CRISPR-Cas Systems in Bacteria: A Review of Mechanisms and Applications
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CRISPR-Cas systems, Bacterial immunity, Gene editing, Cas9 protein, Genome engineering
Abstract
This review analyzes the development and various uses of the CRISPR-Cas systems in bacterial cells, emphasizing their function in adaptive immunity and their potential as effective tools in bioengineering. Consisting of arrays of CRISPR and P proteins, the CRISPR-Cas systems defend bacteria and archaea from viruses by targeting and destroying foreign genetic material sequences. Some of the literature on CRISPR systems subclasses has been reviewed, and basic stages of select bacteria practice modification over the nature and return of that genetic material are described. Class 1 and Class 2 types are particularly stressed, including Cas9 and Cpf1 proteins respectively which made a breakthrough in gene editing technologies. This paper also evaluates the recent trends in the CRISPR technology and its usage in genetic engineering, personalized medicine and diagnostics as well as the recent advances in gene editors, RNA targeting and strategically focused approaches towards antimicrobial resistance. Whether used in genetic stabilizing or cutting precise targeting, the review points out the off-target products and many other ethical issues associated with the techniques including human therapeutic applications in target genome editing. The overall aim of this article to provide guidelines to the researchers willing to employ the CRISPR-Cas systems and the genetic modification technology in developing better biotechnological products and therapeutic techniques in the future.
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References
Lin, H., Li, G., Peng, X., Deng, A., Ye, L., Shi, L., ... & He, J. (2021). The use of CRISPR/Cas9 as a tool to study human infectious viruses. Frontiers in Cellular and Infection Microbiology, 11, 590989.
Nussenzweig, P. M. & Marraffini, L. A. (2020). Molecular mechanisms of CRISPR-Cas immunity in bacteria. Annual review of genetics.
Musharova, O., Medvedeva, S., Klimuk, E., Guzman, N. M., Titova, D., Zgoda, V., ... & Savitskaya, E. (2021). Prespacers formed during primed adaptation associate with the Cas1–Cas2 adaptation complex and the Cas3 interference nuclease–helicase. Proceedings of the National Academy of Sciences, 118(22), e2021291118.
Bhokisham, N., Laudermilch, E., Traeger, L. L., Bonilla, T. D., Ruiz-Estevez, M., & Becker, J. R. (2023). CRISPR-Cas system: the current and emerging translational landscape. Cells, 12(8), 1103.
Mota, D. S., Marques, J. M., Guimarães, J. M., & Mariúba, L. A. M. (2020). CRISPR/Cas Class 2 systems and their applications in biotechnological processes. Genet Mol Res, 20, 1-10.
Chen, Z., Lv, Z., Sun, Y., Chi, Z., & Qing, G. (2020). Recent advancements in polyethyleneimine-based materials and their biomedical, biotechnology, and biomaterial applications. Journal of Materials Chemistry B.
Nidhi, S., Anand, U., Oleksak, P., Tripathi, P., Lal, J. A., Thomas, G., ... & Tripathi, V. (2021). Novel CRISPR–Cas systems: an updated review of the current achievements, applications, and future research perspectives. International journal of molecular sciences, 22(7), 3327.
Davies, K. (2020). Editing humanity: The CRISPR revolution and the new era of genome editing.
Serajian, S., Ahmadpour, E., Oliveira, S. M. R., Pereira, M. D. L., & Heidarzadeh, S. (2021). CRISPR-Cas technology: emerging applications in clinical microbiology and infectious diseases. Pharmaceuticals, 14(11), 1171.
Rizwan, M., Arshad, M., Kashif, M., Durrani, A. Z., Abbas, A., Ahmad, T., ... & Khan, K. (2021). CRIPSR Case System: Biological Role in Bacterial Virulence, Genome Editing and in Antimicrobial Resistance. Punjab University Journal of Zoology, 36(1), 111-118
González-Delgado, A. (2021). The Reverse Transcriptases associated with CRISPR-Cas systems: Phylogenetic relationships and functional characterization.
