2022, Number 1
Introduction to CRISPR systems and their applications in yeasts
Language: Spanish
References: 78
Page: 1-21
PDF size: 835.20 Kb.
ABSTRACT
The adaptive immunity system in bacteria and archaea, responsible for recognizing invasive DNA sequences, is characterized by clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated proteins (Cas) and guide RNAs complementary to specific target DNA sequences are the most widely used gene-editing tools to modify organisms. Currently, the variety of CRISPR/Cas systems has increased, adapting to microorganisms such as yeasts with biotechnological potential. This review aims to facilitate understanding of the basic concepts of the CRISPR/Cas9 system and to recognize some of the varieties of this molecular tool that have been successfully implemented in different yeasts. Likewise, some of the new technologies that are revolutionizing research based on CRISPR are described.REFERENCES
de Puig, H., Lee, R. A., Najjar, D., Tan, X., Soenksen, L. R.,Angenent-Mari, N. M., Donghia, N. M., Weckman, N. E.,Ory, A., Ng, C. F., Nguyen, P. Q., Mao, A. S., Ferrante, T. C.,Lansberry, G., Sallum, H., Niemi, J. & Collins, J. J. (2021).Minimally instrumented SHERLOCK (miSHERLOCK) forCRISPR-based point-of-care diagnosis of SARS-CoV-2 andemerging variants. Science Advances, 7(32), 1-11. https://doi.org/10.1126/sciadv.abh2944
Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V.(2012). Cas9-crRNA ribonucleoprotein complex mediatesspecific DNA cleavage for adaptive immunity in bacteria.Proceedings of the National Academy of Sciences of theUnited States of America, 109(39), E2579-E2586. https://doi.org/10.1073/pnas.1208507109
Geurts, M. H., de Poel, E., Amatngalim, G. D., Oka, R., Meijers,F. M., Kruisselbrink, E., van Mourik, P., Berkers, G., deWinter-de Groot, K. M., Michel, S., Muilwijk, D., Aalbers,B. L., Mullenders, J., Boj, S. F., Suen, S. W., Brunsveld,J. E., Janssens, H. M., Mall, M. A., Graeber, S. Y., vanBoxtel, R., van der Ent, K. C., Beekman, J. & Clevers, H.(2020). CRISPR-Based Adenine Editors Correct NonsenseMutations in a Cystic Fibrosis Organoid Biobank. CellStem Cell, 26(4), 503–510.e7. https://doi.org/10.1016/j.stem.2020.01.019
González, J., Romero-Aguilar, L., Matus-Ortega, G., Pardo,J. P., Flores-Alanis, A. & Segal-Kischinevzky, C. (2020).Levaduras adaptadas al frío: el tesoro biotecnológicode la Antártica. TIP Revista Especializada en CienciasQuímico-Biológicas, 23, 1-14. https://doi.org/10.22201/fesz.23958723e.2020.0.267
Groenen, P. M. A., Bunschoten, A. E, Van Soolingen, D. & vanEmbden, J. D. A. (1993). Nature of DNA polymorphismin the direct repeat cluster of Mycobacterium tuberculosis;application for strain differentiation by a novel typingmethod. Molecular Microbiology, 10(5), 1057-1065. https://doi.org/10.1111/j.1365-2958.1993.tb00976.x
Horwitz, A. A., Walter, J. M., Schubert, M. G., Kung, S. H.,Hawkins, K., Platt, D. M., Hernday, A. D., Mahatdejkul-Meadows, T., Szeto, W., Chandran, S. S. & Newman, J.D. (2015). Efficient Multiplexed Integration of SynergisticAlleles and Metabolic Pathways in Yeasts via CRISPRCas.Cell Systems, 1(1), 88-96. https://doi.org/10.1016/j.cels.2015.02.001
Ishino, Y., Shinagawa, H., Makino, K., Amemura, M. &Nakatura, A. (1987). Nucleotide sequence of the iap gene,responsible for alkaline phosphatase isoenzyme conversionin Escherichia coli, and identification of the gene product.Journal of Bacteriology, 169(12), 5429-5433. https://doi.org/10.1128/jb.169.12.5429-5433.1987
Liu, T. Y., Knott, G. J., Smock, D. C. J., Desmarais, J. J., Son,S., Bhuiya, A., Jakhanwal, S., Prywes, N., Agrawal, S.,Díaz De León Derby, M., Switz, N. A., Armstrong, M.,Harris, A. R., Charles, E. J., Thornton, B. W., Fozouni, P.,Shu, J., Stephens, S. I., Kumar, G. R., Zhao, C., Mok, A., T.lavarone, A., Escajeda, A., McIntosh, R., Kim, S., Dugan,E., IGI testing Consortium, Polland, K., Tan, M., Ott, M.,Fletcher, D., Lareau, L., Hsu, P., Savage, D & Doudna, J. A.(2021). Accelerated RNA detection using tandem CRISPRnucleases. Nature Chemical Biology, 17, 982–988. https://doi.org/10.1038/s41589-021-00842-2
