PROCARIOTIC IMMUNE SYSTEM: MOLECULAR MECHANISMS, APPLICATION IN MICROBIOLOGY
Abstract
During a short time, the CRISPR/Cas system has gained popularity among scientists in various fields of medicine, biology, and chemistry. Prokaryotes use the CRISPR/Cas system to protect their own genome from foreign genetic material, the cassette of which consists of Cas-protein coding genes, leader sequence, speisers and palindromes. Cas-proteins are the main thing without which the CRISPR/Cas system cannot work. While interacting with foreign DNA, the CRISPR/Cas system passes 3 stages: immunization, expression, and interference. Immunization takes place during the first bacterial contact with foreign DNA collecting information about an invasive agent. The next meeting reveals the protein complex creation and the foreign DNA destruction. The differences in the mechanisms of action depend on the system class and type. There are 2 classes of the CRISPR/Cas system separating into 5 types and 16 subtypes. Bioinformation methods are used to find the CRISPR/Cas system in a bacterial cell. Due to the high efficiency and the easy individual component assembly, scientists quickly learned how to benefit from the CRISPR/Cas system, applying it for a wide range of tasks. The CRISPR/Cas system is used in microbiology, genetics, molecular epidemiology, gene engineering, applied medicine, and pharmacology for genome editing, gene expression control, pathological process treatment and modeling, microorganism typing, determination of phylogenetic relationships of microorganisms and so on. The CRISPR/Cas system of N. meningitidis can successfully edit eucariotic genome. But experiments with human genome are connected with biomedical ethics.
About the Authors
A. N. Kharkhal
Republican Research and Practical Center for Epidemiology and Microbiology
Belarus
Junior researcher
Belarus
Junior researcher
L. P. Titov
Republican Research and Practical Center for Epidemiology and Microbiology
Belarus
Corresponding Member, Foreign Member of the RAMS, D. Sc. (Med.), Head of the Laboratory
Belarus
Corresponding Member, Foreign Member of the RAMS, D. Sc. (Med.), Head of the Laboratory
References
1. Titov L. P. Classification, nomenclature and evolution medically significant bacteria. Meditsinskii zhurnal [Medical Journal], 2006, pp. 13–19. (in Russian).
2. Titov L. P., Votyakov V. I., Kozhemiakin A. K., Mosina L. I. Bacterial evolution and it’s medical value. Zdravoohranenie [Health Care], 2002, no. 8, pp. 30–35. (in Russian).
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. Journal of Bacteriology, 1987, vol. 169, no. 12, pp. 5429–5433.
4. Jansen R., Embden J. D., Gaastra W., Schouls L. M. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 2002, vol. 43, no. 6, pp. 1565–1575.
5. Makarova K. S., Grishin N. V., Shabalina S. A., Wolf Y. I., Koonin E. V. 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, vol. 1, p. 7.
6. Sontheimer E. J., Barrangou R. The Bacterial Origins of the CRISPR Genome-Editing Revolution. Human Gene Therapy, 2015, vol. 26, no. 7, pp. 413–424. doi: 10.1089/hum.2015.091.
7. Slaymaker I. M., Gao L., Zetsche B., Scott D. A., Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science, 2016, vol. 351 (6268), pp. 84–88. doi: 10.1126/science. aad5227.
8. Barrangou R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Current Opinion in Immunology, 2015, vol. 32, pp. 36–41. doi: 10.1016/j. coi.2014.12.008.
9. Shashnikova A. V., Goriaev A. A., Smirnova N. I. Structure and functional role of bacterial CRISPR system. Problemy osobo opasnykh infektsii [Problems of Especially Dangerous Infections], 2011, no. 2 (108), pp. 49–52. (in Russian).
10. Peters J. M., Silvis M. R., Zhao D., Hawkins J. S., Gross C. A., Qi L. S. Bacterial CRISPR: accomplishments and prospects. Current Opinion in Microbiology, 2015, vol. 27, pp. 121–126.
