Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint

References

• Makarova KS, Wolf YI, Iranzo J, et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020;18:67–83. doi: 10.1038/s41579-019-0299-x
   PubMed Web of Science ®Google Scholar
• Leenay, Deciphering RT, Beisel CL. Communicating, and engineering the CRISPR PAM. J Mol Biol. 2017;429:177–191. doi: 10.1016/j.jmb.2016.11.024
   PubMed Web of Science ®Google Scholar
• Bikard D, Jiang W, Samai P, et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013;41(15):7429–7437. doi: 10.1093/nar/gkt520
   PubMed Web of Science ®Google Scholar
• Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2021;184(3):844. doi: 10.1016/j.cell.2021.01.019
   PubMed Web of Science ®Google Scholar
• Gaudelli NM, Komor AC, Rees HA, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464–471. doi: 10.1038/nature24644
   PubMed Web of Science ®Google Scholar
• Grünewald J, Zhou R, Lareau CA, et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat Biotechnol. 2020;38(7):861–864. doi: 10.1038/s41587-020-0535-y
   PubMed Web of Science ®Google Scholar
• Komor AC, Kim YB, Packer MS, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–424. doi: 10.1038/nature17946
   PubMed Web of Science ®Google Scholar
• Zhang X, Zhu B, Chen L, et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat Biotechnol. 2020;38(7):856–860. doi: 10.1038/s41587-020-0527-y
   PubMed Web of Science ®Google Scholar
• Klompe SE, Vo PLH, Halpin-Healy TS, et al. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature. 2019;571(7764):219–225. doi: 10.1038/s41586-019-1323-z
   PubMed Web of Science ®Google Scholar
• Strecker J, Ladha A, Gardner Z, et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019;365(6448):48–53. doi: 10.1126/science.aax9181
   PubMed Web of Science ®Google Scholar
• PLH V, Ronda C, Klompe SE, et al. CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering. Nat Biotechnol. 2021;39:480–489. doi: 10.1038/s41587-020-00745-y
   PubMed Web of Science ®Google Scholar
• Anzalone AV, Randolph PB, Davis JR, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):149–157. doi: 10.1038/s41586-019-1711-4
   PubMed Web of Science ®Google Scholar
• Tong Y, Jørgensen TS, Whitford CM, et al. A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Nat Commun. 2021;12(1):5206. doi: 10.1038/s41467-021-25541-3
   PubMed Web of Science ®Google Scholar
• Feng X, Zhao D, Zhang X, et al. CRISPR/Cas9 Assisted Multiplex genome editing technique in escherichia coli. Biotechnol J. 2018;13(9):e1700604. doi: 10.1002/biot.201700604
   PubMed Web of Science ®Google Scholar
• Campa CC, Weisbach NR, Santinha AJ, et al. Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods. 2019;16(9):887–893. doi: 10.1038/s41592-019-0508-6
   PubMed Web of Science ®Google Scholar
• Liao C, Ttofali F, Slotkowski RA, et al. Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis. Nat Commun. 2019;10(1):1–14. doi: 10.1038/s41467-019-10747-3
   PubMedGoogle Scholar
• Jinek M, Chylinski K, Fonfara I, et al. A Programmable dual-RNA–Guided DNA endonuclease in adaptive bacterial immunity. Science2012. 2012;337(6096):816–821. doi: 10.1126/science.1225829 Available from.
