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Li K, Ji L, Gao M, Liang Q, Lan H, Lu W, Zhang W, Zhang Y. Mechanisms of anaerobic treatment of sulfate-containing organic wastewater mediated by Fe 0 under different initial pH values. Bioprocess Biosyst Eng 2024; 47:417-427. [PMID: 38424249 DOI: 10.1007/s00449-024-02974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The anaerobic treatment of sulfide-containing organic wastewater (SCOW) is significantly affected by pH, causing dramatic decrease of treatment efficiency when pH deviates from its appropriate range. Fe0 has proved as an effective strategy on mitigating the impact of pH. However, systematic analysis of the influence mechanism is still lacking. To fill this gap, the impact of different initial pH values on anaerobic treatment efficiency of SCOW with Fe0 addition, the change of fermentation type and methanogens, and intra-extracellular electron transfer were explored in this study. The results showed that Fe0 addition enhanced the efficacy of anaerobic treatment of SCOW at adjusted initial pH values, especially at pH 6. Mechanism analysis showed that respiratory chain-related enzymes and electron shuttle secretion and resistance reduction were stimulated by soluble iron ions generated by Fe0 at pH 6, which accelerated intra-extracellular electron transfer of microorganisms, and ultimately alleviated the impact of acidic pH on the system. While at pH 8, Fe0 addition increased the acetogenic bacteria abundance, as well as optimized the fermentation type and improved the F420 coenzyme activity, resulting in the enhancement of treatment efficiency in the anaerobic system and remission of the effect of alkaline pH on the system. At the neutral pH, Fe0 addition had both advantages as stimulating the secretion of respiratory chain and electron transfer-related enzymes at pH 6 and optimizing the fermentation type pH 8, and thus enhanced the treatment efficacy. This study provides important insights and scientific basis for the application of new SCOW treatment technologies.
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Affiliation(s)
- Ke Li
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Linyu Ji
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Meng Gao
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Qiaochu Liang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Huixia Lan
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
- Yunnan Provincial Key Laboratory of Rural Energy Engineering, Kunming, 650500, China.
| | - Weiwei Lu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Wudi Zhang
- Yunnan Provincial Key Laboratory of Rural Energy Engineering, Kunming, 650500, China
| | - Yang Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
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2
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Balch WE, Ferry JG. The Wolfe cycle of carbon dioxide reduction to methane revisited and the Ralph Stoner Wolfe legacy at 100 years. Adv Microb Physiol 2021; 79:1-23. [PMID: 34836609 DOI: 10.1016/bs.ampbs.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Methanogens are a component of anaerobic microbial consortia decomposing biomass to CO2 and CH4 that is an essential link in the global carbon cycle. One of two major pathways of methanogenesis involves reduction of the methyl group of acetate to CH4 with electrons from oxidation of the carbonyl group while the other involves reduction of CO2 to CH4 with electrons from H2 or formate. Pioneering investigations of the CO2 reduction pathway by Ralph S. Wolfe in the 70s and 80s contributed findings impacting the broader fields of biochemistry and microbiology that directed discovery of the domain Archaea and expanded research on anaerobic microbes for decades that continues to the present. This review presents an historical overview of the CO2 reduction pathway (Wolfe cycle) with recent developments, and an account of Wolfe's larger and enduring impact on the broad field of biology 100 years after his birth.
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Affiliation(s)
- William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.
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3
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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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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5
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Jia X, Xi B, Li M, Liu D, Hou J, Hao Y, Meng F. Metaproteomic analysis of the relationship between microbial community phylogeny, function and metabolic activity during biohydrogen-methane coproduction under short-term hydrothermal pretreatment from food waste. BIORESOURCE TECHNOLOGY 2017; 245:1030-1039. [PMID: 28946205 DOI: 10.1016/j.biortech.2017.08.180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Short-term hydrothermal pretreatment (SHP) is an attractive method for food waste anaerobic digestion, which facilitates the solubilisation of recalcitrant particles. This study employed metaproteomic method to evaluate the relationships among microbial community phylogeny, function, and metabolic activity during two-stage anaerobic digestion under SHP (SHPT) from food waste. The presence of 651 bacterial proteins and 477 archaeal protein has been detected by liquid chromatography online linked to mass spectrometry, revealing a high metabolic heterogeneity during SHPT. The different stages of SHPT highlighted important roles for the bacterial proteins from Gammaproteobacteria, Bacilli, and Clostridia and the archaeal proteins from Methanosarcinales. The identified proteins related to biohydrogen production come from pyruvic acid decarboxylase and formic acid decomposition pathway in carbohydrate metabolism and methanogenesis from acetate, CO2 and a methylotrophic pathway during energy metabolism. This could provide functional evidence of the metabolic activities and biogas production during SHPT.
