RRC ID 47264
Author Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT.
Title Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria.
Journal Microbes Environ
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.
Volume 31(3)
Pages 288-92
Published 2016-9-29
DOI 10.1264/jsme2.ME16057
PMID 27431485
PMC PMC5017805
MeSH Biotransformation Butyrates / metabolism* Clostridiales / genetics* Clostridiales / metabolism* Genome, Bacterial* Genomics Isobutyrates / metabolism* Metabolic Networks and Pathways*
IF 2.575
Times Cited 11
DNA material Genomic DNA of Syntrophomonas wolfei subsp. methylbutyratica JCM 14075T (JGD12758).
General Microbes