Egido, J. E., Costa, A. R., Aparicio-Maldonado, C., Haas, P. J., & Brouns, S. J. (2022). Mechanisms and clinical importance of bacteriophage resistance. FEMS microbiology reviews, 46(1), fuab048.
Münch, P. C., Franzosa, E. A., Stecher, B., McHardy, A. C., & Huttenhower, C. (2021). Identification of natural CRISPR systems and targets in the human microbiome. Cell host & microbe, 29(1), 94-106.
Smith, L. M. (2020). A genome-wide approach identifying regulators of CRISPR-Cas immunity in Serratia.
Schultz, B. M., Acevedo, O. A., Kalergis, A. M., & Bueno, S. M. (2022). Role of extracellular trap release during bacterial and viral infection. Frontiers in Microbiology, 13, 798853.
Alonso-Lerma, B., Jabalera, Y., Samperio, S., Morin, M., Fernandez, A., Hille, L. T., ... & Perez-Jimenez, R. (2023). Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins. Nature microbiology, 8(1), 77-90.
Koonin, E. V. & Makarova, K. S. (2022). Evolutionary plasticity and functional versatility of CRISPR systems. PLoS Biology.
Mortensen, K., Lam, T. J., & Ye, Y. (2021). Comparison of CRISPR–Cas immune systems in healthcare-related pathogens. Frontiers in Microbiology.
Shmakov, S. A., Barth, Z. K., Makarova, K. S., Wolf, Y. I., Brover, V., Peters, J. E., & Koonin, E. V. (2023). Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems. Nucleic Acids Research, 51(15), 8150-8168.
Payne, L. J., Todeschini, T. C., Wu, Y., Perry, B. J., Ronson, C. W., Fineran, P. C., ... & Jackson, S. A. (2021). Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic acids research, 49(19), 10868-10878.
Garcia-Robledo, J. E., Barrera, M. C., & Tobón, G. J. (2020). CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases: CRISPR/Cas9 offers a simple and inexpensive method for disease modeling, genetic screening, and potentially for disease therapy. International Reviews of Immunology, 39(1), 11-20
Javaid, N. & Choi, S. (2021). CRISPR/Cas system and factors affecting its precision and efficiency. Frontiers in cell and developmental biology.
Liao, C. & Beisel, C. L. (2021). The tracrRNA in CRISPR biology and technologies. Annual review of genetics.
Bayoumi, M. & Munir, M. (2021). Potential use of CRISPR/cas13 machinery in understanding virus–host interaction. Frontiers in Microbiology.
Zhang, X., Garrett, S., Graveley, B. R., & Terns, M. P. (2022). Unique properties of spacer acquisition by the type III-A CRISPR-Cas system. Nucleic Acids Research, 50(3), 1562-1582.
Pourcel, C., Touchon, M., Villeriot, N., Vernadet, J. P., Couvin, D., Toffano-Nioche, C., & Vergnaud, G. (2020). CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. Nucleic acids research, 48(D1), D535-D544.
Pfeifer, E., Sousa, J. M., Touchon, M., & Rocha, E. P. (2022). When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Current Opinion in Microbiology, 70, 102230.
Joberty, G., Fälth-Savitski, M., Paulmann, M., Bösche, M., Doce, C., Cheng, A. T., ... & Grandi, P. (2020). A tandem guide RNA-based strategy for efficient CRISPR gene editing of cell populations with low heterogeneity of edited alleles. The CRISPR journal, 3(2), 123-134.
Behler, J. & Hess, W. R. (2020). Approaches to study CRISPR RNA biogenesis and the key players involved. Methods.
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J., ... & Koonin, E. V. (2020). Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2), 67-83.
Özcan, A., Krajeski, R., Ioannidi, E., Lee, B., & Gardner…, A. (2021). Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature.
