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RNA-Guided CRISPR-Cas9 System for Removal of Microbial Pathogens

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Microbial Genomics in Sustainable Agroecosystems

Abstract

CRISPR-Cas9 technology has been cherished and well appreciated by the scientific community. The popularity of CRISPR-Cas9 technology is because it provides simple and efficient directions for genome engineering with feasible applications in a broad range of organisms. It stands to reason that the development of CRISPR-Cas9 is probably among the greatest revolution in the field of molecular biology, ever since the discovery of PCR. Genome engineering of microbes and other organisms may open up newer avenues to achieve a dynamic ecosystem. In this chapter, research on the use of CRISPR-Cas9 technology as an anti-phytopathogenic arsenal has been highlighted. Furthermore, the engineered organism developed using CRISPR-Cas9 technology has also been explained. Besides the applicative side, the background and molecular mechanisms of the CRISPR-Cas9 system have been mentioned and explained thoroughly.

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References

  • Adli M (2018) The CRISPR toolkit for genome editing and beyond. Nat Commun 9(1):1911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz MM (2015) CRISPR/Cas9-mediated viral interference in plants. Genome Biol 16:238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Altenbuchner J (2016) Editing of the Bacillus subtilis genome by the CRISPR-Cas9 system. Appl Environ Microbiol 82(17):5421–5427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andolfo G, Iovieno P, Frusciante L, Ercolano MR (2016) Genome-editing technologies for enhancing plant disease resistance. Front Plant Sci 7:1813

    Article  PubMed  PubMed Central  Google Scholar 

  • Avey D, Tepper S, Li W, Turpin Z, Zhu F (2015) Phosphoproteomic analysis of KSHV-infected cells reveals roles of ORF45-activated RSK during lytic replication. PLoS Pathog 11(7):1004993

    Article  CAS  Google Scholar 

  • Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nat Plants 1:15145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barrios-González J, Miranda RU (2010) Biotechnological production and applications of statins. Appl Microbiol Biotechnol 85(4):869–883

    Article  CAS  PubMed  Google Scholar 

  • Bern C, Kjos S, Yabsley MJ, Montgomery SP (2011) Trypanosoma cruzi and Chagas’ disease in the United States. Clin Microbiol Rev 24(4):655–681

    Article  PubMed  PubMed Central  Google Scholar 

  • Bierle CJ, Anderholm KM, Wang JB, McVoy MA, Schleiss MR (2016) Targeted mutagenesis of guinea pig cytomegalovirus using CRISPR/Cas9-mediated gene editing. J Virol 90(15):6989–6998. https://doi.org/10.1128/JVI.00139-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bikard D, Marraffini LA (2012) Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages. Curr Opin Immunol 24(1):15–20

    Article  CAS  PubMed  Google Scholar 

  • Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41(15):7429–7437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti V, Marraffini LA (2014) Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 32(11):1146–1150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, Van Der Oost J (2008) Small CRISPR RNAs guide antiviral defence in prokaryotes. Science 321(5891):960–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burgio G (2018) Redefining mouse transgenesis with CRISPR/Cas9 genome editing technology. Genome Biol 19(1):27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carr PA, Church GM (2009) Genome engineering. Nat Biotechnol 27(12):1151–1162

    Article  CAS  PubMed  Google Scholar 

  • Carroll D (2017) Genome Editing: Past, Present, and Future. Yale J Biol Med 90(4):653–659

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carte J, Christopher RT, Smith JT, Olson S, Barrangou R, Moineau S, Glover CV III, Graveley BR, Terns RM, Terns MP (2014) The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. Mol Microbiol 93(1):98–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen J, Lai Y, Wang L, Zhai S, Zou G, Zhou Z, Cui C, Wang S (2017) CRISPR/Cas9-mediated efficient genome editing via blastospore-based transformation in entomopathogenic fungus Beauveria bassiana. Sci Rep 7:45763

    Article  CAS  PubMed Central  Google Scholar 

  • Chen YC, Sheng J, Trang P, Liu F (2018) Potential application of the CRISPR/Cas9 system against herpesvirus infections. Viruses 10(6):291

    Article  CAS  PubMed Central  Google Scholar 

  • Chiurillo MA, Lander N, Bertolini MS, Storey M, Vercesi AE, Docampo R (2017) Different roles of mitochondrial calcium uniporter complex subunits in growth and infectivity of Trypanosoma cruzi. MBio 8(3):00574–00517

