Project description:We performed differential RNA-sequencing (dRNA-seq) experiments in both minimal medium (MM) plus β-hydroxybutyrate (β-HB) and MM plus tetralin (THN) of Sphingopyxis granuli strain TFA. The objective was mapping the Transcription Start Site (TSS) of each gene in the genome in both conditions, detecting non-coding RNAs (ncRNAs) and comparing the gene expression profile in a preferential carbon source (β-HB) versus tetralin (an aromatic pollutant). The dRNA-seq technique consists of using a termination exonuclease (TEX) to allow the discrimination of primary and processed transcripts. Furthermore, to detect Hfq-bound RNAs we co-immunoprecipitated RNA from the wild type strain (negative control) and a TFA strain with an Hfq-3xFlag tagged version (MPO501 strain) using an anti-3xFlag antibody and performed RNA-sequencing from the precipitated RNA.
Project description:Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.