Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4

Abstract

Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.

TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12

“…Though a putative relaxase function has been predicted by a recent Rhodococcus megaplasmid sequencing eVort (Sekine et al, 2006), the present study is the Wrst genetic analysis of a determinant of megaplasmid conjugation in Rhodococcus. It is known that the transesteriWcation reaction carried out by all relaxases characterized thus far is dependent on the action and proximity of 3 or 4 key residues at the active site, one of which is the absolutely conserved catalytic tyrosine residue required for the formation of a covalent phosphotyrosyl bond between DNA and protein (Larkin et al, 2005;Pansegrau et al, 1994;Scherzinger et al, 1993;Street et al, 2003).…”

“…Not surprisingly, the putative transfer protein encoded by orf16 (Genbank Accession No. BAE46257) from the pREC1 megaplasmid in R. erythropolis PR4 (Sekine et al, 2006) is one of the closest matches to pREA400 TraA with 34% identity over 1049 residues. The TraA (Genbank Accession No.…”

“…Analysis of pREC1 (Genbank Accession No. NC_007486) revealed that pREC1 Orf16 encodes a putative relaxase (Sekine et al, 2006). This suggests that a single-stranded DNA transfer system similar to other bacterial conjugation systems may function in the transfer of Rhodococcus megaplasmids.…”

“…The sequences and gene annotations of Wve rhodococcal megaplasmidsp33701 from Rhodococcus equi ATCC33701 (Takai et al, 2000), pBD2 from Rhodococcus erythropolis BD2 (Stecker et al, 2003), pRHL3 from Rhodococcus sp. RHA1 (Warren et al, 2004), as well as pREC1 and pREL1 from R. erythropolis PR4 (Sekine et al, 2006)-were recently completed. Analysis of pREC1 (Genbank Accession No.…”

Complete Genome Sequence of the Representative γ-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum UT26

“…One S. japonicum UT26 colony was designated UT26S (NBRC 101211), and its complete genome sequence was determined by a whole-genome shotgun sequencing strategy using the Sanger method (10,15,17). The sequences of ca.…”