    Article  Google Scholar 

  • Cho H, Uehara T, Bernhardt TG (2014) Beta-lactam antibiotics induce a lethal malfunctioning of the bacterial cell wall synthesis machinery. Cell 159(6):1300–1311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chylinski K, Le Rhun A, Charpentier E (2013) The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol 10(5):726–737

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chylinski K, Makarova KS, Charpentier E, Koonin EV (2014) Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res 42(10):6091–6105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Citorik RJ, Mimee M, Lu TK (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 32(11):1141–1145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini L, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Keersmaecker SC, Sonck K, Vanderleyden J (2006) Let LuxS speak up in AI-2 signaling. Trends Microbiol 14(3):114–119

    Article  CAS  PubMed  Google Scholar 

  • Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340):602–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng H, Gao R, Liao X, Cai Y (2017) CRISPR system in filamentous fungi: Current achievements and future directions. Gene 627:212–221

    Article  CAS  PubMed  Google Scholar 

  • DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41(7):4336–4343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dillingham MS, Kowalczykowski SC (2008) RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev 72(4):642–671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diner BA, Lum KK, Toettcher JE, Cristea IM (2016) Viral DNA sensors IFI16 and Cyclic GMP-AMP synthase possess distinct functions in regulating viral gene expression, immune defenses, and apoptotic responses during herpesvirus infection. MBio 7(6):01553–01516

    Article  Google Scholar 

  • Duina AA, Miller ME, Keeney JB (2014) Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. Genetics 197(1):33–48

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang Y, Tyler BM (2016) Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9. Mol Plant Pathol 17(1):127–139

    Article  CAS  PubMed  Google Scholar 

  • Fuller KK, Chen S, Loros JJ, Dunlap JC (2015) Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot Cell 14(11):1073–1080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gantz VM, Jasinskiene N, Tatarenkova O, Fazekas A, Macias VM, Bier E, James AA (2015) Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc Natl Acad Sci U S A 112(49):6736–6743

    Article  CAS  Google Scholar 

  • Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71

    Article  CAS  PubMed  Google Scholar 

  • Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X (2015) CRISPR-Cas adaptive immune systems of the sulfolobales: Unravelling their complexity and diversity. Life 5(1):783–817

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109(39):2579–2586

    Article  Google Scholar 

  • Ghorbal M, Gorman M, Macpherson CR, Martins RM, Scherf A, Lopez-Rubio JJ (2014) Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system. Nat Biotechnol 32(8):819–821

    Article  CAS  PubMed  Google Scholar 

  • Global Health Observatory (GHO) data: HIV/AIDS (2018) World Health Organization http://www.who.int/gho/hiv/en/. Accessed 4 Oct 2018

  • Gohil N, Ramírez-García R, Panchasara H, Patel S, Bhattacharjee G, Singh V (2018) Book Review: Quorum Sensing vs. Quorum Quenching: A Battle With No End in Sight. Front Cell Infect Microbiol 8:106

    Article  CAS  PubMed Central  Google Scholar 

  • Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360(6387):439–444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo JC, Tang YD, Zhao K, Wang TY, Liu JT, Gao JC, Chang XB, Cui HY, Tian ZJ, Cai XH, An TQ (2016) Highly efficient CRISPR/Cas9-mediated homologous recombination promotes the rapid generation of bacterial artificial chromosomes of pseudorabies virus. Front Microbiol 7:2110

    PubMed  PubMed Central  Google Scholar 

  • Gupta RM, Musunuru K (2014) Expanding the genetic editing toolkit: ZFNs, TALENs, and CRISPR-Cas9. J Clin Invest 124(10):4154–4161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamad B (2010) The antibiotics market. Nat Rev Drug Discov 9(9):675–676

    Article  CAS  PubMed  Google Scholar 

  • Harris LJ, Balcerzak M, Johnston A, Schneiderman D, Ouellet T (2016) Host-preferential Fusarium graminearum gene expression during infection of wheat, barley, and maize. Fungal Biol Rev 120(1):111–123

    Article  CAS  Google Scholar 

  • Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA (2015) Cas9 specifies functional viral targets during CRISPR–Cas adaptation. Nature 519(7542):199–202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hisano Y, Sakuma T, Nakade S, Ohga R, Ota S, Okamoto H, Yamamoto T, Kawahara A (2015) Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci Rep 5:8841

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157(6):1262–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang Y, Chen Y, Zeng B, Wang Y, James AA, Gurr GM, Yang G, Lin X, Huang Y, You M (2016) CRISPR/Cas9 mediated knockout of the abdominal-A homeotic gene in the global pest, diamondback moth (Plutella xylostella). Insect Biochem Mol Biol 75:98–106

