The terminal structures of linear plasmids from Rhodococcus opacus

Kalkus, Jutta; Menne, Renate; Reh, Michael; Schlegel, H. G.

doi:10.1099/00221287-144-5-1271

Cited by 28 publications

(24 citation statements)

References 44 publications

(52 reference statements)

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“…Using pulsed-field gel electrophoresis, the genomes of some other, still-unsequenced mycelial Actinobacteria taxa, such as Actinomyces, Amycolatopsis, Actinoplanes, Streptoverticillium, and Micromonospora, were also shown to be linear, with sizes ranging from 7.7 Mb (e.g., Micromonospora chalcea) to 9.7 Mb (Streptoverticillium abikoense), while sometimes also harboring large linear plasmids (362). Linear plasmids, typically possessing short inverted repeats at their termini and protein-bound 5Ј ends, are often present in Actinobacteria (216).…”

Section: Actinobacterial Genome Sequencing Projectsmentioning

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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Section: Actinobacterial Genome Sequencing Projectsmentioning

confidence: 99%

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Ventura

Canchaya

Tauch

et al. 2007

Microbiol Mol Biol Rev

930

638

View full text Add to dashboard Cite

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“…2A, to telomeric regions of pHG207 of Rhodococcus sp. strain MR2253 (30) and to the right telomeres of pRHL2 (56), pBD2 of R. erythropolis (60), pHG201 of R. opacus MR11, and pHG204 of R. opacus MR22 (31). Each of these telomere sequences contains two sets of inverted repeats flanking the GCTXCGC central motif ( Fig.…”

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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“…However, manual alignment of the terminal 100-117 nucleotides of all hitherto available ends of linear Rhodococcus plasmids clearly confirmed the presence of strongly conserved palindromic motifs. Two copies of the motif GCTXCGC were found in each terminus and it was already assumed earlier that these structures are essential for replication (Kalkus et al, 1998;Shimizu et al, 2001). Essentially the same central motif with the potential to form a stable single C-residue loop close to the sheared T : C pairing was found in the linear Streptomyces plasmids pSCL1 (Wu & Roy, 1993), pSLA2 (Hirochika et al, 1984) and SLP2 , as well as in the terminal segments of several linear Streptomyces chromosomes (Huang et al, 1998).…”

Section: Discussionmentioning

confidence: 82%

“…However, in p1CP-J the palindrome of position 12-34 is imperfect because of a mismatch at position 14. Both palindromic structures contain the central motif GCTXCGC, already obtained for other plasmid termini of rhodococci (Kalkus et al, 1998;Shimizu et al, 2001) and streptomycetes (Bey et al, 2000;Huang et al, 1998). Several other regions of striking similarity were identified (alignment positions 1-2, 5-7 and 49-62).…”

Section: +Sds +Sdsmentioning

confidence: 97%

“…One terminal fragment was identified by hybridization of SstII-digested purified p1CP DNA using a DIG-labelled 2?3 kb SalI fragment of the right end of the linear Aut plasmid pHG201 from R. opacus MR11 (Kalkus et al, 1998). Ligation into SstII/EcoRV-digested pBluescript II KS(+) and transformation into E. coli DH5a, followed by colony hybridization, led to the identification of one positive clone, p1CP-S, containing a 1?56 kb SstII/blunt-end insert.…”

Section: Identification Of Genes For (Chloro)aromatic Catabolism On P1cpmentioning

confidence: 99%

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A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP

et al. 2004

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The Gram-positive actinobacterium Rhodococcus opacus 1CP is able to utilize several (chloro)aromatic compounds as sole carbon sources, and gene clusters for various catabolic enzymes and pathways have previously been identified. Pulsed-field gel electrophoresis indicates the occurrence of a 740 kb megaplasmid, designated p1CP. Linear topology and the presence of covalently bound proteins were shown by the unchanged electrophoretic mobility after S1 nuclease treatment and by the immobility of the native plasmid during non-denaturing agarose gel electrophoresis, respectively. Sequence comparisons of both termini revealed a perfect 13 bp terminal inverted repeat (TIR) as part of an imperfect 583/587 bp TIR, as well as two copies of the highly conserved centre (GCTXCGC) of a palindromic motif. An initial restriction analysis of p1CP was performed. By means of PCR and hybridization techniques, p1CP was screened for several genes encoding enzymes of (chloro)aromatic degradation. A single maleylacetate reductase gene macA, the clc gene cluster for 4-chloro-/3,5-dichlorocatechol degradation, and the clc2 gene cluster for 3-chlorocatechol degradation were found on p1CP whereas the cat and pca gene clusters for the catechol and the protocatechuate pathways, respectively, were not. Prolonged cultivation of the wild-type strain 1CP under non-selective conditions led to the isolation of the clc-and clc2-deficient mutants 1CP.01 and 1CP.02 harbouring the shortened plasmid variants p1CP.01 (500 kb) and p1CP.02 (400 kb).

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The terminal structures of linear plasmids from Rhodococcus opacus

Cited by 28 publications

References 44 publications

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

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

A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP

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