1887

Abstract

Bacteria encode clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated genes (), which collectively form an RNA-guided adaptive immune system against invasive genetic elements. surveys have revealed that lactic acid bacteria harbour a prolific and diverse set of CRISPR-Cas systems. Thus, the natural evolutionary role of CRISPR-Cas systems may be investigated in these ecologically, industrially, scientifically and medically important microbes. In this study, 17 strains were investigated and 6 harboured a type II-A CRISPR-Cas system, with considerable diversity in array size and spacer content. Several of the spacers showed similarity to phage and plasmid sequences, which are typical targets of CRISPR-Cas immune systems. Aligning the protospacers facilitated inference of the protospacer adjacent motif sequence, determined to be 5′-NTAA-3′ flanking the 3′ end of the protospacer. The system in JV-V03 and NCK 1342 interfered with transforming plasmids containing sequences matching the most recently acquired CRISPR spacers in each strain. We report the distribution and function of a native type II-A CRISPR-Cas system in the commensal species . Collectively, these results open avenues for applications for bacteriophage protection and genome modification in , and contribute to the fundamental understanding of CRISPR-Cas systems in bacteria.

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2015-09-01
2020-04-07
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. 1990; Basic local alignment search tool. J Mol Biol215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  2. Azcarate-Peril M. A., Altermann E., Goh Y. J., Tallon R., Sanozky-Dawes R. B., Pfeiler E. A., O'Flaherty S., Buck B. L., Dobson A., other authors. 2008; Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol74:4610–4625 [CrossRef][PubMed]
    [Google Scholar]
  3. Barrangou R., Horvath P.. 2012; CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol3:143–162 [CrossRef][PubMed]
    [Google Scholar]
  4. Barrangou R., Marraffini L. A.. 2014; CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell54:234–244 [CrossRef][PubMed]
    [Google Scholar]
  5. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D. A., Horvath P.. 2007; CRISPR provides acquired resistance against viruses in prokaryotes. Science315:1709–1712 [CrossRef][PubMed]
    [Google Scholar]
  6. Baugher J. L., Durmaz E., Klaenhammer T. R.. 2014; Spontaneously induced prophages in Lactobacillus gasseri contribute to horizontal gene transfer. Appl Environ Microbiol80:3508–3517 [CrossRef][PubMed]
    [Google Scholar]
  7. Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L. A.. 2013; Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res41:7429–7437 [CrossRef][PubMed]
    [Google Scholar]
  8. Bondy-Denomy J., Davidson A. R.. 2014; To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol22:218–225 [CrossRef][PubMed]
    [Google Scholar]
  9. Breitbart M., Haynes M., Kelley S., Angly F., Edwards R. A., Felts B., Mahaffy J. M., Mueller J., Nulton J., other authors. 2008; Viral diversity and dynamics in an infant gut. Res Microbiol159:367–373 [CrossRef][PubMed]
    [Google Scholar]
  10. Briner A. E., Barrangou R. 2014; Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity. Appl Environ Microbiol80:994–1001[CrossRef]
    [Google Scholar]
  11. Briner A. E., Donohoue P. D., Gomaa A. A., Selle K., Slorach E. M., Nye C. H., Haurwitz R. E., Beisel C. L., May A. P., Barrangou R.. 2014; Guide RNA functional modules direct Cas9 activity and orthogonality. Mol Cell56:333–339 [CrossRef][PubMed]
    [Google Scholar]
  12. Brouns S. J. J., Jore M. M., Lundgren M., Westra E. R., Slijkhuis R. J. H., Snijders A. P. L., Dickman M. J., Makarova K. S., Koonin E. V., van der Oost J.. 2008; Small CRISPR RNAs guide antiviral defense in prokaryotes. Science321:960–964 [CrossRef][PubMed]
    [Google Scholar]
  13. Casadaban M. J., Cohen S. N.. 1980; Analysis of gene control signals by DNA fusion and cloning in Escherichia coli . J Mol Biol138:179–207 [CrossRef][PubMed]
    [Google Scholar]
  14. Chylinski K., Le Rhun A., Charpentier E.. 2013; The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol10:726–737 [CrossRef][PubMed]
