The number and organization of the rRNA genes of several strains of<i>Mycobacterium simiae</i>

Rivera-Gutierrez, Sandra; Montoro-Cardoso, Ernesto; Valdivia, José A.; Cox, Robert A.; González-y-Merchand, Jorge A.

doi:10.1016/s0378-1097(03)00656-6

Cited by 6 publications

(7 citation statements)

References 30 publications

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“…Published results concerning the rRNA operons, promoters, promoter strengths, and 16S rRNA helix 18 length [24,42,[57][58][59][60][61][62][63][64][65][66][67][68][69], are consistent with, and thus support, the observed distribution of RGM and SGM in the MST-regions model for population structure. RGM Mycobacterium chitae, which falls "outside" the close 16S rRNA similarity values shared by other members of the genus Mycobacterium [68], was also "outside" the compact cluster (though still relatively weakly connected) of RGM in MST-region 1 (Figure 1).…”

Section: The Mst-regions Model Provided a Framework For Genetic Elemesupporting

confidence: 69%

A New Paradigm for Genus Mycobacterium Population Structure

Freidlin¹

2013

J Bacteriol Parasitol

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The genus Mycobacterium contains the pathogenic species tuberculosis and leprae, and additionally at least 148 sometimes opportunistic pathogenic species that occupy environmental niches. The genus Mycobacterium is in the order Actinomycetes along with other acid-fast genera with mycolic acids in their cell walls, such as Corynebacterium, Nocardia, and Rhodococcus. The DNA-dependent RNA polymerase subunit b gene rpoB, is relatively conserved among these bacteria. Sequence polymorphism in a 342bp fragment of rpoB is sufficient to differentiate among most species of Mycobacterium. However, construction of a robust and testable phylogeny or population structure based on this polymorphism, or polymorphism in other genomic regions, has remained elusive. This study presents a new paradigm for the resolution of genus Mycobacterium population structure. A minimum spanning tree (MST) was constructed on restriction enzyme site polymorphisms detected in silico for 5 enzymes, on the 342bp rpoB fragment obtained from GenBank data for 47 Mycobacterium species, and one species each from Corynebacterium, Nocardia and Rhodococcus. The MST was empirically divided into 3 regions. All the rapidly growing mycobacteria (RGM), with a halo of slowly growing mycobacteria (SGM), were found in MST-region 1. The correctness of the MST-regions model of genus Mycobacterium population structure was validated by statistically confirmed linkage disequilibrium of certain restriction site alleles. For certain alleles, SGM in MST-region 1 resembled the RGM of MST-region 1 more than the SGM of MST-region 3. The model provided a framework consistent with published genotypic and phenotypic observations, including expectations from comparative genomics and ribosomal RNA (rRNA) gene properties' distribution among species, and reported cladistic groupings of species. Corynebacterium diphtheriae, Nocardia nova and Rhodococcus equi belonged to MSTregions 2, 3, and 1 respectively. In conclusion, the MST-regions model of genus Mycobacterium population structure was robust, unambiguous, transparent for alleles, consistent with genotypes and phenotypes, and statistically testable.

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Section: The Mst-regions Model Provided a Framework For Genetic Elemesupporting

confidence: 69%

A New Paradigm for Genus Mycobacterium Population Structure

Freidlin¹

2013

J Bacteriol Parasitol

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“…M. marinum and M. chelonae were grown at 30°C and the other mycobacteria at 37°C. (a) [17]; (b) this study (see Section 2); (c) [39]; (d) [40]; (e) [18]; (a) [4]; (b) [5,6]; (c) this study. Mycobacteria were grown in Dubos broth (100 ml) containing 0.1% (w/v) Tween 80 and ADC.…”

Section: Resultsmentioning

confidence: 93%

The pathogen Mycobacterium marinum, a faster growing close relative of Mycobacterium tuberculosis, has a single rRNA operon per genome

HELGUERAREPETTO¹

2004

FEMS Microbiology Letters

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Although Mycobacterium marinum and Mycobacterium tuberculosis are very closely related they differ significantly in their growth rates. The Type strain of M. marinum and one clinical isolate were investigated and, like M. tuberculosis, were found to have a single rRNA (rrn) operon per genome located downstream from murA gene and controlled by two promoters. No sequence differences were found that account for the difference in the growth rates of the two species. We infer that M. tuberculosis has the capacity to synthesize rRNA much faster than it actually does; and propose that the high number of insertion sequences in this species attenuate growth rate to lower values.

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“…The authors propose that these observations can be accounted for in the following way. The ancestral Mycobacterium had one rrnA and one rrnB , 1996aMenendez et al, 2002;Rivera-Gutiérrez et al, 2003;Helguera-Repetto et al, 2004). The asterisk denotes species that are known to have two operons per genome without specification of the identity of the upstream genes; namely, Mycobacterium gilvum (Domenech et al, 1994), Mycobacterium goodii (Brown et al, 1999) and Mycobacterium immunogenum (Wilson et al, 2001).…”

Section: Resultsmentioning

confidence: 99%

“…Mycobacterium celatum was chosen for this study because it is closely related to Mycobacterium simiae. Mycobacterium simiae , which was shown to have a single operon ( rrn A) per genome (Rivera‐Gutiérrez et al , 2003), is included within the same cluster of mycobacteria as M. tuberculosis (Goodfellow & Magee, 1998).…”

Section: Introductionmentioning

confidence: 99%

The organization of two rRNA (rrn) operons of the slow-growing pathogenMycobacterium celatumprovides key insights into mycobacterial evolution

Stadthagen-Gomez¹,

Helguera-Repetto²,

Cerna-Cortés³

et al. 2008

FEMS Microbiology Letters

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The slow-growing Mycobacterium celatum is known to have two different 16S rRNA gene sequences. This study confirms the presence of two rrn operons and describes their organization. One operon (rrnA) was found to be located downstream from murA and the other (rrnB) was found downstream from tyrS. The promoter regions were sequenced, and also the intergenic transcribed spacer (ITS1 and ITS2) regions separating the 16S rRNA, 23S rRNA and 5S rRNA gene coding regions. Analysis of the RNA fraction revealed that rrnA is regulated by two (P1 and PCL1) promoters and rrnB is regulated by one (P1). These data show that the two rrn operons of M. celatum are organized in the same way as the two rrn operons of classical fast-growing mycobacteria. This information was incorporated into a phylogenetic analysis of the genus based on both 16S rRNA gene sequences and (where possible) the number of rrn operons per genome. The results suggest that the ancestral Mycobacterium possessed two (rrnA and rrnB) operons per genome and that subsequently, on two separate occasions, an operon (rrnB) was lost, leading to two clusters of species having a single operon (rrnA); one cluster includes the classical pathogens and the other includes Mycobacterium abscessus and Mycobacterium chelonae.

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The number and organization of the rRNA genes of several strains ofMycobacterium simiae

Cited by 6 publications

References 30 publications

A New Paradigm for Genus Mycobacterium Population Structure

A New Paradigm for Genus Mycobacterium Population Structure

The pathogen Mycobacterium marinum, a faster growing close relative of Mycobacterium tuberculosis, has a single rRNA operon per genome

The organization of two rRNA (rrn) operons of the slow-growing pathogenMycobacterium celatumprovides key insights into mycobacterial evolution

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