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pdCas9-bacteria Citations (67)

Plasmid Article: Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression.
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022.
PubMed Journal

Articles Citing pdCas9-bacteria

Articles
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. Nat Protoc. 2013 Nov;8(11):2180-96. doi: 10.1038/nprot.2013.132. Epub 2013 Oct 17. PubMed
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Li GW, Burkhardt D, Gross C, Weissman JS. Cell. 2014 Apr 24;157(3):624-35. doi: 10.1016/j.cell.2014.02.033. PubMed
Guide RNA functional modules direct Cas9 activity and orthogonality. Briner AE, Donohoue PD, Gomaa AA, Selle K, Slorach EM, Nye CH, Haurwitz RE, Beisel CL, May AP, Barrangou R. Mol Cell. 2014 Oct 23;56(2):333-9. doi: 10.1016/j.molcel.2014.09.019. Epub 2014 Oct 16. PubMed
Protein engineering of Cas9 for enhanced function. Oakes BL, Nadler DC, Savage DF. Methods Enzymol. 2014;546:491-511. doi: 10.1016/B978-0-12-801185-0.00024-6. PubMed
Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis. Lv L, Ren YL, Chen JC, Wu Q, Chen GQ. Metab Eng. 2015 May;29:160-8. doi: 10.1016/j.ymben.2015.03.013. Epub 2015 Mar 31. PubMed
Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi). Hawkins JS, Wong S, Peters JM, Almeida R, Qi LS. Methods Mol Biol. 2015;1311:349-62. doi: 10.1007/978-1-4939-2687-9_23. PubMed
Selection and Validation of Spacer Sequences for CRISPR-Cas9 Genome Editing and Transcription Regulation in Bacteria. Grenier F, Lucier JF, Rodrigue S. Methods Mol Biol. 2015;1334:233-44. doi: 10.1007/978-1-4939-2877-4_15. PubMed
Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology. Jusiak B, Cleto S, Perez-Pinera P, Lu TK. Trends Biotechnol. 2016 Jan 22. pii: S0167-7799(15)00274-7. doi: 10.1016/j.tibtech.2015.12.014. PubMed
CRISPRi-Manipulation of Genetic Code Expansion via RF1 for Reassignment of Amber Codon in Bacteria. Zhang B, Yang Q, Chen J, Wu L, Yao T, Wu Y, Xu H, Zhang L, Xia Q, Zhou D. Sci Rep. 2016 Jan 28;6:20000. doi: 10.1038/srep20000. PubMed
Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system. Lee YJ, Hoynes-O'Connor A, Leong MC, Moon TS. Nucleic Acids Res. 2016 Mar 18;44(5):2462-73. doi: 10.1093/nar/gkw056. Epub 2016 Feb 2. PubMed
Development of a CRISPR-Cas9 toolkit for comprehensive engineering of Bacillus subtilis. Westbrook AW, Moo-Young M, Chou CP. Appl Environ Microbiol. 2016 Jun 3. pii: AEM.01159-16. PubMed

Associated Plasmids

The role of repressor kinetics in relief of transcriptional interference between convergent promoters. Hao N, Palmer AC, Ahlgren-Berg A, Shearwin KE, Dodd IB. Nucleic Acids Res. 2016 Aug 19;44(14):6625-38. doi: 10.1093/nar/gkw600. Epub 2016 Jul 4. PubMed
CRISPR perturbation of gene expression alters bacterial fitness under stress and reveals underlying epistatic constraints. Otoupal PB, Erickson KE, Bordoy AE, Chatterjee A. ACS Synth Biol. 2016 Aug 16. PubMed
CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Kim SK, Han GH, Seong W, Kim H, Kim SW, Lee DH, Lee SG. Metab Eng. 2016 Nov;38:228-240. doi: 10.1016/j.ymben.2016.08.006. Epub 2016 Aug 26. PubMed
Enhanced protein and biochemical production using CRISPRi-based growth switches. Li S, Jendresen CB, Grunberger A, Ronda C, Jensen SI, Noack S, Nielsen AT. Metab Eng. 2016 Nov;38:274-284. doi: 10.1016/j.ymben.2016.09.003. Epub 2016 Sep 16. PubMed
CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942. Huang CH, Shen CR, Li H, Sung LY, Wu MY, Hu YC. Microb Cell Fact. 2016 Nov 15;15(1):196. PubMed
Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system. Yoganand KN, Sivathanu R, Nimkar S, Anand B. Nucleic Acids Res. 2017 Jan 9;45(1):367-381. doi: 10.1093/nar/gkw1151. Epub 2016 Nov 29. PubMed
Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. Cell. 2016 Dec 22. pii: S0092-8674(16)31683-X. doi: 10.1016/j.cell.2016.12.009. PubMed

