Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli

Journal of Basic Microbiology

Volumn 56, Issue 6, 2016, Pages 645-653

  Rahmatabadi, Seyyed Soheil ^a,b   Nezafat, Navid ^b   Negahdaripour, Manica ^a,b   Hajighahramani, Nasim ^a,b   Morowvat, Mohammad Hossein ^b   Ghasemi, Younes ^a,b,c  

^a SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^b SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

Cas; CRISPR; Direct repeat; Escherichia coli; RNA structure

Indexed keywords

BACTERIAL DNA; SPACER DNA; VIRUS DNA;

BACTERIAL GENOME; BACTERIOPHAGE; BIOLOGY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; ESCHERICHIA COLI; GENETICS; PLASMID;

BACTERIOPHAGES; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; DNA, INTERGENIC; DNA, VIRAL; ESCHERICHIA COLI; GENOME, BACTERIAL; PLASMIDS;

EID: 84973100704     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.201500707     Document Type: Article

References (31)

1. Terns, R.M., Terns, M.P., 2014. CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet., 30, 111–118.
2. Lobersli, I., Haugum, K., Lindstedt, B.A., 2012. Rapid and high resolution gen­otyping of all Escherichia coli serotypes using 10 genomic repeat-containing loci. J. Microbiol. Methods, 88, 134–139.
3. Dang, T.N., Zhang, L., Zollner, S., Srinivasan, U., et al., 2013. Uropathogenic Escherichia coli are less likely than paired fecal E. coli to have CRISPR loci. Infect. Genet Evol., J. Mol. Epidemiol. Evolution. Genet. Infect. Dis., 19, 212–218.
4. Wakefield, N., Rajan, R., Sontheimer, E.J., 2015. Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis. FEBS Lett., 20, 3197–3204.
5. Yang, S., Liu, J., Shao, F., Wang, P., et al., 2015. Analysis of the features of 45 identified CRISPR loci in 32 Staphylococcus aureus. Biochem. Biophys. Res. Commun., 464, 894–900.
6. Lillestol, R.K., Redder, P., Garrett, R.A., Brugger, K., 2006. A putative viral defence mechanism in archaeal cells. Archaea, 2, 59–72.
7. Goren, M.G., Yosef, I., Auster, O., Qimron, U., 2012. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J. Microbiol. Methods, 423, 14–16.
8. Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., et al., 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucl. Acids Res., 39, 9275–9282.
9. Pul, U., Wurm, R., Arslan, Z., Geissen, R., et al., 2010. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol. Microbiol., 75, 1495–1512.
10. Horvath, P., Romero, D.A., Coute-Monvoisin, A.C., Richards, M., et al., 2008. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol., 190, 1401–1412.
11. Grissa, I., Vergnaud, G., Pourcel, C., 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform., 8, 172.
12. Diez-Villasenor, C., Almendros, C., Garcia-Martinez, J., Mojica, F.J., 2010. Diversity of CRISPR loci in Escherichia coli. Microbiol., 156, 1351–1361.
13. Kunin, V., Sorek, R., Hugenholtz, P., 2007. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Gen. Biol., 8, 1–7.
14. Bolotin, A., Quinquis, B., Sorokin, A., Ehrlich, S.D., 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiol., 151, 2551–2561.
15. Hsu, P.D., Lander, E.S., Zhang, F., 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157, 1262–1278.
16. Bondy-Denomy, J., Davidson, A.R., 2014. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol., 22, 218–225.
17. Gholami, A., Shahin, S., Mohkam, M., Nezafat, N., et al., 2015. Cloning, characterization and bioinformatics analysis of novel cytosine deaminase from Escherichia coli AGH09. Int. J. Peptide Res. Ther., 21, 365–374.
18. Ghasemi, Y., Dabbagh, F., Rasoul-Amini, S., Borhani Haghighi, A., et al., 2012. The possible role of hsps on behçet's disease. A bioinformatic approach. Comput. Biol. Med., 42, 1079–1085.
19. Nezafat, N., Ghasemi, Y., Javadi, G., Khoshnoud, M.J., et al., 2014. A novel multi-epitope peptide vaccine against cancer. an in silico approach. J. Theor. Biol., 349, 121–134.
20. Zamani, M., Nezafat, N., Negahdaripour, M., Dabbagh, F., et al., 2015. In silico evaluation of different signal peptides for the secretory production of human growth hormone in E. coli. Int. J. Pep. Res. Ther., 21, 261–268.
21. Grissa, I., Vergnaud, G., Pourcel, C., 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucl. Acids Res., 35, 52–57.
22. Zuker, M., Stiegler, P., 1981. Optimal computer folding of lare RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res., 9, 133–148.
23. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., et al., 1990. Basic local alignment search tool. J. Mol. Biol., 215, 403–410.
24. Touchon M., Charpentier S., Clermont O., Rocha E.P., et al., CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 193 2011. 2460–2467.
25. Grissa, I., Bouchon, P., Pourcel, C., Vergnaud, G., 2008. On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing. Biochem., 90, 660–668.
26. Haft, D.H., Selengut, J., Mongodin, E.F., Nelson, K.E., 2005. A guild of forty-five CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol., 6, 60.
27. Greve, B., Jensen, S., Brugger, K., Zillig, W., et al., 2004. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea, 1, 231–239.
28. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J., Soria, E., 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol., 60, 174–182.
29. Pourcel, C., Salvignol, G., Vergnaud, G., 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiol., 151, 653–663.
30. Di, H., Ye, L., Yan, H., Meng, H., et al., 2014. Comparative analysis of CRISPR loci in different Listeria monocytogenes lineages. Biochem. Biophys. Res. Commun., 454, 399–403.
31. Wolfsheimer, S., Hartmann, A.K., 2010. Minimum-free-energy distribution of RNA secondary structures: entropic and thermodynamic properties of rare events. Phys. Rev. E, 82, 021902.