Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5

Abstract

BackgroundOligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium capable of utilizing CO (carbon monoxide) and fixing CO2 (carbon dioxide). We previously published the draft genome of this organism and recently submitted the complete genome sequence to GenBank.ResultsThe genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5 consists of a 3.74-Mb chromosome and a 133-kb megaplasmid that contains the genes responsible for utilization of carbon monoxide, carbon dioxide, and hydrogen. To our knowledge, this strain is the first one to be sequenced in the genus Oligotropha, the closest fully sequenced relatives being Bradyrhizobium sp. BTAi and USDA110 and Nitrobacter hamburgiensis X14. Analysis of the O. carboxidovorans genome reveals potential links between plasmid-encoded chemolithoautotrophy and chromosomally-encoded lipid metabolism. Comparative analysis of O. carboxidovorans with closely related species revealed differences in metabolic pathways, particularly in carbohydrate and lipid metabolism, as well as transport pathways.ConclusionOligotropha, Bradyrhizobium sp and Nitrobacter hamburgiensis X14 are phylogenetically proximal. Although there is significant conservation of genome organization between the species, there are major differences in many metabolic pathways that reflect the adaptive strategies unique to each species.

Complete Genome Sequences of the Chemolithoautotrophic Oligotropha carboxidovorans Strains OM4 and OM5

“…The sequence of the OM5 genome reported here differs from the one reported earlier (4,5), in which only plasmid pHCG3 was described. The sequence of plasmid pOC167 has been found but has been assembled into the chromosome.…”

“…These regions appear to be suitable for homologous recombination. Correspondingly, the pOC167 sequence of the published OM5 genome has been integrated in this area of the chromosome (4,5). We verified the presence of plasmids pOC167 (OM5) and pOC167b (OM4) by PCR-based approaches.…”

The Family Bradyrhizobiaceae

“…Colonies are white or cream colored and are visible on agar plates after 1-4 weeks, depending on the medium. Oligotropha carboxidovorans is the sole species representative of the genus Oligotropha and has had its genome sequenced by Paul et al (2010).…”

C1-carbon sources for chemical and fuel production by microbial gas fermentation

“…The best-studied organism among these carboxidotrophic bacteria is the Gram-negative a-proteobacterium Oligotropha carboxidovorans (formerly Pseudomonas carboxidovorans), an aerobic facultative chemolithoautotroph, that uses an oxygen-tolerant, molybdenum-containing and copper-containing CO dehydrogenase for CO oxidation, the reductive pentose phosphate cycle for CO 2 fixation during autotrophic growth on H 2 , CO 2 and/or CO and grows organoheterotrophically with pyruvate, lactate, acetate, and other organic acids [77]. The genomes of O. carboxidovorans strains OM5 and OM4 have been sequenced, they are nearly identical and both are composed of one chromosome and two (mega)plasmids [78,79]. The genes required for carboxidotrophy, hydrogenotrophy, and CO 2 fixation reside on one of the plasmids, pHCG3 and pHCG3b in strain OM5 and OM4, respectively, and it has been shown that expression of these genes and the proteome adapts to the chemolithoautotrophic or heterotrophic lifestyle [80,81].…”