CRISPRDetect: A flexible algorithm to define CRISPR arrays

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Biswas, Ambarish ^a   Staals, Raymond H J ^a   Morales, Sergio E ^a   Fineran, Peter C ^a   Brown, Chris M ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Bioinformatics; Cas; CRISPR; CrRNA; Horizontal gene transfer; Phage resistance; Plasmids; Repeat elements; Small RNA targets

Indexed keywords

BACTERIOPHAGE; BIOINFORMATICS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENOME; HORIZONTAL GENE TRANSFER; INDEL MUTATION; PIPELINE; PLASMID; ALGORITHM; BACTERIUM; COMPUTER INTERFACE; CRISPR CAS SYSTEM; GENE DELETION; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METABOLISM; MUTATION; NUCLEIC ACID DATABASE; PROCEDURES; PROKARYOTIC CELL; SOFTWARE; TANDEM REPEAT; WORKFLOW;

SPACER DNA;

ALGORITHMS; BACTERIA; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DATABASES, NUCLEIC ACID; DNA, INTERGENIC; GENOME; GENOMICS; MUTAGENESIS, INSERTIONAL; MUTATION; PROKARYOTIC CELLS; SEQUENCE DELETION; SOFTWARE; TANDEM REPEAT SEQUENCES; USER-COMPUTER INTERFACE; WORKFLOW;

EID: 84977517193     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2627-0     Document Type: Article

References (62)

1. Richter C, Chang JT, Fineran PC. Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR Associated (Cas) Systems. Viruses. 2012;4(10):2291-311.
2. Sorek R, Lawrence CM, Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem. 2013;82:237-66.
3. Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J. The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity. Annu Rev Genet. 2012;46:311-39.
4. Samson JE, Magadan AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol. 2013;11(10):675-87.
5. Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J. The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria. Microbiol Mol Biol Rev. 2014;78(1):74-88.
6. Bondy-Denomy J, Davidson AR. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol. 2014;22(4):218-25.
7. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011;9(6):467-77.
8. Dy RL, Richter C, Salmond GPC, Fineran PC. Remarkable Mechanisms in Microbes to Resist Viral Infections. Annu Rev Virol. 2014;2014(1):307-31.
9. van der Oost J, Westra ER, Jackson RN, Wiedenheft B. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol. 2014;12(7):479-92.
10. Westra ER, Buckling A, Fineran PC. CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol. 2014;12:317-326.
11. Ratner HK, Sampson TR, Weiss DS. I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope. Curr Opin Infect Dis. 2015;28(3):267-74.
12. Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol. 2006;62(6):718-29.
13. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209.
14. Minced: Mining CRISPRs in Environmental Datasets [ https://github.com/ctSkennerton/minced/tree/master ]
15. Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics. 2007;8:18.
16. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(Web Server issue):W52-57.
17. Rousseau C, Gonnet M, Le Romancer M, Nicolas J. CRISPI: a CRISPR interactive database. Bioinformatics. 2009;25(24):3317-8.
18. Rho M, Wu YW, Tang H, Doak TG, Ye Y. Diverse CRISPRs evolving in human microbiomes. PLoS Genet. 2012;8(6):e1002441.
19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9.
20. Skennerton CT, Imelfort M, Tyson GW. Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res. 2013;41(10):e105.
21. Riehle MM, Bennett AF, Long AD. Genetic architecture of thermal adaptation in Escherichia coli. Proc Natl Acad Sci U S A. 2001;98(2):525-30.
22. DeBoy RT, Mongodin EF, Emerson JB, Nelson KE. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol. 2006;188(7):2364-74.
23. Tyson GW, Banfield JF. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol. 2008;10(1):200-7.
24. Horvath P, Romero DA, Coute-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol. 2008;190(4):1401-12.
25. Gudbergsdottir S, Deng L, Chen Z, Jensen JV, Jensen LR, She Q, Garrett RA. Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol Microbiol. 2011;79(1):35-49.
26. Jiang W, Maniv I, Arain F, Wang Y, Levin BR, Marraffini LA. Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids. PLoS Genet. 2013;9(9):e1003844.
27. Fineran PC, Charpentier E. Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information. Virology. 2012;434(2):202-9.
28. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315(5819):1709-12.
29. Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature. 2015;527(7579):535-8.
30. Erdmann S, Garrett RA. Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol Microbiol. 2012;85(6):1044-56.
31. Weinberger AD, Wolf YI, Lobkovsky AE, Gilmore MS, Koonin EV. Viral diversity threshold for adaptive immunity in prokaryotes. MBio. 2012;3(6):e00456-00412.
32. Biswas A, Fineran PC, Brown CM. Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. Bioinformatics. 2014;30(13):1805-13.
33. Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics. 2014;30(17):i489-96.
34. Lange SJ, Alkhnbashi OS, Rose D, Will S, Backofen R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 2013;41(17):8034-44.
35. Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013;10(5):817-27.
36. Kunne T, Swarts DC, Brouns SJ. Planting the seed: target recognition of short guide RNAs. Trends Microbiol. 2014;22(2):74-83.
37. Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A. 2011;108(25):10098-103.
38. Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A. 2011;108(25):10092-7.
39. Fineran PC, Gerritzen MJ, Suarez-Diez M, Kunne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A. 2014;111(16):E1629-1638.
40. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, et al. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell. 2015;163(3):759-71.
41. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology. 2009;155(Pt 3):733-40.
42. Kupczok A, Landan G, Dagan T. The Contribution of Genetic Recombination to CRISPR Array Evolution. Genome Biol Evol. 2015;7(7):1925-39.
43. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF. CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus. mBio. 2015;6(2):e00262-15.
44. Cui Y, Li Y, Gorge O, Platonov ME, Yan Y, Guo Z, Pourcel C, Dentovskaya SV, Balakhonov SV, Wang X, et al. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS One. 2008;3(7):e2652.
45. Fabre M, Hauck Y, Soler C, Koeck JL, van Ingen J, van Soolingen D, Vergnaud G, Pourcel C. Molecular characteristics of "Mycobacterium canettii" the smooth Mycobacterium tuberculosis bacilli. Infect Genet Evol. 2010;10(8):1165-73.
46. Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.
47. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947-8.
48. Chylinski K, Makarova KS, Charpentier E, Koonin EV. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res. 2014;42(10):6091-105.
49. Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS, Richter C, Przybilski R, Pitman AR, Fineran PC. Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands. PLoS Genet. 2013;9(4):e1003454.
50. Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 2012;40(12):5569-76.
51. Swarts DC, Mosterd C, van Passel MW, Brouns SJ. CRISPR interference directs strand specific spacer acquisition. PLoS One. 2012;7(4):e35888.
52. Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun. 2012;3:945.
53. Zhang Q, Doak TG, Ye Y. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Res. 2014;42(4):2448-59.
54. Makarova KS, Koonin EV. Annotation and Classification of CRISPR-Cas Systems. Methods Mol Biol. 2015;1311:47-75.
55. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722-36.
56. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci. 2009;1(1):63-7.
57. Huntemann M, Ivanova N, Mavromatis K, Tripp H, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen I, Pati A, et al: The Standard Operating Procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). In.: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA; 2015.
58. Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I, Zaslavsky L: About Prokaryotic Genome Processing and Tools. In: The NCBI Handbook [Internet] 2nd edition Bethesda (MD) National Center for Biotechnology Information; 2014.
59. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5:8365.
60. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16(10):944-5.
61. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92.
62. Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, et al. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One. 2010;5(1):e8926.