CRISPRDetect: A flexible algorithm to define CRISPR arrays

Biswas, Ambarish; Staals, Raymond H.J.; Morales, Sergio E.; Fineran, Peter C.; Brown, Chris M.

doi:10.1186/s12864-016-2627-0

Cited by 302 publications

(250 citation statements)

References 62 publications

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“…Type-IIA CRISPR arrays were identified within individual genomes using CRISPRfinder (Grissa et al, 2007) or CRISPRDetect (Biswas et al, 2016) web utilities. See Figure S1B for a representative L. monocytogenes type II-A CRISPR array.…”

Section: Star Methodsmentioning

confidence: 99%

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch

Silvis

Hultquist

et al. 2017

Cell

440

505

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SUMMARY Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a counter-measure, numerous phages are known that produce proteins to block the function of Class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used Class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages. More than half of L. monocytogenes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR-Cas9 inactivation. Two of these inhibitors also blocked the widely used Streptococcus pyogenes Cas9 when assayed in Escherichia coli and human cells. These natural Cas9-specific “anti-CRISPRs” present tools that can be used to regulate the genome engineering activities of CRISPR-Cas9.

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Section: Star Methodsmentioning

confidence: 99%

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch

Silvis

Hultquist

et al. 2017

Cell

440

505

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“…The replication origin (oriC) was predicted by OriFinder (http://tubic.tju.edu.cn/Ori-Finder; Gao and Zhang, ). The presence of mobile genetic elements in the D. aquatica 174/2 genome was investigated by the following online tools: IslandViewer (http://pathogenomics.sfu.ca/islandviewer; Dhillon et al ., ) for the GI regions, CRISPRDetect (http://brownlabtools.otago.ac.nz/CRISPRDetect/predict_crispr_array.html; Biswas et al ., ) for CRISPR arrays, whereas putative prophage sequences were identified by PHAST and PHASTER analysis (http://phast.wishartlab.com/; Zhou et al ., ; Arndt et al ., ). The genome sequence has been submitted to EMBL database under accession number GCA_900095885 (http://www.ebi.ac.uk/).…”

Section: Methodsmentioning

confidence: 99%

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Duprey

Taïb

Léonard

et al. 2019

Environmental Microbiology

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Summary Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep‐branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in‐depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

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“…The FASTA files for strains RC385, RC586, TMA11079-80, and HC-36A1 were used to identify CRISPR direct repeats and spacers in each sequence using the CRISPRFinder and CRISPRDetect programs (23,24,54). The CRISPRtionary program was used to determine how unique each spacer was to each strain (23,24).…”

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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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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CRISPRDetect: A flexible algorithm to define CRISPR arrays

Cited by 302 publications

References 62 publications

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

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

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