Partial genome sequencing of Rhodococcus equi ATCC 33701

Rahman, Md. Tanvir; Herron, Lisa L.; Kapur, Vivek; Meijer, Wim G.; Byrne, Barbara A.; Ren, Jianwei; Nicholson, Vivian M.; Prescott, John F.

doi:10.1016/s0378-1135(03)00100-7

Cited by 37 publications

(22 citation statements)

References 66 publications

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“…S. avermitilis (13) and Streptomyces coelicolor A3 (2,14), which are nonpathogenic soil bacteria, each have one copy of the mce operon, suggesting that these operons evolved from a common ancestral operon by gene duplication. Similarly, four genes homologous to mycobacterial mce genes (mce1, mce3, and mce4) were identified in an animal pathogen, Rhodococcus equi (18). These data strongly suggest that the multiple copies of mce operons contribute to the virulence of this group of bacteria.…”

Section: Resultsmentioning

confidence: 79%

The complete genomic sequence of Nocardia farcinica IFM 10152

Ishikawa

Yamashita

Mikami

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

272

202

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We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of 6,021,225 bp with an average G؉C content of 70.8% and two plasmids of 184,027 (pNF1) and 87,093 (pNF2) bp with average G؉C contents of 67.2% and 68.4%, respectively. The chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as well as secondary metabolism. Analyses of paralogous protein families suggest that gene duplications have resulted in a bacterium that can survive not only in soil environments but also in animal tissues, resulting in disease.N ocardia are filamentous-growing Gram-positive soil saprophytes that belong to the family Actinomycetales, which also includes clinically and industrially important genera such as Mycobacterium, Streptomyces, Corynebacterium, and Rhodococcus. Many species of Nocardia cause the disease nocardiosis in humans and animals on lung, central nervous system, brain, and cutaneous tissues (1), and a species Nocardia asteroides is suspected to be an etiological agent of Parkinson's disease (2). Nocardiosis is on the rise, with an estimated 109-136 new cases occurring annually in Japan (3) and 500-1,000 in the U.S. (www.cdc.gov͞ncidod͞dbmd͞diseaseinfo͞nocardiosis t.htm). However, there are only a few studies on the mechanisms of nocardial virulence. Nocardia species are resistant to many front-line antibiotics. Because treatment for nocardiosis relies heavily on chemotherapy, their intrinsic multiple drug resistance is a serious problem.Another feature of the nocardia is that many strains, even clinical isolates, also have the capability to produce bioactive molecules such as antibiotics (4, 5) and enzymes that are industrially important (6). A monobactam antibiotic, nocardicin, was isolated from Nocardia sp. (7), and a terpenoid brasilicardin with immunosuppressive activity was isolated from a clinical isolate (4).Nocardia farcinica IFM 10152 was isolated from the bronchus of a 68-year-old male Japanese patient. Despite the complicated taxonomy of the nocardia, the species N. farcinica was found to be nearly homogeneous (8). Subsequently, to elucidate the molecular basis of the versatility of the nocardia, we analyzed the genomic sequence of N. farcinica IFM 10152. MethodsGenome Sequencing and Assembly. The nucleotide sequence of the N. farcinica IFM 10152 genome was determined by a wholegenome shotgun strategy. We constructed small-insert (2 kb) and large-insert (10 kb) genomic libraries and generated 127,077 sequences (giving 9-fold coverage) from both ends of the genomic clones. Sequence assembly was carried out by using the PHRED͞PHRAP͞CONSED package (9). Remaining gaps were closed by transcriptional sequencing (Nippon Gene, Toyama, Japan) or by primer walking. There were no ambiguous nucleotides in the genomic sequence that we could determine. Consistency of the final assembly was confirmed in terms of res...

