The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

doi:10.1186/1471-2105-8-172

Cited by 907 publications

(878 citation statements)

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“…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).…”

Section: Brief History Of Crispr Researchmentioning

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: Brief History Of Crispr Researchmentioning

confidence: 99%

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

2008

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“…The detailed information of CRISPRs was collected from CRISPR database (Grissa et al 2007a) for the genomes of extremophiles. Structural components including spacers, direct repeats (DRs) and CAS in the CRISPR loci were predicted by CRISPR Finder (Grissa et al 2007b) for those genomes whose information not availed in the CRISPR database. Appropriate location of cas genes was explored and identified from their genome maps in the KEGG database.…”

Section: Annotation Of Crispr Components At Genome-scalementioning

confidence: 99%

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Chellapandi

Ranjani

2015

Syst Synth Biol

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. Genomic survey of this study implied that genomic distribution of CRISPR-CAS systems was varied from strain to strain, which was determined by the degree of invading mobiloms. Direct repeats found to be equal in some extent in many thermopiles, but their spacers were differed in each strain. Phylogenetic analyses of CAS superfamily revealed that genes cmr, csh, csx11, HD domain, devR were belonged to the subtypes of cas gene family. The members in cas gene family of thermophiles were functionally diverged within closely related genomes and may contribute to develop several defense strategies. Nevertheless, genome dynamics, geological variation and host defense mechanism were contributed to share their molecular functions across the thermophiles. A thermophilic archaean, Thermococcus gammotolerans and thermophilic bacteria, Petrotoga mobilis and Thermotoga lettingae have shown superoperons-like appearance to cluster cas genes, which were typically evolved for their defense pathways. A cmr operon was identified with a specific promoter in a thermophilic archaean, Caldivirga maquilingensis. Overall, we concluded that knowledge-based genomic survey and phylogeny-based functional assignment have suggested for designing a reliable genetic regulatory circuit naturally from CRISPR-CAS systems, acquired defense pathways, to thermophiles in future synthetic biology.

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“…To identify more CAS proteins, sequences of P. gingivalis CAS that were annotated in the 35 genomes, as well as additional ones found in the NCBI protein database, were used to search against all the proteins annotated in the 35 genomes. Proteins that were not previously annotated as Mfa1 but with ≥90% identity and ≥90% length coverage to the queries were considered additional CRISPR-CAS proteins. e CRISPR: these are the number of CRISPR DNA sequences identified by the online CRISPRfinder programme (http://crispr.i2bc.paris-saclay.fr/Server/) [57]. …”

Section: Introductionmentioning

confidence: 99%

“… e CRISPR: these are the number of CRISPR DNA sequences identified by the online CRISPRfinder programme (http://crispr.i2bc.paris-saclay.fr/Server/) [57]. …”

Section: Introductionmentioning

confidence: 99%

“…Thus, the syntenies, illustrated as the same color across different genomes, of JCVI SC001 appear to be in similar order of those in TDC60 and may not be the true order in this genome. Syntenies were detected with the “MUAVE” program (version 2.4.0) [57] and were illustrated as rectangles of the same colors across all genomes. Two groups of syntenies were indicated with blue and red arrows underneath to exemplify the different rearrangement and inversion events in different genomes for this species. …”

Section: Introductionmentioning

confidence: 99%

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Genetic exchange and reassignment in Porphyromonas gingivalis

Olsen

Chen

Tribble

2018

Journal of Oral Microbiology

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Porphyromonas gingivalis is considered a keystone pathogen in adult periodontitis but has also been associated with systemic diseases. It has a myriad of virulence factors that differ between strains. Genetic exchange and intracellular genome rearrangements may be responsible for the variability in the virulence of P. gingivalis. The present review discusses how the exchange of alleles can convert this bacterium from commensalistic to pathogenic and potentially shapes the host-microbe environment from homeostasis to dysbiosis. It is likely that genotypes of P. gingivalis with increased pathogenic adaptations may spread in the human population with features acquired from a common pool of alleles. The exact molecular mechanisms that trigger this exchange are so far unknown but they may be elicited by environmental pressure.

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The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Cited by 907 publications

References 24 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

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Genetic exchange and reassignment in Porphyromonas gingivalis

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