Associated Plasmids

AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies. Hochrein L, Machens F, Gremmels J, Schulz K, Messerschmidt K, Mueller-Roeber B. Nucleic Acids Res. 2017 Jun 2;45(10):e80. doi: 10.1093/nar/gkx034. PubMed
Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC). Van Hove B, Guidi C, De Wannemaeker L, Maertens J, De Mey M. ACS Synth Biol. 2017 Jun 16;6(6):943-949. doi: 10.1021/acssynbio.7b00017. Epub 2017 Mar 24. PubMed
High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae. Liu X, Gallay C, Kjos M, Domenech A, Slager J, van Kessel SP, Knoops K, Sorg RA, Zhang JR, Veening JW. Mol Syst Biol. 2017 May 10;13(5):931. doi: 10.15252/msb.20167449. PubMed

Associated Plasmids

CRISPR/dCas9-mediated inhibition of gene expression in Staphylococcus aureus. Dong X, Jin Y, Ming D, Li B, Dong H, Wang L, Wang T, Wang D. J Microbiol Methods. 2017 Aug;139:79-86. doi: 10.1016/j.mimet.2017.05.008. Epub 2017 May 15. PubMed
CRISPR Interference (CRISPRi) Inhibition of luxS Gene Expression in E. coli: An Approach to Inhibit Biofilm. Zuberi A, Misba L, Khan AU. Front Cell Infect Microbiol. 2017 May 26;7:214. doi: 10.3389/fcimb.2017.00214. eCollection 2017. PubMed
Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis. Wu MY, Sung LY, Li H, Huang CH, Hu YC. ACS Synth Biol. 2017 Dec 15;6(12):2350-2361. doi: 10.1021/acssynbio.7b00251. Epub 2017 Sep 12. PubMed
Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning. Gao C, Wang S, Hu G, Guo L, Chen X, Xu P, Liu L. Biotechnol Bioeng. 2018 Mar;115(3):661-672. doi: 10.1002/bit.26486. Epub 2017 Nov 22. PubMed
CRISPR-Cas Expands Dynamic Range of Gene Expression From T7RNAP Promoters. McCutcheon SR, Chiu KL, Lewis DD, Tan C. Biotechnol J. 2018 May;13(5):e1700167. doi: 10.1002/biot.201700167. Epub 2017 Dec 6. PubMed
Process optimization for enhancing production of cis-4-hydroxy-L-proline by engineered Escherichia coli. Chen K, Pang Y, Zhang B, Feng J, Xu S, Wang X, Ouyang P. Microb Cell Fact. 2017 Nov 22;16(1):210. doi: 10.1186/s12934-017-0821-7. PubMed
RNA-guided single/double gene repressions in Corynebacterium glutamicum using an efficient CRISPR interference and its application to industrial strain. Park J, Shin H, Lee SM, Um Y, Woo HM. Microb Cell Fact. 2018 Jan 9;17(1):4. doi: 10.1186/s12934-017-0843-1. PubMed
Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli. Gingras H, Dridi B, Leprohon P, Ouellette M. Microb Genom. 2018 Jan 10. doi: 10.1099/mgen.0.000148. PubMed
An enChIP system for the analysis of bacterial genome functions. Fujita T, Yuno M, Fujii H. BMC Res Notes. 2018 Jun 14;11(1):387. doi: 10.1186/s13104-018-3486-3. PubMed

