The subtype I-F CRISPR-Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation

Biochemical Society Transactions

Volumn 41, Issue 6, 2013, Pages 1468-1474

  Richter, Corinna ^a   Fineran, Peter C ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Bacteriophage; Chromosomal targeting; Clustered regularly interspaced short palindromic repeats (CRISPR); Csy; Genome engineering; Genomic island; Horizontal gene transfer

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; CAS2 PROTEIN; CAS3 PROTEIN; CAS6F PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CSY1 PROTEIN; CSY2 PROTEIN; CSY3 PROTEIN; GUIDE RNA; UNCLASSIFIED DRUG;

BACTERIAL CHROMOSOME; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS ASSAY; COMPLEX FORMATION; CONFERENCE PAPER; CONTROLLED STUDY; DEFENSE MECHANISM; GENE DELETION; GENE TARGETING; GENETIC PROCEDURES; NONHUMAN; OPERON; PATHOGENICITY ISLAND; PECTOBACTERIUM; PECTOBACTERIUM ATROSEPTICUM; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN SYNTHESIS;

CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; GENOMIC ISLANDS; PECTOBACTERIUM; RNA, BACTERIAL;

EID: 84887898165     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130151     Document Type: Conference Paper

References (50)

1. Labrie, S.J., Samson, J.E. and Moineau, S. (2010) Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8, 317-327
2. Stern, A. and Sorek, R. (2010) The phage-host arms race: shaping the evolution of microbes. BioEssays 33, 43-51
3. Grissa, I., Vergnaud, G. and Pourcel, C. (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinf. 8, 172
4. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A. and Horvath, P. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712
5. Yosef, I., Goren, M.G. and Qimron, U. (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40, 5569-5576
6. Mojica, F.J., Diéez-Villasenor, C., Soria, E. and Juez, G. (2000) Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36, 244-246
7. Jansen, R., van Embden, J.D., Gaastra, W. and Schouls, L.M. (2002) Identification of a novel family of sequence repeats among prokaryotes. OMICS 6, 23-33
8. Jansen, R., Embden, J.D., Gaastra, W. and Schouls, L.M. (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565-1575
9. Richter, C., Chang, J.T. and Fineran, P.C. (2012) Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. Viruses 4, 2291-2311
10. Fineran, P.C. and Charpentier, E. (2012) Memory of viral infections by CRISPR-Cas adaptive immune systems: acquisition of new information. Virology 434, 202-209
11. Terns, M.P. and Terns, R.M. (2012) CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. 14, 321-327
12. van der Oost, J., Jore, M.M., Westra, E.R., Lundgren, M. and Brouns, S.J. (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401-407
13. Mojica, F.J., Diéez-Villasenor, C., Garciéa- Martiénez, J. and Almendros, C. (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740
14. Shah, S.A., Erdmann, S., Mojica, F.J. and Garrett, R.A. (2013) Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 10, 891-899
15. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F.J., Wolf, Y.I., Yakunin, A.F. et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477
16. Westra, E.R., Swarts, D.C., Staals, R.H., Jore, M.M., Brouns, S.J. and van der Oost, J. (2012) The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu. Rev. Genet. 46, 311-339
17. De Boer, S.H., Li, X. and Ward, L.J. (2012) Pectobacterium spp. associated with bacterial stem rot syndrome of potato in Canada. Phytopathology 102, 937-947
18. Bell, K.S., Sebaihia, M., Pritchard, L., Holden, M.T., Hyman, L.J., Holeva, M.C., Thomson, N.R., Bentley, S.D., Churcher, L.J., Mungall, K. et al. (2004) Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. U.S.A. 101, 11105-11110
19. Evans, T.J., Coulthurst, S.J., Komitopoulou, E. and Salmond, G.P. (2010) Two mobile Pectobacterium atrosepticum prophages modulate virulence. FEMS Microbiol. Lett. 304, 195-202
20. Blower, T.R., Evans, T.J., Przybilski, R., Fineran, P.C. and Salmond, G.P.C. (2012) Viral evasion of a bacterial suicide system by RNA-based molecular mimicry enables infectious altruism. PLoS Genet. 8, e1003023
21. Fineran, P.C., Blower, T.R., Foulds, I.J., Humphreys, D.P., Lilley, K.S. and Salmond, G.P. (2009) The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. U.S.A. 106, 894-899
22. Blower, T.R., Pei, X.Y., Short, F.L., Fineran, P.C., Humphreys, D.P., Luisi, B.F. and Salmond, G.P. (2011) A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nat. Struct. Mol. Biol. 18, 185-190
