SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2

Biochemical Society Transactions

Volumn 41, Issue 6, 2013, Pages 1449-1458

  Erdmann, Susanne ^a   Shah, Shiraz A ^a   Garrett, Roger A ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Archaea; Clustered regularly interspaced short palindromic repeats spacer (CRISPR spacer); PMGB1; Sulfolobus; Sulfolobus monocaudavirus 1 (SMV1); Transposable element

Indexed keywords

DNA FRAGMENT; SPACER DNA;

ARCHAEAL VIRUS; BACTERIOPHAGE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPARATIVE STUDY; COMPUTER MODEL; CONFERENCE PAPER; CONJUGATION; DNA SEQUENCE; DNA STRAND; ENVIRONMENTAL STRESS; GENE ACTIVATION; GENE CASSETTE; GENE LOCUS; GUTTAVIRIDAE; LIPOTHRIXVIRIDAE; MIXED INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; RUDIVIRIDAE; SEGMENTAL DUPLICATION; STREPTOCOCCUS THERMOPHILUS; STRESS; SULFOLOBUS MONOCAUDAVIRUS 1; SULFOLOBUS SOLFATARICUS; SULFOLOBUS SOLFATARICUS P2; VIRUS CELL INTERACTION; VIRUS GENOME;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CONJUGATION, GENETIC; PLASMIDS; SULFOLOBUS SOLFATARICUS; VIRUSES;

EID: 84887891225     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130196     Document Type: Conference Paper

References (48)

