, Reeve JN. Hydrogen regulation of growth, growth yields, and methane gene transcription in Methanobacterium thermoautotrophicum deltaH. J Bacteriol 1997; 179:889-98. [PMID: 9006047 PMCID: PMC178774 DOI: 10.1128/jb.179.3.889-898.1997] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Changes in growth rate, methanogenesis, growth yield (Y(CH4)), and methane gene transcription have been correlated with changes in the supply of H2 to Methanobacterium thermoautotrophicum deltaH cells growing on H2 plus CO2 in fed-batch cultures. Under conditions of excess H2, biomass and methanogenesis increased exponentially and in parallel, resulting in cultures with a constant Y(CH4) and transcription of the mth and mrt genes that encode the H2-dependent N5,N10-methenyltetrahydromethanopterin (methenyl-H4MPT) reductase (MTH) and methyl coenzyme M reductase II (MRII), respectively. Reducing the H2 supply, by decreasing the percentage of H2 in the input gas mixture or by reducing the mixing speed of the fermentor impeller, decreased the growth rate and resulted in lower and constant rates of methanogenesis. Under such H2-limited growth conditions, cultures grew with a continuously increasing Y(CH4) and the mtd and mcr genes that encode the reduced coenzyme F420-dependent N5,N10-methenyl-H4MPT reductase (MTD) and methyl coenzyme M reductase I (MRI), respectively, were transcribed. Changes in the kinetics of growth, methanogenesis, and methane gene transcription directed by reducing the H2 supply could be reversed by restoring a high H2 supply. Methane production continued, but at a low and constant rate, and only mcr transcripts could be detected when the H2 supply was reduced to a level insufficient for growth. ftsA transcripts, which encode coenzyme F390 synthetase, were most abundant in cells growing with high H2 availability, consistent with coenzyme F390 synthesis signaling a high exogenous supply of reductant.
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Affiliation(s)
- R M Morgan
- Department of Microbiology, The Ohio State University, Columbus 43210, USA
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30
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Nölling J, Reeve JN. Growth- and substrate-dependent transcription of the formate dehydrogenase (fdhCAB) operon in Methanobacterium thermoformicicum Z-245. J Bacteriol 1997; 179:899-908. [PMID: 9006048 PMCID: PMC178775 DOI: 10.1128/jb.179.3.899-908.1997] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The formate dehydrogenase-encoding fdhCAB operon and flanking genes have been cloned and sequenced from Methanobacterium thermoformicicum Z-245. fdh transcription was shown to be initiated 21 bp upstream from fdhC, although most fdh transcripts terminated or were processed between fdhC and fdhA. The resulting fdhC, fdhAB, and fdhCAB transcripts were present at all growth stages in cells growing on formate but were barely detectable during early exponential growth on H2 plus CO2. The levels of the fdh transcripts did, however, increase dramatically in cells growing on H2 plus CO2, coincident with the decrease in the growth rate and the onset of constant methanogenesis that occurred when culture densities reached an optical density at 600 nm of approximately 0.5. The mth transcript that encodes the H2-dependent methenyl-H4 MPT reductase (MTH) and the frh and mvh transcripts that encode the coenzyme F420-reducing (FRH) and nonreducing (MVH) hydrogenases, respectively, were also present in cells growing on formate, consistent with the synthesis of three hydrogenases, MTH, FRH, and MVH, in the absence of exogenously supplied H2. Reducing the H2 supply to M. thermoformicicum cells growing on H2 plus CO2 reduced the growth rate and CH4 production but increased frh and fdh transcription and also increased transcription of the mtd, mer, and mcr genes that encode enzymes that catalyze steps 4, 5, and 7, respectively, in the pathway of CO2 reduction to CH4. Reducing the H2 supply to a level insufficient for growth resulted in the disappearance of all methane gene transcripts except the mcr transcript, which increased. Regions flanking the fdhCAB operon in M. thermoformicicum Z-245 were used as probes to clone the homologous region from the Methanobacterium thermoautotrophicum deltaH genome. Sequencing revealed the presence of very similar genes except that the genome of M. thermoautotrophicum, a methanogen incapable of growth on formate, lacked the fdhCAB operon.
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Affiliation(s)
- J Nölling
- Department of Microbiology, The Ohio State University, Columbus 43210, USA
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31
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Thauer RK, Klein AR, Hartmann GC. Reactions with Molecular Hydrogen in Microorganisms: Evidence for a Purely Organic Hydrogenation Catalyst. Chem Rev 1996; 96:3031-3042. [PMID: 11848851 DOI: 10.1021/cr9500601] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rudolf K. Thauer
- Max-Planck-Institut für Terrestrische Mikrobiologie and Laboratorium für Mikrobiologie des Fachbereichs Biologie der Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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32
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Keltjens JT, Vogels GD. Metabolic regulation in methanogenic archaea during growth on hydrogen and CO2. ENVIRONMENTAL MONITORING AND ASSESSMENT 1996; 42:19-37. [PMID: 24193491 DOI: 10.1007/bf00394040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanogenic Archaea represent a unique group of micro-organisms in their ability to derive their energy for growth from the conversion of their substrates to methane. The common substrates are hydrogen and CO2. The energy obtained in the latter conversion is highly dependent on the hydrogen concentration which may dramatically vary in their natural habitats and under laboratory conditions. In this review the bio-energetic consequences of the variations in hydrogen supply will be investigated. It will be described how the organisms seem to be equipped as to their methanogenic apparatus to cope with extremes in hydrogen availability and how they could respond to hydrogen changes by the regulation of their metabolism.
