PH-112 (JTK):

Genome analysis of branched chain fatty acid degrading syntrophs: “Syntrophomonas wolfei subsp. methylbutyratica” strain JCM 14075^T and Syntrophothermus lipocalidus strain TGB-C1^T

Syntrophic degradation of branched chain fatty acid (BCFA) such as 2-methylbutyrate and isobutyrate is an important step to produce methane from proteins/amino acids in anaerobic environments. To date, a few syntrophic BCFA-degrading bacteria have been isolated; however, their metabolic pathways involved in BCFA degradation and energy conservation system remain unclear. In this study, the genome of “Syntrophomonas wolfei subsp. methylbutyratica” strain JCM 14075^T, a mesophilic bacterium capable of degrading butyrate, 3-hydroxybutyrate, and 2-methylbutyrate in syntrophic cooperation with a partner methanogen, was sequenced. In addition, previously reported Syntrophothermus lipocalidus strain TGB-C1^T genome was employed to identify isobutyrate degradation pathway. The genomic DNA of strain JCM 14075^T was subjected to whole genome shotgun sequencing using Illumina MiSeq platform. We constructed and sequenced a paired-end library totaling ca. 2.2 Gb of MiSeq data. Assemblies were performed using a SPAdes software. The strain JCM 14075^T draft genome comprises of 89 scaffolds and has an estimated genome size of 3.2 Mb. More than 2,900 protein coding genes were annotated with Prokka software. We identified a gene cassette of β-oxidation pathway for the degradation of BCFA within the genomes. We also found an isobutyryl-CoA mutase gene cassette that may catalyze the isomerization of isobutyryl-CoA to butyryl-CoA within the strain TGB-C1^T genome. Both genomes encode genes associated with ion-translocating ferredoxin oxidoreductase (IFO)- and electron transfer flavoprotein (ETF)-driven hydrogen generation systems and electron confurcating hydrogenase with high similarity (more than 50% amino acid identity) to those of Syntrophomonas wolfei strain Goettingen. These findings provide genomic insights into syntrophic BCFA degradation in methanogenic ecosystems.

keywords:syntroph,genome,branched chain fatty acid,energy conservation