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Affiliation(s)
- Xuan Jia
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Mingxiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Dongming Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jiaqi Hou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yan Hao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fanhua Meng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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6
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Discovery and characterization of an F 420-dependent glucose-6-phosphate dehydrogenase (Rh-FGD1) from Rhodococcus jostii RHA1. Appl Microbiol Biotechnol 2016; 101:2831-2842. [PMID: 27966048 PMCID: PMC5352752 DOI: 10.1007/s00253-016-8038-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/22/2016] [Accepted: 11/26/2016] [Indexed: 12/16/2022]
Abstract
Cofactor F420, a 5-deazaflavin involved in obligatory hydride transfer, is widely distributed among archaeal methanogens and actinomycetes. Owing to the low redox potential of the cofactor, F420-dependent enzymes play a pivotal role in central catabolic pathways and xenobiotic degradation processes in these organisms. A physiologically essential deazaflavoenzyme is the F420-dependent glucose-6-phosphate dehydrogenase (FGD), which catalyzes the reaction F420 + glucose-6-phosphate → F420H2 + 6-phospho-gluconolactone. Thereby, FGDs generate the reduced F420 cofactor required for numerous F420H2-dependent reductases, involved e.g., in the bioreductive activation of the antitubercular prodrugs pretomanid and delamanid. We report here the identification, production, and characterization of three FGDs from Rhodococcus jostii RHA1 (Rh-FGDs), being the first experimental evidence of F420-dependent enzymes in this bacterium. The crystal structure of Rh-FGD1 has also been determined at 1.5 Å resolution, showing a high similarity with FGD from Mycobacterium tuberculosis (Mtb) (Mtb-FGD1). The cofactor-binding pocket and active-site catalytic residues are largely conserved in Rh-FGD1 compared with Mtb-FGD1, except for an extremely flexible insertion region capping the active site at the C-terminal end of the TIM-barrel, which also markedly differs from other structurally related proteins. The role of the three positively charged residues (Lys197, Lys258, and Arg282) constituting the binding site of the substrate phosphate moiety was experimentally corroborated by means of mutagenesis study. The biochemical and structural data presented here provide the first step towards tailoring Rh-FGD1 into a more economical biocatalyst, e.g., an F420-dependent glucose dehydrogenase that requires a cheaper cosubstrate and can better match the demands for the growing applications of F420H2-dependent reductases in industry and bioremediation.
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7
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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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Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 2014; 5:634. [PMID: 25520705 PMCID: PMC4253957 DOI: 10.3389/fmicb.2014.00634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/05/2014] [Indexed: 11/21/2022] Open
Abstract
Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).
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Affiliation(s)
- Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Jane Lomax
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Hinxton, UK
| | - João C Setubal
- Department of Biochemistry, Universidade de São Paulo São Paulo, Brazil ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Center for Genome Research and Biocomputing, Oregon State University Corvallis, OR, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Department of Biological Sciences, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:706468. [PMID: 25249790 PMCID: PMC4164138 DOI: 10.1155/2014/706468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 11/20/2013] [Accepted: 01/17/2014] [Indexed: 12/30/2022]
Abstract
The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.
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10
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Bashiri G, Rehan AM, Greenwood DR, Dickson JMJ, Baker EN. Metabolic engineering of cofactor F420 production in Mycobacterium smegmatis. PLoS One 2010; 5:e15803. [PMID: 21209917 PMCID: PMC3012119 DOI: 10.1371/journal.pone.0015803] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 11/24/2010] [Indexed: 01/16/2023] Open
Abstract
Cofactor F420 is a unique electron carrier in a number of microorganisms including Archaea and Mycobacteria. It has been shown that F420 has a direct and important role in archaeal energy metabolism whereas the role of F420 in mycobacterial metabolism has only begun to be uncovered in the last few years. It has been suggested that cofactor F420 has a role in the pathogenesis of M. tuberculosis, the causative agent of tuberculosis. In the absence of a commercial source for F420, M. smegmatis has previously been used to provide this cofactor for studies of the F420-dependent proteins from mycobacterial species. Three proteins have been shown to be involved in the F420 biosynthesis in Mycobacteria and three other proteins have been demonstrated to be involved in F420 metabolism. Here we report the over-expression of all of these proteins in M. smegmatis and testing of their importance for F420 production. The results indicate that co–expression of the F420 biosynthetic proteins can give rise to a much higher F420 production level. This was achieved by designing and preparing a new T7 promoter–based co-expression shuttle vector. A combination of co–expression of the F420 biosynthetic proteins and fine-tuning of the culture media has enabled us to achieve F420 production levels of up to 10 times higher compared with the wild type M. smegmatis strain. The high levels of the F420 produced in this study provide a suitable source of this cofactor for studies of F420-dependent proteins from other microorganisms and for possible biotechnological applications.
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Affiliation(s)
- Ghader Bashiri
- Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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11
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Hasan MR, Rahman M, Jaques S, Purwantini E, Daniels L. Glucose 6-phosphate accumulation in mycobacteria: implications for a novel F420-dependent anti-oxidant defense system. J Biol Chem 2010; 285:19135-44. [PMID: 20075070 DOI: 10.1074/jbc.m109.074310] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Glucose 6-phosphate (G6P) is a metabolic intermediate with many possible cellular fates. In mycobacteria, G6P is a substrate for an enzyme, F(420)-dependent glucose-6-phosphate dehydrogenase (Fgd), found in few bacterial genera. Intracellular G6P levels in six Mycobacterium sp. were remarkably higher ( approximately 17-130-fold) than Escherichia coli and Bacillus megaterium. The high G6P level in Mycobacterium smegmatis may result from 10-25-fold higher activity of the gluconeogenic enzyme fructose-1,6-bisphosphatase when grown on glucose, glycerol, or acetate compared with B. megaterium and E. coli. In M. smegmatis this coincided with up-regulation of the first gluconeogenic enzyme, phosphoenolpyruvate carboxykinase, when acetate was the carbon source, suggesting a cellular program for maintaining high G6P levels. G6P was depleted in cells under oxidative stress induced by redox cycling agents plumbagin and menadione, whereas an fgd mutant of M. smegmatis used G6P less well under such conditions. The fgd mutant was more sensitive to these agents and, in contrast to wild type, was defective in its ability to reduce extracellular plumbagin and menadione. These data suggest that intracellular G6P in mycobacteria serves as a source of reducing power and, with the mycobacteria-specific Fgd-F(420) system, plays a protective role against oxidative stress.