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Affiliation(s)
- J T Keltjens
- Department of Microbiology, Faculty of Science, University of Nijmegen, Toernooiveld, NL-6525 ED, Nijmegen, The Netherlands
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33
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Hartmann GC, Klein AR, Linder M, Thauer RK. Purification, properties and primary structure of H2-forming N5 ,N10 -methylenetetrahydromethanopterin dehydrogenase from Methanococcus thermolithotrophicus. Arch Microbiol 1996; 165:187-93. [PMID: 8599536 DOI: 10.1007/bf01692860] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
H2-Forming N5,N10 -methylenetetrahydromethanopterin dehydrogenase (Hmd) is a novel type of hydrogenase found in methanogenic Achaea that contains neither nickel nor iron-sulfur clusters. The enzyme has previously been characterized from Methanobacterium thermoautotrophicum and from Methanopyrus kandleri. We report here on the purification and properties of the enzyme from Methanococcus thermolithotrophicus. The hmd gene was cloned and sequenced. The results indicate that the enzyme from Mc. thermolithotrophicus is functionally and structurally closely related to the H2-forming methylene tetrahydromethanopterin dehydrogenase from Mb. thermoautotrophicum and Mp. kandleri. From amino acid sequence comparisons of the three enzymes, a phylogenetic tree was deduced that shows branching orders similar to those derived from sequence comparisons of the 16S rRNA of the orders Methanococcales, Methanobacteriales, and Methanopyrales.
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Affiliation(s)
- G C Hartmann
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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Hochheimer A, Schmitz RA, Thauer RK, Hedderich R. The tungsten formylmethanofuran dehydrogenase from Methanobacterium thermoautotrophicum contains sequence motifs characteristic for enzymes containing molybdopterin dinucleotide. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 234:910-20. [PMID: 8575452 DOI: 10.1111/j.1432-1033.1995.910_a.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Formylmethanofuran dehydrogenases are molybdenum or tungsten iron-sulfur proteins containing a pterin dinucleotide cofactor. We report here on the primary structures of the four subunits FwdABCD of the tungsten enzyme from Methanobacterium thermoautotrophicum which were determined by cloning and sequencing the encoding genes fwdABCD. FwdB was found to contain sequence motifs characteristic for molybdopterin-dinucleotide-containing enzymes indicating that this subunit harbors the active site. FwdA, FwdC and FwdD showed no significant sequence similarity to proteins in the data bases. Northern blot analysis revealed that the four fwd genes form a transcription unit together with three additional genes designated fwdE, fwdF and fwdG. A 17.8-kDa protein and an 8.6-kDa protein, both containing two [4Fe-4S] cluster binding motifs, were deduced from fwdE and fwdG. The open reading frame fwdF encodes a 38.6-kDa protein containing eight binding motifs for [4Fe-4S] clusters suggesting the gene product to be a novel polyferredoxin. All seven fwd genes were expressed in Escherichia coli yielding proteins of the expected size. The fwd operon was found to be located in a region of the M. thermoautotrophicum genome encoding molybdenum enzymes and proteins involved in molybdopterin biosynthesis.
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Affiliation(s)
- A Hochheimer
- Max-Planck-Institut für terrestrische Mikrobiologie, Philipps-Universität, Marburg, Germany
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35
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Nölling J, Pihl TD, Reeve JN. Cloning, sequencing, and growth phase-dependent transcription of the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductase-encoding genes from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri. J Bacteriol 1995; 177:7238-44. [PMID: 8522533 PMCID: PMC177605 DOI: 10.1128/jb.177.24.7238-7244.1995] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The mer genes, which encode the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductases (CH2 = H4MPT reductases), and their flanking regions have been cloned from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri and sequenced. The mer genes have DNA sequences that are 57% identical and encode polypeptides with amino acid sequences that are 57% identical and 71% similar, with calculated molecular masses of 33.6 and 37.5 kDa, respectively. In M. thermoautotrophicum, mer transcription has been shown to initiate 10 bp upstream from the ATG translation initiating codon and to generate a monocistronic transcript approximately 1 kb in length. This transcript was synthesized at all stages of M. thermoautotrophicum delta H growth in batch cultures but was found to increase in abundance from the earliest stages of exponential growth, reaching a maximum level at the mid-exponential growth phase. For comparison, transcription of the ftr gene from M. thermoautotrophicum delta H that encodes the formylmethanofuran:tetrahydromethanopterin formyltransferase (A. A. DiMarco, K. A. Sment, J. Konisky, and R. S. Wolfe, J. Biol. Chem. 265:472-476, 1990) was included in this study. The ftr transcript was found similarly to be monocistronic and to be approximately 1 kb in length, but, in contrast to the mer transcript, the ftr transcript was present at maximum levels at both the early and the mid-exponential growth stages.
