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Review Article

CRISPeering: Bioengineering the Host Cells through CRISPRCas9 Genome Editing System as the Next-generation of Cell Factories

Author(s): Mohammad H. Morowvat*

Volume 15, Issue 2, 2021

Published on: 19 April, 2021

Page: [137 - 147] Pages: 11

DOI: 10.2174/1872208315666210419102117

Price: $65

Abstract

Background: Nowadays, the CRISPR-Cas9 genome editing system has become a popular bioengineering-based tool for various applications. Owing to its high-target specificity, efficiency, versatility, and simplicity, it has gained attention as a robust tool for molecular biology research, which unveils the biological functions of unexplored genes and engineers the metabolic pathways. Chinese hamster ovary (CHO) cells and Escherichia coli are regarded as the most commonly used expression platforms for industrial- scale production of recombinant proteins. The emergence of the CRISPR-Cas9 genome editing system promotes the current status of expression hosts towards controllable and predictable strains.

Objective: This paper presents the current status of expression hosts for biopharmaceutical production. Some major accomplishments in the utilization of the CRISPR-Cas9 genome editing tool in the different prokaryotic and eukaryotic systems are discussed, and more importantly, the future directions of this newly arrived technology to make the next-generation cell factories with improved or novel properties are suggested. Moreover, the challenges faced in recent patents in this field are also discussed.

Results and Conclusion: The CRISPR-Cas9 genome-editing tool has been adopted to be utilized in some major expression platforms. CRISPeering has been successfully employed for genome editing in different prokaryotic and eukaryotic host cells. The emergence of systems metabolic engineering, systems biology, and synthetic biology fortify the current situation of the CRISPR-Cas9 genome editing system.

Keywords: CRISPR, genome editing, host cell engineering, recent patents, recombinant protein production, synthetic biology.

