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A review of the application of CRISPR-Cas in microbial biotechnology
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Bahareh Nowruzi *1    , Hassan Beiranvand2 , Armita Biglari2 |
1- Associate Professor, Department of Biology, SR.C., Islamic Azad University, Tehran, Iran , bahare77biol@gmail.com
2- MSc Student, Department of Biology, SR.C., Islamic Azad University, Tehran, Iran |
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Abstract: (257 Views) |
| Today, the use of CRISPR-Cas systems for genome editing and modification in diverse microbial species is widespread. Originally identified as bacterial defense mechanisms against viral invaders, CRISPR-Cas systems are present across a broad spectrum of microbial taxa, including bacteria and archaea. These systems are categorized into two main classes: Class 1, comprising multi-subunit protein complexes, and Class 2, distinguished by single-unit Cas protein systems such as Cas9. The flexibility of CRISPR-Cas systems stands out as one of their most attractive features. Various genome editing approaches employed by Class 1 and Class 2 systems reflect their high adaptability in defense mechanisms, which confer protection against viral infections. Furthermore, CRISPR-Cas systems contribute to the stability and integrity of bacterial and archaeal genomes. Currently, these systems serve as essential tools in laboratories for functional genomics, precise genome editing, and targeted gene programming. They play a key role in biotechnology, especially in the engineering of microorganisms for environmental remediation and biofuel production. Beyond laboratory applications, CRISPR-based diagnostics enable rapid and accurate detection of infections and genetic variations, thus facilitating early disease diagnosis. Moreover, the development of targeted antimicrobial strategies utilizing CRISPR has found extensive application in combating drug-resistant microorganisms. Collectively, CRISPR-Cas systems have become indispensable tools in microbial genome engineering and in the advancement of innovative diagnostic and therapeutic approaches in medicine. In this review, data were collected and analyzed through a literature search in Springer, ScienceDirect, Scopus, and John Wiley databases from 2018 to 2025, using MeSH-defined keywords related to microbial CRISPR-Cas systems |
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| Keywords: CRISPR, Bacterial defense mechanism, Microbial biotechnology, Genome editing |
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Full-Text [PDF 1264 kb]
(140 Downloads)
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Semi-pilot: Review |
Subject:
biotechnology
Received: 2025/09/22 | Accepted: 2025/12/9 | Published: 2026/09/1
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1. 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;169:5429-33. [ DOI:10.1128/jb.169.12.5429-5433.1987] 2. Mojica FJ, Díez-Villaseñor Cs, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 2005;60:174-82. [ DOI:10.1007/s00239-004-0046-3] 3. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012;337:816-21. [ DOI:10.1126/science.1225829] 4. Molla KA, Karmakar S, Islam MT. Wide horizons of CRISPR-Cas-derived technologies for basic biology, agriculture, and medicine. In: Islam MT, Bhowmik PK, Molla KA, eds. CRISPR-Cas methods. Humana New York, NY: Springer; 2020. p. 1-23. [ DOI:10.1007/978-1-0716-0616-2_1] 5. Kaushik S. Editorial: Reviews in antibiotic resistance and new antimicrobial drugs. Front Cell Infect Microbiol 2024;14:1434140. [ DOI:10.3389/fcimb.2024.1434140] 6. Nguyen TM, Zhang Y, Pandolfi PP. Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses. Cell Res 2020;30:189-90. [ DOI:10.1038/s41422-020-0290-0] 7. Ding W, Zhang Y, Shi S. Development and application of CRISPR/Cas in microbial biotechnology. Front Bioeng Biotechnol 2020;8:711. [ DOI:10.3389/fbioe.2020.00711] 8. Hampton HG, Watson BN, Fineran PC. The arms race between bacteria and their phage foes. Nature 2020;577:327-36. [ DOI:10.1038/s41586-019-1894-8] 9. Watson BN, Staals RH, Fineran PC. CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction. MBio 2018;9:e02406-17. [ DOI:10.1128/mBio.02406-17] 10. Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, et al. Novel CRISPR-Cas systems: an updated review of the current achievements, applications, and future research perspectives. Int J Mol Sci 2021;22:3327. [ DOI:10.3390/ijms22073327] 11. Bourgeois J, Lazinski DW, Camilli A. Identification of spacer and protospacer sequence requirements in the Vibrio cholerae type IE CRISPR/Cas system. mSphere 2020;5:e00813-20. [ DOI:10.1128/mSphere.00813-20] 12. Sabri S, Mustofa MK, Fouad M, Mukherjee S, Fakruddin M, Shishir MA. Comprehensive Analysis of CRISPR-Cas Systems in Microbial and Their Multifaceted Applications. Microbial Bioactives 2024;7:1-11. [ DOI:10.25163/microbbioacts.719376] 13. Guzmán NM, Esquerra-Ruvira B, Mojica FJ. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021;24:473-98. [ DOI:10.1007/s10123-021-00208-7] 14. Kansal R. The CRISPR-Cas system and clinical applications of CRISPR-based gene editing in hematology with a focus on inherited germline predisposition to hematologic malignancies. Genes 2024;15:863. [ DOI:10.3390/genes15070863] 15. Tong Y, Jørgensen TS, Whitford CM, Weber T, Lee SY. A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Nat Commun 2021;12:5206. [ DOI:10.1038/s41467-021-25541-3] 16. Newsom S, Parameshwaran HP, Martin L, Rajan R. The CRISPR-Cas mechanism for adaptive immunity and alternate bacterial functions fuels diverse biotechnologies. Front Cell Infect Microbiol 2021;10:619763. [ DOI:10.3389/fcimb.2020.619763] 17. Wang LW, Trudeau SJ, Wang C, Gerdt C, Jiang S, Zhao B, et al. Modulating Gene Expression in Epstein‐Barr Virus (EBV)‐Positive B Cell Lines with CRISPRa and CRISPRi. Curr Protoc Mol Biol 2018;121: 31.13.1-31.13.18. [ DOI:10.1002/cpmb.50] 18. Hidalgo-Cantabrana C, Barrangou R. Characterization and applications of Type I CRISPR-Cas systems. Biochem Soc Trans 2020;48:15-23. [ DOI:10.1042/BST20190119] 19. Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, et al. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. Trends Plant Sci 2023;28:1144-65. [ DOI:10.1016/j.tplants.2023.05.012] 20. Lee H, Dhingra Y, Sashital DG. The Cas4-Cas1-Cas2 complex mediates precise prespacer processing during CRISPR adaptation. Elife 2019;8:e44248. [ DOI:10.7554/eLife.44248] 21. Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, et al. Compact RNA editors with small Cas13 proteins. Nat Biotechnol 2022;40:194-97. [ DOI:10.1038/s41587-021-01030-2] 22. Kolesnik MV, Fedorova I, Karneyeva KA, Artamonova DN, Severinov KV. Type III CRISPR-Cas systems: deciphering the most complex prokaryotic immune system. Biochemistry (Mosc) 2021;86:1301-14. [ DOI:10.1134/S0006297921100114] 23. Zhu S, Yung BC, Chandra S, Niu G, Antaris AL, Chen X. Near-infrared-II (NIR-II) bioimaging via off-peak NIR-I fluorescence emission. Theranostics 2018;8:4141. [ DOI:10.7150/thno.27995] 24. Li Y, Li S, Wang J, Liu G. CRISPR/Cas systems towards next-generation biosensing. Trends Biotechnol 2019;37:730-43. [ DOI:10.1016/j.tibtech.2018.12.005] 25. Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR‐Cas13 RNA targeting system. Wiley Interdiscip Rev RNA. 2022;13:e1694. [ DOI:10.1002/wrna.1694] 26. Pawluk A, Davidson AR, Maxwell KL. Anti-CRISPR: discovery, mechanism and function. Nat Rev Microbiol 2018;16:12-17. [ DOI:10.1038/nrmicro.2017.120] 27. Drabavicius G, Sinkunas T, Silanskas A, Gasiunas G, Venclovas Č, Siksnys V. DnaQ exonuclease‐like domain of Cas2 promotes spacer integration in a type I‐E CRISPR‐Cas system. EMBO Rep 2018;19:e45543. [ DOI:10.15252/embr.201745543] 28. Bharathkumar N, Sunil A, Meera P, Aksah S, Kannan M, Saravanan KM, et al. CRISPR/Cas-based modifications for therapeutic applications: a review. Mol Biotechnol 2022;64:355-72. [ DOI:10.1007/s12033-021-00422-8] 29. Demir Ö, Erbaş O. Discovery and applications of CRISPR-Cas9 gene editing technology. Journal of Experimental and Basic Medical Sciences 2023;8:56-67. 30. Camara-Wilpert S, Mayo-Muñoz D, Russel J, Fagerlund RD, Madsen JS, Fineran PC, et al. Bacteriophages suppress CRISPR-Cas immunity using RNA-based anti-CRISPRs. Nature 2023;623:601-7. [ DOI:10.1038/s41586-023-06612-5] 31. Mlaga KD, Garcia V, Colson P, Ruimy R, Rolain J-M, Diene SM. Extensive comparative genomic analysis of Enterococcus faecalis and Enterococcus faecium reveals a direct association between the absence of CRISPR-Cas systems, the presence of anti-endonuclease (ardA) and the acquisition of vancomycin resistance in E. faecium. Microorganisms 2021;9:1118. [ DOI:10.3390/microorganisms9061118] 32. Joseph CE, Jain A, Yaqub MO, Edison LK. CRISPR-Cas Systems: Bridging Bacterial Immunity and Host Interactions. Appl Microbiol 2025;5:118. [ DOI:10.3390/applmicrobiol5040118] 33. Malone LM, Warring SL, Jackson SA, Warnecke C, Gardner PP, Gumy LF, et al. A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nat Microbiol 2020;5:48-55. [ DOI:10.1038/s41564-019-0612-5] 34. Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 2014;5:e00928-13. [ DOI:10.1128/mBio.00928-13] 35. Kiga K, Tan X-E, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato'o Y, et al. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat Commun 2020;11:2934. [ DOI:10.1038/s41467-020-16731-6] 36. Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, et al. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023;18:e0291520. [ DOI:10.1371/journal.pone.0291520] 37. Yang J, Meng X, Pan J, Jiang N, Zhou C, Wu Z, et al. CRISPR/Cas9-mediated noncoding RNA editing in human cancers. RNA Biol 2018;15:35-43. [ DOI:10.1080/15476286.2017.1391443] 38. Dinh H, Semenec L, Kumar SS, Short FL, Cain AK. Microbiology's next top model: Galleria in the molecular age. Pathog Dis 2021;79:ftab006. [ DOI:10.1093/femspd/ftab006] 39. Dimitri A, Herbst F, Fraietta JA. Engineering the next-generation of CAR T-cells with CRISPR-Cas9 gene editing. Mol Cancer 2022;21:78. [ DOI:10.1186/s12943-022-01559-z] 40. Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-based antimicrobials: design, challenges, and bacterial mechanisms of resistance. ACS Infect Dis 2023;9:1283-302. [ DOI:10.1021/acsinfecdis.2c00649] 41. Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L, et al. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell 2020;181:865-76. [ DOI:10.1016/j.cell.2020.04.020] 42. Curti L, Pereyra-Bonnet F, Gimenez C. An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12. BioRxiv 2020;2020. 43. Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 2019;14:2986-3012. [ DOI:10.1038/s41596-019-0210-2] 44. Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science 2014;346:1258096. [ DOI:10.1126/science.1258096] 45. Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA. Mutations in Cas9 enhance the rate of acquisition of viral spacer sequences during the CRISPR-Cas immune response. Mol Cell 2017;65:168-75. [ DOI:10.1016/j.molcel.2016.11.031] 46. Dhokane D, Shaikh A, Yadav A, Giri N, Bandyopadhyay A, Dasgupta S, et al. CRISPR-based bioengineering in microalgae for production of industrially important biomolecules. Front Bioeng Biotechnol 2023;11:1267826. [ DOI:10.3389/fbioe.2023.1267826] 47. Tran Q-G, Le TT, Choi D-Y, Cho D-H, Yun J-H, Choi HI, et al. Progress and challenges in CRISPR/Cas applications in microalgae. J Microbiol 2025;63:e2501028. [ DOI:10.71150/jm.2501028] 48. Dong Z, Chen L, Wang Y, Sun T, Zhang W. Current advances in CRISPR-Cas-mediated gene editing and regulation in cyanobacteria. Blue Biotechnology 2024;1:9. [ DOI:10.1186/s44315-024-00009-3] 49. Huang C-H, Shen CR, Li H, Sung L-Y, Wu M-Y, Hu Y-C. CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942. Microb Cell Fact 2016;15:196. [ DOI:10.1186/s12934-016-0595-3] 50. Gordon GC, Korosh TC, Cameron JC, Markley AL, Begemann MB, Pfleger BF. CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng 2016;38:170-9. [ DOI:10.1016/j.ymben.2016.07.007] 51. Zhang Y-T, Jiang J-Y, Shi T-Q, Sun X-M, Zhao Q-Y, Huang H, et al. Application of the CRISPR/Cas system for genome editing in microalgae. Appl Microbiol Biotechnol 2019;103:3239-48. [ DOI:10.1007/s00253-019-09726-x] 52. Ahmed MM, Kayode HH, Okesanya OJ, Ukoaka BM, Eshun G, Mourid MR, et al. CRISPR-Cas systems in the fight against antimicrobial resistance: current status, potentials, and future directions. Infect Drug Resist 2024:5229-45. [ DOI:10.2147/IDR.S494327] 53. Karthik L, Arivarasan VK, Vignesh MR, Anitha P. CRISPR ERA: Current Applications and Future Perspectives on Actinobacteria. In: Karthik L, ed. Actinobacteria. Singapore: Springer; 2022. [ DOI:10.1007/978-981-16-5835-8_10] 54. Xia Y, Sun L, Liang Z, Guo Y, Li J, Tang D, et al. The construction of a PAM-less base editing toolbox in Bacillus subtilis and its application in metabolic engineering. Chemical Engineering Journal 2023;469:143865. [ DOI:10.1016/j.cej.2023.143865] 55. Du W, Meister LL, van Grinsven T, Branco dos Santos F. Efficient Multiplex Genome Editing of the Cyanobacterium Synechocystis sp. PCC6803 via CRISPR‐Cas12a. Biotechnol Bioeng 2025;122:736-43. [ DOI:10.1002/bit.28910] 56. Mu Y, Zhang C, Li T, Jin F-J, Sung Y-J, Oh H-M, et al. Development and applications of CRISPR/Cas9-based genome editing in Lactobacillus. Int J Mol Sci 2022;23:12852. [ DOI:10.3390/ijms232112852] |
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