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Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A & M Health Science Center, Kingsville, Texas 78363, USA
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Ceh K, Demmer U, Warkentin E, Moll J, Thauer RK, Shima S, Ermler U. Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase. Biochemistry 2009; 48:10098-105. [PMID: 19761261 DOI: 10.1021/bi901104d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.
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Affiliation(s)
- Katharina Ceh
- Max-Planck-Institut fur Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
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Guerra-Lopez D, Daniels L, Rawat M. Mycobacterium smegmatis mc2 155 fbiC and MSMEG_2392 are involved in triphenylmethane dye decolorization and coenzyme F420 biosynthesis. Microbiology (Reading) 2007; 153:2724-2732. [PMID: 17660436 DOI: 10.1099/mic.0.2006/009241-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacteria can tolerate relatively high concentrations of triphenylmethane dyes such as malachite green and methyl violet. To identify mycobacterial genes involved in the decolorization of malachite green, a transposon mutant library of Mycobacterium smegmatis mc2 155 was screened for mutants unable to decolorize this dye. One of the genes identified was MSMEG_5126, an orthologue of Mycobacterium bovis fbiC encoding a 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) synthase, which is essential for the biosynthesis of the electron carrier coenzyme F420. The other gene identified was MSMEG_2392, encoding an alanine-rich protein with a DUF121 domain. The minimum inhibitory concentrations (MICs) for malachite green and methyl violet of the six fbiC mutants and two MSMEG_2392 mutants were one-third and one-fifth, respectively, of the MIC of the parent strain M. smegmatis mc2 155. Representative fbiC and MSMEG_2392 mutant strains were also sensitive to oxidative stress caused by the redox-cycling agents plumbagin and menadione, and the sensitivity was reversed in the complemented strains. HPLC analysis of representative fbiC and MSMEG_2392 strains revealed that, while the fbiC mutant lacked both coenzyme F420 and FO, the MSMEG_2392 mutant contained FO but not coenzyme F420. These results indicate that MSMEG_2392 is involved in the biosynthesis of coenzyme F420.
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Affiliation(s)
- Denise Guerra-Lopez
- Department of Biology, California State University-Fresno, Fresno, CA 937401, USA
| | - Lacy Daniels
- Irma Lerma Rangel College of Pharmacy, Texas A&M Health Science Center, Kingsville, TX 78363, USA
| | - Mamta Rawat
- Department of Biology, California State University-Fresno, Fresno, CA 937401, USA
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Won H, Olson KD, Summers MF, Wolfe RS. F430-Dependent Biocatalysis in Methanogenic Archaebacteria. COMMENT INORG CHEM 2006. [DOI: 10.1080/02603599308035833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Isabelle D, Simpson DR, Daniels L. Large-scale production of coenzyme F420-5,6 by using Mycobacterium smegmatis. Appl Environ Microbiol 2002; 68:5750-5. [PMID: 12406775 PMCID: PMC129890 DOI: 10.1128/aem.68.11.5750-5755.2002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Production of coenzyme F420 and its biosynthetic precursor FO was examined with a variety of aerobic actinomycetes to identify an improved source for these materials. Based on fermentation costs, safety, and ease of growth, Mycobacterium smegmatis was the best source for F420-5,6. M. smegmatis produced 1 to 3 micromol of intracellular F420 per liter of culture, which was more than the 0.85 to 1.0 micromol of F420-2 per liter usually obtained with Methanobacterium thermoautotrophicum and approximately 10-fold higher than what was previously reported for the best aerobic actinomycetes. An improved chromatography system using rapidly flowing quaternary aminoethyl ion-exchange material and Florisil was used to more quickly and easily purify F420 than with previous methods.
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Affiliation(s)
- Dale Isabelle
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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Choi KP, Kendrick N, Daniels L. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F(420) and FO biosynthesis. J Bacteriol 2002; 184:2420-8. [PMID: 11948155 PMCID: PMC134996 DOI: 10.1128/jb.184.9.2420-2428.2002] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using the nitroimidazopyran-based antituberculosis drug PA-824 as a selective agent, transposon-generated Mycobacterium bovis strain BCG (M. bovis) mutants that could not make coenzyme F(420) were identified. Four independent mutants that could not make F(420) or the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in the M. bovis homologue of the Mycobacterium tuberculosis gene Rv1173, which we have named fbiC. Complementation of an M. bovis FbiC(-) mutant with fbiC restored the F(420) phenotype. These data demonstrate that fbiC is essential for F(420) production and that FbiC participates in a portion of the F(420) biosynthetic pathway between pyrimidinedione and FO. Homologues of fbiC were found in all 11 microorganisms that have been fully sequenced and that are known to make F(420). Four of these homologues (all from members of the aerobic actinomycetes) coded for proteins homologous over the entire length of the M. bovis FbiC, but in seven microorganisms two separate genes were found to code for proteins homologous with either the N-terminal or C-terminal portions of the M. bovis FbiC. Histidine-tagged FbiC overexpressed in Escherichia coli produced a fusion protein of the molecular mass predicted from the M. bovis BCG sequence (approximately 95,000 Da), as well as three other histidine-tagged proteins of significantly smaller size, which are thought to be proteolysis products of the FbiC fusion protein.