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[1]
Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339(6121): 819-23.
[http://dx.doi.org/10.1126/science.1231143] [PMID: 23287718]
[2]
Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482(7385): 331-8.
[http://dx.doi.org/10.1038/nature10886] [PMID: 22337052]
[3]
Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR- Cas9. Science 2014; 346(6213): 1258096.
[http://dx.doi.org/10.1126/science.1258096] [PMID: 25430774]
[4]
Yoshimatsu S, Okahara J, Sone T, et al. Robust and efficient knock-in in embryonic stem cells and early-stage embryos of the common marmoset using the CRISPR-Cas9 system. Sci Rep 2019; 9(1): 1528.
[http://dx.doi.org/10.1038/s41598-018-37990-w] [PMID: 30728412]
[5]
Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 1987; 169(12): 5429-33.
[http://dx.doi.org/10.1128/JB.169.12.5429-5433.1987] [PMID: 3316184]
[6]
van Soolingen D, de Haas PE, Hermans PW, Groenen PM, van Embden JD. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol 1993; 31(8): 1987-95.
[http://dx.doi.org/10.1128/JCM.31.8.1987-1995.1993] [PMID: 7690367]
[7]
Groenen PM, Bunschoten AE, Soolingen DV, Embden JDV. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol 2006; 10: 1057-65.
[http://dx.doi.org/10.1111/j.1365-2958.1993.tb00976.x]
[8]
Mojica FJ, Rodriguez-Valera F. The discovery of CRISPR in archaea and bacteria. FEBS J 2016; 283(17): 3162-9.
[http://dx.doi.org/10.1111/febs.13766] [PMID: 27234458]
[9]
Freedman BS, Brooks CR, Lam AQ, et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat Commun 2015; 6: 8715.
[http://dx.doi.org/10.1038/ncomms9715] [PMID: 26493500]
[10]
Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 2013; 10(8): 741-3.
[http://dx.doi.org/10.1038/nmeth.2532] [PMID: 23817069]
[11]
Feng Z, Mao Y, Xu N, et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci USA 2014; 111(12): 4632-7.
[http://dx.doi.org/10.1073/pnas.1400822111] [PMID: 24550464]
[12]
Estrela R, Cate JHD. Energy biotechnology in the CRISPR-Cas9 era. Curr Opin Biotechnol 2016; 38: 79-84.
[http://dx.doi.org/10.1016/j.copbio.2016.01.005] [PMID: 26874259]
[13]
Mollanoori H, Shahraki H, Rahmati Y, Teimourian S. CRISPR/Cas9 and CAR-T cell, collaboration of two revolutionary technologies in cancer immunotherapy, an instruction for successful cancer treatment. Hum Immunol 2018; 79(12): 876-82.
[http://dx.doi.org/10.1016/j.humimm.2018.09.007] [PMID: 30261221]
[14]
Li Q, Sapkota M, van der Knaap E. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. Horticult Res 2020; 7: 1-11.
[15]
Khan FA, Pandupuspitasari NS, Chun-Jie H, et al. CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases. Oncotarget 2016; 7(32): 52541-52.
[http://dx.doi.org/10.18632/oncotarget.9646] [PMID: 27250031]
[16]
Citorik RJ, Mimee M, Lu TK. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 2014; 32(11): 1141-5.
[http://dx.doi.org/10.1038/nbt.3011] [PMID: 25240928]
[17]
Broughton JP, Deng X, Yu G, et al. CRISPR- Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38(7): 870-4.
[http://dx.doi.org/10.1038/s41587-020-0513-4] [PMID: 32300245]
[18]
Alphey L. Can CRISPR-Cas9 gene drives curb malaria? Nat Biotechnol 2016; 34(2): 149-50.
[http://dx.doi.org/10.1038/nbt.3473] [PMID: 26849518]
[19]
First CRISPR therapy dosed. Nat Biotechnol 2020; 38(4): 382-2.
[http://dx.doi.org/10.1038/s41587-020-0493-4] [PMID: 32265555]
[20]
Ferreira R, David F, Nielsen J. Advancing biotechnology with CRISPR/Cas9: recent applications and patent landscape. J Ind Microbiol Biotechnol 2018; 45(7): 467-80.
[http://dx.doi.org/10.1007/s10295-017-2000-6] [PMID: 29362972]
[21]
Lim D. Disruption and development: the evolving CRISPR patent and technology landscape. Pharm Pat Anal 2018; 7(4): 141-5.
[http://dx.doi.org/10.4155/ppa-2018-0010] [PMID: 29882718]
[22]
Martin-Laffon J, Kuntz M, Ricroch AE. Worldwide CRISPR patent landscape shows strong geographical biases. Nat Biotechnol 2019; 37(6): 613-20.
[http://dx.doi.org/10.1038/s41587-019-0138-7] [PMID: 31164740]
[23]
Wang Q. The dispute on the CRISPR patent and the lessons for Chinese researchers. Kexue Tongbao. Chin Sci Bull 2017; 62: 1091-4.
[http://dx.doi.org/10.1360/N972017-00333]
[24]
Stasi A, Rodrigues IP. Dealing with patent fragmentation in genetics: can patent pools facilitate the development of CRISPR gene-editing technology? J Law Med 2019; 26(4): 866-73.
[PMID: 31682364]
[25]
Aggarwal RS. What’s fueling the biotech engine-2012 to 2013. Nat Biotechnol 2014; 32(1): 32-9.