Taylor, H. N., Laderman, E., Armbrust, M., Hallmark, T., Keiser, D., Bondy-Denomy, J., & Jackson, R. N. (2021). Positioning diverse type IV structures and functions within class 1 CRISPR-Cas systems. Frontiers in microbiology, 12, 671522.
Munawar, N. & Ahmad, A. (2021). CRISPR/Cas system: an introduction. CRISPR Crops: The Future of Food Security.
Liu, Z., Dong, H., Cui, Y., Cong, L., & Zhang, D. (2020). Application of different types of CRISPR/Cas-based systems in bacteria. Microbial cell factories.
Zhu, H., Li, C., & Gao, C. (2020). Applications of CRISPR–Cas in agriculture and plant biotechnology. Nature Reviews Molecular Cell Biology.
Chaudhuri, A., Halder, K., & Datta, A. (2022). Classification of CRISPR/Cas system and its application in tomato breeding. Theoretical and Applied Genetics.
Bhatia, S. & Yadav, S. K. (2023). CRISPR-Cas for genome editing: classification, mechanism, designing and applications. International Journal of Biological Macromolecules
Budhathoki, J. B., Xiao, Y., Schuler, G., Hu, C., Cheng, A., Ding, F., & Ke, A. (2020). Real-time observation of CRISPR spacer acquisition by Cas1–Cas2 integrase. Nature structural & molecular biology, 27(5), 489-499.
Deckers, M., Deforce, D., Fraiture, M. A., & Roosens, N. H. C. (2020). Genetically modified micro-organisms for industrial food enzyme production: An overview. Foods.
Li, H., Yang, Y., Hong, W., Huang, M., Wu, M., & Zhao, X. (2020). Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal transduction and targeted therapy, 5(1), 1.
Khan, S. H., Tariq, H., Farooq, I., Tasleeem, H., Ghouri, M. Z., Mubarik, M. S., & Khan, Z. (2022). Applications of CRISPR/Cas system in plants. The CRISPR/cas tool kit for genome editing, 285-309.
Wang, J., Zhang, X., Cheng, L., & Luo, Y. (2020). An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools. RNA biology.
Boti, M. A., Athanasopoulou, K., Adamopoulos, P. G., Sideris, D. C., & Scorilas, A. (2023). Recent advances in genome-engineering strategies. Genes, 14(1), 129.
Nadakuduti, S. S. & Enciso-Rodríguez, F. (2021). Advances in genome editing with CRISPR systems and transformation technologies for plant DNA manipulation. Frontiers in plant science.
Ali, A., Zafar, M. M., Farooq, Z., Ahmed, S. R., Ijaz, A., Anwar, Z., ... & Maozhi, R. (2023). Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnology Journal, 18(8), 2200642.
Wang, S. W., Gao, C., Zheng, Y. M., Yi, L., Lu, J. C., Huang, X. Y., ... & Ke, A. W. (2022). Current applications and future perspective of CRISPR/Cas9 gene editing in cancer. Molecular cancer, 21(1), 57.
Schleidgen, S., Dederer, H. G., Sgodda, S., Cravcisin, S., Lüneburg, L., Cantz, T., & Heinemann, T. (2020). Human germline editing in the era of CRISPR-Cas: risk and uncertainty, inter-generational responsibility, therapeutic legitimacy. BMC Medical Ethics, 21, 1-12.
Naeem, M., Majeed, S., Hoque, M. Z., & Ahmad, I. (2020). Latest developed strategies to minimize the off-target effects in CRISPR-Cas-mediated genome editing. Cells.
Alpaslan-Roodenberg, S., Anthony, D., Babiker, H., Bánffy, E., Booth, T., Capone, P., ... & Zahir, M. (2021). Ethics of DNA research on human remains: five globally applicable guidelines. Nature, 599(7883), 41-46.
Piergentili, R., Del Rio, A., Signore, F., Umani Ronchi, F., Marinelli, E., & Zaami, S. (2021). CRISPR-Cas and its wide-ranging applications: From human genome editing to environmental implications, technical limitations, hazards and bioethical issues. Cells, 10(5), 969.