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Affiliation(s)
- Kwang-Pil Choi
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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17
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Choi KP, Bair TB, Bae YM, Daniels L. Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG. J Bacteriol 2001; 183:7058-66. [PMID: 11717263 PMCID: PMC95553 DOI: 10.1128/jb.183.24.7058-7066.2001] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three transposon Tn5367 mutagenesis vectors (phAE94, pPR28, and pPR29) were used to create a collection of insertion mutants of Mycobacterium bovis strain BCG. A strategy to select for transposon-generated mutants that cannot make coenzyme F(420) was developed using the nitroimidazopyran-based antituberculosis drug PA-824. One-third of 134 PA-824-resistant mutants were defective in F(420) accumulation. Two mutants that could not make F(420)-5,6 but which made the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in two adjacent homologues of Mycobacterium tuberculosis genes, which we have named fbiA and fbiB for F(420) biosynthesis. Homologues of fbiA were found in all seven microorganisms that have been fully sequenced and annotated and that are known to make F(420). fbiB homologues were found in all but one such organism. Complementation of the fbiA mutant with fbiAB and complementation of the fbiB mutant with fbiB both restored the F(420)-5,6 phenotype. Complementation of the fbiA mutant with fbiA or fbiB alone did not restore the F(420)-5,6 phenotype, but the fbiA mutant complemented with fbiA produced F(420)-2,3,4 at levels similar to F(420)-5,6 made by the wild-type strain, but produced much less F(420)-5. These data demonstrate that both genes are essential for normal F(420)-5,6 production and suggest that the fbiA mutation has a partial polar effect on fbiB. Reverse transcription-PCR data demonstrated that fbiA and fbiB constitute an operon. However, very low levels of fbiB mRNA are produced by the fbiA mutant, suggesting that a low-level alternative start site is located upstream of fbiB. The specific reactions catalyzed by FbiA and FbiB are unknown, but both function between FO and F(420)-5,6, since FO is made by both mutants.
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Affiliation(s)
- K P Choi
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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18
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Membrane-bound F420H2-dependent heterodisulfide reductase in methanogenic bacterium strain Göl andMethanolobus tindarius. FEBS Lett 2001. [DOI: 10.1016/0014-5793(90)80670-e] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Zirngibl C, Hedderich R, Thauer R. N5,N10-Methylenetetrahydromethanopterin dehydrogenase fromMethanobacterium thermoautotrophicumhas hydrogenase activity. FEBS Lett 2001. [DOI: 10.1016/0014-5793(90)80649-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Formylmethanofuran dehydrogenase activity in cell extracts ofMethanobacterium thermoautotrophicumand ofMethanosarcina barkeri. FEBS Lett 2001. [DOI: 10.1016/0014-5793(89)81153-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Abstract
The established pathway for the last two steps in purine biosynthesis, the conversion of 5-aminoimidazole-4-carboxamide ribonucleotide (ZMP) to IMP, is known to utilize 10-formyl-tetrahydrofolate as the required C1 donor cofactor. The biosynthetic conversion of ZMP to IMP in three members of the domain Archaea, Methanobacterium thermoautotrophicum deltaH, M. thermoautotrophicum Marburg, and Sulfolobus solfataricus, however, has been demonstrated to occur with only formate and ATP serving as cofactors. Thus, in these archaea, which use methanopterin (MPT) or another modified folate in place of folate as the C1 carrier coenzyme, neither folate nor a modified folate serves as a cofactor for this biosynthetic transformation. It is concluded that archaea, which function with modified folates such as MPT, are able to carry out purine biosynthesis without the involvement of folates or modified folates.
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Affiliation(s)
- R H White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA.
