2018 / 02

Следующая статья
DOI: 10.24075/vrgmu.2018.016

ОБЗОР

CRISPR-Cas системы Mусоbacterium tuberculosis: структура модуля, изменение в процессе эволюции у различных линий, возможная роль в формировании вирулентности и лекарственной устойчивости

М. В. Зайчикова1, Н. В. Захаревич1, М. С. Чекалина, В. Н. Даниленко1,2
Информация об авторах

1 Институт общей генетики имени Н. И. Вавилова Российской академии наук, Москва

2 Кафедра биоинформатики, факультет биологической и медицинской физики,
Московский физико-технический институт (государственный университет), Долгопрудный

Для корреспонденции: Зайчикова Марина Викторовна
ул. Губкина, д. 3, г. Москва, 119991; ur.xednay@51zaniram, ur.ggiv@direlav

Статья получена: 15.03.2018 Статья принята к печати: 20.03.2018 Опубликовано online: 09.06.2018
|
  1. Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet. 2010; 11 (3): 181–190.
  2. 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. doi:10.1186/1471-2105-8-172.
  3. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987; 169 (12): 5429–33.
  4. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005; 151 (8): 2551–61.
  5. 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: 1709–1712.
  6. Westra ER, Buckling A, Fineran PC. CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol. 2014; 12 (5): 317– 326. DOI: 10.1038/nrmicro3241.
  7. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. Journal of Clinical Microbiology. 1997; 35 (4): 907–14.
  8. van Embden JD, van Gorkom T, Kremer K, Jansen R, van Der Zeijst BA, Schouls LM. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J Bacteriol. 2000 May; 182 (9): 2393–401.
  9. Haft DH, Selengut J, Mongodin EF, Nelson KE. A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/ Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. 2005; 1 (6): e60.
  10. Gogleva AA, Gelfand MS, Artamonova II. Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs. BMC Genomics. 2014; 15 (1): 202. DOI:10.1186/1471-2164-15- 202.
  11. Takeuchi N, Wolf YI, Makarova KS, Koonin EV. Nature and Intensity of Selection Pressure on CRISPR-Associated Genes. J Bacteriol. 2012; 194 (5): 1216–25.
  12. Makarova KS, Wolf YI, Alkhnbashi OS, et al. An updated evolutionary classification of CRISPR–Cas systems. Nature reviews Microbiology. 2015; 13 (11): 722–36. DOI:10.1038/ nrmicro3569.
  13. Makarova KS, Zhang F, Koonin EV. SnapShot: Class 1 CRISPRCas Systems. Cell. 2017; 168 (5): 946–46.
  14. Goeders N, van Melderen L. Toxin-Antitoxin Systems as Multilevel Interaction Systems. Toxins. 2014; 6 (1): 304–24.
  15. Makarova KS, Anantharaman V, Aravind L, Koonin EV. Live virusfree or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct. 2012; 7: 40.
  16. Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. Regulation of dev, an Operon That Includes Genes Essential for Myxococcus xanthus Development and CRISPR-Associated Genes and Repeats . J Bacteriol. 2007; 189 (10): 3738–50.
  17. Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011; 79 (2): 484–502.
  18. Heussler GE, Cady KC, Koeppen K, Bhuju S, Stanton BA, O’Toole GA. Clustered Regularly Interspaced Short Palindromic Repeat-Dependent, Biofilm-Specific Death of Pseudomonas aeruginosa Mediated by Increased Expression of Phage-Related Genes. mBio. 2015; 6 (3): e00129-15.
  19. Sampson TR, Saroj SD, Llewellyn AC, Tzeng Y-L, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013; 497: 254–7.
  20. Louwen R, Horst-Kreft D, de Boer AG, van der Graaf L, de Knegt G, Hamersma M, et al. A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome. Eur J Clin Microbiol Infect Dis. 2013; 32 (2): 207–26.
  21. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012; 482, 331–38.
  22. Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet. 2011; 45: 273–97.
  23. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 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. Biology Direct. 2006; 1: 7.
  24. Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007; 7 (5): 328–37.
  25. Прозоров А. А., Даниленко В. Н. Микобактерии туберкулезного комплекса: геномика, молекулярная эпидемиология, пути эволюции. Успехи современной биологии. 2011; 131 (3): 227– 43.