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I.& Koonin, E. V. (2006). A putative RNA-interferencebasedimmune system in prokaryotes: computationalanalysis of the predicted enzymatic machinery, functionalanalogies with eukaryotic RNAi, and hypotheticalmechanisms of action. Biology Direct, 1(7), 1-26. https://doi.org/10.1186/1745-6150-1-7
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F.,Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J.J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S.,Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M. F.,Yakunin, A. F., Garrett, R. A., van der Oost, J. Backofen, R. &Koonin, E. V. (2015). An updated evolutionary classificationof CRISPR–Cas systems. Nature Reviews Microbiology,13, 722–736. https://doi.org/10.1038/nrmicro3569
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A.,Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng,D., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M.,Scott, D., Shah, S. A., Siksnys, V., Terns, M. P., Venclovas,Č., White, M. F., Yakunin, A. F., Yan, W., Zhang, F.,Garret, R. A., Backofen, R., van der Oost, J., Barrangou,R. & Koonin, E. V. (2020). Evolutionary classificationof CRISPR–Cas systems: a burst of class 2 and derivedvariants. Nature Reviews Microbiology, 18, 67–83. https://doi.org/10.1038/s41579-019-0299-x
Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M.,Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. & Kondo, A. (2016). Targeted nucleotideediting using hybrid prokaryotic and vertebrate adaptiveimmune systems. Science, 353(6305), 1-8. https://doi.org/10.1126/science.aaf8729
Segal-Kischinevzky, C., Romero-Aguilar, L., Alcaraz, L.D.,López-Ortiz, G., Martínez-Castillo, B., Torres-Ramírez,N., Sandoval, G. & González, J. (2022). Yeasts InhabitingExtreme Environments and Their BiotechnologicalApplications. Microorganisms, 10(4), 1-26. https://doi.org/10.3390/microorganisms10040794
Shmakov, S., Smargon, A., Scott, D., Cox, D., Pyzocha, N.,Yan, W., Abudayyeh, O. O., Gootenberg, J. S., Makarova,K. S., Wolf, Y. I., Severinov, K., Zhang, F. & Koonin, E.V. (2017). Diversity and evolution of class 2 CRISPRCassystems. Nature Reviews Microbiology, 15, 169–182.https://doi.org/10.1038/nrmicro.2016.184
Smith, A. M. C., Takeuchi, R., Pellenz, S., Davis, L., Maizels,N., Monnat, R. J. & Stoddard, B. L. (2009). Generation of anicking enzyme that stimulates site-specific gene conversionfrom the I-Anil LAGLIDADG homing endonuclease.Proceedings of the National Academy of Sciences of theUnited States of America, 106(13), 5099–5104. https://doi.org/10.1073/pnas.0810588106
Spasskaya, D. S., Kotlov, M. I., Lekanov, D. S., Tutyaeva,V. V., Snezhkina, A. V., Kudryavtseva, A. V., Karpov,V. L. & Karpov, D. S. (2021). CRISPR/Cas9-MediatedGenome Engineering Reveals the Contribution of the 26SProteasome to the Extremophilic Nature of the Yeast. ACSSynthetic Biology, 10(2), 297–308. https://doi.org/10.1021/acssynbio.0c00426
Stadtmauer, E. A., Fraietta, J. A., Davis, M. M., Cohen, A. D.,Weber, K. L., Lancaster, E., Mangan, P. A., Kulikovskaya,I., Gupta, M., Chen, F., Tian, L., Gonzalez, V. E., Xu, J.,Jung, I. Y., Melenhorst, J. J., Plesa, G., Shea, J., Matlawski,T., Cervini, A., Gaymon, A. L., Desjardins, S., Lamontagne,A., Salas-Mckee, J., Fesnak, A., Siegel, D. L., Levine, B. L.,Jadlowsky, J. K., Young, R. M., Chew, A., Hwang, W.-T.,Hexner, E. O., Carreno, B. M., Nobles, C. L., Bushman, F.D., Parker, K. R., Qi, Y., Satpathy, A. T., Chang, H. Y., Zhao,Y., Lacey, S. F. & June, C. H. (2020). CRISPR-engineered Tcells in patients with refractory cancer. Science, 367(6481),1-12. https://doi.org/10.1126/science.aba7365
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead,E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber,J. E., Qi, L. S. & Lim, W. A. (2015). Engineering complexsynthetic transcriptional programs with CRISPR RNAscaffolds. Cell, 160, 339-350. https://doi.org/10.1016/j.cell.2014.11.052
Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I.,Kneppers, J., DeGennaro, E. M., Winblad, N., Choudhury,S. R., Abudayyeh, O. O., Gootenberg, J. S., Wu, W. Y.,Scott, D. A., Severinov, K., van der Oost, J. & Zhang, F.(2017). Multiplex gene editing by CRISPR–Cpf1 using asingle crRNA array. Nature Biotechnology, 35(1), 31-34.https://doi.org/10.1038/nbt.3737