IJBTT

Gene editing: A potential tool to enhance field crop production

	International Journal of Biotech Trends and Technology (IJBTT)
	© 2020 by IJBTT Journal
	Volume - 10 Issue - 1
	Year of Publication : 2020
	Authors : Mahnoor Imran, Maria Butt, Abdul Hannan, Asma Manzoor, Uzma Qaisar
	DOI :  10.14445/22490183/IJBTT-V10I1P612

Citation

MLA Style:Mahnoor Imran, Maria Butt, Abdul Hannan, Asma Manzoor, Uzma Qaisar"Gene editing: A potential tool to enhance field crop production" International Journal of Biotech Trends and Technology 10.1 (2020): 72-82.

APA Style:Mahnoor Imran, Maria Butt, Abdul Hannan, Asma Manzoor, Uzma Qaisar. Gene editing: A potential tool to enhance field crop production  International Journal of Biotech Trends and Technology, 10(1), 72-82.

Abstract

Genome editing of crops has been observed to be rapidly advancing technology to introduce targeted mutations in plant genomes. The advances in clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) protein systems have enabled targeted genome editing for crop improvement as compared to the previous methods including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) that were time consuming and expensive. This technology works by repairing the double stranded breaks (DSB) by nonhomologous end joining (NHEJ) and homology directed repair (HDR) and targets the gene of interest more precisely. In this review, we highlight the basic mechanism of CRISPR Cas9 system including the adaptation of CRISPR Cas9 system and its variants in plant editing. A RNA guided endonuclease, Cas9 has been used for generating stable knock out and knock in mutants in several plant species. We further review the delivery systems and the applications of CRISPR in trait improvement of crops. We outline the future perspectives of CRISPR Cas9 genome editing for regulating the gene expression and increasing the editing efficiency in medicine and agriculture. Application of CRISPR Cas9 for non-GMO crop editing with desirable trait can lead to increased yield of crops under environmental stress conditions.

References

[1] Stephens, J. and A. Barakate, Gene editing technologies–ZFNs, TALENs, and CRISPR/Cas9. 2017.
[2] Chen, K. and C. Gao, Targeted genome modification technologies and their applications in crop improvements. Plant Cell Reports, 2014. 33(4): p. 575-583.
[3] Jinek, M., et al., A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. science, 2012. 337(6096): p. 816-821.
[4] Waltz, E., With a free pass, CRISPR-edited plants reach market in record time. 2018, Nature Publishing Group.
[5] Koo, T., J. Lee, and J.-S. Kim, Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9. Molecules and cells, 2015. 38(6): p. 475.
[6] Ran, F.A., et al., Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 2013. 154(6): p. 1380-1389.
[7] Malzahn, A., L. Lowder, and Y. Qi, Plant genome editing with TALEN and CRISPR. Cell & bioscience, 2017. 7(1): p. 21.
[8] Chen, K. and C. Gao, TALENs: customizable molecular DNA scissors for genome engineering of plants. Journal of Genetics and Genomics, 2013. 40(6): p. 271-279.
[9] Cermak, T., et al., Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research, 2011. 39(12): p. e82-e82.
[10] Zhang, Y., et al., Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant physiology, 2013. 161(1): p. 20-27.
[11] Shan, Q., et al., Targeted genome modification of crop plants using a CRISPR-Cas system. Nature biotechnology, 2013. 31(8): p. 686.
[12] Ishino, Y., et al., Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology, 1987. 169(12): p. 5429-5433.
[13] Mojica, F.J., G. Juez, and F. Rodriguez?Valera, Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Molecular microbiology, 1993. 9(3): p. 613-621.
[14] Mojica, F.J., J. García-Martínez, and E. Soria, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of molecular evolution, 2005. 60(2): p. 174-182.
[15] Bortesi, L. and R. Fischer, The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnology advances, 2015. 33(1): p. 41-52.
[16] Bolotin, A., et al., Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology, 2005. 151(8): p. 2551-2561.
[17] Jansen, R., et al., Identification of genes that are associated with DNA repeats in prokaryotes. Molecular microbiology, 2002. 43(6): p. 1565-1575.
[18] Pourcel, C., G. Salvignol, and G. Vergnaud, CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology, 2005. 151(3): p. 653-663.
[19] Barrangou, R., et al., CRISPR provides acquired resistance against viruses in prokaryotes. Science, 2007. 315(5819): p. 1709-1712.
[20] Kunin, V., R. Sorek, and P. Hugenholtz, Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome biology, 2007. 8(4): p. R61.
[21] Mojica, F.J., et al., Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology, 2009. 155(3): p. 733-740.
[22] Makarova, K.S., et al., 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, 2006. 1(1): p. 7.
[23] Brouns, S.J., et al., Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 2008. 321(5891): p. 960-964.
[24] Garneau, J.E., et al., The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 2010. 468(7320): p. 67.
[25] Deltcheva, E., et al., CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature, 2011. 471(7340): p. 602.
[26] Sapranauskas, R., et al., The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic acids research, 2011. 39(21): p. 9275-9282.
[27] Gasiunas, G., et al., Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences, 2012. 109(39): p. E2579-E2586.
[28] Cong, L., et al., Multiplex genome engineering using CRISPR/Cas systems. Science, 2013. 339(6121): p. 819-823.
[29] Makarova, K.S., et al., An updated evolutionary classification of CRISPR–Cas systems. Nature Reviews Microbiology, 2015. 13(11): p. 722.
[30] Sternberg, S.H., et al., DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 2014. 507(7490): p. 62.
[31] Makarova, K.S., Y.I. Wolf, and E.V. Koonin, The basic building blocks and evolution of CRISPR–Cas systems. 2013, Portland Press Limited.
[32] Sashital, D.G., B. Wiedenheft, and J.A. Doudna, Mechanism of foreign DNA selection in a bacterial adaptive immune system. Molecular cell, 2012. 46(5): p. 606-615.
[33] van Duijn, E., et al., Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Molecular & Cellular Proteomics, 2012. 11(11): p. 1430-1441.
[34] Zhang, J., et al., Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Molecular cell, 2012. 45(3): p. 303-313.
[35] Makarova, K.S., et al., Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biology direct, 2011. 6(1): p. 38.
[36] Babu, M., et al., A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair. Molecular microbiology, 2011. 79(2): p. 484-502.
[37] Haurwitz, R.E., et al., Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science, 2010. 329(5997): p. 1355-1358.
[38] Kleanthous, C., et al., Structural and mechanistic basis of immunity toward endonuclease colicins. Nature Structural & Molecular Biology, 1999. 6(3): p. 243.
[39] Jakubauskas, A., et al., Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. Journal of molecular biology, 2007. 370(1): p. 157-169.
[40] Hale, C.R., et al., RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell, 2009. 139(5): p. 945-956.
[41] Marraffini, L.A. and E.J. Sontheimer, CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. science, 2008. 322(5909): p. 1843-1845.
[42] Sinkunas, T., et al., Cas3 is a single?stranded DNA nuclease and ATP?dependent helicase in the CRISPR/Cas immune system. The EMBO journal, 2011. 30(7): p. 1335-1342.
[43] Ricroch, A., P. Clairand, and W. Harwood, Use of CRISPR systems in plant genome editing: toward new opportunities in agriculture. Emerging Topics in Life Sciences, 2017. 1(2): p. 169-182.
[44] Yin, K., C. Gao, and J.-L. Qiu, Progress and prospects in plant genome editing. Nature plants, 2017. 3(8): p. 17107.
[45] Belhaj, K., et al., Editing plant genomes with CRISPR/Cas9. Current opinion in biotechnology, 2015. 32: p. 76-84.
[46] Xu, R., et al., Generation of targeted mutant rice using a CRISPR?Cpf1 system. Plant biotechnology journal, 2017. 15(6): p. 713-717.
[47] Li, P., et al., The Arabidopsis UDP?glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation. The Plant Journal, 2017. 89(1): p. 85-103.
[48] Svitashev, S., et al., Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nature communications, 2016. 7: p. 13274.
[49] Liang, Z., et al., Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature communications, 2017. 8: p. 14261.
[50] Ali, Z., et al., CRISPR/Cas9-mediated immunity to geminiviruses: differential interference and evasion. Scientific reports, 2016. 6: p. 26912.