[http://dx.doi.org/10.1038/nbt.2794] [PMID: 24406926]
[26]
Walsh G. Biopharmaceutical benchmarks 2018. Nat Biotechnol 2018; 36(12): 1136-45.
[http://dx.doi.org/10.1038/nbt.4305] [PMID: 30520869]
[27]
Walsh G. Biopharmaceutical benchmarks 2014. Nat Biotechnol 2014; 32(10): 992-1000.
[http://dx.doi.org/10.1038/nbt.3040] [PMID: 25299917]
[28]
Yin J, Li G, Ren X, Herrler G. Select what you need: a comparative evaluation of the advantages and limitations of frequently used expression systems for foreign genes. J Biotechnol 2007; 127(3): 335-47.
[http://dx.doi.org/10.1016/j.jbiotec.2006.07.012] [PMID: 16959350]
[29]
Schmidt FR. Recombinant expression systems in the pharmaceutical industry. Appl Microbiol Biotechnol 2004; 65(4): 363-72.
[http://dx.doi.org/10.1007/s00253-004-1656-9] [PMID: 15480623]
[30]
Jinek M, Jiang F, Taylor DW, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014; 343(6176): 1247997.
[http://dx.doi.org/10.1126/science.1247997] [PMID: 24505130]
[31]
Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc Lond B Biol Sci 2016; 371(1707): 20150496.
[http://dx.doi.org/10.1098/rstb.2015.0496] [PMID: 27672148]
[32]
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 2014; 507(7490): 62-7.
[http://dx.doi.org/10.1038/nature13011] [PMID: 24476820]
[33]
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013; 31(3): 233-9.
[http://dx.doi.org/10.1038/nbt.2508] [PMID: 23360965]
[34]
Banno S, Nishida K, Arazoe T, Mitsunobu H, Kondo A. Deaminase-mediated multiplex genome editing in Escherichia coli. Nat Microbiol 2018; 3(4): 423-9.
[http://dx.doi.org/10.1038/s41564-017-0102-6] [PMID: 29403014]
[35]
Sun J, Wang Q, Jiang Y, et al. Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system. Microb Cell Fact 2018; 17(1): 41.
[http://dx.doi.org/10.1186/s12934-018-0887-x] [PMID: 29534717]
[36]
Li K, Cai D, Wang Z, He Z, Chen S. Development of an efficient genome editing tool in Bacillus licheniformis using CRISPR-Cas9 nickase. Appl Environ Microbiol 2018; 84(6): 84.
[http://dx.doi.org/10.1128/AEM.02608-17] [PMID: 29330178]
[37]
Peng F, Wang X, Sun Y, et al. Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system. Microb Cell Fact 2017; 16(1): 201.
[http://dx.doi.org/10.1186/s12934-017-0814-6] [PMID: 29137643]
[38]
Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013; 152(5): 1173-83.
[http://dx.doi.org/10.1016/j.cell.2013.02.022] [PMID: 23452860]
[39]
Bachu R, Bergareche I, Chasin LA. CRISPR-Cas targeted plasmid integration into mammalian cells via non-homologous end joining. Biotechnol Bioeng 2015; 112(10): 2154-62.
[http://dx.doi.org/10.1002/bit.25629] [PMID: 25943095]
[40]
Ronda C, Pedersen LE, Hansen HG, et al. Accelerating genome editing in CHO cells using CRISPR- Cas9 and CRISPy, a web-based target finding tool. Biotechnol Bioeng 2014; 111(8): 1604-16.
[http://dx.doi.org/10.1002/bit.25233] [PMID: 24827782]
[41]
Shi TQ, Liu GN, Ji RY, et al. CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art. Appl Microbiol Biotechnol 2017; 101(20): 7435-43.
[http://dx.doi.org/10.1007/s00253-017-8497-9] [PMID: 28887634]
[42]
Zhang Y, Wang J, Wang Z, et al. A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae. Nat Commun 2019; 10(1): 1053.
[http://dx.doi.org/10.1038/s41467-019-09005-3] [PMID: 30837474]
[43]
Holkenbrink C, Dam MI, Kildegaard KR, et al. EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica. Biotechnol J 2018; 13(9): e1700543.
[PMID: 29377615]
[44]
Cai P, Gao J, Zhou Y. CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications. Microb Cell Fact 2019; 18(1): 63.
[http://dx.doi.org/10.1186/s12934-019-1112-2] [PMID: 30940138]
[45]
Stovicek V, Borodina I, Forster J. CRISPR-Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab Eng Commun 2015; 2: 13-22.
[http://dx.doi.org/10.1016/j.meteno.2015.03.001]
[46]
Mabashi-Asazuma H, Jarvis DL. CRISPR-Cas9 vectors for genome editing and host engineering in the baculovirus-insect cell system. Proc Natl Acad Sci USA 2017; 114(34): 9068-73.
[http://dx.doi.org/10.1073/pnas.1705836114] [PMID: 28784806]
[47]
Gori JL. Optimized CRISPR/cas9 systems and methods for gene editing in stem cells. US20180282762A1, 2018.
[48]
Verwaal R, Meijrink B, Wiessenhaan N, Vonk B, Roubos JA. CRISPR-CAS system for a yeast host cell. US10619170B2, 2020.
[49]
Zhang F. CRISPR-Cas component systems, methods and compositions for sequence manipulation. US20180305704A1, 2014.
[50]
Zhang F. CRISPR-Cas systems and methods for altering expression of gene products. US8697359B1, 2014.
