<i>Corynebacterium diphtheriae</i> spoligotyping based on combined use of two CRISPR loci

Mokrousov, Igor; Limeschenko, Elena; Vyazovaya, Anna; Narvskaya, Olga

doi:10.1002/biot.200700035

Cited by 67 publications

(46 citation statements)

References 20 publications

(27 reference statements)

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“…2A). This has become the standard method for genotyping of M. tuberculosis strains as part of ongoing efforts to control tuberculosis outbreaks 37,38 , and is also used for the typing of Corynebacterium diphtheriae 39 . Nonspoligotyping based methods for strain typing using CRISPR arrays are also used to study Campylobacter jejuni, Thermotoga neapolitana and other bacterial strains 40,41 , and Russell and colleagues recently filed a patent application on CRISPR-based methods to type Lactobacillus strains (US Patent application 20060199190).…”

Section: Current and Future Applicationsmentioning

confidence: 99%

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

2008

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Arrays of clustered, regularly spaced short palindromic repeats (CRISPR) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats sized 24-47 bp separated by similarly sized non-repetitive sequences (spacers). It was recently experimentally shown that CRISPR arrays, along with a group of associated proteins, confer resistance to phage. Following exposure to phage, bacteria integrate new spacer sequences that are derived from the phage genome. Acquisition of these spacers enables the bacterial cell to shutdown the phage attack, presumably by an RNA-interference-like mechanism. This Progress discusses the structure and function of CRISPRs and the implications of this new antiviral mechanism in bacteria.2 Bacteriophages constitute the most populous life-forms on Earth 1 . In sea water, an environment in which phage abundance has been extensively studied, it has been estimated that there are 5-10 phage for every bacterial cell 2 . Despite being outnumbered by phage, bacteria proliferate and avoid extinction by using a battery of innate phageresistance mechanisms such as restriction enzymes and abortive infection 3 . In this Progress article we describe the CRISPR system, a recently discovered defence mechanism, which is remarkable because it confers acquired phage resistance in Bacteria and Archaea. A hallmark of this system are arrays of short direct repeats interspersed by non-repetitive spacer sequences, the so-called Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). Additional components of the system include CRISPRassociated (CAS) genes and a leader sequence (Fig. 1A). Brief history of CRISPR researchThe first report that described a CRISPR array, in 1987, was from Ishino et al. who found 14 repeats of 29bp interspersed by 32-33bp non-repeating spacer sequences 4,5 , adjacent to the isozyme converting alkaline phosphatase (iap) gene in Escherichia coli. In subsequent years similar CRISPR arrays were found in Mycobacterium tuberculosis 6 , Haloferax mediterranei 7 , Methanocaldococcus jannaschii 8 , Thermotoga maritima 9 and other bacteria and archaea. The accumulation of sequenced microbial genomes allowed genome-wide computational searches for CRISPRs (the first such analysis was carried out by Mojica et al. in 2000 10 ), and the most recent computational analyses revealed that CRISPRs are found in ~40% of bacterial and ~90% of archaeal genomes sequenced to date 11, 12 (Box 1).In parallel to the initial appreciation of the abundance of CRISPRs 13 , Jansen et al. identified four CRISPR-associated (CAS) genes that were almost always found adjacent to the repeat arrays 14 . Subsequent studies initiated by Koonin and colleagues 15, 16 and Haft et al. 17 uncovered 25-45 additional CAS genes appearing in close proximity to the arrays. The same set of genes is absent from genomes that lack CRISPRs.Several hypotheses for the function of CRISPRs have been proposed. Early in 1995 Mojica et al. suggested that the repeats were involved i...

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Section: Current and Future Applicationsmentioning

confidence: 99%

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

2008

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“…Spoligotyping is based on differences between CRISPR-Cas systems to identify bacterial strains (315). This technique helps investigations of evolution and geographical and/or historical studies (316,317) and permits the identification of microbial populations (318) or the analysis of pathogen outbreaks (319).…”

Section: Genetic Elements Controlling the Stability Of Mobile Elementsmentioning

confidence: 99%

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

337

289

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SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

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“…Louwen et al thus established that not only the spacer variation of the CRISPR array but also single nucleotide polymorphisms (SNPs) of the cas genes in C. jejuni are useful for typing purposes (30). Likewise, in Corynebacterium diphtheriae, the CRISPR-Cas systems (type I-E and type II-C) were found to be useful for typing purposes (32,33). Remarkably, spoligotyping, a technique making use of sequence information contained within the CRISPR spacers, was found to provide enhanced discriminatory power in C. diphtheriae compared to pulsed-field gel electrophoresis (PFGE), random amplification of polymorphic DNA (RAPD), and AFLP analyses (33).…”

Section: Figmentioning

confidence: 99%

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Louwen

Staals

Endtz

et al. 2014

Microbiol Mol Biol Rev

216

178

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SUMMARY Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

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Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci

Cited by 67 publications

References 20 publications

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

Bacterial Genome Instability

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

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