Microbial Bioactives
MicroBio Pharmaceuticals and Pharmacology | Online ISSN 2209-2161
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Contents Vol 7 (1)

Comprehensive Analysis of CRISPR-Cas Systems in Microbial and Their Multifaceted Applications

Suriana Sabri 1, Md Kawsar Mustofa 2,  M. T. Fouad 3, Saikat Mukherjee 4, Md Fakruddin 5*, Md Asaduzzaman Shishir 6

+ Author Affiliations

Microbial Bioactives 7 (1) 1-11 https://doi.org/10.25163/microbbioacts.719376

Submitted: 26 November 2023 Revised: 23 January 2024  Published: 29 January 2024 

Abstract

Scientific interest in CRISPR-Cas systems is immense due to their emergence as groundbreaking tools for genome editing and modification in various microbes. Initially recognized as bacterial defenses against viral invaders, CRISPR-Cas systems have been found in a wide range of microbial species, including bacteria and archaea. They are classified into two main classes: Class 1, consisting of multi-subunit complexes, and Class 2, characterized by single-protein Cas9 systems. These classes display remarkable diversity, with numerous subtypes and variants enabling adaptation to various ecological niches. The versatility of CRISPR-Cas systems is one of their most appealing attributes. They employ diverse genome editing strategies, reflecting their adaptability and evolution as adaptive immune systems in microorganisms, co-evolving in response to viral threats. Beyond viral defense, these systems contribute to genome stability and integrity in bacteria and archaea. CRISPR-Cas systems have become indispensable tools in laboratories for functional genomics, precise genome editing, and gene reprogramming. They play pivotal roles in synthetic biology and biotechnology, facilitating the engineering of microorganisms for environmental remediation and biofuel production. Furthermore, CRISPR-based diagnostics enable rapid and precise identification of infections and genetic alterations, promising a transformative impact on disease diagnosis. Additionally, the potential of CRISPR-based antimicrobials to combat drug-resistant microorganisms holds significant promise in medicine. In conclusion, the diverse applications of CRISPR-Cas systems underscore the remarkable adaptability of life and the potential for scientific and medical advancements. Continued exploration and optimization of these systems will unlock new avenues for research and transformative applications across various industries. Harnessing the defensive mechanisms of microbial CRISPR-Cas systems exemplifies both the power of nature and human ingenuity for societal benefit and scientific progress.

Keywords: CRISPR-Cas, Microbial genetics, Gene editing, Microbial biotechnology, Antimicrobial defense

References

Abbott, T. R., Dhamdhere, G., Liu, Y., Lin, X., Goudy, L., & Zeng, L. (2020). Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell, 181, 865–e12.

Amitai, G., & Sorek, R. (2016). CRISPR-Cas adaptation: Insights into the mechanism of action. Nature Reviews Microbiology, 14, 67–76.

Arslan, Z., Hermanns, V., Wurm, R., Wagner, R., & Pul, Ü. (2014). Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system. Nucleic Acids Research, 42, 7884–7893.

Athukoralage, J. S., McMahon, S. A., Zhang, C., Grüschow, S., Graham, S., & Krupovic, M. (2020). An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature, 577, 572–575.

Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., & Nocek, B. (2011). A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Molecular Microbiology, 79, 484–502.

Barrangou, R., & Horvath, P. (2017). A decade of discovery: CRISPR functions and applications. Nature Microbiology, 2, 17092–17099.

Barrangou, R., & Marraffini, L. A. (2014). CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Molecular Cell, 54, 234–244.

Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., & Moineau, S. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315, 1709–1712.

Béguin, P. B., Charpin, N., Koonin, E. V., Forterre, P., & Krupovic, M. (2016). Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems. Nucleic Acids Research, 44, 10367.

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in Bacteria and Archaea: Versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45, 273–297.

Bikard, D., & Barrangou, R. (2017). Using CRISPR-Cas systems as antimicrobials. Current Opinion in Microbiology, 37, 155–160.

Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., & Duportet, X. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnology, 32, 1146–1150.

Bikard, D., Hatoum-Aslan, A., Mucida, D., & Marraffini, L. A. (2012). CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host & Microbe, 12, 177–186.

Bondy-Denomy, J., Garcia, B., Strum, S., Du, M., Rollins, M. F., & Hidalgo-Reyes, Y. (2015). Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature, 526, 136–139.