[51]
Xu S, Wang Q, Zeng W, Li Y, Shi G, Zhou J. Construction of a heat-inducible Escherichia coli strain for efficient de novo biosynthesis of L-tyrosine. Process Biochem 2020; 92: 85-92.
[http://dx.doi.org/10.1016/j.procbio.2020.02.023]
[52]
Rojas-Sánchez U, López-Calleja AC, Millán-Chiu BE, Fernández F, Loske AM, Gómez-Lim MA. Enhancing the yield of human erythropoietin in Aspergillus niger by introns and CRISPR-Cas9. Prot Express Pur 2020; 168: 105570.
[53]
Mo XH, Zhang H, Wang TM, et al. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104(10): 4515-32.
[http://dx.doi.org/10.1007/s00253-020-10543-w] [PMID: 32215707]
[54]
Lee SS, Park J, Heo YB, Woo HM. Case study of xylose conversion to glycolate in Corynebacterium glutamicum: current limitation and future perspective of the CRISPR-Cas systems. Enz Microb Technol 2020; 132: 109395.
[55]
Ha TK, Hansen AH, Kildegaard HF, Lee GM. Knockout of sialidase and pro-apoptotic genes in Chinese hamster ovary cells enables the production of recombinant human erythropoietin in fed-batch cultures. Metab Eng 2020; 57: 182-92.
[http://dx.doi.org/10.1016/j.ymben.2019.11.008] [PMID: 31785386]
[56]
Dong L, Yu D, Lin X, Wang B, Pan L. Improving expression of thermostable trehalase from Myceliophthora sepedonium in Aspergillus niger mediated by the CRISPR/Cas9 tool and its purification, characterization. Prot Express Pur 2020; 165.
[57]
Sasaki Y, Mitsui R, Yamada R, Ogino H. Secretory overexpression of the endoglucanase by Saccharomyces cerevisiaevia CRISPR-δ-integration and multiple promoter shuffling. Enzyme Microb Technol 2019; 121: 17-22.
[http://dx.doi.org/10.1016/j.enzmictec.2018.10.014] [PMID: 30554640]
[58]
Mensah EO, Guo XY, Gao XD, Fujita M. Establishment of DHFR-deficient HEK293 cells for high yield of therapeutic glycoproteins. J Biosci Bioeng 2019; 128(4): 487-94.
[http://dx.doi.org/10.1016/j.jbiosc.2019.04.005] [PMID: 31031194]
[59]
Matsuo K, Atsumi G. CRISPR/Cas9-mediated knockout of the RDR6 gene in Nicotiana benthamiana for efficient transient expression of recombinant proteins. Planta 2019; 250(2): 463-73.
[http://dx.doi.org/10.1007/s00425-019-03180-9] [PMID: 31065786]
[60]
Li SW, Yu B, Byrne G, et al. Identification and CRISPR/Cas9 inactivation of the C1s protease responsible for proteolysis of recombinant proteins produced in CHO cells. Biotechnol Bioeng 2019; 116(9): 2130-45.
[http://dx.doi.org/10.1002/bit.27016] [PMID: 31087560]
[61]
Chen H, Zhu C, Zhu M, et al. High production of valencene in Saccharomyces cerevisiae through metabolic engineering. Microb Cell Fact 2019; 18(1): 195.
[http://dx.doi.org/10.1186/s12934-019-1246-2] [PMID: 31699116]
[62]
Besada-Lombana PB, Da Silva NA. Engineering the early secretory pathway for increased protein secretion in Saccharomyces cerevisiae. Metab Eng 2019; 55: 142-51.
[http://dx.doi.org/10.1016/j.ymben.2019.06.010] [PMID: 31220665]
[63]
Wang L, Deng A, Zhang Y, et al. Efficient CRISPR-Cas9 mediated multiplex genome editing in yeasts. Biotechnol Biofuels 2018; 11: 277.
[http://dx.doi.org/10.1186/s13068-018-1271-0] [PMID: 30337956]
[64]
Westbrook AW, Ren X, Moo-Young M, Chou CP. Engineering of cell membrane to enhance heterologous production of hyaluronic acid in Bacillus subtilis. Biotechnol Bioeng 2018; 115(1): 216-31.
[http://dx.doi.org/10.1002/bit.26459] [PMID: 28941282]
[65]
Peng R, Wang Y, Feng WW, et al. CRISPR/dCas9- mediated transcriptional improvement of the biosynthetic gene cluster for the epothilone production in Myxococcus xanthus. Microb Cell Fact 2018; 17(1): 15.
[http://dx.doi.org/10.1186/s12934-018-0867-1] [PMID: 29378572]
[66]
Amann T, Hansen AH, Kol S, Lee GM, Andersen MR, Kildegaard HF. CRISPR/Cas9-multiplexed editing of Chinese hamster ovary B4Gal-T1, 2, 3, and 4 tailors N-glycan profiles of therapeutics and secreted host cell proteins. Biotechnol J 2018; 13(10): e1800111.
[http://dx.doi.org/10.1002/biot.201800111] [PMID: 29862652]
[67]
Arendt P, Miettinen K, Pollier J, De Rycke R, Callewaert N, Goossens A. An endoplasmic reticulum-engineered yeast platform for overproduction of triterpenoids. Metab Eng 2017; 40: 165-75.
[http://dx.doi.org/10.1016/j.ymben.2017.02.007] [PMID: 28216107]
[68]
Li H, Shen CR, Huang CH, Sung LY, Wu MY, Hu YC. CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production. Metab Eng 2016; 38: 293-302.
[http://dx.doi.org/10.1016/j.ymben.2016.09.006] [PMID: 27693320]

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