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Section: Resultsmentioning

confidence: 79%

The complete genomic sequence of Nocardia farcinica IFM 10152

Ishikawa

Yamashita

Mikami

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

272

202

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“…The inability of R. equi ␣5G12 to grow in the presence of 80 M 2,2-dipyridyl is therefore probably due to a failure to translocate a siderophore-iron complex into the cell. To date, siderophores have not been identified in R. equi, although analysis of a partial genome sequence revealed sequences that are similar to mycobactin and exochelin biosynthesis genes (36). The iupABC genes are highly similar to the cchCDE genes of S. coelicolor, which are part of gene cluster that is predicted to produce a novel hydroxamate siderophore, coelichelin (10).…”

Section: Discussionmentioning

confidence: 99%

“…We therefore propose that the putative siderophore translocated by the iupABC-encoded ABC transport system is required for saprophytic growth, whereas a second siderophore is required for growth of R. equi in macrophages. Analysis of the partial genome sequence of R. equi identified sequences similar to mycobactin biosynthesis genes (36). The relevance of these for virulence is currently being analyzed.…”

Section: Discussionmentioning

confidence: 99%

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The Iron-Regulated iupABC Operon Is Required for Saprophytic Growth of the Intracellular Pathogen Rhodococcus equi at Low Iron Concentrations

et al. 2005

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Rhodococcus equi is a facultative intracellular pathogen which proliferates rapidly in both manure-enriched soil and alveolar macrophages. Although both environments are characterized by extremely low concentrations of free iron, very little is known regarding the strategies employed by R. equi to thrive under these conditions. This paper reports the characterization of an R. equi transposome mutant that fails to grow at low iron concentrations. The transposome was shown to be inserted into iupA, the first gene of the iupABC operon encoding an ABC transport system highly similar to siderophore uptake systems. Disruption of the iupA gene also resulted in a failure of R. equi to utilize heme and hemoglobin as a source of iron. Introduction of the iupABC operon in trans restored the wild-type phenotype of the mutant strain. iupABC transcripts were 180-fold more abundant in R. equi grown in iron-depleted medium than in organisms grown in iron-replete medium. Proliferation of the iupABC mutant strain in macrophages was comparable to that of the wild-type strain. Furthermore, the iupABC mutant was not attenuated in mice, showing that the iupABC operon is not required for virulence.

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“…The latter is highlighted by a partial genome sequence of R. equi which showed that the majority of R. equi genes are most similar to those of M. tuberculosis [55]. R. equi and Mycobacterium species belong to the Mycolata, a phylogenetically distinct group of high G+C Gram-positive bacteria that contains a number of pathogens, including species of the genera Rhodococcus, Nocardia, Corynebacterium and Mycobacterium [26].…”

Section: Introductionmentioning

confidence: 99%

Rhodococcus equi

2004

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-Rhodococcus equi is an important cause of subacute or chronic abscessating bronchopneumonia of foals up to 3-5 months of age. It shares the lipid-rich cell wall envelope characteristic of the mycolata, including Mycobacterium tuberculosis, as well as the ability of pathogenic members of this group to survive within macrophages. The possession of a large virulence plasmid in isolates recovered from pneumonic foals is crucial for virulence. The plasmid contains an 27 kb pathogenicity island (PI) that encodes seven related virulence-associated proteins (Vaps), including the immunodominant surface-expressed protein, VapA. Only PI genes are differentially expressed when the organism is grown in macrophages in vitro. Ten of the PI genes, including six Vap genes, have signal sequences, suggesting that they are exported from the cell to interact with the macrophage. Different PI genes are regulated by temperature, pH, iron, oxidative stress and probably also by magnesium, all environmental changes encountered after environmental R. equi are inhaled in dust and are ingested into macrophages in the lung. The basis of pathogenicity of R. equi is its ability to multiply in and eventually to destroy alveolar macrophages. Infectivity is largely or exclusively limited to cells of the monocyte-macrophage lineage. Current evidence suggests that infection of foals with virulent R. equi results in some foals in subversion of cellmediated immunity and development of an ineffective and sometimes lethal Th2-based immune response. Significant progress has been made recently in the development of R. equi-E. coli shuttle vectors, transformation and random and site specific mutagenesis procedures, all of which will be important in molecular dissection of the mechanisms by which R. equi subverts normal macrophage killing mechanisms and cell-mediated immunity.

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Partial genome sequencing of Rhodococcus equi ATCC 33701

Cited by 37 publications

References 66 publications

The complete genomic sequence of Nocardia farcinica IFM 10152

The complete genomic sequence of Nocardia farcinica IFM 10152

The Iron-Regulated iupABC Operon Is Required for Saprophytic Growth of the Intracellular Pathogen Rhodococcus equi at Low Iron Concentrations

Rhodococcus equi

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