Investigation of direct repeats, spacers and proteins associated with clustered regularly interspaced short palindromic repeat (CRISPR) system of Vibrio parahaemolyticus

Baliga, Pallavi; Shekar, Malathi; Venugopal, M. N.

doi:10.1007/s00438-018-1504-8

Cited by 11 publications

(12 citation statements)

References 49 publications

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“…In this study, the DRs detected in CRISPR loci were 28-bp in length and its sequences have also been reported [16]. These characteristics were identical to those found in the reference strain of V. parahaemolyticus RIMD 2210633.…”

Section: Discussionsupporting

confidence: 82%

“…Although a combination of CRISPR spacer sequences with hemolysin genes (tdh, trh1, and trh2) was used for subtyping V. parahaemolyticus, the association between spacer groups and hemolysin genotypes has not been clearly addressed. Moreover, only a few studies document the presence of CRISPR among seafood isolates of V. parahaemolyticus [16,17].…”

Section: Introductionmentioning

confidence: 99%

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Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources

et al. 2021

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Vibrio parahaemolyticus is one of the significant seafood-borne pathogens causing gastroenteritis in humans. Clustered regularly interspaced short palindromic repeats (CRISPR) are commonly detected in the genomes of V. parahaemolyticus and the polymorphism of CRISPR patterns has been applied as a genetic marker for tracking its evolution. In this work, a total of 15 pandemic and 36 non-pandemic V. parahaemolyticus isolates obtained from seafood between 2000 and 2012 were characterized based on hemolytic activity, antimicrobial susceptibility, and CRISPR elements. The results showed that 15/17 of the V. parahaemolyticus seafood isolates carrying the thermostable direct hemolysin gene (tdh+) were Kanagawa phenomenon (KP) positive. The Multiple Antibiotic Resistance (MAR) index ranged between 0.1 and 0.4, and 45% of the isolates have an MAR index ≥ 0.2. A total of 19 isolates were positive for CRISPR detection, including all tdh+ trh− isolates, two of tdh− trh+, and each of tdh+ trh+ and tdh− trh−. Four spacer types (Sp1 to Sp4) were identified, and CRISPR-positive isolates had at least one type of spacer homolog to the region of Vibrio alginolyticus megaplasmid. It is of interest that a specific CRISPR profile and spacer sequence type was observed with correlations to the hemolysin genotype (tdh/trh). Thus, these provide essential data on the exposure of foreign genetic elements and indicate shared ancestry within different genotypes of V. parahaemolyticus isolates.

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Section: Discussionsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources

et al. 2021

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“…In prokaryotes harboring the CRISPR-cas type I-F system, the Cas6-associated protein functions as an endoribonuclease bringing about cleavage of the CRISPR RNAs and generation of pre-crRNA [16]. In V. parahemolyticus , a previous study with cas6 showed the gene sequences to be diverse and broadly classified into four genotypes [20]. The primers designed in this study could be used in the identification of the cas6 genotypes in V. parahaemolyticus .…”

Section: Resultsmentioning

confidence: 99%

“…Cas5 and Cas7 also belong to the RAMP superfamily and are implicated in interference and stabilization stages of crRNA generation [26]. Bioinformatics-based analysis of the V. parahaemolyticus cas6 sequence showed the existence of four different sequence subtypes ( cas6 -a- cas6 -d), with a majority of strains analyzed seen associated with cas6 -a subtype [20]. The subtypes cas6-b and cas6-c were not detected in the strains studied which probably is due to the under-representation of environmental strains taken for analysis.…”

Section: Discussionmentioning

confidence: 99%

“…In our previous study, based on computational analysis of existing V. parahaemolyticus cas6 gene sequences in database, we have shown the existence of four subtypes for cas6 , designated cas6 -a, cas6 -b, cas6 -c, and cas6 -d [20]. In this study, we designed novel primers for the polymerase chain reaction (PCR) detection and characterization of cas6 gene variants in V. parahaemolyticus .…”

Section: Introductionmentioning

confidence: 99%

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Detection and characterization of clustered regularly interspaced short palindromic repeat-associated endoribonuclease gene variants in Vibrio parahaemolyticus isolated from seafoods and environment

2019

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Aim: In Vibrio parahaemolyticus, the clustered regularly interspaced short palindromic repeat (CRISPR)-associated cas6 endoribonuclease gene has been shown to exhibit sequence diversity and has been subtyped into four major types based on its length and composition. In this study, we aimed to detect and characterize the cas6 gene variants prevalent among V. parahaemolyticus strains isolated from seafoods and environment. Materials and Methods: Novel primers were designed for each of the cas6 subtypes to validate their identification in V. parahaemolyticus by polymerase chain reaction (PCR). In total, 38 V. parahaemolyticus strains isolated from seafoods and environment were screened for the presence of cas6 gene. Few representative PCR products were sequenced, and their phylogenetic relationship was established to available cas6 gene sequences in GenBank database. Results: Of the 38 V. parahaemolyticus isolates screened, only about 40% of strains harbored the cas6 endoribonuclease gene, among which 31.6% and 7.9% of the isolates were positive for the presence of the cas6-a and cas6-d subtypes of the gene, respectively. The subtypes cas6-b and cas6-c were absent in strains studied. Sequence and phylogenetic analysis also established the cas6 sequences in this study to match GenBank sequences for cas6-a and cas6-d subtypes. Conclusion: In V. parahaemolyticus, the Cas6 endoribonuclease is an associated protein of the CRISPR-cas system. CRISPR-positive strains exhibited genotypic variation for this gene. Primers designed in this study would aid in identifying the cas6 genotype and understanding the role of these genotypes in the CRISPR-cas immune system of the pathogen.

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Investigation into the prevalent CRISPR–Cas systems among the Aeromonas genus

Baliga

Shekar

et al. 2021

J Basic Microbiol

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Clustered regularly interspaced short palindromic repeats (CRISPR) is a prokaryotic adaptive immune system that checks invasion by mobile genetic elements through nuclease targeting. In this study, we investigated the occurrence, diversity, and features of the CRISPR system in the genus Aeromonas using bioinformatics tools. Only 13 out of 122 complete genomes (10.66%) of the genus Aeromonas from the NCBI GenBank database harbored the CRISPR system. The Type I–F system was the most prevalent CRISPR system among the Aeromonads, followed by the Type I–E system. Only one strain harbored a Type I–C CRISPR system. Among the Aeromonads, Aeromonas caviae (22.7%) and Aeromonas veronii (20%) had a higher prevalence rate of the complete CRISPR system. The analysis of direct repeat (DR) sequences showed that all could form stable RNA secondary structures. A phylogenetic tree generated for the Cas1 protein classified CRISPR subtypes into three distinct clusters. Among the 748 spacers investigated, 41.98% and 17.25% showed perfect homology to phage and plasmid sequences, respectively. Some arrays had duplicated spacers. The CRISPR loci are closely linked to antibiotic resistance genes in most strains. Collectively, our results would contribute to research on antibiotic resistance in the Aeromonas group, and provide new insights into the diversity and evolution of the CRISPR–Cas system.

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Investigation of direct repeats, spacers and proteins associated with clustered regularly interspaced short palindromic repeat (CRISPR) system of Vibrio parahaemolyticus

Cited by 11 publications

References 49 publications

Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources

Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources

Detection and characterization of clustered regularly interspaced short palindromic repeat-associated endoribonuclease gene variants in Vibrio parahaemolyticus isolated from seafoods and environment

Investigation into the prevalent CRISPR–Cas systems among the Aeromonas genus

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