Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen,
            <i>Eubacterium limosum</i>
            KIST612

Roh, Hanseong; Ko, Hyeok Jin; Kim, Dae–Hee; Choi, Dong Geon; Park, Shinyoung; Kim, Sujin; Chang, In Seop; Choi, In Geol

doi:10.1128/jb.01217-10

Cited by 69 publications

(40 citation statements)

References 15 publications

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“…We searched the published genome sequence of E. limosum strain KIST612 (16) for genes located downstream of the regulatory elements known as cobalamin riboswitches. These regulatory sequences are commonly found adjacent to genes involved in cobamide biosynthesis and transport, including bluB (3,17).…”

Section: Identification Of Putative Dmb Biosynthesis Genes Adjacent Tomentioning

confidence: 99%

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂

Hazra

Han

Mehta

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

102

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Vitamin B 12 (cobalamin) is required by humans and other organisms for diverse metabolic processes, although only a subset of prokaryotes is capable of synthesizing B 12 and other cobamide cofactors. The complete aerobic and anaerobic pathways for the de novo biosynthesis of B 12 are known, with the exception of the steps leading to the anaerobic biosynthesis of the lower ligand, 5,6-dimethylbenzimidazole (DMB). Here, we report the identification and characterization of the complete pathway for anaerobic DMB biosynthesis. This pathway, identified in the obligate anaerobic bacterium Eubacterium limosum, is composed of five previously uncharacterized genes, bzaABCDE, that together direct DMB production when expressed in anaerobically cultured Escherichia coli. Expression of different combinations of the bza genes revealed that 5-hydroxybenzimidazole, 5-methoxybenzimidazole, and 5-methoxy-6-methylbenzimidazole, all of which are lower ligands of cobamides produced by other organisms, are intermediates in the pathway. The bza gene content of several bacterial and archaeal genomes is consistent with experimentally determined structures of the benzimidazoles produced by these organisms, indicating that these genes can be used to predict cobamide structure. The identification of the bza genes thus represents the last remaining unknown component of the biosynthetic pathway for not only B 12 itself, but also for three other cobamide lower ligands whose biosynthesis was previously unknown. Given the importance of cobamides in environmental, industrial, and human-associated microbial metabolism, the ability to predict cobamide structure may lead to an improved ability to understand and manipulate microbial metabolism.

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Section: Identification Of Putative Dmb Biosynthesis Genes Adjacent Tomentioning

confidence: 99%

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂

Hazra

Han

Mehta

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

102

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“…While only a single acetogen had been sequenced before mid-2010, several genome sequences have since been released [91,101,102,144,173,174,228]. However, only very few transcriptomic studies have been published to date [54,176], looking at certain sets of genes rather than gene expression on a global basis.…”

Section: Strain Improvementmentioning

confidence: 99%

Commercial Biomass Syngas Fermentation

2012

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Abstract:The use of gas fermentation for the production of low carbon biofuels such as ethanol or butanol from lignocellulosic biomass is an area currently undergoing intensive research and development, with the first commercial units expected to commence operation in the near future. In this process, biomass is first converted into carbon monoxide (CO) and hydrogen (H 2 )-rich synthesis gas (syngas) via gasification, and subsequently fermented to hydrocarbons by acetogenic bacteria. Several studies have been performed over the last few years to optimise both biomass gasification and syngas fermentation with significant progress being reported in both areas. While challenges associated with the scale-up and operation of this novel process remain, this strategy offers numerous advantages compared with established fermentation and purely thermochemical approaches to biofuel production in terms of feedstock flexibility and production cost. In recent times, metabolic engineering and synthetic biology techniques have been applied to gas fermenting organisms, paving the way for gases to be used as the feedstock for the commercial production of increasingly energy dense fuels and more valuable chemicals.

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“…Eubacterium limosum KIST612 is a Gram-positive acetogen that grows on syngas, H 2 ϩ CO 2 or CO (16,17). Interestingly, during growth on CO it produces butyrate alongside acetate (18).…”

mentioning

confidence: 99%

Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612

Jeong

Bertsch

Hess

et al. 2015

Appl Environ Microbiol

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c Eubacterium limosum KIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. We have used a genome-guided analysis to delineate the path of butyrate formation, the enzymes involved, and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the acetyl-coenzyme A (CoA) synthase/CO dehydrogenase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex and Na ؉ dependent. Consistent with the finding of a Na ؉ -dependent Rnf complex is the presence of a conserved Na ؉ -binding motif in the c subunit of the ATP synthase. Butyrate formation is from acetyl-CoA via acetoacetyl-CoA, hydroxybutyryl-CoA, crotonyl-CoA, and butyryl-CoA and is consistent with the finding of a gene cluster that encodes the enzymes for this pathway. The activity of the butyryl-CoA dehydrogenase was demonstrated. Reduction of crotonyl-CoA to butyryl-CoA with NADH as the reductant was coupled to reduction of ferredoxin. We postulate that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding of etfA and etfB genes next to it. The overall ATP yield was calculated and is significantly higher than the one obtained with H 2 ؉ CO 2 . The energetic benefit may be one reason that butyrate is formed only from CO but not from H 2 ؉ CO 2 .A cetogenic bacteria are a phylogenetically diverse group of strictly anaerobic bacteria able to reduce two molecules of CO 2 to acetate by the Wood-Ljungdahl pathway (WLP) (1-4). Electrons may derive from molecular hydrogen (autotrophic growth), from carbon monoxide, or from organic donors (heterotrophic growth) such as hexoses, pentoses, formate, lactate, alcohols, or methyl group donors (1). Not only does the WLP provide the cell with organic material for biomass formation, but it is also coupled to energy conservation for ATP supply by a chemiosmotic mechanism (2, 5). Every acetogen examined to date uses reduced ferredoxin (Fd) as the electron donor for an ion-translocating membrane protein complex, and acetogens can have either an Fd:NAD ϩ oxidoreductase (Rnf) or an Fd:H ϩ oxidoreductase (Ech) complex for generation of an ion motive force (5). In both cases, the ion gradient can be either an H ϩ or an Na ϩ gradient. The electrochemical ion gradient thus established is then used by a membrane bound, H ϩ -or Na ϩ -translocating F 1 F o ATP synthase (2).Acetate production from CO 2 proceeds via formate that is converted to formyl-tetrahydrofolate (THF) in an ATP-consuming reaction (6). Water is split off from formyl-THF to yield methenyl-THF, which is reduced via methylene-THF to methyl-THF. The latter is condensed with CO (derived from another molecule of CO 2 ) and coenzyme A (CoA) to acetyl-CoA, which is the starting molecule for biosynthetic reactions (4,7,8). Acetyl-CoA is also the precursor of the end product, acetate, that is produced by the enzymes acetyltransferase and acetate kinase. ATP production in the acetate kinase reaction is of special...

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Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen, Eubacterium limosum KIST612

Cited by 69 publications

References 15 publications

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂

Commercial Biomass Syngas Fermentation

Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612

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Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen, Eubacterium limosum KIST612

Cited by 69 publications

References 15 publications

Anaerobic biosynthesis of the lower ligand of vitamin B 12

Anaerobic biosynthesis of the lower ligand of vitamin B 12

Commercial Biomass Syngas Fermentation

Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612

Contact Info

Product

Resources

About

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂

Anaerobic biosynthesis of the lower ligand of vitamin B ₁₂