11. Hale C. R., Zhao P., Olson S., Duff M. O., Graveley B. R., Wells L., Terns R. M., Terns M. P. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell, 2009, vol. 139, no. 5, pp. 945–956.
12. Abby S. S., Neron B., Menager H., Touchon M., Rocha E. P. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLOS ONE, 2014, vol. 9, no. 10, pp. 1–9.
13. Borisenko A. Iu., Dzhioev Iu. P., Paramonov A. I., Bukin Iu. S., Stepanenko L. A., Kolbaseeva O. V., Zlobin I. V. The use of bioinformatics software methods for search CRISPR/Cas systems in genomes of the strains of Staphylococcus aureus. Sibirskii meditsinskii zhurnal (Irkutsk) [Siberian Medical Journal (Irkutsk)], 2015, vol. 133, no. 2, pp. 71–74. (in Russian).
14. Savitskaya E. E., Musharova O. S., Severinov K. V. Diversity of CRISPR-Cas-mediated mechanisms of adaptive immunity in prokaryotes and their application in biotechnology. Biochemistry, 2016, vol. 81, no. 7, pp. 653–661.
15. Lee C., Cradick T., Bao G. The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells. Molecular Therapy, 2016, vol. 24, no. 3, pp. 645–654.
16. Barrangou R. Diversity of CRISPR-Cas immune systems and molecular machines. Genome Biology, 2015, vol. 16, pp. 247–257.
17. Van Houte S., Ekroth A. K., Broniewski, Chabas H., Ashby B., Bondy-Denomy J., Gandon S., Boots M., Paterson S., Buckling A., Westra E. R. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature, 2016, vol. 532 (7599), pp. 385–388. doi: 10.1038/nature17436.
18. O’Connell M. R., Oakes B. L., Sternberg S. H., East-Seletsky A., Kaplan M., Doudna J. A. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature, 2014, vol. 516, no. 7530, pp. 263–266.
19. Makarova K. S., Koonin E. V. Annotation and Classification of CRISPR-Cas Systems. Methods in Molecular Biology, 2015, vol. 1311, pp. 47–75.
20. Makarova K. S., Wolf Y. I., Alkhnbashi O. S., Costa F., Shah S. A., Saunders S. J., Barrangou R., Brouns S. J., Charpentier E., Haft D. H., Horvath P., Moineau S., Mojica F. J., Terns R. M., Terns M. P., White M. F., Yakunin A. F., Garrett R. A., van der Oost J., Backofen R., Koonin E. V. An updated evolutionary classification of CRISPR-Cas systems. Nature Reviews: Microbiology, 2015, vol. 13, no. 11, pp. 722–736.
21. Bondy-Denomy J., Garcia B., Strum S., Du M., Rollins M. F., Hidalgo-Reyes Y., Wiedenheft B., Maxwell K. L., Davidson A. R. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature, 2015, vol. 526 (7571), pp. 136–139.
22. Hilton I. B., Gersbach C. A. Genetic engineering: Chemical control for CRISPR editing. Nature Chemical Biology, 2017, vol. 13, pp. 2–3.
23. Sashital D. G., Wiedenheft B., Doudna J. A. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Cell, 2012, vol. 46, pp. 606–615.
24. Sangal V., Fineran P. C., Hoskisson P. A. Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphteriae. Microbiology, 2013, no. 159, pp. 2118–2126.
25. Chylinski K., Makarova K. S., Charpentier E., Koonin E. V. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Research, 2014, vol. 42, no. 10, pp. 6091–6105.
26. Fonfara I., Le Rhun A., Chylinski K., Makarova K. S., Lйcrivain A. L., Bzdrenga J., Koonin E. V., Charpentier E. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Research, 2014, vol. 42, no. 4, pp. 2577–2590.
