pgRNA-bacteria Citations (62)
Originally described in: 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 pgRNA-bacteria
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| 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 |
One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces.
Huang H, Zheng G, Jiang W, Hu H, Lu Y.
Acta Biochim Biophys Sin (Shanghai). 2015 Apr;47(4):231-43. doi: 10.1093/abbs/gmv007. Epub 2015 Mar 3.
PubMed
Associated Plasmids |
| 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 |
| Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins. Fujii H, Fujita T. Int J Mol Sci. 2015 Sep 9;16(9):21802-12. doi: 10.3390/ijms160921802. 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 |
Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli.
Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin AP, Gill RT.
ACS Synth Biol. 2016 Apr 22.
PubMed
Associated Plasmids |
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 (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 |
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS.
Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048.
PubMed
Associated Plasmids |
tCRISPRi: tunable and reversible, one-step control of gene expression.
Li XT, Jun Y, Erickstad MJ, Brown SD, Parks A, Court DL, Jun S.
Sci Rep. 2016 Dec 20;6:39076. doi: 10.1038/srep39076.
PubMed
Associated Plasmids |
| CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Liang L, Liu R, Garst AD, Lee T, Nogue VSI, Beckham GT, Gill RT. Metab Eng. 2017 May;41:1-10. doi: 10.1016/j.ymben.2017.02.009. Epub 2017 Feb 16. 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 |
| 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 |
Targeted DNA methylation in human cells using engineered dCas9-methyltransferases.
Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD.
Sci Rep. 2017 Jul 27;7(1):6732. doi: 10.1038/s41598-017-06757-0.
PubMed
Associated Plasmids |
| 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 |
| Programmable DNA looping using engineered bivalent dCas9 complexes. Hao N, Shearwin KE, Dodd IB. Nat Commun. 2017 Nov 20;8(1):1628. doi: 10.1038/s41467-017-01873-x. 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 |
| Rapid identification of unknown carboxyl esterase activity in Corynebacterium glutamicum using RNA-guided CRISPR interference. Lee SS, Shin H, Jo S, Lee SM, Um Y, Woo HM. Enzyme Microb Technol. 2018 Jul;114:63-68. doi: 10.1016/j.enzmictec.2018.04.004. Epub 2018 Apr 9. PubMed |
| CRISPR interference-mediated metabolic engineering of Corynebacterium glutamicum for homo-butyrate production. Yoon J, Woo HM. Biotechnol Bioeng. 2018 Aug;115(8):2067-2074. doi: 10.1002/bit.26720. Epub 2018 May 8. PubMed |
Anaerobic production of medium-chain fatty alcohols via a beta-reduction pathway.
Mehrer CR, Incha MR, Politz MC, Pfleger BF.
Metab Eng. 2018 Jul;48:63-71. doi: 10.1016/j.ymben.2018.05.011. Epub 2018 May 25.
PubMed
Associated Plasmids |
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 |
| Metabolic engineering of Bacillus subtilis for l-valine overproduction. Westbrook AW, Ren X, Moo-Young M, Chou CP. Biotechnol Bioeng. 2018 Nov;115(11):2778-2792. doi: 10.1002/bit.26789. Epub 2018 Sep 25. 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 |
| 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 Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism.
Schober AF, Mathis AD, Ingle C, Park JO, Chen L, Rabinowitz JD, Junier I, Rivoire O, Reynolds KA.
Cell Rep. 2019 Jun 11;27(11):3359-3370.e7. doi: 10.1016/j.celrep.2019.05.030.