   PubMed Web of Science ®Google Scholar
• Kabadi AM, Ousterout DG, Hilton IB, et al. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res. 2014;42(19):e147. doi: 10.1093/nar/gku749
   PubMed Web of Science ®Google Scholar
• Reis AC, Halper SM, Vezeau GE, et al. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nat Biotechnol. 2019;37(11):1294–1301. doi: 10.1038/s41587-019-0286-9
   PubMed Web of Science ®Google Scholar
• Ferreira R, Skrekas C, Nielsen J, et al. Multiplexed CRISPR/Cas9 genome editing and gene regulation using Csy4 in Saccharomyces cerevisiae. ACS Synth Biol. 2018;7:10–15. doi: 10.1021/acssynbio.7b00259
   PubMed Web of Science ®Google Scholar
• He Y, Zhang T, Yang N, et al. Self-cleaving ribozymes enable the production of guide RNAs from unlimited choices of promoters for CRISPR/Cas9 mediated genome editing. J Genet Genomics. 2017;44(9):469–472. doi: 10.1016/j.jgg.2017.08.003
   PubMed Web of Science ®Google Scholar
• Kurata M, Wolf NK, Lahr WS, et al. Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays. PLoS One. 2018;13(9):e0198714. doi: 10.1371/journal.pone.0198714
   PubMed Web of Science ®Google Scholar
• 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. doi: 10.1038/s41467-019-09005-3
   PubMedGoogle Scholar
• Zetsche B, Heidenreich M, Mohanraju P, et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol. 2017;35:31–34. doi: 10.1038/nbt.3737
   PubMed Web of Science ®Google Scholar
• McGinn J, Marraffini LA. Molecular mechanisms of CRISPR–Cas spacer acquisition. Nat Rev Microbiol. 2018;17:7–12. doi: 10.1038/s41579-018-0071-7
   Web of Science ®Google Scholar
• Swiat MA, Dashko S, den Ridder M, et al. FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae. Nucleic Acids Res. 2017;45(21):12585–12598. doi: 10.1093/nar/gkx1007
   PubMed Web of Science ®Google Scholar
• Ciurkot K, Gorochowski TE, Roubos JA, et al. Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a. Nucleic Acids Res. 2021;49(13):7775–7790. doi: 10.1093/nar/gkab529
   PubMed Web of Science ®Google Scholar
• Zhang Y, Ren Q, Tang X, et al. Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems. Nat Commun. 2021;12(1):1944. doi: 10.1038/s41467-021-22330-w
   PubMed Web of Science ®Google Scholar
• Ao X, Yao Y, Li T, et al. A Multiplex genome editing method for Escherichia coli based on CRISPR-Cas12a. Front Microbiol. 2018 [cited 2022 Feb 2]. Internet. 10.3389/fmicb.2018.02307
   Web of Science ®Google Scholar
• Port F, Starostecka M, Boutros M. Multiplexed conditional genome editing with Cas12a in Drosophila. Proc Natl Acad Sci U S A. 2020;117(37):22890–22899. doi: 10.1073/pnas.2004655117
   PubMed Web of Science ®Google Scholar
• Bryson JW, Auxillos JY, Rosser SJ. Multiplexed activation in mammalian cells using a split-intein CRISPR/Cas12a based synthetic transcription factor. Nucleic Acids Res. 2021;50:549–560. doi: 10.1093/nar/gkab1191
   Web of Science ®Google Scholar
• Charpentier E, Richter H, van der Oost J, et al. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev. 2015;39(3):428–441. doi: 10.1093/femsre/fuv023
   PubMed Web of Science ®Google Scholar
• Deltcheva E, Chylinski K, Sharma CM, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471(7340):602–607. doi: 10.1038/nature09886
   PubMed Web of Science ®Google Scholar
• Sternberg SH, LaFrance B, Kaplan M, et al. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature. 2015;527:110–113. doi: 10.1038/nature15544
   PubMed Web of Science ®Google Scholar
• Cui L, Vigouroux A, Rousset F, et al. A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9. Nat Commun. 2018;9(1):1–10. doi: 10.1038/s41467-018-04209-5
   PubMedGoogle Scholar
• Liao C, Slotkowski RA, Beisel CL. CRATES: a one-step assembly method for class 2 CRISPR arrays. Methods Enzymol. 2019;629. Available from: https://pubmed.ncbi.nlm.nih.gov/31727255/
   PubMed Web of Science ®Google Scholar
• Shin J, Noireaux V. Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70. J Biol Eng. 2010;4(1):8. doi: 10.1186/1754-1611-4-8
   PubMedGoogle Scholar
• Jiang W, Bikard D, Cox D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 2013;31:233–239. doi: 10.1038/nbt.2508 Available from.
