Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors

Mot, René De; Nagy, István; Schrijver, Adinda De; Pattanapipitpaisal, Pranee; Schoofs, Geert; Vanderleyden, Jos

doi:10.1099/00221287-143-10-3137

Cited by 74 publications

(49 citation statements)

References 65 publications

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“…The TnpA transposase of S. fradiae is the closest relative of R. ruber TnpA, with 49% identity. The orf5 product of S. fradiae Tn4556 is a potential resolvase of Tn4556 whose similarity with the R. ruber TnpR extends into the upstream region of this ORF, disregarding a TAG stop codon as mentioned by De Mot et al (6). The deduced polypeptide of 324 residues is 31% identical to TnpR of R. ruber.…”

Section: Resultsmentioning

confidence: 81%

“…The deduced polypeptide of 324 residues is 31% identical to TnpR of R. ruber. The closest relative of R. ruber TnpR is R. erythropolis PmrA (62% identity), which is a site-specific recombinase of the integrase family and may be involved in stabilization of the cryptic plasmid pFAJ2600 (6). Amino acid comparisons revealed that other proteins related to R. ruber TnpR are almost exclusively sitespecific recombinases of the integrase family.…”

Section: Resultsmentioning

confidence: 99%

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Cloning of a Genetically Unstable Cytochrome P-450 Gene Cluster Involved in Degradation of the Pollutant Ethyl tert -Butyl Ether by Rhodococcus ruber

Chauvaux¹,

Chevalier

Dantec

et al. 2001

J Bacteriol

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Section: Resultsmentioning

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Cloning of a Genetically Unstable Cytochrome P-450 Gene Cluster Involved in Degradation of the Pollutant Ethyl tert -Butyl Ether by Rhodococcus ruber

Chauvaux¹,

Chevalier

Dantec

et al. 2001

J Bacteriol

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“…However, the mechanisms of plasmid replication, inheritance, and host ranges have not yet received much attention. The two replication proteins (RepA and RepB) found in most small plasmids of Nocardia, as well as those of the closely related Rhodococcus, resemble replication proteins of the theta-type replicating Mycobacterium plasmid pAL5000 (111,177,241). The replication protein of Nocardia plasmid pNI100 (308a) resembles the rolling-circle replication proteins encoded by the Streptomyces plasmids pIJ101 and pSG5 (238,277).…”

Section: Extrachromosomal Dna Elements In Nocardiamentioning

confidence: 99%

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Ventura

Canchaya

Tauch

et al. 2007

Microbiol Mol Biol Rev

930

638

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SUMMARY Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

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“…RHL3.237, designated rep1, encodes a 444-residue protein that shares up to 25% amino acid sequence identity with rep genes of mycobacterial and rhodococcal plasmids (3,5,16,46) (Table 1). RHL3.235 encodes a protein that shares 34% sequence identity to ParA protein from R. erythropolis (15). Both pJBG6 and pBTSBK contain rep1.…”

Section: Vol 186 2004mentioning

confidence: 99%

Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1

Warren¹,

Hsiao

Kudo

et al. 2004

J Bacteriol

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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.Rhodococcus is a widely occurring genus of aerobic, nonmotile soil bacteria that are closely related to three other genera of GC-rich actinomycetes: Gordonia, Nocardia, and Mycobacterium. Rhodococci degrade an extraordinarily wide variety of organic substrates and thus play an important role in the global C cycle. The unusual armamentarium of enzymatic activities involved in these processes has been exploited in applications ranging from commodity chemical production to the desulfurization of fossil fuels (6). Consequently, the metabolic capabilities of rhodococci are of interest to the pharmaceutical, environmental, chemical, and energy sectors.Rhodococcus sp. strain RHA1 is characterized by its exceptional ability to transform polychlorinated biphenyls (PCBs) (53), a particularly widespread and persistent class of environmental pollutants. It is generally thought that in aerobic bacteria, PCBs are cometabolized by the bph pathway, which is responsible for the aerobic degradation of biphenyl (23). The upper bph pathway consists of four enzymatic activities that together transform biphenyl to benzoate and 2-hydroxypenta-2,4-dienoate. For each of these four steps, RHA1 appears to possess multiple isozymes, which may help explain the strain's superior PCB-transforming capabilities. Thus, the strain contains at least three bph-type ring-hydroxylating di...

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Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors

Cited by 74 publications

References 65 publications

Cloning of a Genetically Unstable Cytochrome P-450 Gene Cluster Involved in Degradation of the Pollutant Ethyl tert -Butyl Ether by Rhodococcus ruber

Cloning of a Genetically Unstable Cytochrome P-450 Gene Cluster Involved in Degradation of the Pollutant Ethyl tert -Butyl Ether by Rhodococcus ruber

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1

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