Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus

Molecular Microbiology

Volumn 91, Issue 5, 2014, Pages 900-917

  Erdmann, Susanne ^a   Le Moine Bauer, Sven ^a,b   Garrett, Roger A ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; SPACER DNA; VIRUS DNA;

ARTICLE; CONTROLLED STUDY; CRISPR IMMUNE SYSTEM; HOST CELL; IMMUNE SYSTEM; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; SMV1 VIRUS; STSV2 VIRUS; SULFOLOBUS; SULFOLOBUS ISLANDICUS; VIRAL GENETICS; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS INFECTION; VIRUS STRAIN;

SULFOLOBUS;

BASE SEQUENCE; CLONE CELLS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COLD-SHOCK RESPONSE; DNA REPLICATION; DNA, BACTERIAL; DNA, INTERGENIC; DNA, VIRAL; GENETIC LOCI; GENOME, VIRAL; HOST-PATHOGEN INTERACTIONS; MICROBIAL VIABILITY; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SULFOLOBUS; VIRAL PROTEINS; VIRION; VIRUS REPLICATION; VIRUSES;

EID: 84896738064     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/mmi.12503     Document Type: Article

References (49)

1. Arnold, H.P., Zillig, W., Ziese, U., Holz, I., Crosby, M., Utterback, T., etal. (2000) A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. Virology 267: 252-266.
2. Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., Nocek, B., etal. (2011) A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 79: 484-502.
3. Barrangou, R., and Van der Oost, J. (eds) (2013) CRISPR-Cas Systems. Heidelberg: Springer Press, pp. 1-291.
4. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., etal. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
5. Beloglazova, N., Brown, G., Zimmerman, M.D., Proudfoot, M., Makarova, K.S., Kudritska, M., etal. (2008) A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem 283: 20361-20371.
6. Bondy-Denomy, J., Pawluk, A., Maxwell, K.L., and Davidson, A.R. (2012) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493: 429-432.
7. 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.
8. Deng, L., Zhu, H., Chen, Z., Liang, Y.X., and She, Q. (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13: 735-746.
9. Deng, L., Garrett, R.A., Shah, S.A., Peng, X., and She, Q. (2013) A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol Microbiol 87: 1088-1099.
10. Deveau, H., Barrangou, R., Garneau, J.E., Labonté, J., Fremaux, C., Boyaval, P., etal. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190: 1390-1400.
11. Díez-Villaseñor, C., Guzmán, N.M., Almendros, C., García-Martínez, J., and Mojica, F.J.M. (2013) CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol 10: 792-802.
12. Erdmann, S., and Garrett, R.A. (2012) Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol. Microbiol. 85: 1044-1056. Corrigendum. Mol Microbiol 86: 757.
13. Erdmann, S., Shah, S.A., and Garrett, R.A. (2013) SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem Soc Trans 41: 1449-1458.
14. Erdmann, S., Chen, B., Huang, X., Deng, L., Liu, C., Shah, S.A., etal. (2014) A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles 18: 51-60.
15. Garrett, R.A., Vestergaard, G., and Shah, S.A. (2011) Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol 19: 549-556.
16. Goulet, A., Vestergaard, G., Felisberto-Rodrigues, C., Campanacci, V., Garrett, R.A., Cambillau, C., etal. (2010) Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV. Acta Crystallogr D Biol Crystallogr D66: 304-308.
17. Gudbergsdottir, S., Deng, L., Chen, Z., Jensen, J.V., Jensen, L.R., She, Q., etal. (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.
18. Guo, L., Brügger, K., Liu, C., Shah, S.A., Zheng, H., Zhu, Y., etal. (2011) Genome analyses of Icelandic strains of Sulfolobus islandicus: model organisms for genetic and virus-host interaction studies. J Bacteriol 193: 1672-1680.
19. Häring, M., Rachel, R., Peng, X., Garrett, R.A., and Prangishvili, D. (2005) Viral diversity in hot springs of Pozzuoli, Italy, including a unique bottle-shaped virus ABV from a new family the Ampullaviridae. J Virol 79: 9904-9911.
20. Lillestøl, R.K., Redder, P., Garrett, R.A., and Brügger, K. (2006) A putative viral defence mechanism in archaeal cells. Archaea 2: 59-72.
