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
2022-01-18
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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 Biol 215:403–410 [View Article][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 Microbiol 74:4610–4625 [View Article][PubMed]
    [Google Scholar]
  3. Barrangou R., Horvath P. 2012; CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol 3:143–162 [View Article][PubMed]
    [Google Scholar]
  4. Barrangou R., Marraffini L. A. 2014; CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 54:234–244 [View Article][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. Science 315:1709–1712 [View Article][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 Microbiol 80:3508–3517 [View Article][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 Res 41:7429–7437 [View Article][PubMed]
    [Google Scholar]
  8. Bondy-Denomy J., Davidson A. R. 2014; To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol 22:218–225 [View Article][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 Microbiol 159:367–373 [View Article][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 Microbiol 80:994–1001 [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 Cell 56:333–339 [View Article][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. Science 321:960–964 [View Article][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 Biol 138:179–207 [View Article][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 Biol 10:726–737 [View Article][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 Res 42:6091–6105 [View Article][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 Leeuwenhoek 82:303–321 [View Article][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 Microbiol 10:141–145[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. Nature 471:602–607 [View Article][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 Bacteriol 190:1390–1400 [View Article][PubMed]
    [Google Scholar]
  22. Doudna J. A., Charpentier E. 2014; The new frontier of genome engineering with CRISPR-Cas9. Science 346:1258096 [View Article][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 Methods 10:1116–1121 [View Article][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. Nature 468:67–71 [View Article][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 A 109:E2579–E2586 [View Article][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. MBio 5:e00928-13 [View Article][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 Bioinformatics 8:172 [View Article][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 Res 35:(Web Server)W52–W57 [View Article][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 Microbiol 43:199–207 [View Article][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 Bacteriol 190:1401–1412 [View Article][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 Microbiol 131:62–70 [View Article][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 Microbiol 58:648–653 [View Article][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 Genet 9:e1003844 [View Article][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. Science 337:816–821 [View Article][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 Microbiol 48:726–731[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 Microbiol 89:511–516 [View Article][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 Genet 9:e1003312 [View Article][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 Res 43:674–681 [View Article][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 Microbiol 9:467–477 [View Article][PubMed]
    [Google Scholar]
  41. Marraffini L. A., Sontheimer E. J. 2008; CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–1845 [View Article][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 Res 21:1616–1625 [View Article][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. Microbiology 155:733–740 [View Article][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 Commun 4:1430 [View Article][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 Microbiol 55:2206–2213[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 Microbes 3:15–24 [View Article][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 Res 39:9275–9282 [View Article][PubMed]
    [Google Scholar]
  48. Selle K., Barrangou R. 2015; Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol 23:225–232 [View Article][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 Rev 37:915–935 [View Article][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 A 108:10098–10103 [View Article][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 Microbiol 34:164–173 [View Article][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 Microbiol 15:463–470 [View Article][PubMed]
    [Google Scholar]
  53. Walker D. C., Aoyama K., Klaenhammer T. R. 1996; Electrotransformation of Lactobacillus acidophilus group A1. FEMS Microbiol Lett 138:233–237 [View Article][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 A 108:10092–10097 [View Article][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 One 7:e38077 [View Article][PubMed]
    [Google Scholar]
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