1. Zillig, W., Arnold, H.P., Holz, I., Prangishvili, D., Schweier, A., Stedman, K., She, Q., Phan, H., Garrett, R. and Kristjansson, J.K. (1998) Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles 2, 131-140
2. Prangishvili, D., Forterre, P. and Garrett, R.A. (2006) Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4, 837-848
3. Pina, M., Bize, A., Forterre, P. and Prangishvili, D. (2011) The archaeoviruses. FEMS Microbiol. Rev. 35, 1035-1054
4. Lawrence, C.M., Menon, S., Eilers, B.J., Bothner, B., Khayat, R., Douglas, T. and Young, M.J. (2009) Structural and functional studies of archaeal viruses. J. Biol. Chem. 284, 12599-12603
5. Brumfield, S.K., Ortmann, A.C., Ruigrok, V., Suci, P., Douglas, T. and Young, M.J. (2009) Particle assembly and ultrastructural features associated with replication of the lytic archaeal virus Sulfolobus turreted icosahedral virus. J. Virol. 83, 5964-5970
6. Bize, A., Karlsson, E.A., Ekefjard, K., Quax, T.E., Pina, M., Prevost, M.C., Forterre, P., Tenaillon, O., Bernander, R. and Prangishvili, D. (2009) A unique virus release mechanism in Archaea. Proc. Natl. Acad. Sci. U.S.A. 106, 11306-11311
7. Prangishvili, D., Vestergaard, G., Haring, M., Aramayo, R., Basta, T., Rachel, R. and Garrett, R.A. (2006) Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Mol. Biol. 359, 1203-1216
8. She, Q., Phan, H., Garrett, R.A., Albers, S.-V., Stedman, K.M. and Zillig, W. (1998) Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles 2, 417-425
9. Stedman, K.M., She, Q., Phan, H., Holz, I., Singh, H., Prangishvili, D., Garrett, R.A. and Zillig, W. (2000) The pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota. J. Bacteriol. 182, 7014-7020
10. Greve, B., Jensen, S., Brugger, K., Zillig, W. and Garrett, R.A. (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1, 231-239
11. Erauso, G., Stedman, K.M., van de Werken, H.J., Zillig, W. and van der Oost, J. (2006) Two novel conjugative plasmids from a single strain of Sulfolobus. Microbiology 152, 1951-1968
12. Aagaard, C., Dalgaard, J. and Garrett, R.A. (1995) Intercellular mobility and homing of an archaeal rDNA intron confers selective advantage over intron- cells of Sulfolobus acidocaldarius. Proc. Natl. Acad. Sci. U.S.A. 92, 12285-12289
13. Hansen, J.E., Dill, A.C. and Grogan, D.W. (2005) Conjugational genetic exchange in the hyperthermophilic archaeon Sulfolobus acidocaldarius: intragenic recombination with minimal dependence on marker separation. J. Bacteriol. 187, 805-809
14. Guo, L., Brugger, K., Liu, C., Shah, S.A., Zheng, H., Zhu, Y., Wang, S., Lillestøl, R.K., Chen, L., Frank, J. et al. (2011) Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. J. Bacteriol. 193, 1672-1680
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. Held, N.L., Herrera, A., Cadillo-Quiroz, H. and Whitaker, R.J. (2010) CRISPR associated diversity within a population of Sulfolobus islandicus. PLoS ONE 5, e12988
17. Lillestøl, R.K., Redder, P., Garrett, R.A. and Brugger, K. (2006) A putative viral defence mechanism in archaeal cells. Archaea 2, 59-72
18. Lillestøl, R.K., Shah, S.A., Brugger, K., Redder, P., Phan, H., Christiansen, J. and Garrett, R.A. (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol. Microbiol. 72, 259-272
19. 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
20. Shah, S.A., Vestergaard, G. and Garrett, R.A. (2011) CRISPR/Cas and CRISPR/Cmr immune systems of archaea. In Regulatory RNAs in Prokaryotes (Marchfelder, A. and Hess, W., eds), pp. 163-181, Springer Verlag, Berlin
21. 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
22. 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
23. 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
24. 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
25. Erratum (2012) Mol. Microbiol. 86, 757
26. 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
27. Deveau, H., Barrangou, R., Garneau, J.E., Labonteé, J., Fremaux, C., Boyaval, P., Romero, D.A., Horvath, P. and Moineau, S. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190, 1390-1400
28. Garneau, J.E., Dupuis, M.E., Villion, M., Romero, D.A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadaén, A.H. and Moineau, S. (2010) The CRISPR/cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67-71
29. 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
30. 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
31. Diéez-Villasenor, C., Guzmaén, N.M., Almendros, C., Garciéa-Martiénez, 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
32. Arnold, H.P., Zillig, W., Ziese, U., Holz, I., Crosby, M., Utterback, T., Weidmann, J.F., Kristjansson, J., Klenk, H.P., Nelson, K.E. and Fraser, C.M. (2000) A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. Virology 267, 252-266
33. Haring, M., Vestergaard, G., Brugger, K., Rachel, R., Garrett, R.A. and Prangishvili, D. (2005) Structure and genome organisation of AFV2, a novel filamentous archaeal virus with unusual terminal structures. J. Bacteriol. 187, 3855-3858
34. Xiang, X., Chen, L., Huang, X., Luo, Y., She, Q. and Huang, L. (2005) Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J. Virol. 79, 8677-8686
35. Pornillos, O., Garrus, J.E. and Sundquist, W.I. (2002) Mechanism of enveloped RNA virus budding. Trends Cell. Biol. 12, 569-579
36. Garrett, R.A., Shah, S.A., Vestergaard, G., Deng, L., Gudbergsdottir, S., Kenchappa, C.S., Erdmann, S. and She, Q. (2011) CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem. Soc. Trans. 39, 51-57
37. Berkner, S. and Lipps, G. (2007) An active nonautonomous mobile element in Sulfolobus islandicus REN1H1. J. Bacteriol. 189, 2145-2149
38. Zillig, W., Prangishvili, D., Schleper, C., Elferink, M., Holz, I., Albers, S., Janekovic, D. and Gotz., D. (1996) Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol. Rev. 18, 225-236
39. Vestergaard, G., Shah, S.A., Bize, A., Reitberger, W., Reuter, M., Phan, H., Briegel, A., Rachel, R., Garrett, R.A. and Prangishvili, D. (2008) SRV, a new rudiviral isolate from Stygioglobus and the interplay of crenarchaeal rudiviruses with the host viral-defence CRISPR system. J. Bacteriol. 190, 6837-6845
40. Hale, C.R., Majumdar, S., Elmore, J., Pfister, N., Compton, M., Olson, S., Resch, A.M., Glover, C.V., Graveley, B.R., Terns, R.M. and Terns, M.P. (2012) Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45, 292-302
41. Zhang, J., Kasciukovic, T. and White, M.F. (2012) The CRISPR-associated protein Cas4 is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster. PLoS ONE 7, e47232
42. Paez-Espino, D., Morovic, W., Sun, C.L., Thomas, B.C., Ueda, K., Stahl, B., Barrangou, R. and Banfield, J.F. (2013) Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat. Commun. 4, 1430
43. Goren, M.G., Yosef, I., Auster, O. and Qimron, U. (2012) Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J. Mol. Biol. 423, 14-16
44. 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
45. Bolduc, B., Shaughnessy, D.P., Wolf, Y.I., Koonin, E.V., Roberto, F.F. and Young, M. (2012) Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 86, 5562-5573
46. Brugger, K., Redder, P., She, Q., Confalonieri, F., Zivanovic, Y. and Garrett, R.A. (2002) Mobile elements in archaeal genomes. FEMS Microbiol. Lett. 206, 131-141
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. Arnold, H.P., Ziese, U. and Zillig, W. (2000) SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Virology 272, 409-416