21. Lillestøl, R.K., Shah, S.A., Brügger, K., Redder, P., Phan, H., Christiansen, J., etal. (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72: 259-272.
22. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J., Charpentier, E., Horvath, P., etal. (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9: 467-477.
23. Makarova, K.S., Anatharaman, V., Aravind, L., and Koonin, E.V. (2012) Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct 7: 40.
24. Manica, A., Zebec, Z., Teichmann, D., and Schleper, C. (2011) In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Mol Microbiol 80: 481-491.
25. Manica, A., Zebec, Z., Steinkellner, J., and Schleper, C. (2013) Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus. Nucleic Acids Res 41: 10509-10517.
26. Nam, K.H., Ding, F., Haitjema, C., Huang, Q., Delisa, M.P., and Ke, A. (2012) Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J Biol Chem 287: 35943-35952.
27. Paez-Espino, D., Morovic, W., Sun, C.L., Thomas, B.C., Ueda, K., Stahl, B., etal. (2013) Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun 4: 1430.
28. Peng, N., Xia, Q., Chen, Z., Liang, Y.X., and She, Q. (2009) An upstream activation element exerting differential transcriptional activation on an archaeal promoter. Mol Microbiol 74: 928-939.
29. Peng, X., Blum, H., She, Q., Domdey, H., Mallok, S., Brügger, K., etal. (2001) Sequences and replication of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291: 226-234.
30. Pina, M., Bize, A., Forterre, P., and Prangishvili, D. (2011) The archaeoviruses. FEMS Microbiol Rev 35: 1035-1054.
31. Prangishvili, D., and Garrett, R.A. (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13: 535-542.
32. Prangishvili, D., Forterre, P., and Garrett, R.A. (2006a) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4: 837-848.
33. Prangishvili, D., Vestergaard, G., Häring, M., Aramayo, R., Basta, T., Rachel, R., and Garrett, R.A. (2006b) Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J Mol Biol 359: 1203-1216.
34. 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.
35. Scheele, U., Erdmann, E., Ungewickell, E.J., Felisberto-Rodrigues, C., Ortiz-Lombardía, M., and Garrett, R.A. (2011) Chaperone role for proteins p618 and p892 in the extra-cellular tail development of Acidianus two-tailed virus ATV. J Virol 85: 4812-4821.
36. Shah, S.A., and Garrett, R.A. (2011) CRISPR/Cas and Cmr modules - mobility and evolution of an adaptive immune system. Res Microbiol 162: 27-38.
37. Shah, S.A., Hansen, N.R., and Garrett, R.A. (2009) Distributions of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem Soc Trans 37: 23-28.
38. Shah, S.A., Vestergaard, G., and Garrett, R.A. (2011) CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea. Regulatory RNAs in Prokaryotes. Marchfelder, A., and Hess, W. (eds). Vienna: Springer Press, pp. 163-181.
39. Shah, S.A., Erdmann, S., Mojica, F.J.M., and Garrett, R.A. (2013) Protospacer motifs: mixed identities and functional diversity. RNA Biol 10: 891-899.
40. 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.
41. Terns, M.P., and Terns, R.M. (2011) CRISPR-based adaptive immune systems. Curr Opin Microbiol 14: 321-327.
42. Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S.M., Ma, W., and Doudna, J.A. (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17: 904-912.
43. Wiedenheft, B., Sternberg, S.H., and Doudna, J.A. (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482: 331-338.
44. 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.
45. Yosef, I., Shitrit, D., Goren, M.G., Burstein, D., Pupko, T., and Qimron, U. (2013) DNA motifs determining the efficiency of adaptation into Escherichia coli CRISPR array. Proc Natl Acad Sci USA 110: 14396-14401.
46. Zerbino, D.R., and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
47. Zhang, J., Rouillon, C., Kerou, M., Reeks, J., Brügger, K., Graham, S.J., etal. (2012) Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell 45: 303-313.
48. Zhang, Y., Heidrich, N., Ampattu, B.J., Gunderson, C.W., Seifert, H.S., Schoen, C., etal. (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 50: 488-503.
49. Zillig, W., Kletzin, A., Schleper, C., Holz, I., Janekovic, D., Hain, J., etal. (1994) Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. Syst Appl Microbiol 16: 109-128.