  26. Jagielski T, van Ingen J, Rastogi N, Dziadek J, Mazur PK, Bielecki J. Current methods in the molecular typing of Mycobacterium tuberculosis and other Mycobacteria. Biomed Res Int. 2014; 2014:645802.
  27. Прозоров А. А., Федорова И.А., Беккер О. Б., Даниленко В. Н. Факторы вирулентности Mycobacterium tuberculosis: генетический контроль, новые концепции. Генетика. 2014; 50 (8): 885–908.
  28. Reiling N, Homolka S, Walter K, Brandenburg J, Niwinski L, Ernst M et al. Clade specific virulence patterns of Mycobacterium tuberculosis complex strains in human primarymacrophages and aerogenically infected mice. MBio. 2013; 4 (4): pii: e00250-13.
  29. Lasunskaia E, Ribeiro SC, Manicheva O, Gomes LL, Suffys PN, Mokrousov I, et al. Emerging multidrug resistant Mycobacterium tuberculosis strains of the Beijing genotype circulating in Russia express a pattern of biological properties associated with enhanced virulence. Microbes Infect. 2010; 12 (6): 467–75.
  30. Hanekom M, Gey van Pittius NC, McEvoy C, Victor TC, Van Helden PD, Warren RM. Mycobacterium tuberculosis Beijing genotype: a template for success. Tuberculosis (Edinb). 2011; 91 (6): 510–23.
  31. Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008; 4 (9): e1000160.
  32. Mokrousov I. The quiet and controversial: Ural family of Mycobacterium tuberculosis. Infect Genet Evol. 2012; 12 (4): 619–29.
  33. Mikheecheva NE, Zaychikova MV, Melerzanov AV, Danilenko VN. A nonsynonymous SNP catalog of Mycobacterium tuberculosis virulence genes and its use for detecting new potentially virulent sublineages. Genome Biol Evol. 2017; 9 (4): 887–99.
  34. He L, Fan X, Xie J. Comparative genomic structures of Mycobacterium CRISPR-Cas. J Cell Biochem. 2012; 113 (7): 2464–73.
  35. Brosch R, Pym AS, Gordon SV, Cole ST. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 2001; 9 (9): 452–58.
  36. Homolka S, Projahn M, Feuerriegel S, Ubben T, Diel R, Nübel U et al. High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms. PLoS One. 2012; 7 (7): e39855.
  37. Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015; 47 (3): 242–49.
  38. Zaychikova MV, Zakharevich NV, Sagaidak MO, Bogolubova NA, Smirnova TG, Andreevskaya SN, et al. Mycobacterium tuberculosis Type II Toxin-Antitoxin Systems: Genetic Polymorphisms and Functional Properties and the Possibility of Their Use for Genotyping. PLoS One. 2015; 10: e0143682.
  39. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, References et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007; 8: 209.
  40. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007; 35: 52–7.
  41. Numata T, Inanaga H, Sato C, Osawa T. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex. J Mol Biol. 2015; 427 (2): 259–73.
  42. Mestre O, Luo T, Dos Vultos T, Kremer K, Murray A, Namouchi A, et al. Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair. PLoS One. 2011; 6 (1): e16020.
  43. Freidlin PJ, Nissan I, Luria A, Goldblatt D, Schaffer L, KaidarShwartz H, et al. Structure and variation of CRISPR and CRISPRflanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains. BMC Genomics. 2017; 18 (1): 168.
  44. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 1999; 96 (8): 4285–8.
  45. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology. 2015; 16: 157.
  46. Count CM.: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010; 26 (15): 1910–2.
  47. Sokal R, Michener C. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin. 1958; 38: 1409–1438.
  48. Monu, Meena LS. Roles of Triolein and Lipolytic Protein in the Pathogenesis and Survival of Mycobacterium tuberculosis: a Novel Therapeutic Approach. Appl Biochem Biotechnol. 2016; 178 (7): 1377–89.
  49. Deb C, Lee CM, Dubey VS, Daniel J, Abomoelak B, Sirakova TD, et al. A Novel In Vitro Multiple-Stress Dormancy Model for Mycobacterium tuberculosis Generates a Lipid-Loaded, DrugTolerant, Dormant Pathogen. PLoS ONE. 2009; 4 (6): e6077.
  50. Braibant M, Gilot P, Content J. The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. FEMS Microbiol Rev. 2000; 24 (4): 449–67.