Bondy-Denomy, J., Pawluk, A., Maxwell, K. L., & Davidson, A. R. (2013). Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature, 493, 429–432.

Bourgogne, A., Garsin, D. A., Qin, X., Singh, K. V., Sillanpaa, J., & Yerrapragada, S. (2008). Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biology, 9, R110.

Brockhurst, M. A., Harrison, E., Hall, J. P. J., Richards, T., McNally, A., & MacLean, C. (2019). The ecology and evolution of pangenomes. Current Biology, 29(20), R1094–R1103.

Brodt, A., Lurie-Weinberger, M. N., & Gophna, U. (2011). CRISPR loci reveal networks of gene exchange in archaea. Biology Direct, 6, 65.

Brouns, S. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J., & Snijders, A. P. (2008). Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 321(80), 960–964.

Carroll, M., & Zhou, X. (2017). Panacea in progress: CRISPR and the future of its biological research introduction. Microbiological Research, 201, 63–74.

Charpentier, E., Richter, H., Van Der Oost, J., & White, M. F. (2015). Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiology Reviews, 39, 428–441.

Chen, W., Zhang, Y., Zhang, Y., Pi, Y., Gu, T., & Song, L. (2018). CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species. iScience, 6, 222–231.

Chylinski, K., Le Rhun, A., & Charpentier, E. (2013). The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biology, 10, 726–737.

Citorik, R. J., Mimee, M., & Lu, T. K. (2014). Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnology, 32, 1141–1145.

Cox, D. B. T., Gootenberg, J. S., Abudayyeh, O. O., Franklin, B., Kellner, M. J., & Joung, J. (2017). RNA editing with CRISPR-Cas13. Science, 358, 1019–1027.

Cui, L., Wang, X., Huang, D., Zhao, Y., Feng, J., & Lu, Q. (2020). CRISPR-Cas3 of Salmonella upregulates bacterial biofilm formation and virulence to host cells by targeting quorum-sensing systems. Pathogens, 9, 53.

Curti, L., Pereyra-Bonnet, F., & Gimenez, C. (2020). An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12. bioRxiv, 2020.02.29.971127.

Dai, W., Xu, X., Wang, D., Wu, J., & Wang, J. (2019). Cancer therapy with a CRISPR-assisted telomerase-activating gene expression system. Oncogene, 38, 4110–4124.

Díez-Villaseñor, C., Guzmán, N. M., Almendros, C., García-Martínez, J., & Mojica, F. J. (2013). CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biology, 10, 792–802.

Ding, X., Yin, K., Li, Z., & Liu, C. (2020). All-in-one dual CRISPR-Cas12a (AIOD-CRISPR) assay: A case for rapid, ultrasensitive and visual detection of novel coronavirus SARS-CoV-2 and HIV virus. bioRxiv, 2020.03.19.998724.

Dong, D., Guo, M., Wang, S., Zhu, Y., Wang, S., & Xiong, Z. (2017). Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Nature, 546, 436–439.

Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., & Keren, M. (2018). Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 359.

Doudna, J. A., & Charpentier, E. (2014). Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346, 1258096.

Faure, G., Shmakov, S. A., Yan, W. X., Cheng, D. R., Scott, D. A., & Peters, J. E. (2019). CRISPR–Cas in mobile genetic elements: Counter-defence and beyond. Nature Reviews Microbiology, 17, 513–525.

Fineran, P. C., & Charpentier, E. (2012). Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information. Virology, 434, 202–209.

Gao, N. J., Al-Bassam, M. M., Poudel, S., Wozniak, J. M., Gonzalez, D. J., & Olson, J. (2019). Functional and proteomic analysis of Streptococcus pyogenes virulence upon loss of its native Cas9 nuclease. Frontiers in Microbiology, 10, 1967.

García-Gutiérrez, E., Almendros, C., Mojica, F. J., Guzmán, N. M., & García-Martínez, J. (2015). CRISPR content correlates with the pathogenic potential of Escherichia coli. PloS One, 10, e0131935.

García-Martínez, J., Maldonado, R. D., Guzmán, N. M., & Mojica, F. J. M. (2018). The CRISPR conundrum: Evolve and maybe die, or survive and risk stagnation. Microbial Cell, 5, 262–268.

Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., & Whitehead, E. H. (2014). Genome-scale CRISPR-mediated control of gene repression and activation. Cell, 159, 647–661.

