Inteins in mycobacterial GyrA are a taxonomic character

“…New intein genes can be identified by amplifying genes known to include inteins in some species from other related species (Davis et al ., 1994; Fsihi et al ., 1996; Sander et al ., 1998; Saves et al ., 2000; Lazarevic, 2001). However, all known inteins are randomly distributed, and only one case was found of closely related species with consistent intein distribution (Sander et al ., 1998). Usually only a few of the examined species were found to contain inteins.…”

Section: Discussionmentioning

confidence: 99%

Distribution of split DnaE inteins in cyanobacteria

Caspi¹,

Amitai²,

Belenkiy³

et al. 2003

Molecular Microbiology

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SummaryInteins are genetic elements found inside the coding regions of different host proteins and are translated in frame with them. The intein-encoded protein region is removed by an autocatalytic protein-splicing reaction that ligates the host protein flanks with a peptide bond. This reaction can also occur in trans with the intein and host protein split in two. After translation of the two genes, the two intein parts ligate their flanking protein parts to each other, producing the mature protein. Naturally split inteins are only known in the DNA polymerase III alpha subunit (polC or dnaE gene) of a few cyanobacteria. Analysing the phylogenetic distribution and probable genetic propagation mode of these split inteins, we conclude that they are genetically fixed in several large cyanobacterial lineages. To test our hypothesis, we sequenced parts of the dnaE genes from five diverse cyanobacteria and found all species to have the same type of split intein. Our results suggest the occurrence of a genetic rearrangement in the ancestor of a large division of cyanobacteria. This event fixed the dnaE gene in a unique two-genes one-protein configuration in the progenitor of many cyanobacteria. Our hypothesis, findings and the cloning procedure that we established allow the identification and acquisition of many naturally split inteins. Having a large and diverse repertoire of these unique inteins will enable studies of their distinct activity and enhance their use in biotechnology.

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“…1; Table 2), the high degree of conservation of the mycobacterial 16S rRNA gene may explain why PRPA of the 16S rRNA genes of M. ulcerans and M. marinum is not useful for discriminating between these two species. Other molecular methods have tried to circumvent this limitation in species discrimination (27), including sequence analysis of a 360-bp gene fragment characteristic for GyrA lacking an intein and the 16-kDa HSP, an ␣-crystalline homologue (I. C. Shamputa, unpublished data). However, none of these methods so far permits an unequivocal differentiation between M. ulcerans and M. marinum.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of PCR-Restriction Profile Analysis and IS 2404 Restriction Fragment Length Polymorphism and Amplified Fragment Length Polymorphism Fingerprinting for Identification and Typing of Mycobacterium ulcerans and M. marinum

et al. 2001

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Mycobacterium ulcerans and M. marinum are emerging necrotizing mycobacterial pathogens that reside in common reservoirs of infection and exhibit striking pathophysiological similarities. Furthermore, the interspecific taxonomic relationship between the two species is not clear as a result of the very high phylogenetic relatedness (i.e., >99.8% 16S rRNA sequence similarity), in contrast to only 25 to 47% DNA relatedness. To help understand the genotypic affiliation between these two closely related species, we performed a comparative analysis including PCR restriction profile analysis (PRPA), IS2404 restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) on a set of M. ulcerans (n ‫؍‬ 29) and M. marinum Mycobacterium ulcerans and M. marinum are slow-growing mycobacterial species with optimal growth temperatures of 30 to 33°C. These organisms are emerging as clinically significant pathogens associated with skin infections (5, 9). M. ulcerans infection, or Buruli ulcer (BU), was first described in Bairnsdale, Australia, in 1948 (17) and was subsequently found in numerous, mostly tropical countries in Africa, the Americas, Southeast Asia, and the central Pacific. Recent reports describe increases in the incidence of BU in Benin (13), Australia (6,8,12,34), and Côte d'Ivoire (18). M. ulcerans causes chronic necrotizing ulcers in the skin of humans (22) and other mammals (22, 23). The epidemiology of BU is poorly understood, but most foci are associated with slow-flowing or stagnant water; however, the natural reservoir of M. ulcerans remains unknown. M. marinum, first described in Sweden (1), gives rise to infections in temperate climates and is the cause of fish tank and swimming pool granulomas (16).M. ulcerans is often difficult to isolate from clinical specimens and usually requires 6 to 8 weeks to produce visible growth in primary culture (23,24). Definitive identification of M. ulcerans is thus time-consuming; however, it can be recognized by classic molecular and microbiologic methods (20,24). M. marinum, once cultured, is readily identified by using conventional mycobacterial characterization methods. It grows relatively quickly (1 to 2 weeks) and is easily recognized as a result of its photochromogenicity (20). While infections due to M. marinum can usually be treated with antimycobacterial drugs, very few cases of BU lesions respond favorably to antimicrobial therapy (2), making wide surgical excision and skin grafting the treatment of choice.In the last decade, various DNA-based techniques have been used to classify mycobacteria (15,25,26,30). All such studies have demonstrated a high taxonomic affiliation between M. ulcerans and M. marinum. Other attempts have targeted the 3Ј end of 16S rRNA gene and found four subtypes of M. ulcerans related to their geographic origin, except for one isolate from Suriname, which exhibited the same sequence as M. marinum (20). The use of IS2404 resriction fragment length polymorphism (RFLP) analysis (2) led to the classification...

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Inteins in mycobacterial GyrA are a taxonomic character

Cited by 17 publications

References 14 publications

The PRP8 inteins in Cryptococcus are a source of phylogenetic and epidemiological information

The PRP8 inteins in Cryptococcus are a source of phylogenetic and epidemiological information

Distribution of split DnaE inteins in cyanobacteria

Evaluation of PCR-Restriction Profile Analysis and IS 2404 Restriction Fragment Length Polymorphism and Amplified Fragment Length Polymorphism Fingerprinting for Identification and Typing of Mycobacterium ulcerans and M. marinum

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