CRISPR-Cas: A continuously evolving technology

SARITA KUMARI; SUMEET KUMAR SINGH; VINAY KUMAR SHARMA; RAJESH KUMAR; MANAS MATHUR; TARUN KUMAR UPADHYAY; RAKESH KUMAR PRAJAPAT

doi:10.56093/ijas.v91i9.116069

Authors

SARITA KUMARI Rajendra Prasad Central Agricultural University, Pusa, Samastipur 848 125, India
SUMEET KUMAR SINGH Rajendra Prasad Central Agricultural University, Pusa, Samastipur 848 125, India
VINAY KUMAR SHARMA Rajendra Prasad Central Agricultural University, Pusa, Samastipur 848 125, India
RAJESH KUMAR Rajendra Prasad Central Agricultural University, Pusa, Samastipur 848 125, India
MANAS MATHUR School of Agriculture, Suresh Gyan Vihar University, Jaipur
TARUN KUMAR UPADHYAY School of Agriculture, Suresh Gyan Vihar University, Jaipur
RAKESH KUMAR PRAJAPAT School of Agriculture, Suresh Gyan Vihar University, Jaipur

https://doi.org/10.56093/ijas.v91i9.116069

Keywords:

CRISPR/Cas, Cpf1, Covid-19, Genome editing, Transgene free technology

Abstract

The discovery of the CRISPR/Cas microbial adaptive immune system and its ongoing development as a genome editing tool represents the work of many scientists around the world. The time line of CRISPR/Cas system shows that this technology is improving continuously to remove the demerits of preceding one with the aim of development of highly efficient, specific with low off target effect and ultimately transgene free technology in light of ethical and environmental issues related with transgenic technology. Initially, CRISPR/Cas9 was developed as method of choice as it provides targeted mutagenesis under in vivo condition and all the homeoalleles of a gene can be targeted in same plant, especially in case of polyploid species efficiently which is difficult through other existing technology. No residual or foreign gene insertion is required and modification is permanent. Now, CRISPR/Cpf1 has been developed as more potent, efficient and simpler than CRISPR/Cas9. Different forms of Cas enzymes provide new avenues for regulation of genomic component. In view of the present devastating COVID-19 disaster the scientists used this novel technology for detection of virus in humans at an early stage of infection thus saving human lives. The evolution of CRISPR/Cas technology, their advantages, apprehensions and solution, experimental design and updates of this technology is discussed in the present review.

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References

Barrangou R, Fremaux C, Deveau H, Richards M and Boyaval P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes, Science 315: 1709–12. DOI: https://doi.org/10.1126/science.1138140

Belhaj K, Garcia A C, Kamoun S, Patron N J and Nekrasov V. 2015. Editing plant genomes with CRISPR/Cas9. Current Opinion in Biotechnology 32: 76–84. DOI: https://doi.org/10.1016/j.copbio.2014.11.007

Bolotin A, Quinquis B, Sorokin A and Ehrlich S D. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551–61. DOI: https://doi.org/10.1099/mic.0.28048-0

Bortesi L and Fischer R. 2015. The CRISPR/Cas9 system for plant genome editing and beyond, Biotechnology Advances 33: 41–52. DOI: https://doi.org/10.1016/j.biotechadv.2014.12.006

Brouns S J, Jore M M, Lundgren M, Westra E R and Slijkhuis R J. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960–64. DOI: https://doi.org/10.1126/science.1159689

Cong L, Ran F A, Cox D, Lin S and Barretto R. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819–23. DOI: https://doi.org/10.1126/science.1231143

Deltcheva E, Chylinski K, Sharma C M, Gonzales K and Chao Y. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471: 602–07. DOI: https://doi.org/10.1038/nature09886

Feng Z, Zhang B, Ding W, Liu X and Yang D L. 2013. Efficient genome editing in plants using a CRISPR/Cas system, Cell Research 23: 1229–32. DOI: https://doi.org/10.1038/cr.2013.114

Garneau J E, Dupuis M È, Villion M, Romero D A and Barrangou R. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468: 67–71. DOI: https://doi.org/10.1038/nature09523