Gleditzsch, D., Pausch, P., Müller-Esparza, H., Özcan, A., Guo, X., & Bange, G. (2019). PAM identification by CRISPR-Cas effector complexes: Diversified mechanisms and structures. RNA Biology, 16, 504–517.

Gomaa, A. A., Klumpe, H. E., Luo, M. L., Selle, K., Barrangou, R., & Beisel, C. L. (2014). Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. mBio, 5, e00928.

Gong, T., Tang, B., Zhou, X., Zeng, J., Lu, M., & Guo, X. (2018). Genome editing in Streptococcus mutans through self-targeting CRISPR arrays. Molecular Oral Microbiology, 33, 440–449.

Gophna, U., Kristensen, D. M., Wolf, Y. I., Popa, O., Drevet, C., & Koonin, E. V. (2015). No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME Journal, 9, 2021–2027.

Grissa, I., Vergnaud, G., & Pourcel, C. (2007). CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Research, 35, W52.

Gunderson, F. F., & Cianciotto, N. P. (2013). The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. mBio, 4, e00074.

Haft, D. H., Selengut, J., Mongodin, E. F., & Nelson, K. E. (2005). A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology, 1, e60.

Hampton, H. G., Watson, B. N. J., & Fineran, P. C. (2020). The arms race between bacteria and their phage foes. Nature, 577, 327–336.

Han, P., Niestemski, L. R., Barrick, J. E., & Deem, M. W. (2013). Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. Physical Biology, 10, 025004.

Heidrich, N., Hagmann, A., Bauriedl, S., Vogel, J., & Schoen, C. (2019). The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells. RNA Biology, 16, 390–396.

Makarova, K. S., Aravind, L., Grishin, N. V., Rogozin, I. B., & Koonin, E. V. (2002). A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. Nucleic Acids Research, 30, 482–496.

Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (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. Biology Direct, 1, 7.

Mandin, P., Repoila, F., Vergassola, M., Geissmann, T., & Cossart, P. (2007). Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Research, 35(3), 962–974.

Mangas, E. L., Rubio, A., Álvarez-Marín, R., Labrador-Herrera, G., Pachón, J., & Pachón-Ibáñez, M. E. (2019). Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation. Microbial Genomics, 5.

McDonald, N. D., Regmi, A., Morreale, D. P., Borowski, J. D., & Boyd, E. F. (2019). CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics, 20, 105.

Metsky, H. C., Freije, C. A., Kosoko-Thoroddsen, T.-S. F., Sabeti, P. C., & Myhrvold, C. (2020). CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design. bioRxiv, 2020.02.26.967026.

Nguyen, T. M., Zhang, Y., & Pandolfi, P. P. (2020). Virus against virus: A potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses. Cell Research, 30, 189–190.

Nishimasu, H., & Nureki, O. (2017). Structures and mechanisms of CRISPR RNA-guided effector nucleases. Current Opinion in Structural Biology, 43, 68–78.

Palmer, K. L., & Gilmore, M. S. (2010). Multidrug-resistant enterococci lack CRISPR-Cas. mBio, 1.

Patterson, A. G., Jackson, S. A., Taylor, C., Evans, G. B., Salmond, G. P. C., & Przybilski, R. (2016). Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR-Cas systems. Molecular Cell, 64, 1102–1108.

Pawluk, A., Amrani, N., Zhang, Y., Garcia, B., Hidalgo-Reyes, Y., & Lee, J. (2016). Naturally occurring off-switches for CRISPR-Cas9. Cell, 167, 1829–e9.

Samanta, M. K., Dey, A., & Gayen, S. (2016). CRISPR/Cas9: An advanced tool for editing plant genomes. Transgenic Research, 25, 561–573.

Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y. L., & Weiss, D. S. (2013). A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature, 497, 254–257.

Schaeffer, S. M., & Nakata, P. A. (2015). CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field. Plant Science, 240, 130–142.

Seed, K. D. (2015). Battling phages: How bacteria defend against viral attack. PloS Pathogens, 11(6), e1004847.

van Belkum, A., Soriaga, L. B., LaFave, M. C., Akella, S., Veyrieras, J. B., Barbu, E. M., et al. (2015). Phylogenetic distribution of CRISPR-Cas systems in antibiotic-resistant Pseudomonas aeruginosa. mBio, 6, e01796.

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