    Article  CAS  PubMed  Google Scholar 

  • Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169(12):5429–5433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jakočiūnas T, Bonde I, Herrgård M, Harrison SJ, Kristensen M, Pedersen LE, Jensen MK, Keasling JD (2015) Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28:213–222

    Article  CAS  PubMed  Google Scholar 

  • Ji X, Zhang H, Zhang Y, Wang Y, Gao C (2015) Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants. Nat Plants 1:15144

    Article  CAS  PubMed  Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343(6176):1247997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson KE, Bottero V, Flaherty S, Dutta S, Singh VV, Chandran B (2014) IFI16 restricts HSV-1 replication by accumulating on the hsv-1 genome, repressing HSV-1 gene expression, and directly or indirectly modulating histone modifications. PLoS Pathog 10(11):1004503

    Article  CAS  Google Scholar 

  • Kanda T, Furuse Y, Oshitani H, Kiyono T (2016) Highly efficient CRISPR/Cas9-mediated cloning and functional characterization of gastric cancer-derived Epstein-Barr virus strains. J Virol 90(9):4383–4393 90(9):4383-4393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang S, Kim J, Hur JK, Lee SS (2017) CRISPR-based genome editing of clinically important Escherichia coli SE15 isolated from indwelling urinary catheters of patients. J Med Microbiol 66(1):18–25

    Article  PubMed  Google Scholar 

  • Karginov FV, Hannon GJ (2010) The CRISPR system: small RNA-guided defence in bacteria and archaea. Mol Cell 37(1):7–19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V (2013) crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 10(5):841–851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K, Maruyama JI (2016) Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett 38(4):637–642

    Article  CAS  PubMed  Google Scholar 

  • Khambhati K, Bhattacharjee G, Singh V (2018) Current progress in CRISPR-based diagnostic platforms. J Cell Biochem. https://doi.org/10.1002/jcb.27690

  • Khatodia S, Bhatotia K, Tuteja N (2017) Development of CRISPR/Cas9 mediated virus resistance in agriculturally important crops. Bioengineered 8(3):274–279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knott GJ, Doudna JA (2018) CRISPR-Cas guides the future of genetic engineering. Science 361(6405):866–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuang D, Qiao J, Li Z, Wang W, Xia H, Jiang L, Dai J, Fang Q, Dai X (2017) Tagging to endogenous genes of Plasmodium falciparum using CRISPR/Cas9. Parasit Vectors 10(1):595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kucheria R, Dasgupta P, Sacks SH, Khan MS, Sheerin NS (2005) Urinary tract infections: new insights into a common problem. Postgrad Med J 81(952):83–86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuivanen J, Wang YMJ, Richard P (2016) Engineering Aspergillus niger for galactaric acid production: elimination of galactaric acid catabolism by using RNA sequencing and CRISPR/Cas9. Microb Cell Factories 15(1):210

    Article  CAS  Google Scholar 

  • Kumar A, Jha A (2017) Antifungals used against candidiasis. In: Kumar A, Jha A (eds) Anticandidal agents. Academic Press/Elsevier, New York, pp 11–39. ISBN 9780128113110

    Chapter  Google Scholar 

  • La Russa MF, Qi LS (2015) The new state of the art: CRISPR for gene activation and repression. Mol Cell Biol 35(22):3800–3809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lander N, Li ZH, Niyogi S, Docampo R (2015) CRISPR/Cas9-induced disruption of paraflagellar rod protein 1 and 2 genes in Trypanosoma cruzireveals their role in flagellar attachment. MBio 6(4):01012–01015

    Article  CAS  Google Scholar 

  • Lecellier A, Gaydou V, Mounier J, Hermet A, Castrec L, Barbier G, Ablain W, Manfait M, Toubas D, Sockalingum GD (2015) Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds. Food Microbiol 45:126–134

    Article  CAS  PubMed  Google Scholar 

  • Levy A, Goren MG, Yosef I, Auster O, Manor M, Amitai G, Edgar R, Qimron U, Sorek R (2015) CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 520(7548):505–510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu R, Chen L, Jiang Y, Zhou Z, Zou G (2015) Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov 1:15007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Chen Y, Li Q, Wu L, Wen T (2017) Dcf1 regulates neuropeptide expression and maintains energy balance. Neurosci Lett 650:1–7

