The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plant-derived compounds in an O(2)-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms.
McLeod
Michael P
MP
Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
Warren
René L
RL
Hsiao
William W L
WW
Araki
Naoto
N
Myhre
Matthew
M
Fernandes
Clinton
C
Miyazawa
Daisuke
D
Wong
Wendy
W
Lillquist
Anita L
AL
Wang
Dennis
D
Dosanjh
Manisha
M
Hara
Hirofumi
H
Petrescu
Anca
A
Morin
Ryan D
RD
Yang
George
G
Stott
Jeff M
JM
Schein
Jacqueline E
JE
Shin
Heesun
H
Smailus
Duane
D
Siddiqui
Asim S
AS
Marra
Marco A
MA
Jones
Steven J M
SJ
Holt
Robert
R
Brinkman
Fiona S L
FS
Miyauchi
Keisuke
K
Fukuda
Masao
M
Davies
Julian E
JE
Mohn
William W
WW
Eltis
Lindsay D
LD
D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics; D005075:Biological Evolution; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D008660:Metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D012240:Rhodococcus / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins