Abstract
Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. In this study, the structure and function of the CRISPR-Cas system in 120 Vibrio strains were analyzed by bioinformatics methods, as well as the correlation between CRISPR and mobile genetic elements (MEGs). Only 61 Vibrio strains contained one or more CRISPR structures, and finally 102 CRISPRs were identified. The typical repeat size was 28 bp, and the total length of CRISPRs is nearly 60 bp, which was the most stable length of CRISPR in Vibrio strains. The types of CRISPR-Cas present in 61 strains were I-C, I-E, I-F, II-B, III-B, III-D and the rare type IV systems. Through principal component analysis, we found that Cas gene was most closely related to CRISPR. In addition, phages and plasmids were also highly correlated, showing negative correlation with CRISPR-Cas system. CRISPR-Cas predominantly present on chromosome within Vibrio while rarely in plasmids. Comparing the structural characteristics of plasmids containing CRISPR and without CRISPR, we found plasmid pMBL287 with CRISPR contained a bacteriophage f237, with more MGES, suggesting the diversity was greater. In addition, the same mobile genetic elements IS256 and ISL3 were found in the upstream and downstream of CRISPR. This study provides the prevalence, diversity and phylogenetic distribution of CRISPR-Cas in Vibrio, revealing which type of CRISPR-Cas system is predominant, and the factors affecting its function, as well as its relationship with mobile genetic elements.
Similar content being viewed by others
References
Azuma Y et al (2009) Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res 37:5768–5783
Baliga P, Shekar M, Venugopal MN (2019) Investigation of direct repeats, spacers and proteins associated with clustered regularly interspaced short palindromic repeat (CRISPR) system of Vibrio parahaemolyticus. Mol Genet Genom 294:253–262. https://doi.org/10.1007/s00438-018-1504-8
Barrangou R (2013) CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4:267–278. https://doi.org/10.1002/wrna.1159
Box AM, McGuffie MJ, O’Hara BJ, Seed KD (2016) Functional analysis of bacteriophage immunity through a Type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J Bacteriol 198:578–590. https://doi.org/10.1128/jb.00747-15
Carpenter MR, Kalburge SS, Borowski JD, Peters MC, Colwell RR, Boyd EF (2017) CRISPR-Cas and contact-dependent secretion systems present on excisable pathogenicity islands with conserved recombination modules. J Bacteriol. https://doi.org/10.1128/jb.00842-16
Chakraborty S, Waise TM, Hassan F, Kabir Y, Smith MA, Arif M (2009) Assessment of the evolutionary origin and possibility of CRISPR-Cas (CASS) mediated RNA interference pathway in Vibrio cholerae O395. Silico Biol 9:245–254
Denman RB (1993) Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques 15:1090–1095
Deveau H, Garneau JE, Moineau S (2010) CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 64:475–493
Guo X et al (2015) Detection and analysis of CRISPRs of Shigella. Curr Microbiol 70:85–90
Hille F, Charpentier E (2016) CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc B. https://doi.org/10.1098/rstb.2015.0496
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170. https://doi.org/10.1126/science.1179555
Horvath P et al (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190:1401–1412. https://doi.org/10.1128/jb.01415-07
Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL (2015) Comparative analysis of the orphan CRISPR2 locus in 242 Enterococcus faecalis Strains. PLoS ONE 10:e0138890. https://doi.org/10.1371/journal.pone.0138890
Jorth P, Whiteley M (2012) An evolutionary link between natural transformation and CRISPR adaptive immunity. Mbio. https://doi.org/10.1128/mBio.00309-12
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78. https://doi.org/10.1016/j.mib.2017.05.008
Labbate M et al (2016) A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. Sci Rep 6:36891. https://doi.org/10.1038/srep36891
Makarova KS et al (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467–477
Makarova KS et al (2015) An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13:722–736. https://doi.org/10.1038/nrmicro3569
Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P (2007) Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res 35:962–974. https://doi.org/10.1093/nar/gkl1096
Mcdonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF (2019) CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. BMC Genom 20:105. https://doi.org/10.1186/s12864-019-5439-1
Naser IB, Hoque MM, Nahid MA, Tareq TM, Rocky MK, Faruque SM (2017) Analysis of the CRISPR-Cas system in bacteriophages active on epidemic strains of Vibrio cholerae in Bangladesh. Sci Rep 7:14880. https://doi.org/10.1038/s41598-017-14839-2
Nishimasu H, Nureki O (2017) Structures and mechanisms of CRISPR RNA-guided effector nucleases. Curr Opin Struct Biol 43:68–78. https://doi.org/10.1016/j.sbi.2016.11.013
Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA (2014) Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol 21:528–534. https://doi.org/10.1038/nsmb.2820
Reeks J, Naismith JH, White MF (2013) CRISPR interference: a structural perspective. Biochem J 453:155–166. https://doi.org/10.1042/bj20130316
Sanozky-Dawes R, Selle K, O’Flaherty S, Klaenhammer T, Barrangou R (2015) Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri. Microbiology 161:1752–1761. https://doi.org/10.1099/mic.0.000129
Seed KD, Lazinski DW, Calderwood SB, Camilli A (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494:489–491. https://doi.org/10.1038/nature11927
Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform. https://doi.org/10.1002/0471250953.bi0203s00
Touchon M et al (2012) Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiol Sgm 158:2997–3004. https://doi.org/10.1099/mic.0.060814-0
van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34:401–407. https://doi.org/10.1016/j.tibs.2009.05.002
Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338. https://doi.org/10.1038/nature10886
Yin S, Jensen MA, Bai J, Debroy C, Barrangou R, Dudley EG (2013) The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. Appl Environ Microbiol 79:5710–5720. https://doi.org/10.1128/aem.00950-13
Yosef I, Goren MG, Qimron U (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 40:5569–5576. https://doi.org/10.1093/nar/gks216
Zhang M et al (2019) Analysis of the structures of confirmed and questionable CRISPR loci in 325 Staphylococcus genomes. J Basic Microbiol 59:901–913. https://doi.org/10.1002/jobm.201900124
Acknowledgements
This work was supported by National Natural Science Foundation of China (No. 32172188). We gratefully acknowledge the anonymous reviewers for their constructive comments and suggestions.
Funding
This work was supported by National Natural Science Foundation of China (No. 32172188) and Key Research and Development Program of Zhejiang Province (No. 2020C02031 and No. 2018C02024).
Author information
Authors and Affiliations
Contributions
Not applicable.
Corresponding authors
Ethics declarations
Conflict of interest
The authors have no conflicts of interest to declare that are relevant to the content of this article.
Availability of data and materials
All data generated or analyzed during this study are included in this published article [and its supplementary information files].
Code availability
Not applicable.
Ethics approval
Not applicable.
Consent to participate
Not applicable.
Consent for publication
All the authors consent to this submission.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Zhang, E., Zhou, W., Zhou, J. et al. CRISPR-Cas systems are present predominantly on chromosome and its relationship with MEGs in Vibrio species. Arch Microbiol 204, 76 (2022). https://doi.org/10.1007/s00203-021-02656-1
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-021-02656-1