    Article  CAS  PubMed  Google Scholar 

  • Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (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. Biol Direct 1(1):7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10(10):957–963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsu-ura T, Baek M, Kwon J, Hong C (2015) Efficient gene editing in Neurospora crassa with CRISPR technology. Fungal Biol Biotechnol 2(1):4

    Article  PubMed  PubMed Central  Google Scholar 

  • Miyagishi M, Taira K (2002) U6 promoter–driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol 20(5):497–500

    Article  CAS  PubMed  Google Scholar 

  • Mojica FJ, Díez-Villaseñor C, García-Martínez J, Almendros C (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155(3):733–740

    Article  CAS  PubMed  Google Scholar 

  • Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM (2012) Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PloS ONE 7(9):44638

    Article  CAS  Google Scholar 

  • Nielsen J, Fussenegger M, Keasling J, Lee SY, Liao JC, Prather K, Palsson B (2014) Engineering synergy in biotechnology. Nat Chem Biol 10(5):319–322

    Article  CAS  PubMed  Google Scholar 

  • Ophinni Y, Inoue M, Kotaki T, Kameoka M (2018) CRISPR/Cas9 system targeting regulatory genes of HIV-1 inhibits viral replication in infected T-cell cultures. Sci Rep 8(1):7784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, Edraki A, Shah M, Sontheimer EJ, Maxwell KL, Davidson AR (2016) Naturally occurring off-switches for CRISPR-Cas9. Cell 167(7):1829–1838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Payungwoung T, Shinzawa N, Hino A, Nishi T, Murata Y, Yuda M, Iwanaga S (2018) CRISPR/Cas9 system in Plasmodium falciparum using the centromere plasmid. Parasitol Int 67(5):605–608

    Article  CAS  PubMed  Google Scholar 

  • Pohl C, Kiel JAKW, Driessen AJM, Bovenberg RAL, Nygard Y (2016) CRISPR/Cas9 based genome editing of Penicillium chrysogenum. ACS Synth Biol 5(7):754–764

    Article  CAS  PubMed  Google Scholar 

  • Pursey E, Sünderhauf D, Gaze WH, Westra ER, van Houte S (2018) CRISPR-Cas antimicrobials: Challenges and future prospects. PLoS Pathog 14(6):1006990

    Article  CAS  Google Scholar 

  • Rath D, Amlinger L, Rath A, Lundgren M (2015) The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 117:119–128

    Article  CAS  PubMed  Google Scholar 

  • Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J (2017) Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 168(1–2):150–158

    Article  CAS  PubMed  Google Scholar 

  • Roberts RJ (2005) How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci U S A 102(17):5905–5908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rutherford ST, Bassler BL (2012) Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med 2(11):012427

    Article  CAS  Google Scholar 

  • Sajith S, Priji P, Sreedevi S, Benjamin S (2016) An overview on fungal cellulases with an industrial perspective. J Nutr Food Sci 6(1):461

    Google Scholar 

  • Schuster M, Schweizer G, Reissmann S, Kahmann R (2016) Genome editing in Ustilagomaydis using the CRISPR–Cas system. Fungal Genet Biol 89:3–9

    Article  CAS  PubMed  Google Scholar 

  • Shabbir MA, Hao H, Shabbir MZ, Wu Q, Sattar A, Yuan Z (2016) Bacteria vs. bacteriophages: parallel evolution of immune arsenals. Front Microbiol 7:1292

    Article  PubMed  PubMed Central  Google Scholar 

  • Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013) Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 10(5):891–899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi TQ, Liu GN, Ji RY, Shi K, Song P, Ren LJ, Huang H, Ji XJ (2017) CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art. Appl Microbiol Biotechnol 101(20):7435–7443

    Article  CAS  PubMed  Google Scholar 

  • Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA (2017) Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv 3(7):e1701620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shokri J, Adibkia K (2013) Application of cellulose and cellulose derivatives in pharmaceutical industries. In: van de Ven T, Godbout L (eds) Cellulose-medical, pharmaceutical and electronic applications. InTechOpen. https://doi.org/10.5772/55178

  • Singh V, Braddick D, Dhar PK (2017) Exploring the potential of genome editing CRISPR-Cas9 technology. Gene 599:1–18

    Article  CAS  PubMed  Google Scholar 

  • Singh V, Gohil N, Ramírez-García R, Braddick D, Fofié CK (2018) Recent advances in CRISPR-Cas9 genome editing technology for biological and biomedical investigations. J Cell Biochem 119(1):81–94