23. Przybilski, R., Richter, C., Gristwood, T., Clulow, J.S., Vercoe, R.B. and Fineran, P.C. (2011) Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biol. 8, 517-528
24. Cook, G.M., Robson, J.R., Frampton, R.A., McKenzie, J., Przybilski, R., Fineran, P.C. and Arcus, V.L. (2013) Ribonucleases in bacterial toxin-antitoxin systems. Biochim. Biophys. Acta 1829, 523-531
25. Biswas, A., Gagnon, J.N., Brouns, S.J., Fineran, P.C. and Brown, C.M. (2013) CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 10, 817-827
26. Vercoe, R.B., Chang, J.T., Dy, R.L., Taylor, C., Gristwood, T., Clulow, J.S., Richter, C., Przybilski, R., Pitman, A.R. and Fineran, P.C. (2013) Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet. 9, e1003454
27. Kunin, V., Sorek, R. and Hugenholtz, P. (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, 1-7
28. Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Snijders, A.P., Dickman, M.J., Makarova, K.S., Koonin, E.V. and van der Oost, J. (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964
29. Cady, K.C. and O'Toole, G.A. (2011) Non-identity targeting of Yersinia-subtype CRISPR-prophage interaction requires the Csy and Cas3 proteins. J. Bacteriol. 193, 3433-3445
30. Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. and Doudna, J.A. (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358
31. Sternberg, S.H., Haurwitz, R.E. and Doudna, J.A. (2012) Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18, 661-672
32. Richter, C., Gristwood, T., Clulow, J.S. and Fineran, P.C. (2012) In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas system. PLoS ONE 7, e49549
33. Haurwitz, R.E., Sternberg, S.H. and Doudna, J.A. (2012) Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 31, 2824-2832
34. Wiedenheft, B., van Duijn, E., Bultema, J., Waghmare, S., Zhou, K., Barendregt, A., Westphal, W., Heck, A., Boekema, E., Dickman, M. and Doudna, J.A. (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
35. Wiedenheft, B., Lander, G.C., Zhou, K., Jore, M.M., Brouns, S.J., van der Oost, J., Doudna, J.A. and Nogales, E. (2011) Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486-489
36. Nam, K.H., Haitjema, C., Liu, X., Ding, F., Wang, H., DeLisa, M.P. and Ke, A. (2012) Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 20, 1574-1584
37. Lintner, N.G., Kerou, M., Brumfield, S.K., Graham, S., Liu, H., Naismith, J.H., Sdano, M., Peng, N., She, Q., Copieé, V. et al. (2011) Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J. Biol. Chem. 286, 21643-21656
38. Westra, E.R., van Erp, P.B., Kunne, T., Wong, S.P., Staals, R.H., Seegers, C.L., Bollen, S., Jore, M.M., Semenova, E., Severinov, K. et al. (2012) CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by cascade and Cas3. Mol. Cell 46, 595-605
39. Sinkunas, T., Gasiunas, G., Waghmare, S.P., Dickman, M.J., Barrangou, R., Horvath, P. and Siksnys, V. (2013) In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J. 32, 385-394
40. Datsenko, K.A., Pougach, K., Tikhonov, A., Wanner, B.L., Severinov, K. and Semenova, E. (2012) Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun. 3, 945
41. Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. and Koonin, E.V. (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7
42. Swarts, D.C., Mosterd, C., van Passel, M.W. and Brouns, S.J. (2012) CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7, e35888
43. Stern, A., Keren, L., Wurtzel, O., Amitai, G. and Sorek, R. (2010) Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26, 335-340
44. Mandin, P., Repoila, F., Vergassola, M., Geissmann, T. and Cossart, P. (2007) Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res. 35, 962-974
45. Almendros, C., Guzman, N.M., Diéez-Villasenor, C., Garciéa-Martiénez, J. and Mojica, F.J. (2012) Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli. PLoS ONE 7, e50797
46. Semenova, E., Jore, M.M., Datsenko, K.A., Semenova, A., Westra, E.R., Wanner, B., van der Oost, J., Brouns, S.J. and 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
47. Gudbergsdottir, S., Deng, L., Chen, Z., Jensen, J.V., Jensen, L.R., She, Q. and Garrett, R.A. (2011) Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol. Microbiol. 79, 35-49
48. Diéez-Villasenor, C., Almendros, C., Garciéa- Martiénez, J. and Mojica, F.J. (2010) Diversity of CRISPR loci in Escherichia coli. Microbiology 156, 1351-1361
49. Touchon, M., Charpentier, S., Clermont, O., Rocha, E.P., Denamur, E. and Branger, C. (2011) CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 193, 2460-2467
50. Brodt, A., Lurie-Weinberger, M.N. and Gophna, U. (2011) CRISPR loci reveal networks of gene exchange in archaea. Biol. Direct 6, 65