    [Google Scholar]
  15. Chylinski K., Makarova K. S., Charpentier E., Koonin E. V.. 2014; Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res42:6091–6105 [CrossRef][PubMed]
    [Google Scholar]
  16. Clark R. H.. 2001; Distribution and strain polymorphisms in probiotic lactobacilli MS thesis, North Carolina State University, Raleigh, NC, USA
    [Google Scholar]
  17. Coffey A., Ross R. P.. 2002; Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application. Antonie van Leeuwenhoek82:303–321 [CrossRef][PubMed]
    [Google Scholar]
  18. Crowell D.. 1998; Microbial analysis of human intestinal flora after feeding Lactobacillus acidophilus MS thesis, North Carolina State University, Raleigh, NC, USA
    [Google Scholar]
  19. Delgado S., Suárez A., Mayo B.. 2007; Dominant cultivable Lactobacillus species from the feces of healthy adults in northern Spain. Int Microbiol10:141–145[PubMed]
    [Google Scholar]
  20. Deltcheva E., Chylinski K., Sharma C. M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J., Charpentier E.. 2011; CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature471:602–607 [CrossRef][PubMed]
    [Google Scholar]
  21. Deveau H., Barrangou R., Garneau J. E., Labonté J., Fremaux C., Boyaval P., Romero D. A., Horvath P., Moineau S.. 2008; Phage response to CRISPR-encoded resistance in Streptococcus thermophilus . J Bacteriol190:1390–1400 [CrossRef][PubMed]
    [Google Scholar]
  22. Doudna J. A., Charpentier E.. 2014; The new frontier of genome engineering with CRISPR-Cas9. Science346:1258096 [CrossRef][PubMed]
    [Google Scholar]
  23. Esvelt K. M., Mali P., Braff J. L., Moosburner M., Yaung S. J., Church G. M.. 2013; Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods10:1116–1121 [CrossRef][PubMed]
    [Google Scholar]
  24. Garneau J. E., Dupuis M.-È., Villion M., Romero D. A., Barrangou R., Boyaval P., Fremaux C., Horvath P., Magadán A. H., Moineau S.. 2010; The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature468:67–71 [CrossRef][PubMed]
    [Google Scholar]
  25. Gasiunas G., Barrangou R., Horvath P., Siksnys V.. 2012; Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A109:E2579–E2586 [CrossRef][PubMed]
    [Google Scholar]
  26. Gomaa A. A., Klumpe H. E., Luo M. L., Selle K., Barrangou R., Beisel C. L.. 2014; Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio5:e00928-13 [CrossRef][PubMed]
    [Google Scholar]
  27. Grissa I., Vergnaud G., Pourcel C.. 2007a; The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics8:172 [CrossRef][PubMed]
    [Google Scholar]
  28. Grissa I., Vergnaud G., Pourcel C.. 2007b; CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res35:(Web Server)W52–W57 [CrossRef][PubMed]
    [Google Scholar]
  29. Hanahan D.. 1985; Techniques for Transformation of Escherchia coli Oxford: IRL Press;
    [Google Scholar]
  30. Healy M., Huong J., Bittner T., Lising M., Frye S., Raza S., Schrock R., Manry J., Renwick A., other authors. 2005; Microbial DNA typing by automated repetitive-sequence-based PCR. J Clin Microbiol43:199–207 [CrossRef][PubMed]
    [Google Scholar]
  31. Horvath P., Romero D. A., Coûté-Monvoisin A.-C., Richards M., Deveau H., Moineau S., Boyaval P., Fremaux C., Barrangou R.. 2008; Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus . J Bacteriol190:1401–1412 [CrossRef][PubMed]
    [Google Scholar]
  32. Horvath P., Coûté-Monvoisin A.-C., Romero D. A., Boyaval P., Fremaux C., Barrangou R.. 2009; Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol131:62–70 [CrossRef][PubMed]
    [Google Scholar]
  33. Ismail E. A., Neve H., Geis A., Heller K. J.. 2009; Characterization of temperate Lactobacillus gasseri phage LgaI and its impact as prophage on autolysis of its lysogenic host strains. Curr Microbiol58:648–653 [CrossRef][PubMed]
    [Google Scholar]
  34. Jiang W., Maniv I., Arain F., Wang Y., Levin B. R., Marraffini L. A.. 2013; Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet9:e1003844 [CrossRef][PubMed]
    [Google Scholar]
  35. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E.. 2012; A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science337:816–821 [CrossRef][PubMed]
    [Google Scholar]