    Article  CAS  PubMed  Google Scholar 

  • Sollelis L, Ghorbal M, MacPherson CR, Martins RM, Kuk N, Crobu L, Bastien P, Scherf A, Lopez-Rubio JJ, Sterkers Y (2015) First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites. Cell Microbiol 17(10):1405–1412

    Article  CAS  PubMed  Google Scholar 

  • Sternberg SH, LaFrance B, Kaplan M, Doudna JA (2015) Conformational control of DNA target cleavage by CRISPR–Cas9. Nature 527(7576):110–113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sturbelle RT, de Avila LFDC, Roos TB, Borchardt JL, Dellagostin OA, Leite FPL (2015) The role of quorum sensing in Escherichia coli (ETEC) virulence factors. Vet Microbiol 180(3-4):245–252

    Article  CAS  PubMed  Google Scholar 

  • Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R (2014) Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci U S A 111(27):9798–9803

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thrane U, Anderson B, Frisvad JC, Smedsgaard J (2007) The exo-metabolome in filamentous fungi. In: Nielsen J, Jewett MC (eds) Metabolomics. (Topics in current genetics), vol 18. Springer, Berlin, pp 235–252

    Google Scholar 

  • Umesha S, Singh P, Singh R (2017) Microbiology biotechnology and sustainable agriculture. In: Singh RL, Mondal S (eds) Biotechnology for sustainable agriculture: emerging approaches and strategies. Woodhead Publishing, Cambridge, UK, pp 185–205

    Google Scholar 

  • Van Diemen FR, Lebbink RJ (2017) CRISPR/Cas9, a powerful tool to target human herpesviruses. Cell Microbiol 19(2). https://doi.org/10.1111/cmi.12694

  • Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015) Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163(4):840–853

    Article  CAS  PubMed  Google Scholar 

  • Wang D, Wang XW, Peng XC, Xiang Y, Song SB, Wang YY, Chen L, Xin VW, Lyu YN, Ji J, Ma ZW (2018) CRISPR/Cas9 genome editing technology significantly accelerated herpes simplex virus research. Cancer Gene Ther 25(5-6):93–105

    Article  CAS  PubMed  Google Scholar 

  • Ward OP (2012) Production of recombinant proteins by filamentous fungi. Biotechnol Adv 30(5):1119–1139

    Article  CAS  PubMed  Google Scholar 

  • Weber J, Valiante V, Nødvig CS, Mattern DJ, Slotkowski RA, Mortensen UH, Brakhage AA (2016) Functional reconstitution of a fungal natural product gene cluster by advanced genome editing. ACS Synth Biol 6(1):62–68

    Article  CAS  PubMed  Google Scholar 

  • Wei Y, Chesne MT, Terns RM, Terns MP (2015) Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus. Nucleic Acids Res 43(3):1749–1758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wiles MV, Qin W, Cheng AW, Wang H (2015) CRISPR–Cas9-mediated genome editing and guide RNA design. Mamm Genome 26(9-10):501–510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woloshuk CP, Shim WB (2013) Aflatoxins, fumonisins, and trichothecenes: a convergence of knowledge. FEMS Microbiol Rev 37(1):94–109

    Article  CAS  PubMed  Google Scholar 

  • Wright AV, Nuñez JK, Doudna JA (2016) Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering. Cell 164(1-2):29–44

    Article  CAS  PubMed  Google Scholar 

  • Xu X, Fan S, Zhou J, Zhang Y, Che Y, Cai H, Wang L, Guo L, Liu L, Li Q (2016) The mutated tegument protein UL7 attenuates the virulence of herpes simplex virus 1 by reducing the modulation of α-4 gene transcription. Virol J 13:152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu D, Ellis HM, Lee EC, Jenkins NA, Copeland NG (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A 97(11):5978–5983

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang D, Li Z, Li JF (2015) Genome editing: new antiviral weapon for plants. Nat Plants 1(10):15146

    Article  CAS  Google Scholar 

  • Zhang C, Meng X, Wei X, Lu L (2016) Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet Biol 86:47–57

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by Puri Foundation for Education in India.

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Correspondence to Vijai Singh .

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Bhattacharjee, G., Khambhati, K., Singh, V. (2019). RNA-Guided CRISPR-Cas9 System for Removal of Microbial Pathogens. In: Tripathi, V., Kumar, P., Tripathi, P., Kishore, A. (eds) Microbial Genomics in Sustainable Agroecosystems. Springer, Singapore. https://doi.org/10.1007/978-981-13-8739-5_12

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