Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector‐borne viral and plasmid genes and protospacers

Abstract

Summary The adaptive immune CRISPR/Cas and CRISPR/Cmr systems of the crenarchaeal thermoacidophile Sulfolobus were challenged by a variety of viral and plasmid genes, and protospacers preceded by different dinucleotide motifs. The genes and protospacers were constructed to carry sequences matching individual spacers of CRISPR loci, and a range of mismatches were introduced. Constructs were cloned into vectors carrying pyrE/pyrF genes and transformed into uracil auxotrophic hosts derived from Sulfolobus solfataricus P2 or Sulfolobus islandicus REY15A. Most constructs, including those carrying different protospacer mismatches, yielded few viable transformants. These were shown to carry either partial deletions of CRISPR loci, covering a broad spectrum of sizes and including the matching spacer, or deletions of whole CRISPR/Cas modules. The deletions occurred independently of whether genes or protospacers were transcribed. For family I CRISPR loci, the presence of the protospacer CC motif was shown to be important for the occurrence of deletions. The results are consistent with a low level of random dynamic recombination occurring spontaneously, either inter‐genomically or intra‐genomically, at the repeat regions of Sulfolobus CRISPR loci. Moreover, the relatively high incidence of single‐spacer deletions observed for S. islandicus suggests that an additional more directed mechanism operates in this organism.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 35

1. 1.

   Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709-1712.

   Not in our library10.1126/science.1138140

2. 2.

   Bernander R. The cell cycle of Sulfolobus. Mol Microbiol. 2007;66:557-562.

   Not in our library10.1111/j.1365-2958.2007.05917.x

3. 3.

   Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005;151:2551-2561.

   Not in our library10.1099/mic.0.28048-0

4. 4.

   Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321:960-964.

   Not in our library10.1126/science.1159689

5. 5.

   Deng L, Zhu H, Chen Z, Liang YX, She Q. Unmarked gene deletion and host–vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles. 2009;13:735-746.

   Not in our library10.1007/s00792-009-0254-2

6. 6.

   Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol. 2008;190:1390-1400.

   Not in our library10.1128/jb.01412-07

7. 7.

   Grissa I, Vergnaud G, Pourcel C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2008;36:145-148.

   Not in our library10.1093/nar/gkn228

8. 8.

   Hale C, Kleppe K, Terns RM, Terns MP. Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA. 2008;14:1-8.

   Not in our library10.1261/rna.1246808

9. 9.

   Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, et al. RNA-guided RNA cleavage by a CRISPR RNA–Cas protein complex. Cell. 2009;139:945-956.

   Not in our library10.1016/j.cell.2009.07.040

10. 10.

    Heckman KL, Pease LR. Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc. 2007;2:924-932.

    Not in our library10.1038/nprot.2007.132

11. 11.

    Held NL, Whitaker RJ. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol. 2009;11:457-466.

    Not in our library10.1111/j.1462-2920.2008.01784.x

12. 12.

    Horvath P, Romero DA, Coûté-Monvoisin A-C, Richards M, Deveau H, Moineau S, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol. 2008;190:1401-1412.

    Not in our library10.1128/jb.01415-07

13. 13.

    Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43:1565-1575.

    Not in our library10.1046/j.1365-2958.2002.02839.x

14. 14.

    Karginov FV, Hannon GJ. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell. 2010;37:7-19.

    Not in our library10.1016/j.molcel.2009.12.033

15. 15.

    Lillestøl RK, Redder P, Garrett RA, Brügger K. A putative viral defence mechanism in archaeal cells. Archaea. 2006;2:59-72.

    Not in our library10.1155/2006/542818

16. 16.

    Lillestøl RK, Shah SA, Brügger K, Redder P, Phan H, Christiansen J, Garrett RA. CRISPR families of the crenarchaeal genius Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol. 2009;72:259-272.

    Not in our library10.1111/j.1365-2958.2009.06641.x

17. 17.
    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 · 2006

    No notice
18. 18.

    Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA. Science. 2008;322:1843-1845.

    Not in our library10.1126/science.1165771

19. 19.

    Marraffini LA, Sontheimer EJ. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature. 2010;463:568-571.

    Not in our library10.1038/nature08703

20. 20.

    Martusewitsch E, Sensen CW, Schleper C. High spontaneous mutation rate in the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by transposable elements. J Bacteriol. 2000;182:2574-2581.

    Not in our library10.1128/jb.182.9.2574-2581.2000

21. 21.

    Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60:174-182.

    Not in our library10.1007/s00239-004-0046-3

22. 22.

    Peng N, Xia Q, Chen Z, Liang YX, She Q. An upstream activation element exerting differential transcription activation on an archaeal promoter. Mol Microbiol. 2009;74:928-939.

    Not in our library10.1111/j.1365-2958.2009.06908.x

23. 23.

    Peng X, Brügger K, Shen B, Chen L, She Q, Garrett RA. Genus-specific protein binding to the large clusters of DNA repeats (Short Regularly Spaced Repeats) present in Sulfolobus genomes. J Bacteriol. 2003;185:2410-2417.

    Not in our library10.1128/jb.185.8.2410-2417.2003

24. 24.

    Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151:653-663.

    Not in our library10.1099/mic.0.27437-0

25. 25.

    Prangishvili D, Forterre P, Garrett RA. Viruses of the Archaea: a unifying view. Nat Rev Microbiol. 2006a;11:837-848.

    Not in our library10.1038/nrmicro1527

26. 26.

    Prangishvili D, Vestergaard G, Häring M, Aramayo R, Basta T, Rachel R, Garrett RA. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J Mol Biol. 2006b;359:1203-1216.

    Not in our library10.1016/j.jmb.2006.04.027

27. 27.

    Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol. 2010;75:1495-1512.

    Not in our library10.1111/j.1365-2958.2010.07073.x

28. 28.

    Redder P, Garrett RA. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol. 2006;188:4198-4206.

    Not in our library10.1128/jb.00061-06

29. 29.

    Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 2001.

    Not in our library

30. 30.

    Shah SA, Garrett RA. CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol. 2010.

    Not in our library10.1016/j.resmic.2010.09.001

31. 31.

    Shah SA, Hansen NR, Garrett RA. Distributions of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem Soc Trans. 2009;37:23-28.

    Not in our library10.1042/bst0370023

32. 32.

    She Q, Phan H, Garrett RA, Albers S-V, Stedman KM, Zillig W. Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles. 1998;2:417-425.

    Not in our library10.1007/s007920050087

33. 33.

    Sunkar R, Girke T, Zhu JK. Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res. 2005;33:4443-4454.

    Not in our library10.1093/nar/gki758

34. 34.

    Tang T-H, Bachellerie J-P, Rozhdestvensky T, Bortolin M-L, Huber H, Drungowski M, et al. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci USA. 2002;99:7536-7541.

    Not in our library10.1073/pnas.112047299

35. 35.

    Tang T-H, Polacek N, Zywicki M, Huber H, Brügger K, Garrett R, et al. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol. 2005;55:469-481.

    Not in our library10.1111/j.1365-2958.2004.04428.x

Cited by papers we hold 10

• Anti-CRISPR-Based and CRISPR-Based Genome Editing of <i>Sulfolobus islandicus</i> Rod-Shaped Virus 2 · 2018
  Not checked
• PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures · 2018
  No notice
• Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium · 2016
  No notice
• CRISPRDetect: A flexible algorithm to define CRISPR arrays · 2016
  No notice
• Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids · 2013
  No notice
• CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein · 2013
  No notice
• Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition · 2013
  No notice
• Versatile genetic tool box for the crenarchaeote Sulfolobus acidocaldarius · 2012
  Not checked
• Persisting Viral Sequences Shape Microbial CRISPR-based Immunity · 2012
  No notice
• Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms · 2012
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.