144
Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome
engineering. Cell 157(6):1262–1278. https://doi.org/10.1016/j.cell.2014.05.010
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
Jiang W, Maniv I, Arain F, Wang Y, Levin BR, Marraffini LA (2013) Dealing with the evolutionary
downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet 9(9):e1003844.
https://doi.org/10.1371/journal.pgen.1003844
Jiang Y, Qian F, Yang J, Liu Y, Dong F, Xu C, Sun B, Chen B, Xu X, Li Y, Wang R, Yang S
(2017) CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun
8:15179. https://doi.org/10.1038/ncomms15179
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dualRNA- guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821.
https://doi.org/10.1126/science.1225829
Jorth P, Turner KH, Gumus P, Nizam N, Buduneli N, Whiteley M (2014) Metatranscriptomics of
the human oral microbiome during health and disease.. MBio5(2):e01012–14. doi: https://doi.
org/10.1128/mBio.01012-14
Karimi Z, Ahmadi A, Najafi A, Ranjbar R (2018) Bacterial CRISPR regions: General features and
their potential for epidemiological molecular typing studies. Open Micro. J. 12:59–70. https://
doi.org/10.2174/1874285801812010059
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. https://doi.org/10.4161/rna.24203
Kim JS, Cho DH, Park M, Chung WJ, Shin D, Ko KS (2015) CRISPR/cas9-mediated re- sensitization
of antibiotic-resistant Escherichia coli harboring extended-spectrum β-lactamases. J Microbiol
Biotechnol 26:394–401. https://doi.org/10.4014/jmb.1508.08080
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas
systems. Curr Opin Microbiol 37:67–78. https://doi.org/10.1016/j.mib.2017.05.008
Lillestøl RK, Shah SA, Brügger K, Redder P, Phan H, Christiansen J et al (2009) CRISPR families
of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol
Microbiol 72(1):259–272. https://doi.org/10.1111/j.1365-2958.2009.06641.x
Lima R, Del Fiol FS, Balcão VM (2019) Prospects for the use of new technologies to combat multidrug- resistant bacteria. Front Pharmacol 21(10):692. https://doi.org/10.3389/
fphar.2019.00692
Liu C, ZhangL LH, Cheng K (2017) Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications. J Control Release 266:17–26. https://doi.org/10.1016/j.
jconrel.2017.09.012
Makarova KS, Koonin EV (2015) Annotation and classification of CRISPR-Cas systems. Methods
Mol Biol 1311:47–75. https://doi.org/10.1007/978-1-4939-2687-9_4
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ et al (2015) An updated
evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13(11):722–736.
https://doi.org/10.1038/nrmicro3569
Marbouty M, Baudry L, Cournac A, Koszul R (2017) Scaffolding bacterial genomes and probing
host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.
Sci Adv 3(2):e1602105. https://doi.org/10.1126/sciadv.1602105
Marraffini LA, Sontheimer EJ (2010) CRISPR interference: RNA-directed adaptive immunity in
bacteria and archaea. Nat Rev Genet 11(3):181–190. https://doi.org/10.1038/nrg2749
McDonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF (2019) CRISPR-Cas systems
are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics
20(1):105. https://doi.org/10.1186/s12864-019-5439-1
A. P. Sarma et al.
Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome
engineering. Cell 157(6):1262–1278. https://doi.org/10.1016/j.cell.2014.05.010
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
Jiang W, Maniv I, Arain F, Wang Y, Levin BR, Marraffini LA (2013) Dealing with the evolutionary
downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet 9(9):e1003844.
https://doi.org/10.1371/journal.pgen.1003844
Jiang Y, Qian F, Yang J, Liu Y, Dong F, Xu C, Sun B, Chen B, Xu X, Li Y, Wang R, Yang S
(2017) CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun
8:15179. https://doi.org/10.1038/ncomms15179
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dualRNA- guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821.
https://doi.org/10.1126/science.1225829
Jorth P, Turner KH, Gumus P, Nizam N, Buduneli N, Whiteley M (2014) Metatranscriptomics of
the human oral microbiome during health and disease.. MBio5(2):e01012–14. doi: https://doi.
org/10.1128/mBio.01012-14
Karimi Z, Ahmadi A, Najafi A, Ranjbar R (2018) Bacterial CRISPR regions: General features and
their potential for epidemiological molecular typing studies. Open Micro. J. 12:59–70. https://
doi.org/10.2174/1874285801812010059
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. https://doi.org/10.4161/rna.24203
Kim JS, Cho DH, Park M, Chung WJ, Shin D, Ko KS (2015) CRISPR/cas9-mediated re- sensitization
of antibiotic-resistant Escherichia coli harboring extended-spectrum β-lactamases. J Microbiol
Biotechnol 26:394–401. https://doi.org/10.4014/jmb.1508.08080
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas
systems. Curr Opin Microbiol 37:67–78. https://doi.org/10.1016/j.mib.2017.05.008
Lillestøl RK, Shah SA, Brügger K, Redder P, Phan H, Christiansen J et al (2009) CRISPR families
of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol
Microbiol 72(1):259–272. https://doi.org/10.1111/j.1365-2958.2009.06641.x
Lima R, Del Fiol FS, Balcão VM (2019) Prospects for the use of new technologies to combat multidrug- resistant bacteria. Front Pharmacol 21(10):692. https://doi.org/10.3389/
fphar.2019.00692
Liu C, ZhangL LH, Cheng K (2017) Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications. J Control Release 266:17–26. https://doi.org/10.1016/j.
jconrel.2017.09.012
Makarova KS, Koonin EV (2015) Annotation and classification of CRISPR-Cas systems. Methods
Mol Biol 1311:47–75. https://doi.org/10.1007/978-1-4939-2687-9_4
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ et al (2015) An updated
evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13(11):722–736.
https://doi.org/10.1038/nrmicro3569
Marbouty M, Baudry L, Cournac A, Koszul R (2017) Scaffolding bacterial genomes and probing
host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.
Sci Adv 3(2):e1602105. https://doi.org/10.1126/sciadv.1602105
Marraffini LA, Sontheimer EJ (2010) CRISPR interference: RNA-directed adaptive immunity in
bacteria and archaea. Nat Rev Genet 11(3):181–190. https://doi.org/10.1038/nrg2749
McDonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF (2019) CRISPR-Cas systems
are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics
20(1):105. https://doi.org/10.1186/s12864-019-5439-1
A. P. Sarma et al.