Bioinformatic and Functional Analysis of the pSID Siderophore Biosynthesis Plasmid of Rhodococcus pyridinivorans 5Ap

Abstract—

Complete genome sequencing of R. pyridinivorans strain 5Ap revealed the pSID plasmid (CP063453.1) 250 428 bp in size. The gene responsible for replication of this plasmid is, most probably, dnaB. The genes which may be involved in the replication (dnaB, ssb) and plasmid separation after replication (parA) showed the highest similarity to the determinants located on large (224‒343 kb) plasmids of rhodococci: unnamed1 of R. pyridinivorans YF3, unnamed1 of R. rhodochrous LH-B3, pRJH1 of R. pyridinivorans YC-JH2, pRDE01 of Rhodococcus sp. RDE2, and pRho-VOC14-C342 of R. opacus VOC-14. The pSID plasmid was found to contain two loci responsible for the synthesis of secondary metabolites, one of them determining the synthesis of a polyketide compound (similar sequences have been revealed on plasmids of other rhodococci) and the other one probably determines the synthesis of a siderophore: the genes for biosynthesis of this compound (sid1–5) exhibited the highest similarity (not exceeding 75%) with the sequences from Streptomyces vilmorinianum YP1 (CP040244.1), S. ficellus NRRL 8067 (CP034279.1), Streptomyces sp. NBC00162 (CP102509.1), and some other streptomycetes, while showing no similarity to the known siderophore biosynthesis genes of rhodococci. The locus of the pSID plasmid responsible for the siderophore synthesis had a unique organization, since transcription of the sid5 (iucC) gene occurs in the opposite direction, while in other bacteria it belongs to an operon and is located at one of its termini. Inactivation of the sid1 gene was found to result in decreased antagonistic activity of R. pyridinivorans 5Ap against plant-pathogenic bacteria P. carotovorum 2.18, lower resistance to iron and cadmium ions and arsenate, as well as in emergence of phytotoxic properties against radish, while wild-type bacteria exhibit plant growth-promoting activity.