  36. Kok J., van der Vossen J. M., Venema G.. 1984; Construction of plasmid cloning vectors for lactic streptococci which also replicate in Bacillus subtilis and Escherichia coli . Appl Environ Microbiol48:726–731[PubMed]
    [Google Scholar]
  37. Kullen M. J., Sanozky-Dawes R. B., Crowell D. C., Klaenhammer T. R.. 2000; Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol89:511–516 [CrossRef][PubMed]
    [Google Scholar]
  38. Levin B. R., Moineau S., Bushman M., Barrangou R.. 2013; The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity. PLoS Genet9:e1003312 [CrossRef][PubMed]
    [Google Scholar]
  39. Luo M. L., Mullis A. S., Leenay R. T., Beisel C. L.. 2015; Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Res43:674–681 [CrossRef][PubMed]
    [Google Scholar]
  40. Makarova K. S., Haft D. H., Barrangou R., Brouns S. J. J., Charpentier E., Horvath P., Moineau S., Mojica F. J. M., Wolf Y. I., other authors. 2011; Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol9:467–477 [CrossRef][PubMed]
    [Google Scholar]
  41. Marraffini L. A., Sontheimer E. J.. 2008; CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science322:1843–1845 [CrossRef][PubMed]
    [Google Scholar]
  42. Minot S., Sinha R., Chen J., Li H., Keilbaugh S. A., Wu G. D., Lewis J. D., Bushman F. D.. 2011; The human gut virome: inter-individual variation and dynamic response to diet. Genome Res21:1616–1625 [CrossRef][PubMed]
    [Google Scholar]
  43. Mojica F. J. M., Díez-Villaseñor C., García-Martínez J., Almendros C.. 2009; Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology155:733–740 [CrossRef][PubMed]
    [Google Scholar]
  44. Paez-Espino D., Morovic W., Sun C. L., Thomas B. C., Ueda K., Stahl B., Barrangou R., Banfield J. F.. 2013; Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun4:1430 [CrossRef][PubMed]
    [Google Scholar]
  45. Raya R. R., Kleeman E. G., Luchansky J. B., Klaenhammer T. R.. 1989; Characterization of the temperate bacteriophage phi adh and plasmid transduction in Lactobacillus acidophilus ADH. Appl Environ Microbiol55:2206–2213[PubMed]
    [Google Scholar]
  46. Rodrigues da Cunha L., Fortes Ferreira C. L. L., Durmaz E., Goh Y. J., Sanozky-Dawes R., Klaenhammer T.. 2012; Characterization of Lactobacillus gasseri isolates from a breast-fed infant. Gut Microbes3:15–24 [CrossRef][PubMed]
    [Google Scholar]
  47. Sapranauskas R., Gasiunas G., Fremaux C., Barrangou R., Horvath P., Siksnys V.. 2011; The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli . Nucleic Acids Res39:9275–9282 [CrossRef][PubMed]
    [Google Scholar]
  48. Selle K., Barrangou R.. 2015; Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol23:225–232 [CrossRef][PubMed]
    [Google Scholar]
  49. Selle K., Klaenhammer T. R.. 2013; Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev37:915–935 [CrossRef][PubMed]
    [Google Scholar]
  50. Semenova E., Jore M. M., Datsenko K. A., Semenova A., Westra E. R., Wanner B., van der Oost J., Brouns S. J. J., Severinov K.. 2011; Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A108:10098–10103 [CrossRef][PubMed]
    [Google Scholar]
  51. Shariat N., DiMarzio M. J., Yin S., Dettinger L., Sandt C. H., Lute J. R., Barrangou R., Dudley E. G.. 2013; The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. Food Microbiol34:164–173 [CrossRef][PubMed]
    [Google Scholar]
  52. Sun C. L., Barrangou R., Thomas B. C., Horvath P., Fremaux C., Banfield J. F.. 2013; Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol15:463–470 [CrossRef][PubMed]
    [Google Scholar]
  53. Walker D. C., Aoyama K., Klaenhammer T. R.. 1996; Electrotransformation of Lactobacillus acidophilus group A1. FEMS Microbiol Lett138:233–237 [CrossRef][PubMed]
    [Google Scholar]
  54. Wiedenheft B., van Duijn E., Bultema J. B., Waghmare S. P., Zhou K., Barendregt A., Westphal W., Heck A. J. R., Boekema E. J., other authors. 2011; RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A108:10092–10097 [CrossRef][PubMed]
    [Google Scholar]
  55. Young J. C., Dill B. D., Pan C., Hettich R. L., Banfield J. F., Shah M., Fremaux C., Horvath P., Barrangou R., Verberkmoes N. C.. 2012; Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus . PLoS One7:e38077 [CrossRef][PubMed]
    [Google Scholar]
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