Gasiunas G, Barrangou R, Horvath P and Siksnys V. 2012. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS 109: 2579–86. DOI: https://doi.org/10.1073/pnas.1208507109

Hale C R, Zhao P, Olson S, Duff M O and Graveley B R. 2014. RNA Guided RNA Cleavage by a CRISPR RNA Cas Protein Complex. Cell 139: 945–56. DOI: https://doi.org/10.1016/j.cell.2009.07.040

Ishino Y, Shinagawa H, Makino K, Amemura M and Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli and identification of the gene product. Journal of Bacteriology 169(12): 5429–33. DOI: https://doi.org/10.1128/jb.169.12.5429-5433.1987

Jansen R, Embden J D A V, Gaastra W and Schouls L M. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology 43(6): 1565–75. DOI: https://doi.org/10.1046/j.1365-2958.2002.02839.x

Jinek M, Chylinski K, Fonfara I, Hauer M and Doudna J A. 2012. A programmable dual RNA guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–21. DOI: https://doi.org/10.1126/science.1225829

Kellner M J, Koob J G, Gootenberg J S, Abudayyeh O O and Zhang F. 2019. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nature Protocols 14: 2986–3012. DOI: https://doi.org/10.1038/s41596-019-0210-2

Lander E S. 2016. The Heroes of CRISPR. Cell 64–175.

Makarova K S, Grishin N V, Shabalina S A, Wolf Y I and 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. DOI: https://doi.org/10.1186/1745-6150-1-7

Makarova K S, Haft D H, Barrangou R, Brouns S J J, Charpentier E. 2008. Evolution and classification of the CRISPR–Cas systems. Nature Reviews Microbiology 9(2011): 467–77. DOI: https://doi.org/10.1038/nrmicro2577

Marraffini L A and Sontheimer E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843–45. DOI: https://doi.org/10.1126/science.1165771

Mojica F J M, DezVillaseor C S, Garca Martnez J S and Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution 60: 174–82. DOI: https://doi.org/10.1007/s00239-004-0046-3

Mojica F J M, Ferrer C, Juez G & Rodrı´guez-Valera F. 1995. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Moleclular Microbiology 17: 85–93. DOI: https://doi.org/10.1111/j.1365-2958.1995.mmi_17010085.x

O’Connell M R, Oakes B L, Sternberg S H, Seletsky A E and Kaplan M. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516: 263–66. DOI: https://doi.org/10.1038/nature13769

Pourcel C, Salvignol G and Vergnaud G. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA and provide additional tools for evolutionary studies. Microbiology 151: 653–63. DOI: https://doi.org/10.1099/mic.0.27437-0

Prajapat R K and Mahajan M M, 2016. Thanks to genome editing: A tool for genomic revolution. The Indian Research Journal of Genetics and Biotechnology 8(2): 93–100.

Shan Q, Wang Y, Li J and Gao C. 2014. Genome editfing in rice and wheat using the CRISPR/Cas system. Nature protocols 9(10): 2395–10. DOI: https://doi.org/10.1038/nprot.2014.157

Sorek R, Lawrence C M and Wiedenheft B. 2013. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistry 82: 237–66. DOI: https://doi.org/10.1146/annurev-biochem-072911-172315

Srivastava V. Indian scientists wage frontline battle against coronavirus, Nature India (2020) doi:10.1038/nindia.2020.56.

Voytas D F and Gao C. 2014. Precision genome engineering and agriculture: Opportunities and regulatory challenges. PLOS Biology 12(6): 1001877–83. DOI: https://doi.org/10.1371/journal.pbio.1001877

Wang Y, Cheng X, Shan Q, Zhang Y and Liu J. 2014. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature biotechnology 32(9): 947–52. DOI: https://doi.org/10.1038/nbt.2969

Woo J W, Kim J, Kwon S I, Corvalán C and Cho S W. 2015. DNA -free genome editing in plants with preassembled CRIS PR-Cas9 ribonucleoproteins. Nature Biotechnology 33: 1162–64. DOI: https://doi.org/10.1038/nbt.3389