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22
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White RH. Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus. Biochemistry 1993; 32:745-53. [PMID: 8422380 DOI: 10.1021/bi00054a003] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The structures of the modified folates present in Pyrococcus furiosus have been determined. This was accomplished largely by the characterization of the arylamines resulting from the air oxidative cleavage of the reduced modified folates present in these cells, using both chemical and enzymatic methods. Cell extracts separated on DEAE-Sephadex columns showed one major peak containing the arylamines derived from the modified folates. These arylamines were not retained on the DEAE-Sephadex columns, indicating that they contained no net negative charge. Purification of the azo dye derivatives of these arylamines on a Bio-Gel P-6 column showed the presence of three different compounds (compounds 1, 2, and 3) in an average amount of 4.1, 7.6, and 22 nmol/g dry weight of cells, respectively. Each of these compounds readily underwent mild acid hydrolysis (0.1 M HCl, 110 degrees C, 1 min) to produce the azo dye derivative of 5-(p-aminophenyl)-1,2,3,4-tetrahydroxypentane (pAPT). The structure and stereochemistry (ribo) of the pAPT was the same as the pAPT present in methanopterin. In addition, compounds 1, 2, and 3 were each shown to contain 1 mol equiv of ribose and 1, 2, and 3 mol equiv of N-acetylglucosamine (gluNAc), respectively, and were designated as the azo dye derivatives of pAPT-ribose-gluNAc, pAPT-ribose-(gluNAc)2, and pAPT-ribose-(gluNAc)3. Each of these compounds was readily cleaved to the azo dye derivative of pAPT-ribose by the enzymatic action of beta-N-acetylglucosaminidase, indicating that all the gluNAc residues were beta-linked.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- R H White
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308
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23
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Chapter 4 Bioenergetics and transport in methanogens and related thermophilic archaea. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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25
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Blaut M, Müller V, Gottschalk G. Energetics of methanogenesis studied in vesicular systems. J Bioenerg Biomembr 1992; 24:529-46. [PMID: 1459985 DOI: 10.1007/bf00762346] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methanogenesis is restricted to a group of prokaryotic microorganisms which thrive in strictly anaerobic habitats where they play an indispensable role in the anaerobic food chain. Methanogenic bacteria possess a number of unique cofactors and coenzymes that play an important role in their specialized metabolism. Methanogenesis from a number of simple substrates such as H2 + CO2, formate, methanol, methylamines, and acetate is associated with the generation of transmembrane electrochemical gradients of protons and sodium ions which serve as driving force for a number of processes such as the synthesis of ATP via an ATP synthase, reverse electron transfer, and solute uptake. Several unique reactions of the methanogenic pathways have been identified that are involved in energy transduction. Their role and importance for the methanogenic metabolism are described.
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Affiliation(s)
- M Blaut
- Institut für Mikrobiologie, Georg-August-Universität Göttingen, Germany
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26
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von Bünau R, Zirngibl C, Thauer RK, Klein A. Hydrogen-forming and coenzyme-F420-reducing methylene tetrahydromethanopterin dehydrogenase are genetically distinct enzymes in Methanobacterium thermoautotrophicum (Marburg). EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:1205-8. [PMID: 1765081 DOI: 10.1111/j.1432-1033.1991.tb16491.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A coenzyme-F420-reducing and an H2-forming methylenetetrahydromethanopterin dehydrogenase have been isolated from Methanobacterium thermoautotrophicum (Marburg). Indirect evidence suggested that the former enzyme (32 kDa) might be derived from the latter enzyme (42 kDa) by proteolysis. To test this hypothesis the gene sequence of the H2-forming dehydrogenase was determined and compared with the N-terminal amino acid sequence of the F420-reducing dehydrogenase. No corresponding sequences were found indicating that the two dehydrogenases are genetically distinct enzymes. With purified enzyme preparations it is shown that the activity of the F420-reducing dehydrogenase is inhibited in the presence of the H2-forming enzyme. This finding is discussed in terms of substrate competition.
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Affiliation(s)
- R von Bünau
- Molekulargenetik, Fachbereich Biologie, Philipps-Universität Marburg, Lahn, Federal Republic of Germany
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27
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te Brömmelstroet BW, Geerts WJ, Keltjens JT, van der Drift C, Vogels GD. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1079:293-302. [PMID: 1911853 DOI: 10.1016/0167-4838(91)90072-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
5,10-Methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase have been purified to homogeneity by a factor of 86 and 68, respectively, from methanol-grown Methanosarcina barkeri cells. The dehydrogenase was isolated as a hexamer of a single 35 kDa subunit, whereas the reductase was composed of four identical 38 kDa subunits. The purified oxygen-stable enzymes catalyzed the oxidation of 5,10-methylenetetrahydromethanopterin and methyltetrahydromethanopterin with Vmax values of 3000 and 200 mumol min-1 mg-1, respectively. The methanogenic electron carrier coenzyme F420 was a specific electron acceptor for both enzymes. Steady state kinetics for the two enzymes were in agreement with ternary complex (sequential) mechanisms. Methylene reductase and methylene dehydrogenase are proposed to function in the methanol oxidation step to CO2.
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Affiliation(s)
- B W te Brömmelstroet
- Department of Microbiology, Faculty of Science, University of Nijmegen, The Netherlands
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28
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Coenzyme F420 dependent N5, N10-methylenetetrahydromethanopterin dehydrogenase in methanol grown Methanosarcina barkeri. Arch Microbiol 1991. [DOI: 10.1007/bf00244966] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Activities of formylmethanofuran dehydrogenase, methylenetetrahydromethanopterin dehydrogenase, methylenetetrahydromethanopterin reductase, and heterodisulfide reductase in methanogenic bacteria. Arch Microbiol 1991. [DOI: 10.1007/bf00244962] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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te Brömmelstroet BW, Hensgens CM, Keltjens JT, van der Drift C, Vogels GD. Purification and characterization of coenzyme F420-dependent 5,10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum strain delta H. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1073:77-84. [PMID: 1991149 DOI: 10.1016/0304-4165(91)90185-j] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
5,10-Methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum strain delta H was purified to homogeneity with nearly complete recovery. The aerobically stable monofunctional enzyme catalyzed the reversible oxidation of 5,10-methylene-5,6,7,8-tetrahydromethanopterin to its 5,10-methenyl derivative. For the reaction a midpoint potential E'0 = - 362 mV was calculated at 60 degrees C. The methanogenic electron carrier coenzyme F420 was strictly required as the co-substrate. The dehydrogenase (Mr 216,000) was purified as an apparent hexamer of six identical 36 kDa subunits. Oxidation of 5,10-methylenetetrahydromethanopterin coupled to coenzyme F420 reduction catalyzed by the dehydrogenase with a turnover number of 2400 S-1 proceeded via a ternary complex mechanism. High concentrations of monovalent cations markedly stimulated the reaction.