Associated Plasmids

Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi). Woolston BM, Emerson DF, Currie DH, Stephanopoulos G. Metab Eng. 2018 Jul;48:243-253. doi: 10.1016/j.ymben.2018.06.006. Epub 2018 Jun 15. PubMed
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance. Wang T, Guan C, Guo J, Liu B, Wu Y, Xie Z, Zhang C, Xing XH. Nat Commun. 2018 Jun 26;9(1):2475. doi: 10.1038/s41467-018-04899-x. PubMed

Associated Plasmids

CRISPRi allows optimal temporal control of N-acetylglucosamine bioproduction by a dynamic coordination of glucose and xylose metabolism in Bacillus subtilis. Wu Y, Chen T, Liu Y, Lv X, Li J, Du G, Ledesma-Amaro R, Liu L. Metab Eng. 2018 Sep;49:232-241. doi: 10.1016/j.ymben.2018.08.012. Epub 2018 Aug 31. PubMed
Filamentation and restoration of normal growth in Escherichia coli using a combined CRISPRi sgRNA/antisense RNA approach. Muckl A, Schwarz-Schilling M, Fischer K, Simmel FC. PLoS One. 2018 Sep 11;13(9):e0198058. doi: 10.1371/journal.pone.0198058. eCollection 2018. PubMed
Regulation of ATP levels in Escherichia coli using CRISPR interference for enhanced pinocembrin production. Tao S, Qian Y, Wang X, Cao W, Ma W, Chen K, Ouyang P. Microb Cell Fact. 2018 Sep 18;17(1):147. doi: 10.1186/s12934-018-0995-7. PubMed
CRISPR Gene Perturbations Provide Insights for Improving Bacterial Biofuel Tolerance. Otoupal PB, Chatterjee A. Front Bioeng Biotechnol. 2018 Sep 4;6:122. doi: 10.3389/fbioe.2018.00122. eCollection 2018. PubMed
Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis. Otoupal PB, Cordell WT, Bachu V, Sitton MJ, Chatterjee A. Commun Biol. 2018 Sep 3;1:129. doi: 10.1038/s42003-018-0135-2. eCollection 2018. PubMed

Associated Plasmids

Selective Enrichment of Slow-Growing Bacteria in a Metabolism-Wide CRISPRi Library with a TIMER Protein. Beuter D, Gomes-Filho JV, Randau L, Diaz-Pascual F, Drescher K, Link H. ACS Synth Biol. 2018 Nov 16. doi: 10.1021/acssynbio.8b00379. PubMed
A step forward: Compatible and dual-inducible expression vectors for gene co-expression in Corynebacterium glutamicum. Gauttam R, Desiderato C, Jung L, Shah A, Eikmanns BJ. Plasmid. 2019 Jan;101:20-27. doi: 10.1016/j.plasmid.2018.12.004. Epub 2018 Dec 27. PubMed
CRISPR-Cas9 In Situ engineering of subtilisin E in Bacillus subtilis. Price MA, Cruz R, Baxter S, Escalettes F, Rosser SJ. PLoS One. 2019 Jan 7;14(1):e0210121. doi: 10.1371/journal.pone.0210121. eCollection 2019. PubMed
Combining orthogonal CRISPR and CRISPRi systems for genome engineering and metabolic pathway modulation in Escherichia coli. Sung LY, Wu MY, Lin MW, Hsu MN, Truong VA, Shen CC, Tu Y, Hwang KY, Tu AP, Chang YH, Hu YC. Biotechnol Bioeng. 2019 May;116(5):1066-1079. doi: 10.1002/bit.26915. Epub 2019 Feb 8. PubMed
Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. Sander T, Farke N, Diehl C, Kuntz M, Glatter T, Link H. Cell Syst. 2019 Jan 23;8(1):66-75.e8. doi: 10.1016/j.cels.2018.12.005. Epub 2019 Jan 9. PubMed
A xylose-inducible expression system and a CRISPRi-plasmid for targeted knock-down of gene expression in Clostridioides difficile. Muh U, Pannullo AG, Weiss DS, Ellermeier CD. J Bacteriol. 2019 Feb 11. pii: JB.00711-18. doi: 10.1128/JB.00711-18. PubMed

