Molecular Genetics and Genomics

, Volume 294, Issue 1, pp 253–262 | Cite as

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

  • Pallavi Baliga
  • Malathi ShekarEmail author
  • Moleyur Nagarajappa Venugopal
Original Article


Vibrio parahaemolyticus, a ubiquitous bacterium of the marine environment is an important food-borne pathogen responsible for gastroenteritis worldwide. In this study, we aimed to investigate the occurrence and diversity of the CRISPR–Cas system in V. parahaemolyticus genomes using a bioinformatics approach. The CRISPR–Cas system functions as an adaptive immune system in prokaryotes that provides immunity against foreign genetic elements. In total, 570 genomes V. parahaemolyticus genomes were analyzed of which 200 confirmed for the presence of CRISPR–Cas system. The CRISPR–Cas loci were further analyzed for their repeats, spacers and associated Cas proteins. Among the 200 V. parahaemolyticus strains analyzed, 16 (8%) strains possessed the CRISPR–Cas system of complete subtype I-F, while the remaining 184 (92%) harbored the minimalistic type, a subtype I-F variant. Orphan CRISPR repeats and Cas genes were found in one strain each. The CRISPR-associated direct repeat had an unit length of 28 bases. The number of repeat units in each array ranged from 3 to 5 or 5–41 depending on whether they belonged to the minimalistic or complete subtype-IF CRISPR–Cas system, respectively. Of the 768 spacers analyzed in this study, 295 were found to be unique to V. parahaemolyticus. Homology analysis of the conserved spacers revealed matches to plasmids, phages and gut viruses and self chromosomes. Among the CRISPR-associated proteins, Cas5 and Cas7 proteins were found to be conserved. However, variations were seen in the Cas6 protein, which could be grouped into four different types based on their protein length as well as amino acid composition. We present here the diversity and main features of the CRISPR–Cas system in V. parahaemolyticus, which could provide valuable insights in elucidating the role and mechanism of CRISPR/Cas elements in this pathogen.


Vibrio parahaemolyticus CRISPR Type IF CRISPR Direct repeat Spacer Cas proteins 



The financial support from the Department of Biotechnology, Government of India, under the Bioinformatics Centre programme (BT/BI/04/049/99) is gratefully acknowledged.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Supplementary material

438_2018_1504_MOESM1_ESM.xlsx (52 kb)
Supplementary material 1 (XLSX 52 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Pallavi Baliga
    • 1
  • Malathi Shekar
    • 1
    Email author
  • Moleyur Nagarajappa Venugopal
    • 1
  1. 1.Bioinformatics Centre, Department of Fisheries Microbiology, College of FisheriesKarnataka Veterinary, Animal and Fisheries Sciences UniversityMangaloreIndia

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