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Affiliation(s)
- B W te Brömmelstroet
- Department of Microbiology, Faculty of Science; University of Nijmegen, The Netherlands
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31
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Keltjens JT, Brömmelstroet BW, Kengen S, Drift C, Vogels GD. 5,6,7,8-Tetrahydromethanopterin-dependent enzymes involved in methanogenesis. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04932.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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32
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Abstract
The biosynthetic pathway for the generation of the methylated pterin in methanopterins was determined for the methanogenic bacteria Methanococcus volta and Methanobacterium formicicum. Extracts of M. volta were found to readily cleave L-7,8-dihydroneopterin to 7,8-dihydro-6-(hydroxymethyl)pterin, which was confirmed to be a precursor of the pterin portion of the methanopterin. [methylene-2H]-6-(Hydroxymethyl)pterin was incorporated into methanopterin by growing cells of M. volta to an extent of 30%. Both the C-11 and C-12 methyl groups of methanopterin originate from [methyl-2H3]methionine, as confirmed by the incorporation of two C2H3 groups into 6-ethyl-7-methylpterin, a pterin-containing fragment derived from methanopterin. Cells grown in the presence of [methylene-2H]-6-(hydroxymethyl)pterin, [ethyl-2H4]-6-[1 (RS)-hydroxyethyl]pterin, [methyl-2H3]-6- (hydroxymethyl)-7-methylpterin, [ethyl-2H4, methyl-2H3]-6-[1 (RS)-hydroxyethyl]-7-methylpterin, and [1-ethyl-3H]-6-[1 (RS)-hydroxyethyl]-7-methylpterin showed that only the non-7-methylated pterins were incorporated into methanopterin. Cells extracts of M. formicicum readily condensed synthetic [methylene-3H]-7,8-H2-6-(hydroxymethyl)pterin-PP with methaniline to generate demethylated methanopterin, which is then methylated to methanopterin by the cell extract in the presence of S-adenosylmethionine. These observations indicate that the pterin portion of methanopterin is biosynthetically derived from 7,8-H2-6-(hydroxymethyl)pterin, which is coupled to methaniline by a pathway analogous to the biosynthesis of folic acid. This pathway for the biosynthesis of methanopterin represents the first example of the modification of the specificity of a coenzyme through a methylation reaction.
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Affiliation(s)
- R H White
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061
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33
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Jablonski PE, DiMarco AA, Bobik TA, Cabell MC, Ferry JG. Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila. J Bacteriol 1990; 172:1271-5. [PMID: 2307649 PMCID: PMC208594 DOI: 10.1128/jb.172.3.1271-1275.1990] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cell extract protein content of acetate- and methanol-grown Methanosarcina thermophila TM-1 was examined by two-dimensional polyacrylamide gel electrophoresis. More than 100 mutually exclusive spots were present in acetate- and methanol-grown cells. Spots corresponding to acetate kinase, phosphotransacetylase, and the five subunits of the carbon monoxide dehydrogenase complex were identified in acetate-grown cells. Activities of formylmethanofuran dehydrogenase, formylmethanofuran:tetrahydromethanopterin formyltransferase, 5,10-methenyltetrahydromethanopterin cyclohydrolase, methylene tetrahydromethanopterin:coenzyme F420 oxidoreductase, formate dehydrogenase, and carbonic anhydrase were examined in acetate- and methanol-grown Methanosarcina thermophila. Levels of formyltransferase in either acetate- or methanol-grown Methanosarcina thermophila were approximately half the levels detected in H2-CO2-grown Methanobacterium thermoautotrophicum. All other enzyme activities were significantly lower in acetate- and methanol-grown Methanosarcina thermophila.
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Affiliation(s)
- P E Jablonski
- Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg 24061-0305
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34
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te Brömmelstroet BW, Hensgens CM, Geerts WJ, Keltjens JT, van der Drift C, Vogels GD. Purification and properties of 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri. J Bacteriol 1990; 172:564-71. [PMID: 2298699 PMCID: PMC208478 DOI: 10.1128/jb.172.2.564-571.1990] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri was purified 313-fold to a specific activity of 470 mumol min-1 mg-1 at 37 degrees C and pH 7.8. At this stage, the enzyme was pure as judged from polyacrylamide gel electrophoresis. The monofunctional enzyme was oxygen stable, but the presence of a detergent proved to be essential for its stability. Like the cyclohydrolase purified from Methanobacterium thermoautotrophicum (A. A. Dimarco, M. I. Donnelly, and R. S. Wolfe, J. Bacteriol. 168:1372-1377, 1986), the protein showed an apparent Mr of 82,000, and it is composed of two identical subunits as was concluded from nondenaturating and denaturating polyacrylamide gel electrophoresis. The enzymes from M. thermoautotrophicum and M. barkeri markedly differ with respect to the hydrolysis product of 5,10-methenyltetrahydromethanopterin: 5-formyl- and 10-formyltetrahydromethanopterin, respectively. The apparent Km for 5,10-methenyltetrahydromethanopterin was 0.57 mM at 37 degrees C and pH 7.8.
