The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse

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 plantderived compounds in an O2-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.biodegradation ͉ actinomycete ͉ linear chromosome ͉ aromatic pathways ͉ oxygenase

Biodegradation of the xenobiotic organic disulphide 4,4′-dithiodibutyric acid by Rhodococcus erythropolis strain MI2 and comparison with the microbial utilization of 3,3′-dithiodipropionic acid and 3,3′-thiodipropionic acid

“…H. Wübbeler and others, unpublished results). Considering the available data on the completely sequenced genome of Rhodococcus strain RHA1 (McLeod et al, 2006), more than 500 ORFs that encode reductases, including six genes encoding paralogues of dihydrolipoamide dehydrogenases, are present. Moreover, A. mimigardefordensis strain DPN7 and R. erythropolis strain MI2 were both able to cleave The second proposed step in the catabolism of DTDB is the oxidation of 4MB to the corresponding carboxylic acid 4-oxo-4-sulphanylbutanoic acid.…”

Gene Expression Analysis of Methylotrophic Oxidoreductases Involved in the Oligotrophic Growth ofRhodococcus erythropolisN9T-4

“…8) S-Hydroxymethyl-mycothiol is formed nonenzymatically from mycothiol and formaldehyde in Gram-positive methylotrophs; mFADH then catalyzes NAD-dependent dehydrogenation of S-hydroxymethylmycothiol to produce S-formyl-mycothiol. 9) The genetic organization in the vicinity of the mFADH gene in the N9T-4 genome was compared with that in the R. erythropolis PR4 and R. jostii RHA1 genomes 10) which have been completely sequenced (Fig. 1a).…”

Identification of a novel ATP-binding cassette transporter involved in long-chain fatty acid import and its role in triacylglycerol accumulation in Rhodococcus jostii RHA1

“…cell envelope, inclusion bodies, etc.). In this context, a large portion of the R. jostii RHA1 genome codes for enzymes involved in lipid metabolism (McLeod et al, 2006). Fatty acids are probably key intermediates in rhodococci for the biosynthesis of many of the lipid species which perform important functions in their interaction with the environment (Fig.…”