[51] Ding, Y., et al., Recent advances in genome editing using CRISPR/Cas9. Frontiers in plant science, 2016. 7: p. 703.
[52] Li, J.-F., et al., Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature biotechnology, 2013. 31(8): p. 688.
[53] Kuhn, J. and S. Binder, RT–PCR analysis of 5? to 3?-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria. Nucleic acids research, 2002. 30(2): p. 439-446.
[54] Mao, Y., et al., Application of the CRISPR–Cas system for efficient genome engineering in plants. Molecular plant, 2013. 6(6): p. 2008-2011.
[55] Campenhout, C.V., et al., Guidelines for optimized gene knockout using CRISPR/Cas9. BioTechniques, 2019. 66(6): p. 295-302.
[56] Ray, A. and M. Langer, Homologous recombination: ends as the means. Trends in plant science, 2002. 7(10): p. 435-440.
[57] Baltes, N.J., et al., DNA replicons for plant genome engineering. The Plant Cell, 2014. 26(1): p. 151-163.
[58] Komor, A.C., et al., Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 2016. 533(7603): p. 420.
[59] Zong, Y., et al., Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nature biotechnology, 2017. 35(5): p. 438.
[60] Ma, Y., et al., Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nature methods, 2016. 13(12): p. 1029.
[61] Lu, Y. and J.-K. Zhu, Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Molecular plant, 2017. 10(3): p. 523-525.
[62] Li, J., et al., Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Molecular plant, 2017. 10(3): p. 526-529.
[63] Peng, A., et al., Engineering canker?resistant plants through CRISPR/Cas9?targeted editing of the susceptibility gene Cs LOB 1 promoter in citrus. Plant biotechnology journal, 2017. 15(12): p. 1509-1519.
[64] Jia, H., et al., Modification of the PthA4 effector binding elements in Type I Cs LOB 1 promoter using Cas9/sg RNA to produce transgenic Duncan grapefruit alleviating Xcc?pthA4: dCs LOB 1.3 infection. Plant biotechnology journal, 2016. 14(5): p. 1291-1301.
[65] Hsu, P.D., E.S. Lander, and F. Zhang, Development and applications of CRISPR-Cas9 for genome engineering. Cell, 2014. 157(6): p. 1262-1278.
[66] Mao, X., et al., OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance in rice. Biochemical and biophysical research communications, 2018. 495(1): p. 461-467.
[67] Wang, F., et al., Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS one, 2016. 11(4): p. e0154027.
[68] Lou, D., et al., OsSAPK2 confers abscisic acid sensitivity and tolerance to drought stress in rice. Frontiers in plant science, 2017. 8: p. 993.
[69] Li, J., et al., Gene replacements and insertions in rice by intron targeting using CRISPR–Cas9. Nature plants, 2016. 2(10): p. 16139.
[70] Sun, Y., et al., Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Molecular plant, 2016. 9(4): p. 628-631.
[71] Zhou, J., et al., Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice. The Plant Journal, 2015. 82(4): p. 632-643.
[72] Connorton, J.M., et al., Wheat vacuolar iron transporter TaVIT2 transports Fe and Mn and is effective for biofortification. Plant physiology, 2017. 174(4): p. 2434-2444.
[73] Kim, D., B. Alptekin, and H. Budak, CRISPR/Cas9 genome editing in wheat. Functional & integrative genomics, 2018. 18(1): p. 31-41.
[74] Wang, Y., et al. CDnet 2014: an expanded change detection benchmark dataset. in Proceedings of the IEEE conference on computer vision and pattern recognition workshops. 2014.
[75] Shi, J., et al., ARGOS 8 variants generated by CRISPR?Cas9 improve maize grain yield under field drought stress conditions. Plant biotechnology journal, 2017. 15(2): p. 207-216.
[76] Liang, P., et al., CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein & cell, 2015. 6(5): p. 363-372.
[77] Baltes, N.J., et al., Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nature Plants, 2015. 1(10): p. 15145.
[78] Nekrasov, V., et al., Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Scientific reports, 2017. 7(1): p. 482.
[79] Ali, Z., et al., CRISPR/Cas9-mediated viral interference in plants. Genome biology, 2015. 16(1): p. 238.
[80] Wang, L., et al., Reduced drought tolerance by CRISPR/Cas9-mediated SlMAPK3 mutagenesis in tomato plants. Journal of agricultural and food chemistry, 2017. 65(39): p. 8674-8682.
[81] Li, R., et al., Multiplexed CRISPR/Cas9?mediated metabolic engineering of ??aminobutyric acid levels in Solanum lycopersicum. Plant biotechnology journal, 2018. 16(2): p. 415-427.
[82] Butler, N.M., et al., Geminivirus-mediated genome editing in potato (Solanum tuberosum L.) using sequence-specific nucleases. Frontiers in plant science, 2016. 7: p. 1045.
[83] Du, H., et al., Efficient targeted mutagenesis in soybean by TALENs and CRISPR/Cas9. Journal of biotechnology, 2016. 217: p. 90-97.
[84] Odipio, J., et al., Efficient CRISPR/Cas9 genome editing of phytoene desaturase in cassava. Frontiers in plant science, 2017. 8: p. 1780.
[85] Chen, X., et al., Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system. Scientific reports, 2017. 7: p. 44304.
[86] Iqbal, Z., M.N. Sattar, and M. Shafiq, CRISPR/Cas9: a tool to circumscribe cotton leaf curl disease. Frontiers in plant science, 2016. 7: p. 475.
[87] Andersson, M., et al., Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant cell reports, 2017. 36(1): p. 117-128.
[88] Steinert, J., et al., Highly efficient heritable plant genome engineering using Cas9 orthologues from Streptococcus thermophilus and Staphylococcus aureus. The Plant Journal, 2015. 84(6): p. 1295-1305.
[89] Ali, Z., A. Mahas, and M. Mahfouz, CRISPR/Cas13 as a tool for RNA interference. Trends in plant science, 2018. 23(5): p. 374-378.
[90] Cox, D.B., et al., RNA editing with CRISPR-Cas13. Science, 2017. 358(6366): p. 1019-1027.
[91] Aman, R., et al., RNA virus interference via CRISPR/Cas13a system in plants. Genome biology, 2018. 19(1): p. 1.
[92] Qi, L.S., et al., Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 2013. 152(5): p. 1173-1183.
[93] Piatek, A., et al., RNA?guided transcriptional regulation in planta via synthetic dC as9?based transcription factors. Plant biotechnology journal, 2015. 13(4): p. 578-589.
[94] Lowder, L.G., et al., A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant physiology, 2015. 169(2): p. 971-985.
[95] Ren, Q., et al., Bidirectional promoter based CRISPR-Cas9 systems for plant genome editing. Frontiers in Plant Science, 2019. 10: p. 1173.

Keywords
CRISPR Cas, GMOs, TALEN, sgRNA