Associated Plasmids

A Self-Actuated Cellular Protein Delivery Machine. Ahan RE, Kirpat BM, Saltepe B, Seker UOS. ACS Synth Biol. 2019 Apr 19;8(4):686-696. doi: 10.1021/acssynbio.9b00062. Epub 2019 Mar 12. PubMed

Associated Plasmids

A simple dual-inducible CRISPR interference system for multiple gene targeting in Corynebacterium glutamicum. Gauttam R, Seibold GM, Mueller P, Weil T, Weiss T, Handrick R, Eikmanns BJ. Plasmid. 2019 May;103:25-35. doi: 10.1016/j.plasmid.2019.04.001. Epub 2019 Apr 4. PubMed
Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Nat Commun. 2019 May 9;10(1):2127. doi: 10.1038/s41467-019-09985-2. PubMed
Analysis of lipoprotein transport depletion in Vibrio cholerae using CRISPRi. Caro F, Place NM, Mekalanos JJ. Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17013-17022. doi: 10.1073/pnas.1906158116. Epub 2019 Aug 1. PubMed
Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Liu Y, Wan X, Wang B. Nat Commun. 2019 Aug 26;10(1):3693. doi: 10.1038/s41467-019-11479-0. PubMed
A broad-host-range CRISPRi toolkit for silencing gene expression in Burkholderia. Hogan AM, Rahman ASMZ, Lightly TJ, Cardona ST. ACS Synth Biol. 2019 Sep 6. doi: 10.1021/acssynbio.9b00232. PubMed