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Affiliation(s)
- J Nölling
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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36
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Klein AR, Hartmann GC, Thauer RK. Hydrogen isotope effects in the reactions catalyzed by H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 233:372-6. [PMID: 7588769 DOI: 10.1111/j.1432-1033.1995.372_1.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea, which is a novel hydrogenase containing neither nickel nor iron-sulfur clusters, catalyzes the reversible reduction of N5,N10-methenyltetrahydomethanopterin (CH identical to H4MPT+) with H2 to N5,N10-methylenetetrahydromethanopterin (CH2 = H4MPT) and a proton (delta G degree' = -5.5 kJ/mol). The enzyme also catalyzes a CH identical to H4MPT(+)-dependent H2/H+ exchange. We report here on kinetic deuterium isotope effects in these reactions. When CH identical to H4MPT+ reduction was performed with D2 instead of H2, Vmax and the Km did not change. A primary isotope effect of 1 was found at all pH and temperatures tested and independent of whether H2O or D2O was the solvent. The findings indicate that a step other than the activation of H2 was rate-determining in CH identical to H4MPT+ reduction with H2. This was substantiated by the observation that also the CH identical to H4MPT(+)-dependent H2/H+ exchange reaction did not exhibit an appreciable deuterium isotope effect. Vmax for CH2 = H4MPT dehydrogenation to CH identical to H4MPT+ and H2 was only 2-3 times higher than for CD2 = H4MPT dehydrogenation to CD identical to H4MPT+ and HD. Such a small primary isotope effect indicates that the breakage of the C-H bond in the methylene group of CH2 = H4MPT was only rate-limiting when hydrogen was substituted by a deuterium.
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Affiliation(s)
- A R Klein
- Max-Planck-Institut für terrestrische Mikrobiologie, Philipps-Universität Marburg, Germany
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Nölling J, Ishii M, Koch J, Pihl TD, Reeve JN, Thauer RK, Hedderich R. Characterization of a 45-kDa flavoprotein and evidence for a rubredoxin, two proteins that could participate in electron transport from H2 to CO2 in methanogenesis in Methanobacterium thermoautotrophicum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:628-38. [PMID: 7649162 DOI: 10.1111/j.1432-1033.1995.0628d.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Methanobacterium thermoautotrophicum strains contain a flavoprotein (flavoprotein A) that copurifies with the H2:heterodisulfide oxidoreductase complex. In this study, we report the iron-dependent synthesis and biochemical properties of flavoprotein A, cloning and sequencing of the flavoprotein-A-encoding gene (fpaA) and the co-transcription of fpaA with two downstream open reading frames, one of which (rdxA) appears to encode a rubredoxin. Native flavoprotein A has been shown to be a homodimer of a 45-kDa polypeptide that contains 1.3 mol FMN/45-kDa subunit but no iron or acid-labile sulfur. Catalytic amounts of the H2:heterodisulfide oxidoreductase complex or of the F420-reducing hydrogenase reduced flavoprotein A with H2, at specific rates of 0.3-0.4 U/mg enzyme, generating up to 70% flavin semiquinone before reduction to the flavin hydroquinone was observed. This intermediate accumulation of the semiquinone species had a kinetic rather than a thermodynamic basis, because the semiquinone form of flavoprotein A, generated by photoreduction, disproportionated quantitatively to the quinone and hydroquinone species. The midpoint potential of the quinone/hydroquinone couple was estimated to be 230 +/- 15 mV, at pH 7.6, versus the normal hydrogen electrode. Quantitation of Western blots demonstrated that flavoprotein A constituted approximately 1.5% of the soluble protein in cells grown in an iron-sufficient medium but that this increased to about 6% of the cellular protein when the iron the medium was depleted. The increase in the flavoprotein A content of cells grown under iron-limiting conditions was mirrored by a decrease in the content of the iron-rich polyferredoxin that also copurified with the H2:heterodisulfide oxidoreductase complex. The fpaA gene, cloned and sequenced from M. thermoautotrophicum strain delta H, encodes 404 amino acids in a sequence that has a C-terminal domain (approximately 130 amino acid residues) with features consistent with a flavodoxin structure. The remainder of flavoprotein A has sequences that are also predicted to be present in the N-terminal region of the orf14 gene product, which also appears to be an enlarged flavodoxin, encoded in the nif region of Rhodobacter capsulatus. Immediately downstream from fpaA, two open reading frames designated orfX and rdxA, have been located and shown by Northern-blot analyses to be co-transcribed with fpaA, although approximately 50% of fpaA-orfX-rdxA transcripts terminated or were cleaved within rdxA. Primer extension studies revealed that transcription of this transcriptional unit (the fpa operon) was initiated 32 nucleotides upstream of fpaA, at a site 25 nucleotides downstream from a sequence consistent with an archaeal TATA-box promoter element.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- J Nölling
- Department of Microbiology, Ohio State University, Columbus, USA
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