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Affiliation(s)
- B W te Brömmelstroet
- Department of Microbiology, Faculty of Science, University of Nijmegen, The Netherlands
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35
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te Brömmelstroet BW, Hensgens CM, Keltjens JT, van der Drift C, Vogels GD. Purification and properties of 5,10-methylenetetrahydromethanopterin reductase, a coenzyme F420-dependent enzyme, from Methanobacterium thermoautotrophicum strain delta H. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39907-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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36
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Raemakers-Franken PC, Kortstee AJ, van der Drift C, Vogels GD. Methanogenesis involving a novel carrier of C1 compounds in Methanogenium tationis. J Bacteriol 1990; 172:1157-9. [PMID: 2105296 PMCID: PMC208554 DOI: 10.1128/jb.172.2.1157-1159.1990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The pathway of CO2 reduction to methane in Methanogenium tationis and Methanogenium thermophilicum is similar to that observed in other methanogens. In M. tationis a novel pterin, tatiopterin, is present. This pterin appears to be a structural and functional analog of methanopterin and sarcinapterin. Folate could not substitute for tatiopterin.
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Affiliation(s)
- P C Raemakers-Franken
- Department of Microbiology, Faculty of Science, University of Nijmegen, The Netherlands
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37
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Affiliation(s)
- A D Moodie
- Department of Biochemistry and Microbiology, University of St Andrews, UK
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38
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DiMarco AA, Sment KA, Konisky J, Wolfe RS. The formylmethanofuran:tetrahydromethanopterin formyltransferase from Methanobacterium thermoautotrophicum delta H. Nucleotide sequence and functional expression of the cloned gene. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40254-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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39
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Abstract
In this review, I focus on the bioenergetics of the methanogenic bacteria, with particular attention directed to the roles of transmembrane electrochemical gradients of sodium and proton. In addition, the mechanism of coupling ATP synthesis to methanogenic electron transfer is addressed. Evidence is reviewed which suggests that the methanogens possess great diversity in their bioenergetic machinery. In particular, in some methanogens the primary ion which is translocated coupled to metabolic energy is the proton, while others appear to utilize sodium. In addition, ATP synthesis driven by methanogenic electron transfer is accomplished in some organisms by a chemiosmotic mechanism and is coupled by a more direct mechanism in others. A possible explanation for this diversity (which is consistent with the relatedness of these organisms to each other and to other members of the Archaebacteria as determined by molecular biological techniques) is discussed.
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Affiliation(s)
- J R Lancaster
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300
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40
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Widdel F, Wolfe RS. Expression of secondary alcohol dehydrogenase in methanogenic bacteria and purification of the F420-specific enzyme from Methanogenium thermophilum strain TCI. Arch Microbiol 1989. [DOI: 10.1007/bf00425168] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Kaesler B, Schönheit P. The role of sodium ions in methanogenesis. Formaldehyde oxidation to CO2 and 2H2 in methanogenic bacteria is coupled with primary electrogenic Na+ translocation at a stoichiometry of 2-3 Na+/CO2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 184:223-32. [PMID: 2550228 DOI: 10.1111/j.1432-1033.1989.tb15010.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cell suspensions of Methanosarcina barkeri were found to oxidize formaldehyde to CO2 and 2H2 (delta G0' = -27 kJ/mol CO2), when methanogenesis was inhibited by 2-bromoethanesulfonate. We report here that this reaction is coupled with (a) primary electrogenic Na+ translocation at a stoichiometry of 2-3 Na+/CO2, (b) with secondary H+ translocation via a Na+/H+ antiporter and (c) with ATP synthesis driven by an electrochemical proton potential. This is concluded from the following findings. Formaldehyde oxidation to CO2 and 2H2 was dependent on Na+ ions, 2-3 mol Na+/mol formaldehyde oxidized were extruded. Na+ translocation was inhibited by Na+ ionophores, but not affected by protonophores of Na+/H+ antiport inhibitors. Formaldehyde oxidation was associated with the build up of a membrane potential in the order of 100 mV (inside negative), which could be dissipated by sodium ionophores rather than by protonophores. Formaldehyde oxidation was coupled with ATP synthesis, which could be inhibited by Na+ ionophores, Na+/H+ antiport inhibitors, by protonophores and by the H+-translocating-ATP-synthase inhibitor, dicyclohexylcarbodiimide. With cell suspensions of Methanobacterium thermoautotrophicum similar results were obtained.
