Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA

Abstract

BackgroundSphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA.ResultsThe TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100 %) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided.ConclusionsSphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2411-1) contains supplementary material, which is available to authorized users.

Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA

“…Reads that passed these filters were mapped using 43 to generate read alignments using the Sphingopyxis granuli strain TFA genome (RefSeq: NZ_CP012199.1) as ref. 18 . Differential transcript expression was then computed using DESeq2.…”

SuhB, a small non‐coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA

“…In addition to the TSS analysis, a search was made for genes encoding sRNAs in the TFA genome using the Infernal software using the Rfam database and discarding those predictions with an e-value of ≥10 −5 (García-Romero et al, 2016). Besides ribosomal and transfer RNAs and several well-known cis-regulatory elements (e.g., the glycine, cobalamin and TPP riboswitches and the serC element), housekeeping sRNAs including the tm-RNA, 6S-RNA, RnpB and 4.5S-RNA were identified although the predicted coordinates did not always fit well with the TSS detection (Supporting Information Table S2).…”

“…Media and growth conditions Escherichia coli strains were grown aerobically in Luria-Bertani (LB) medium at 37 C. Sphingopyxis granuli strains were grown at 30 C in MML medium or MM medium (Hernáez et al, 1999) supplied with tetralin in the vapour phase, 8 or 40 mM βHB, 16 mM sebacic acid or a combination of them as the carbon and energy sources. Nitrate was added to the medium at 20 mM for anaerobic growth (García-Romero et al, 2016).…”

“…Little is known about the molecular mechanism of CCR in nonmodel bacteria such as the oligotrophic members of the Sphingomonadaceae family. Sphingopyxis granuli strain TFA is an oligotrophic α-proteobacterium whose genome has been sequenced (García-Romero et al, 2016). One of the main metabolic features of this bacterium is its ability to grow aerobically using tetralin (1,2,3,4-tetrahydronaphthalene) as the only carbon and energy source (Hernáez et al, 1999).…”

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

“…2014; Zheng et al. 2014; García-Romero et al. 2016), comprehensive analyses of these horizontally transferred “selfish genetic elements” are conspicuously missing.…”