   PubMed Web of Science ®Google Scholar
• Vigouroux A, Oldewurtel E, Cui L, et al. Tuning dCas9’s ability to block transcription enables robust, noiseless knockdown of bacterial genes. Mol Syst Biol. 2018;14(3):e7899. doi: 10.15252/msb.20177899
   PubMed Web of Science ®Google Scholar
• Magnusson JP, Rios AR, Wu L, et al. Enhanced Cas12a multi-gene regulation using a CRISPR array separator. Elife 2021;10. Available from 10.7554/eLife.66406.
   Web of Science ®Google Scholar
• Creutzburg SCA, Wu WY, Mohanraju P, et al. Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a. Nucleic Acids Res. 2020;48(6):3228–3243. doi: 10.1093/nar/gkz1240
   PubMed Web of Science ®Google Scholar
• Reimann V, Alkhnbashi OS, Saunders SJ, et al. Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRnas. Nucleic Acids Res. 2017;45(2):915–925. doi: 10.1093/nar/gkw786
   PubMed Web of Science ®Google Scholar
• Zadeh JN, Steenberg CD, Bois JS, et al. NUPACK: Analysis and design of nucleic acid systems. J Comput Chem. 2011;32:170–173. doi: 10.1002/jcc.21596
   PubMed Web of Science ®Google Scholar
• Rhoads A, Au KF. PacBio sequencing and its applications. Int J Genomics Proteomics. 2015;13(5):278–289. doi: 10.1016/j.gpb.2015.08.002
   Google Scholar
• Lu H, Giordano F, Ning Z. Oxford nanopore MinION sequencing and genome assembly. Int J Genomics Proteomics. 2016;14(5):265–279. doi: 10.1016/j.gpb.2016.05.004
   Google Scholar
• Pollard MO, Gurdasani D, Mentzer AJ, et al. Long reads: their purpose and place. Hum Mol Genet. 2018;27(R2):R234–41. doi: 10.1093/hmg/ddy177
   PubMed Web of Science ®Google Scholar
• Wang T, Guan C, Guo J, et al. Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance. Nat Commun. 2018;9(1):2475. doi: 10.1038/s41467-018-04899-x
   PubMedGoogle Scholar
• Rousset F, Cui L, Siouve E, et al. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet. 2018;14(11):e1007749. doi: 10.1371/journal.pgen.1007749
   PubMed Web of Science ®Google Scholar
• de Bakker V, Liu X, Bravo AM, et al. Crispri-seq for genome-wide fitness quantification in bacteria. Nat Protoc. 2022;17(2):252–281. doi: 10.1038/s41596-021-00639-6
   PubMed Web of Science ®Google Scholar
• Liu Y, Wang R, Liu J, et al. Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum. Sci Adv. 2022;8(35):eabq2157. doi: 10.1126/sciadv.abq2157
   PubMed Web of Science ®Google Scholar
• Konstantakos V, Nentidis A, Krithara A, et al. CRISPR-Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning. Nucleic Acids Res. 2022;50:3616–3637. doi: 10.1093/nar/gkac192
   PubMed Web of Science ®Google Scholar
• Chuai G, Ma H, Yan J, et al. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol. 2018;19(1):80. doi: 10.1186/s13059-018-1459-4
   PubMedGoogle Scholar
• Diehl V, Wegner M, Grumati P, et al. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res. 2021;49(10):5684–5704. doi: 10.1093/nar/gkab309
   PubMed Web of Science ®Google Scholar
• Joung J, Konermann S, Gootenberg JS, et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017;12(4):828–863. doi: 10.1038/nprot.2017.016
   PubMed Web of Science ®Google Scholar
• Bock C, Datlinger P, Chardon F, et al. High-content CRISPR screening. Nat Rev Methods Primers. 2022;2:1–23. doi: 10.1038/s43586-021-00093-4
   Google Scholar
• Liao C, Beisel CL. The tracrRNA in CRISPR Biology and technologies. Ann Rev Genet. 2021;55(1):161–181. doi: 10.1146/annurev-genet-071719-022559
   PubMedGoogle Scholar
• Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol. 2023;75:102353. doi: 10.1016/j.mib.2023.102353
   PubMed Web of Science ®Google Scholar
• Miller JH, editor. Assay of β-galactosidase. In: Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1972. p. 352–355.
   Google Scholar