Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.
Warren
René
R
Genome Sciences Centre, Vancouver, Canada.
Hsiao
William W L
WW
Kudo
Hisashi
H
Myhre
Matt
M
Dosanjh
Manisha
M
Petrescu
Anca
A
Kobayashi
Hiroyuki
H
Shimizu
Satoru
S
Miyauchi
Keisuke
K
Masai
Eiji
E
Yang
George
G
Stott
Jeff M
JM
Schein
Jacquie E
JE
Shin
Heesun
H
Khattra
Jaswinder
J
Smailus
Duane
D
Butterfield
Yaron S
YS
Siddiqui
Asim
A
Holt
Robert
R
Marra
Marco A
MA
Jones
Steven J M
SJ
Mohn
William W
WW
Brinkman
Fiona S L
FS
Fukuda
Masao
M
Davies
Julian
J
Eltis
Lindsay D
LD
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001673:Biodegradation, Environmental; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D022761:Gene Transfer, Horizontal; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D011078:Polychlorinated Biphenyls / Q000378:metabolism*; D018741:Replication Origin; D012240:Rhodococcus / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D016615:Telomere
D001426:Bacterial Proteins; D003577:Cytochrome P-450 Enzyme System; D011078:Polychlorinated Biphenyls