PAM-Expanded Streptococcus thermophilus Cas9 C-to-T and C-to-G Base Editors for Programmable Base Editing in Mycobacteria

World Health Organization. Global tuberculosis report 2018. Report. 2018. Gandhi, 2010, Multidrug-resistant and extensively drug-resistant tuberculosis: a threat to global control of tuberculosis, Lancet, 375, 1830, 10.1016/S0140-6736(10)60410-2 Udwadia, 2012, Totally drug-resistant tuberculosis in India, Clin Infect Dis, 54, 579, 10.1093/cid/cir889 Balasubramanian, 1996, Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates, J Bacteriol, 178, 273, 10.1128/jb.178.1.273-279.1996 Bardarov, 2002, Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis, Microbiology, 148, 3007, 10.1099/00221287-148-10-3007 van Kessel, 2007, Recombineering in Mycobacterium tuberculosis, Nat Methods, 4, 147, 10.1038/nmeth996 Murphy, 2018, ORBIT: a new paradigm for genetic engineering of mycobacterial chromosomes, MBio, 9, e01467, 10.1128/mBio.01467-18 Yan, 2020, A CRISPR-assisted nonhomologous end-joining strategy for efficient genome editing in Mycobacterium tuberculosis, MBio, 11, e02364, 10.1128/mBio.02364-19 Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033 Ge, 2016, CRISPR/Cas9-AAV mediated knock-in at NRL locus in human embryonic stem cells, Mol Ther Nucleic Acids, 5, 10.1038/mtna.2016.100 Cobb, 2015, High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system, ACS Synth Biol, 4, 723, 10.1021/sb500351f Yang, 2017, CRISPR/Cas9-loxP-mediated gene editing as a novel site-specific genetic manipulation tool, Mol Ther Nucleic Acids, 7, 378, 10.1016/j.omtn.2017.04.018 Tong, 2015, CRISPR-Cas9 based engineering of actinomycetal genomes, ACS Synth Biol, 4, 1020, 10.1021/acssynbio.5b00038 Jiang, 2013, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat Biotechnol, 31, 233, 10.1038/nbt.2508 Chen, 2017, Rapid and efficient genome editing in Staphylococcus aureus by using an engineered CRISPR/Cas9 system, J Am Chem Soc, 139, 3790, 10.1021/jacs.6b13317 Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022 Gilbert, 2013, CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, 154, 442, 10.1016/j.cell.2013.06.044 Choudhary, 2015, Gene silencing by CRISPR interference in mycobacteria, Nat Commun, 6, 6267, 10.1038/ncomms7267 Singh, 2016, Investigating essential gene function in Mycobacterium tuberculosis using an efficient CRISPR interference system, Nucleic Acids Res, 44, 10.1093/nar/gkw625 Rock, 2017, Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform, Nat Microbiol, 2, 16274, 10.1038/nmicrobiol.2016.274 Fleck, 2021, A Cas12a-based CRISPR interference system for multigene regulation in mycobacteria, J Biol Chem, 297, 10.1016/j.jbc.2021.100990 Komor, 2016, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature, 533, 420, 10.1038/nature17946 Gaudelli, 2017, Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage, Nature, 551, 464, 10.1038/nature24644 Jin, 2019, Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice, Science, 364, 292, 10.1126/science.aaw7166 Tong, 2019, Highly efficient DSB-free base editing for Streptomycetes with CRISPR-BEST, Proc Natl Acad Sci USA, 116, 20366, 10.1073/pnas.1913493116 Gu, 2018, Highly efficient base editing in Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase, Chem Sci, 9, 3248, 10.1039/C8SC00637G Wang, 2019, A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii to understand the H2O2-sensing mechanism of OxyR, Cell Chem Biol, 26, 1732, 10.1016/j.chembiol.2019.09.003 Zheng, 2018, Highly efficient base editing in bacteria using a Cas9-cytidine deaminase fusion, Commun Biol, 1, 32, 10.1038/s42003-018-0035-5 Li, 2019, CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii, Biotechnol Bioeng, 116, 1475, 10.1002/bit.26949 Chen, 2018, CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species, iScience, 6, 222, 10.1016/j.isci.2018.07.024 Wang, 2018, CRISPR-Cas9 and CRISPR-assisted cytidine deaminase enable precise and efficient genome editing in Klebsiella pneumoniae, Appl Environ Microbiol, 84, e01834, 10.1128/AEM.01834-18 Banno, 2018, Deaminase-mediated multiplex genome editing in Escherichia coli, Nat Microbiol, 3, 423, 10.1038/s41564-017-0102-6 Wang, 2018, MACBETH: multiplex automated Corynebacterium glutamicum base editing method, Metab Eng, 47, 200, 10.1016/j.ymben.2018.02.016 Gibson, 2009, Enzymatic assembly of DNA molecules up to several hundred kilobases, Nat Methods, 6, 343, 10.1038/nmeth.1318 Kluesner, 2018, EditR: a method to quantify base editing from sanger sequencing, CRISPR J, 1, 239, 10.1089/crispr.2018.0014 Altenbuchner, 2016, Editing of the bacillus subtilis genome by the CRISPR-Cas9 system, Appl Environ Microbiol, 82, 5421, 10.1128/AEM.01453-16 Huang, 2016, CRISPR/Cas9-based efficient genome editing in Clostridium ljungdahlii, an autotrophic gas-fermenting bacterium, ACS Synth Biol, 5, 1355, 10.1021/acssynbio.6b00044 Leenay, 2019, Genome editing with CRISPR-Cas9 in Lactobacillus plantarum revealed that editing outcomes can vary across strains and between methods, Biotechnol J, 14, 10.1002/biot.201700583 Jiang, 2015, Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, Appl Environ Microbiol, 81, 2506, 10.1128/AEM.04023-14 Li, 2018, Base editing with a Cpf1-cytidine deaminase fusion, Nat Biotechnol, 36, 324, 10.1038/nbt.4102 Zhang, 2020, Catalytic-state structure and engineering of Streptococcus thermophilus Cas9, Nat Catal, 3, 813, 10.1038/s41929-020-00506-9 Komor, 2017, Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T: a base editors with higher efficiency and product purity, Sci Adv, 3, 10.1126/sciadv.aao4774 Zhao, 2021, Glycosylase base editors enable C-to-A and C-to-G base changes, Nat Biotechnol, 39, 35, 10.1038/s41587-020-0592-2 Kurt, 2021, CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells, Nat Biotechnol, 39, 41, 10.1038/s41587-020-0609-x Chen, 2021, Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins, Nat Commun, 12, 1384, 10.1038/s41467-021-21559-9 Koblan, 2021, Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning, Nat Biotechnol, 39, 1414, 10.1038/s41587-021-00938-z Billon, 2017, CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons, Mol Cell, 67, 1068, 10.1016/j.molcel.2017.08.008 Yu, 2020, CRISPR-CBEI: a designing and analyzing tool kit for cytosine base editor-mediated gene inactivation, mSystems, 5, e00350, 10.1128/mSystems.00350-20 Gupta, 2017, A novel calcium uptake transporter of uncharacterized P-type ATPase family supplies calcium for cell surface integrity in Mycobacterium smegmatis, MBio, 8, e01388, 10.1128/mBio.01388-17 Unissa, 2016, Overview on mechanisms of isoniazid action and resistance in Mycobacterium tuberculosis, Infect Genet Evol, 45, 474, 10.1016/j.meegid.2016.09.004