Associated Plasmids

Selective degradation of plasmid-derived mRNAs by MCPIP1 RNase. Qian Y, Li X, Miao R, Liu S, Xin HB, Huang X, Wang TT, Fu M. Biochem J. 2019 Oct 15;476(19):2927-2938. doi: 10.1042/BCJ20190646. PubMed
Expanding and understanding the CRISPR toolbox for Bacillus subtilis with MAD7 and dMAD7. Price MA, Cruz R, Bryson J, Escalettes F, Rosser SJ. Biotechnol Bioeng. 2020 Jun;117(6):1805-1816. doi: 10.1002/bit.27312. Epub 2020 Mar 3. PubMed
Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function. Shields RC, Walker AR, Maricic N, Chakraborty B, Underhill SAM, Burne RA. PLoS Pathog. 2020 Mar 9;16(3):e1008344. doi: 10.1371/journal.ppat.1008344. eCollection 2020 Mar. PubMed
Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation. Wiles TJ, Schlomann BH, Wall ES, Betancourt R, Parthasarathy R, Guillemin K. PLoS Biol. 2020 Mar 20;18(3):e3000661. doi: 10.1371/journal.pbio.3000661. eCollection 2020 Mar. PubMed
bolA gene involved in curli amyloids and fimbriae production in E. coli: exploring pathways to inhibit biofilm and amyloid formation. Azam MW, Zuberi A, Khan AU. J Biol Res (Thessalon). 2020 Jun 17;27:10. doi: 10.1186/s40709-020-00120-7. eCollection 2020 Dec. PubMed
Programmable CRISPR-Cas transcriptional activation in bacteria. Ho HI, Fang JR, Cheung J, Wang HH. Mol Syst Biol. 2020 Jul;16(7):e9427. doi: 10.15252/msb.20199427. PubMed
Bacteria Modify Their Sensitivity to Chemerin-Derived Peptides by Hindering Peptide Association With the Cell Surface and Peptide Oxidation. Godlewska U, Bilska B, Majewski P, Pyza E, Zabel BA, Cichy J. Front Microbiol. 2020 Aug 11;11:1819. doi: 10.3389/fmicb.2020.01819. eCollection 2020. PubMed
Strain engineering for high-level 5-aminolevulinic acid production in Escherichia coli. Miscevic D, Mao JY, Kefale T, Abedi D, Moo-Young M, Perry Chou C. Biotechnol Bioeng. 2021 Jan;118(1):30-42. doi: 10.1002/bit.27547. Epub 2020 Sep 9. PubMed
A multiplex CRISPR interference tool for virulence gene interrogation in Legionella pneumophila. Ellis NA, Kim B, Tung J, Machner MP. Commun Biol. 2021 Feb 4;4(1):157. doi: 10.1038/s42003-021-01672-7. PubMed
QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus. Yang Q, Zou P, Cao Z, Wang Q, Fu S, Xie G, Huang J. Front Cell Infect Microbiol. 2021 Jan 21;10:594652. doi: 10.3389/fcimb.2020.594652. eCollection 2020. PubMed
Inhibition of Escherichia coli Lipoprotein Diacylglyceryl Transferase Is Insensitive to Resistance Caused by Deletion of Braun's Lipoprotein. Diao J, Komura R, Sano T, Pantua H, Storek KM, Inaba H, Ogawa H, Noland CL, Peng Y, Gloor SL, Yan D, Kang J, Katakam AK, Volny M, Liu P, Nickerson NN, Sandoval W, Austin CD, Murray J, Rutherford ST, Reichelt M, Xu Y, Xu M, Yanagida H, Nishikawa J, Reid PC, Cunningham CN, Kapadia SB. J Bacteriol. 2021 Jun 8;203(13):e0014921. doi: 10.1128/JB.00149-21. Epub 2021 Jun 8. PubMed
A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Tong Y, Jorgensen TS, Whitford CM, Weber T, Lee SY. Nat Commun. 2021 Sep 1;12(1):5206. doi: 10.1038/s41467-021-25541-3. PubMed
Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli. Silvis MR, Rajendram M, Shi H, Osadnik H, Gray AN, Cesar S, Peters JM, Hearne CC, Kumar P, Todor H, Huang KC, Gross CA. mBio. 2021 Oct 26;12(5):e0256121. doi: 10.1128/mBio.02561-21. Epub 2021 Oct 12. PubMed
New Method for Genome-Scale Functional Genomic Study in Bacteria with Superior Performance: CRISPR Interference Screen. Liao X, Xing XH, Zhang C. Methods Mol Biol. 2022;2377:123-141. doi: 10.1007/978-1-0716-1720-5_7. PubMed
Potentiating antibiotic efficacy via perturbation of non-essential gene expression. Otoupal PB, Eller KA, Erickson KE, Campos J, Aunins TR, Chatterjee A. Commun Biol. 2021 Nov 5;4(1):1267. doi: 10.1038/s42003-021-02783-x. PubMed
Strain engineering and bioprocessing strategies for biobased production of porphobilinogen in Escherichia coli. Lall D, Miscevic D, Bruder M, Westbrook A, Aucoin M, Moo-Young M, Perry Chou C. Bioresour Bioprocess. 2021;8(1):122. doi: 10.1186/s40643-021-00482-3. Epub 2021 Dec 13. PubMed
CRISPR Interference (CRISPRi) Mediated Suppression of OmpR Gene in E. coli: An Alternative Approach to Inhibit Biofilm. Zuberi A, Azam MW, Khan AU. Curr Microbiol. 2022 Jan 29;79(3):78. doi: 10.1007/s00284-021-02760-x. PubMed
CRISPR Interference Modules as Low-Burden Logic Inverters in Synthetic Circuits. Bellato M, Frusteri Chiacchiera A, Salibi E, Casanova M, De Marchi D, Castagliuolo I, Cusella De Angelis MG, Magni P, Pasotti L. Front Bioeng Biotechnol. 2022 Jan 28;9:743950. doi: 10.3389/fbioe.2021.743950. eCollection 2021. PubMed

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