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. 2006 Oct 17;103(42):15582-7.
doi: 10.1073/pnas.0607048103. Epub 2006 Oct 9.

The Complete Genome of Rhodococcus Sp. RHA1 Provides Insights Into a Catabolic Powerhouse

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Free PMC article

The Complete Genome of Rhodococcus Sp. RHA1 Provides Insights Into a Catabolic Powerhouse

Michael P McLeod et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Physical map of the Rhodococcus sp. RHA1 genome. The four maps represent each of the replicons. Ticks on the bottom scale are spaced every 100 kbp. The rows represent (counting from the bottom scale): 1, %G+C calculated over 20 kbp using a 2-kbp sliding window (red and black are below and above the mean, respectively); 2, G+C skew calculated over 5 kbp using a 1-kbp sliding window (G−C)/(C+G) (red <0 ≤ black); 3 and 4, genes in the forward (blue) and reverse (red) strands (box width reflects gene size); 5, tRNA (black), rRNA (green), and nonribosomal peptide synthetase and polyketide synthase (purple) genes; 6, genes associated with mobility (pink); 7, manually curated GIs (green) (Table 4); and 8, aromatic pathway genes (orange) (Table 3). Black triangles indicate the predicted oriC positions.
Fig. 2.
Fig. 2.
Phylogenetic relationship of ParA proteins from 44 different replicons. Names in black and red identify ParAs from circular and linear replicons, respectively. Green shading identifies chromosomal ParAs. Yellow shading identifies ParAs from B. burgdorferi plasmids. A tree based on 90 sequences is provided in Fig. 3, together with the methods used.

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