Genome analysis of branched chain fatty acid degrading syntrophs: “Syntrophomonas wolfei subsp. methylbutyratica” strain JCM 14075T and Syntrophothermus lipocalidus strain TGB-C1T
1Bioproduction Research Institute, AIST, 2University of Illinois at Urbana-Champaign
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 14075T, 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-C1T genome was employed to identify isobutyrate degradation pathway. The genomic DNA of strain JCM 14075T 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 14075T 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-C1T 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