ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs

Journal of Bacteriology

Volumn 198, Issue 5, 2016, Pages 797-807

  Kapitonov, Vladimir V ^a   Makarova, Kira S ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; BACTERIAL PROTEIN; CAS9 PROTEIN; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; ENDONUCLEASE; TRANSPOSON;

AMINO ACID SEQUENCE; ARCHAEAL GENOME; ARCHAEON; ARTICLE; BACTERIAL GENOME; CONSENSUS SEQUENCE; CRISPR CAS SYSTEM; INSERTION SEQUENCES CAS9 LIKE; INVERTED REPEAT; LACTOBACILLUS DELBRUECKII; METHANOSARCINA; MICROCYSTIS AERUGINOSA; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TERMINAL SEQUENCE; TRANSPOSON; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGY; PROTEIN MOTIF;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; BASE SEQUENCE; CRISPR-CAS SYSTEMS; DNA TRANSPOSABLE ELEMENTS; ENDONUCLEASES; GENE EXPRESSION REGULATION, ARCHAEAL; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PHYLOGENY;

EID: 84961166483     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00783-15     Document Type: Article

References (35)

1. Chylinski K, Makarova KS, Charpentier E, Koonin EV. 2014. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res 42:6091-6105. http://dx.doi.org/10.1093/nar/gku241.
2. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 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. http://dx.doi.org/10.1186/1745-6150-1-7.
3. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816-821. http://dx.doi.org/10.1126/science.1225829.
4. 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. http://dx.doi.org/10.1073/pnas.1208507109.
5. Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. 2015. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519:199-202. http://dx.doi.org/10.1038/nature14245.
6. Makarova KS, Aravind L, Wolf YI, Koonin EV. 2011. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 6:38. http://dx.doi.org/10.1186/1745-6150-6-38.
7. Siguier P, Gourbeyre E, Chandler M. 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38:865-891. http://dx.doi.org/10.1111/1574-6976.12067.
8. Pasternak C, Dulermo R, Ton-Hoang B, Debuchy R, Siguier P, Coste G, Chandler M, Sommer S. 2013. ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB. Mol Microbiol 88:443-455. http://dx.doi.org/10.1111/mmi.12194.
9. He S, Guynet C, Siguier P, Hickman AB, Dyda F, Chandler M, Ton-Hoang B. 2013. IS200/IS605 family single-strand transposition: mechanism of IS608 strand transfer. Nucleic Acids Res 41:3302-3313. http://dx.doi.org/10.1093/nar/gkt014.
10. Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61-D65. http://dx.doi.org/10.1093/nar/gkl842.
11. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. http://dx.doi.org/10.1093/nar/25.17.3389.
12. Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH. 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41:D348-D352. http://dx.doi.org/10.1093/nar/gks1243.
13. Drozdetskiy A, Cole C, Procter J, Barton GJ. 2015. JPred4: a protein secondary structure prediction server. Nucleic Acids Res 43(W1):W389-W394. http://dx.doi.org/10.1093/nar/gkv332.
14. Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244-W248. http://dx.doi.org/10.1093/nar/gki408.
15. Wheeler D, Bhagwat M. 2007. BLAST QuickStart: example-driven webbased BLAST tutorial. Methods Mol Biol 395:149-176. http://dx.doi.org/10.1007/978-1-59745-514-5_9.
16. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. http://dx.doi.org/10.1093/nar/gkh340.
17. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. http://dx.doi.org/10.1371/journal.pone.0009490.
18. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704. http://dx.doi.org/10.1080/10635150390235520.
19. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474. http://dx.doi.org/10.1186/1471-2105-7-474.
20. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772-780. http://dx.doi.org/10.1093/molbev/mst010.
21. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277. http://dx.doi.org/10.1016/S0168-9525(00)02024-2.
22. Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D. 2011. Haloquadratum walsbyi: limited diversity in a global pond. PLoS One 6:e20968. http://dx.doi.org/10.1371/journal.pone.0020968.
23. Siguier P, Gourbeyre E, Varani A, Ton-Hoang B, Chandler M. 2015. Everyman's guide to bacterial insertion sequences. Microbiol Spectr 3:MDNA3-0030-2014. http://dx.doi.org/10.1128/microbiolspec.MDNA3-0030-2014.
24. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32-D36. http://dx.doi.org/10.1093/nar/gkj014.
25. Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F. 2005. Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. Mol Cell 20:143-154. http://dx.doi.org/10.1016/j.molcel.2005.07.026.
26. Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G, Ton-Hoang B. 2013. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11:525-538. http://dx.doi.org/10.1038/nrmicro3067.
27. He S, Corneloup A, Guynet C, Lavatine L, Caumont-Sarcos A, Siguier P, Marty B, Dyda F, Chandler M, Ton Hoang B. 2015. The IS200/IS605 family and "peel and paste" single-strand transposition mechanism. Microbiol Spectr 3. http://dx.doi.org/10.1128/microbiolspec.MDNA3-0039-2014.
28. Boocock MR, Rice PA. 2013. A proposed mechanism for IS607-family serine transposases. MobDNA4:24. http://dx.doi.org/10.1186/1759-8753-4-24.
29. Kersulyte D, Mukhopadhyay AK, Shirai M, Nakazawa T, Berg DE. 2000. Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J Bacteriol 182:5300-5308. http://dx.doi.org/10.1128/JB.182.19.5300-5308.2000.
30. Ariyoshi M, Vassylyev DG, Iwasaki H, Nakamura H, Shinagawa H, Morikawa K. 1994. Atomic structure of the RuvC resolvase: a Holliday junction-specific endonuclease from E. coli. Cell 78:1063-1072. http://dx.doi.org/10.1016/0092-8674(94)90280-1.
31. Lilley DM, White MF. 2001. The junction-resolving enzymes. Nat Rev Mol Cell Biol 2:433-443. http://dx.doi.org/10.1038/35073057.
32. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:1247997. http://dx.doi.org/10.1126/science.1247997.
33. Koonin EV, Krupovic M. 2015. Evolution of adaptive immunity from transposable elements combined with innate immune systems. Nat Rev Genet 16:184-192. http://dx.doi.org/10.1038/nrg3859.
34. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost Regev A, Koonin EV, Zhang F. 2015. Cpf1 Is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759-771. http://dx.doi.org/10.1016/j.cell.2015.09.038.
35. Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV. 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60:385-397. http://dx.doi.org/10.1016/j.molcel.2015.10.008.