CRISPRTarget

Biswas, Ambarish; Gagnon, Joshua N.; Brouns, Stan J. J.; Fineran, Peter C.; Brown, Chris M.

doi:10.4161/rna.24046

Cited by 293 publications

(170 citation statements)

References 85 publications

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“…We used the CRISPRMap program to assign type and subtype to each of the CRISPR-Cas regions (37). The spacer dictionaries generated by the CRISPRFinder and CRISPRDetect programs were used in the CRISPRTarget program to identify the most likely targets of CRISPR RNA spacers in the NCBI GenBank-phage and RefSeq-plasmid databases for all V. cholerae strains examined (55). Putative spacer target sequences were identified following a BLASTn search of the plasmid and bacteriophage databases (55).…”

Section: Methodsmentioning

confidence: 99%

“…The spacer dictionaries generated by the CRISPRFinder and CRISPRDetect programs were used in the CRISPRTarget program to identify the most likely targets of CRISPR RNA spacers in the NCBI GenBank-phage and RefSeq-plasmid databases for all V. cholerae strains examined (55). Putative spacer target sequences were identified following a BLASTn search of the plasmid and bacteriophage databases (55). A cutoff score of 20 (the default value) was used for the analysis to filter out low-scoring hits from the output.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules

et al. 2017

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Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs. IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and catalyze their incorporation into bacterial chromosomes, which could convert a strain into a pathogen with very different disease pathologies. Each island had the ability to excise from the chromosome as distinct, complete units for possible transfer. Evolutionary analysis of these regions indicates that they were acquired by horizontal transfer and that PAIs are the units of transfer. Similar to the case for phage evolution, PAIs have a modular structure where different functional regions are acquired by identical recombination modules.KEYWORDS CRISPR-Cas, type III secretion, Vibrio cholerae, pathogenicity islands V ibrio cholerae is the causative agent of the severe diarrheal disease cholera. The factors necessary for manifestation of this disease were acquired by horizontal gene transfer. The cholera toxin (CT), a potent enterotoxin whose effects are respon-

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules

et al. 2017

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“…The cas genes were previously annotated by Watanabe et al (26). Individual spacer sequences present in four identified CRISPR arrays were used to search for potential protospacer sequences by using CRISPRTarget (39). Consensus repeat sequences for each of the identified CRISPR arrays were used to search the CRISPRmap database to identify structural motifs and sequence families (40).…”

Section: Methodsmentioning

confidence: 99%

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems

et al. 2015

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The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and transposons. It is present in the majority of Archaea and almost half of species of Bacteria. Porphyromonas gingivalis is an important human pathogen that has been proven to be an etiological agent of periodontitis and has been linked to systemic conditions, such as rheumatoid arthritis and cardiovascular disease. At least 95% of clinical strains of P. gingivalis carry CRISPR arrays, suggesting that these arrays play an important function in vivo. Here we show that all four CRISPR arrays present in the P. gingivalis W83 genome are transcribed. For one of the arrays, we demonstrate in vivo activity against double-stranded DNA constructs containing protospacer sequences accompanied at the 3= end by an NGG protospacer-adjacent motif (PAM). Most of the 44 spacers present in the genome of P. gingivalis W83 share no significant similarity with any known sequences, although 4 spacers are similar to sequences from bacteria found in the oral cavity and the gastrointestinal tract. Four spacers match genomic sequences of the host; however, none of these is flanked at its 3= terminus by the appropriate PAM element. IMPORTANCEThe CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression.

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“…Publicly available complete sequences of plasmids, phages, and microbial genomes were obtained from the BLAST database. The CRISPRTarget databases provided GenBank-Phage, RefSeq-Plasmid, and RefSeq-Microbial and RefSeq-viral, and the cutoff score was the default parameter value [29].…”

Section: Data Validationmentioning

confidence: 99%

Bioinformatic analysis of Listeria monocytogenes CRISPR

Qu¹,

Shen²,

Xu³

et al. 2018

Oncotarget

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Listeria monocytogenes is a leading causes of death from food-borne pathogens. Bioinformatics approach was applied to investigate the features of L. monocytogenes CRISPR structure and the relationship between CRISPR and plasmid transposase content. Among 93 L. monocytogenes genomes, 95 confirmed CRISPR structure loci were identified and classified into 5 groups based on repeat size. RNA secondary structure and minimum free energy indicated that the secondary structure of Group 5 (36 bp) was more stable than other groups. Type I-B or II-A Cas genes were found in 36 strains, and the CRISPR-Cas system of type I-B was more conserved than type II-A. Furthermore, CRISPR loci affected the enzyme transposase content of L. monocytogenes plasmid. This study examined the diversity of the CRISPR-Cas system in L. monocytogenes, classified CRISPR structure and repeats, and demonstrated the influence of the CRISPR-Cas system on the number of transposase in plasmid.

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CRISPRTarget

Cited by 293 publications

References 85 publications

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems

Bioinformatic analysis of Listeria monocytogenes CRISPR

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