27. Vasil’eva E. A., Melino D., Barlev N. A. CRISPR/Cas system for genome editing in pluripotent stem cells. Tsitologiia [Cytology], 2015, vol. 57, no. 1, pp. 19–30. (in Russian).
28. Hou Z., Zhang Y., Propson N. E., Howden S. E., Chu L. F., Sontheimer E. J., Sontheimer B., Thomson J. A. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedings of the National Academy of Sciences of the United States of America, 2013, no. 110, pp. 15644–15649.
29. Merkett S., Martin U. Site-specific genome engineering in human pluripotent stem cells. International Journal of Molecular Sciences, 2016, vol. 17 (1000), pp. 1–11.
30. Samson J. E., Magadan A. H., Moineau S. The CRISPR-Cas immune system and genetic transfers: reaching an equilibrium. Microbiology Spectrum, 2015, vol. 3, no. 1, pp. 209–218.
31. Bassuk A. G., Zheng A., Li Y., Tsang S. H., Mahajan V. B. Precision medicine: genetic repair of retinitis pigmentosa in patient-derived stem cells. Scientific Reports, 2016, vol. 6, p. 19969. doi:10.1038/srep19969.
32. Yang Y., Zhang X., Yi L., Hou Z., Chen J., Kou X., Zhao Y., Wang H., Sun X. F., Jiang C., Wang Y., Gao S. Naïve induced pluripotent stem cells generated from β-thalassemia fibroblasts allow efficient gene correction with CRISPR/Cas9. Stem Cells Translational Medicine, 2016, vol. 5, no. 1, pp. 8–19.
33. Goodman M. A., Malik P., Rothenberg M. E. CRISPR/Cas9 in allergic and immunologic diseases. Expert Review of Clinical Immunology, 2016, pp. 1–5.
34. Wang D., Ma Ning, Hui Yang, Gao Xu. The application of CRISPR/Cas9 genome editing technology in cancer research. Yi Chuan, 2016, vol. 38, no. 1, pp. 1–8. doi: 10.16288/j. yczz.15–252.
35. Li Y., Song Y. H., Liu B., Yu X. Y. The potential application and challenge of powerful CRISPR/Cas9 system in cardiovascular research. International Journal of Cardiology, 2016, vol. 9, pp. 191–193.
36. Freedman B. S., Brooks C. R., Lam A. Q., Fu H., Morizane R., Agrawal V., Saad A. F., Li M. K., Hughes M. R., Werff R. V., Peters D. T., Lu J., Baccei A., Siedlecki A. M., Valerius M. T., Musunuru K., McNagny K. M., Steinman T., Zhou J., Lerou P. H., Bonventre J. V. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nature Communications, 2015, vol. 6, pp. 1–13. doi: 10.1038/ncomms9715.
37. Yin H., Xue W., Chen S., Bogorad R. L., Benedetti E., Grompe M., Koteliansky V., Sharp P. A., Jacks T., Anderson D. G. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nature Biotechnology, 2014, vol. 32, no. 6, pp. 551–553. doi: 10.1038/nbt.2884.
38. Niemann H., Petersen B. The production of multi-transgenic pigs: update and perspectives for xenotransplantation. Transgenic Research, 2016, pp. 1–14.
39. Schiml S., Puchta H. Revolutionizing plant biology: multiple ways of genome engineering by CRISPR/Cas. Plant Methods, 2016, vol. 12, no. 8, pp. 1–9.
40. Schwartz M. L., Jorgensen E. M. SapTrap, a toolkit for high-throughput CRISPR/Cas9 gene modification in Caenorhabditis elegans. Genetics, 2016, vol. 202, no. 4, pp. 1277–1288. doi: 10.1534/genetics.115.184275.
Review
For citations:
Kharkhal A.N., Titov L.P. PROCARIOTIC IMMUNE SYSTEM: MOLECULAR MECHANISMS, APPLICATION IN MICROBIOLOGY. Proceedings of the National Academy of Sciences of Belarus, Medical series. 2017;(3):121-128. (In Russ.)
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