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Affiliation(s)
- B Kaesler
- Fachbereich Biologie-Mikrobiologie, Philipps-Universität Marburg
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42
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Function of methanofuran, tetrahydromethanopterin, and coenzyme F420 in Archaeoglobus fulgidus. Arch Microbiol 1989. [DOI: 10.1007/bf00425174] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Kengen S, Keltjens JT, Vogels GD. The ATP-dependent synthesis of factor 390 by cell-free extracts of Methanobacterium thermoautotrophicum(strain ÎH). FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03409.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Baron SF, Ferry JG. Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum. J Bacteriol 1989; 171:3846-53. [PMID: 2738024 PMCID: PMC210134 DOI: 10.1128/jb.171.7.3846-3853.1989] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The membrane-associated coenzyme F420-reducing hydrogenase of Methanobacterium formicicum was purified 87-fold to electrophoretic homogeneity. The enzyme contained alpha, beta, and gamma subunits (molecular weights of 43,000, 36,700, and 28,800, respectively) and formed aggregates (molecular weight, 1,020,000) of a coenzyme F420-active alpha 1 beta 1 gamma 1 trimer (molecular weight, 109,000). The hydrogenase contained 1 mol of flavin adenine dinucleotide (FAD), 1 mol of nickel, 12 to 14 mol of iron, and 11 mol of acid-labile sulfide per mol of the 109,000-molecular-weight species, but no selenium. The isoelectric point was 5.6. The amino acid sequence I-N3-P-N2-R-N1-EGH-N6-V (where N is any amino acid) was conserved in the N-termini of the alpha subunits of the F420-hydrogenases from M. formicicum and Methanobacterium thermoautotrophicum and of the largest subunits of nickel-containing hydrogenases from Desulfovibrio baculatus, Desulfovibrio gigas, and Rhodobacter capsulatus. The purified F420-hydrogenase required reductive reactivation before assay. FAD dissociated from the enzyme during reactivation unless potassium salts were present, yielding deflavoenzyme that was unable to reduce coenzyme F420. Maximal coenzyme F420-reducing activity was obtained at 55 degrees C and pH 7.0 to 7.5, and with 0.2 to 0.8 M KCl in the reaction mixture. The enzyme catalyzed H2 production at a rate threefold lower than that for H2 uptake and reduced coenzyme F420, methyl viologen, flavins, and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Specific antiserum inhibited the coenzyme F420-dependent but not the methyl viologen-dependent activity of the purified enzyme.
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Affiliation(s)
- S F Baron
- Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg 24061
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Fischer R, Thauer RK. Methyltetrahydromethanopterin as an intermediate in methanogenesis from acetate in Methanosarcina barkeri. Arch Microbiol 1989. [DOI: 10.1007/bf00416607] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bobik TA, Wolfe RS. Activation of formylmethanofuran synthesis in cell extracts of Methanobacterium thermoautotrophicum. J Bacteriol 1989; 171:1423-7. [PMID: 2921239 PMCID: PMC209762 DOI: 10.1128/jb.171.3.1423-1427.1989] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In cell extracts of Methanobacterium thermoautotrophicum, formylmethanofuran (formyl-MFR) synthesis (an essential CO2 fixation reaction that is an early step in CO2 reduction to methane) is subject to a complex activation that involves a heterodisulfide of coenzyme M and N-(7-mercaptoheptanoyl)threonine O3-phosphate (CoM-S-S-HTP). In this paper we report that titanium(III) citrate, a low-potential reducing agent, stimulated CO2 reduction to methane and activated formyl-MFR synthesis in cell extracts. Titanium(III) citrate functioned as the sole source of electrons for formyl-MFR synthesis and enabled this reaction to occur independently of CoM-S-S-HTP. In addition, CoM-S-S-HTP was found to activate an unknown electron carrier that reduced metronidazole. The activation of formyl-MFR synthesis by CoM-S-S-HTP may involve the activation of a low-potential electron carrier.
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Affiliation(s)
- T A Bobik
- Department of Microbiology, University of Illinois, Urbana 61801
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Baron SF, Williams DS, May HD, Patel PS, Aldrich HC, Ferry JG. Immunogold localization of coenzyme F420-reducing formate dehydrogenase and coenzyme F420-reducing hydrogenase in Methanobacterium formicicum. Arch Microbiol 1989. [DOI: 10.1007/bf00406556] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Webb EC. Enzyme nomenclature. Recommendations 1984. Supplement 2: corrections and additions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 179:489-533. [PMID: 2920724 DOI: 10.1111/j.1432-1033.1989.tb14579.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- E C Webb
- Nomenclature Committe of the International Union od Biochemistry (NC-IUB)
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Rogers KR, Gillies K, Lancaster JR. Iron-sulfur centers involved in methanogenic electron transfer in Methanobacterium thermoautotrophicum (delta-H). Biochem Biophys Res Commun 1988; 153:87-95. [PMID: 2837216 DOI: 10.1016/s0006-291x(88)81193-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Utilizing a subcellular particulate preparation from Methanobacterium thermoautotrophicum (delta-H) which contains all detectable methanogenic electron transfer activity, we present the results of the effects of the anaerobic addition of oxidized factor F420 and of methyl coenzyme M plus ATP on the EPR signals from reduced iron-sulfur centers and a rapidly-relaxing radical species. Based on these results, we report the existence of a minimum of three iron-sulfur centers which are capable of donating electrons to these cofactors.
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Affiliation(s)
- K R Rogers
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300
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