title: Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria.
abstract: The syntrophic degradation of branched-chain fatty acids (BCFAs) such as 2-methylbutyrate and isobutyrate is an essential step in the production of methane from proteins/amino acids in anaerobic ecosystems. While a few syntrophic BCFA-degrading bacteria have been isolated, their metabolic pathways in BCFA and short-chain fatty acid (SCFA) degradation as well as energy conservation systems remain unclear. In an attempt to identify these pathways, we herein performed comparative genomics of three syntrophic bacteria: 2-methylbutyrate-degrading "Syntrophomonas wolfei subsp. methylbutyratica" strain JCM 14075(T) (=4J5(T)), isobutyrate-degrading Syntrophothermus lipocalidus strain TGB-C1(T), and non-BCFA-metabolizing S. wolfei subsp. wolfei strain Göttingen(T). We demonstrated that 4J5 and TGB-C1 both encode multiple genes/gene clusters involved in β-oxidation, as observed in the Göttingen genome, which has multiple copies of genes associated with butyrate degradation. The 4J5 genome possesses phylogenetically distinct β-oxidation genes, which may be involved in 2-methylbutyrate degradation. In addition, these Syntrophomonadaceae strains harbor various hydrogen/formate generation systems (i.e., electron-bifurcating hydrogenase, formate dehydrogenase, and membrane-bound hydrogenase) and energy-conserving electron transport systems, including electron transfer flavoprotein (ETF)-linked acyl-CoA dehydrogenase, ETF-linked iron-sulfur binding reductase, ETF dehydrogenase (FixABCX), and flavin oxidoreductase-heterodisulfide reductase (Flox-Hdr). Unexpectedly, the TGB-C1 genome encodes a nitrogenase complex, which may function as an alternative H2 generation mechanism. These results suggest that the BCFA-degrading syntrophic strains 4J5 and TGB-C1 possess specific β-oxidation-related enzymes for BCFA oxidation as well as appropriate energy conservation systems to perform thermodynamically unfavorable syntrophic metabolism.
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
authors.forename: Takashi
authors.initials: T
authors.lastname: Narihiro
authors.forename: Masaru K
authors.initials: MK
authors.lastname: Nobu
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Tamaki
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sekiguchi
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
mesh_terms: D001711:Biotransformation; D002087:Butyrates / Q000378:metabolism*; D000068016:Eubacteriales / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D023281:Genomics; D058610:Isobutyrates / Q000378:metabolism*; D053858:Metabolic Networks and Pathways
chemical_list: D002087:Butyrates; D058610:Isobutyrates; C020380:isobutyric acid; C019475:2-methylbutanoic acid