Li, C., Chu, W., Gill, R. A., Sang, S., Shi, Y., Hu, X., ... & Zhang, B. (2023). Computational tools and resources for CRISPR/Cas genome editing. Genomics, proteomics & bioinformatics, 21(1), 108-126.
Newsom, S., Parameshwaran, H. P., Martin, L., & Rajan, R. (2021). The CRISPR-Cas mechanism for adaptive immunity and alternate bacterial functions fuels diverse biotechnologies. Frontiers in cellular and infection microbiology, 10, 619763.
Fillol-Salom, A., Miguel-Romero, L., Marina, A., Chen, J., & Penadés, J. R. (2020). Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation. Current Opinion in Microbiology, 56, 52-58.
Malone, L. M., Birkholz, N., & Fineran, P. C. (2021). Conquering CRISPR: how phages overcome bacterial adaptive immunity. Current opinion in biotechnology.
Ganger, S., Harale, G., & Majumdar, P. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated (CRISPR/Cas) Systems: Discovery, Structure, Classification, and General Mechanism. In CRISPR/Cas-Mediated Genome Editing in Plants (pp. 65-97). Apple Academic Press.
Cornuault, J. K., Moncaut, E., Loux, V., Mathieu, A., Sokol, H., Petit, M. A., & De Paepe, M. (2020). The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition. The ISME journal, 14(3), 771-787.
Bonsma-Fisher, M. J. (2022). Population Dynamics of CRISPR Adaptive Immunity in Communities of Bacteria and Phages: a Window into Another World.
Fage, C., Lemire, N., & Moineau, S. (2021). Delivery of CRISPR-Cas systems using phage-based vectors. Current opinion in biotechnology.
Gao, Z., Fan, M., Das, A. T., Herrera-Carrillo, E., & Berkhout, B. (2020). Extinction of all infectious HIV in cell culture by the CRISPR-Cas12a system with only a single crRNA. Nucleic Acids Research, 48(10), 5527-5539.
Sharrock, J. & Sun, J. C. (2020). Innate immunological memory: from plants to animals. Current opinion in immunology.
Vedadghavami, A., Zhang, C., & Bajpayee, A. G. (2020). Overcoming negatively charged tissue barriers: Drug delivery using cationic peptides and proteins. Nano today.
Zhang, D., Hussain, A., Manghwar, H., Xie, K., Xie, S., Zhao, S., ... & Ding, F. (2020). Genome editing with the CRISPR‐Cas system: an art, ethics and global regulatory perspective. Plant biotechnology journal, 18(8), 1651-1669.
Rajput, M., Choudhary, K., Kumar, M., Vivekanand, V., Chawade, A., Ortiz, R., & Pareek, N. (2021). RNA interference and CRISPR/Cas gene editing for crop improvement: Paradigm shift towards sustainable agriculture. Plants, 10(9), 1914.
Uddin, F., Rudin, C. M., & Sen, T. (2020). CRISPR gene therapy: applications, limitations, and implications for the future. Frontiers in oncology.
Arroyo-Olarte, R. D., Bravo Rodriguez, R., & Morales-Ríos, E. (2021). Genome editing in bacteria: CRISPR-Cas and beyond. Microorganisms.
Lewens, T. (2020). Blurring the germline: Genome editing and transgenerational epigenetic inheritance. Bioethics.
Kan, M. J. & Doudna, J. A. (2022). Treatment of genetic diseases with CRISPR genome editing. Jama.
D’Souza, R. F., Mathew, M., & Surapaneni, K. M. (2024). Attitudes of Algorithms: An Exploration of the Ethics of CRISPR Cas9 through the Lens of ChatGPT. Indian Journal of Clinical Biochemistry, 1-8.
Subica, A. M. (2023). CRISPR in public health: the health equity implications and role of community in gene-editing research and applications. American Journal of Public Health
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