PubMed
Associated Plasmids |
| 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 |
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 |
| Quorum Sensing and Metabolic State of the Host Control Lysogeny-Lysis Switch of Bacteriophage T1. Laganenka L, Sander T, Lagonenko A, Chen Y, Link H, Sourjik V. mBio. 2019 Sep 10;10(5). pii: mBio.01884-19. doi: 10.1128/mBio.01884-19. PubMed |
| CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ. Microb Cell Fact. 2020 Apr 25;19(1):93. doi: 10.1186/s12934-020-01345-w. PubMed |
| Addressing the role of centromere sites in activation of ParB proteins for partition complex assembly. Audibert S, Tanguy-le-Gac N, Rech J, Turlan C, Bouet JY, Bystricky K, Lane D. PLoS One. 2020 May 7;15(5):e0226472. doi: 10.1371/journal.pone.0226472. eCollection 2020. 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 |
| 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 |
| 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 |
| Paratransgenic manipulation of a tsetse microRNA alters the physiological homeostasis of the fly's midgut environment. Yang L, Weiss BL, Williams AE, Aksoy E, de Silva Orfano A, Son JH, Wu Y, Vigneron A, Karakus M, Aksoy S. PLoS Pathog. 2021 Jun 9;17(6):e1009475. doi: 10.1371/journal.ppat.1009475. eCollection 2021 Jun. PubMed |
| Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Nat Commun. 2021 Sep 27;12(1):5664. doi: 10.1038/s41467-021-25992-8. 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 |
| 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 |
| MCR-1-dependent lipid remodelling compromises the viability of Gram-negative bacteria. Feng S, Liang W, Li J, Chen Y, Zhou D, Liang L, Lin D, Li Y, Zhao H, Du H, Dai M, Qin LN, Bai F, Doi Y, Zhong LL, Tian GB. Emerg Microbes Infect. 2022 Dec;11(1):1236-1249. doi: 10.1080/22221751.2022.2065934. PubMed |
| Establishment of genetic tools for genomic DNA engineering of Halomonas sp. KM-1, a bacterium with potential for biochemical production. Tsuji A, Takei Y, Azuma Y. Microb Cell Fact. 2022 Jun 20;21(1):122. doi: 10.1186/s12934-022-01797-2. PubMed |
| Efficient Suppression of Natural Plasmid-Borne Gene Expression in Carbapenem-Resistant Klebsiella pneumoniae Using a Compact CRISPR Interference System. Yao S, Wei D, Tang N, Song Y, Wang C, Feng J, Zhang G. Antimicrob Agents Chemother. 2022 Nov 15;66(11):e0089022. doi: 10.1128/aac.00890-22. Epub 2022 Oct 12. PubMed |
CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling.
Barber KW, Shrock E, Elledge SJ.
Cell Rep Methods. 2022 Oct 17;2(10):100318. doi: 10.1016/j.crmeth.2022.100318. eCollection 2022 Oct 24.
PubMed
Associated Plasmids |
| High-Fidelity Cytosine Base Editing in a GC-Rich Corynebacterium glutamicum with Reduced DNA Off-Target Editing Effects. Heo YB, Hwang GH, Kang SW, Bae S, Woo HM. Microbiol Spectr. 2022 Dec 21;10(6):e0376022. doi: 10.1128/spectrum.03760-22. Epub 2022 Nov 14. PubMed |
| Effect of chromosomal integration on catalytic performance of a multi-component P450 system in Escherichia coli. Luelf UJ, Bohmer LM, Li S, Urlacher VB. Biotechnol Bioeng. 2023 Jul;120(7):1762-1772. doi: 10.1002/bit.28404. Epub 2023 Apr 27. PubMed |
A metabolomics pipeline highlights microbial metabolism in bloodstream infections.
Mayers JR, Varon J, Zhou RR, Daniel-Ivad M, Beaulieu C, Bholse A, Glasser NR, Lichtenauer FM, Ng J, Vera MP, Huttenhower C, Perrella MA, Clish CB, Zhao SD, Baron RM, Balskus EP.
Cell. 2024 Jun 11:S0092-8674(24)00579-8. doi: 10.1016/j.cell.2024.05.035.
PubMed
Associated Plasmids |
| CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration. Boob AG, Zhu Z, Intasian P, Jain M, Petrov VA, Lane ST, Tan SI, Xun G, Zhao H. Nucleic Acids Res. 2024 Apr 12;52(6):e30. doi: 10.1093/nar/gkae062. PubMed |
| Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria. Wang P, Du X, Zhao Y, Wang W, Cai T, Tang K, Wang X. Appl Environ Microbiol. 2024 Apr 17;90(4):e0009524. doi: 10.1128/aem.00095-24. Epub 2024 Mar 18. PubMed |
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