Literature DB >> 33285498

Bacterial CRISPR screens for gene function.

Horia Todor1, Melanie R Silvis1, Hendrik Osadnik1, Carol A Gross2.   

Abstract

In this review we describe the application of CRISPR tools for functional genomics screens in bacteria, with a focus on the use of interference (CRISPRi) approaches. We review recent developments in CRISPRi titration, which has enabled essential gene functional screens, and genome-scale pooled CRISPRi screens. We summarize progress toward enabling CRISPRi screens in non-model and pathogenic bacteria, including the development of new dCas9 variants. Taking into account the current state of the field, we provide a forward-looking analysis of CRISPRi strategies for determining gene function in bacteria.
Copyright © 2020. Published by Elsevier Ltd.

Entities:  

Year:  2020        PMID： 33285498      PMCID： PMC8331264          DOI： 10.1016/j.mib.2020.11.005

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN： 1369-5274            Impact factor:   7.934


  57 in total

1.  A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance.

Authors:  James K Martin; Joseph P Sheehan; Benjamin P Bratton; Gabriel M Moore; André Mateus; Sophia Hsin-Jung Li; Hahn Kim; Joshua D Rabinowitz; Athanasios Typas; Mikhail M Savitski; Maxwell Z Wilson; Zemer Gitai
Journal:  Cell       Date:  2020-06-03       Impact factor: 41.582

2.  Modulating Pathogenesis with Mobile-CRISPRi.

Authors:  Jiuxin Qu; Neha K Prasad; Michelle A Yu; Shuyan Chen; Amy Lyden; Nadia Herrera; Melanie R Silvis; Emily Crawford; Mark R Looney; Jason M Peters; Oren S Rosenberg
Journal:  J Bacteriol       Date:  2019-10-21       Impact factor: 3.490

3.  Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis.

Authors:  John S Hawkins; Melanie R Silvis; Byoung-Mo Koo; Jason M Peters; Hendrik Osadnik; Marco Jost; Cameron C Hearne; Jonathan S Weissman; Horia Todor; Carol A Gross
Journal:  Cell Syst       Date:  2020-10-19       Impact factor: 10.304

4.  High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae.

Authors:  Xue Liu; Clement Gallay; Morten Kjos; Arnau Domenech; Jelle Slager; Sebastiaan P van Kessel; Kèvin Knoops; Robin A Sorg; Jing-Ren Zhang; Jan-Willem Veening
Journal:  Mol Syst Biol       Date:  2017-05-10       Impact factor: 11.429

5.  Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria.

Authors:  Chen Dong; Jason Fontana; Anika Patel; James M Carothers; Jesse G Zalatan
Journal:  Nat Commun       Date:  2018-06-27       Impact factor: 14.919

6.  Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi).

Authors:  Sara Cleto; Jaide Vk Jensen; Volker F Wendisch; Timothy K Lu
Journal:  ACS Synth Biol       Date:  2016-02-16       Impact factor: 5.110

7.  Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent.

Authors:  Marco Jost; Yuwen Chen; Luke A Gilbert; Max A Horlbeck; Lenno Krenning; Grégory Menchon; Ankit Rai; Min Y Cho; Jacob J Stern; Andrea E Prota; Martin Kampmann; Anna Akhmanova; Michel O Steinmetz; Marvin E Tanenbaum; Jonathan S Weissman
Journal:  Mol Cell       Date:  2017-10-05       Impact factor: 17.970

8.  Programmable CRISPR-Cas transcriptional activation in bacteria.

Authors:  Hsing-I Ho; Jennifer R Fang; Jacky Cheung; Harris H Wang
Journal:  Mol Syst Biol       Date:  2020-07       Impact factor: 11.429

9.  Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes.

Authors:  Lun Yao; Kiyan Shabestary; Sara M Björk; Johannes Asplund-Samuelsson; Haakan N Joensson; Michael Jahn; Elton P Hudson
Journal:  Nat Commun       Date:  2020-04-03       Impact factor: 14.919

10.  Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes.

Authors:  Timothy J de Wet; Kristy R Winkler; Musa Mhlanga; Valerie Mizrahi; Digby F Warner
Journal:  Elife       Date:  2020-11-06       Impact factor: 8.713
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  9 in total

1.  Computational pipeline for designing guide RNAs for mismatch-CRISPRi.

Authors:  Jordi van Gestel; John S Hawkins; Horia Todor; Carol A Gross
Journal:  STAR Protoc       Date:  2021-05-05

2.  CRISPR Interference Efficiently Silences Latent and Lytic Viral Genes in Kaposi's Sarcoma-Associated Herpesvirus-Infected Cells.

Authors:  Kevin Brackett; Ameera Mungale; Mary Lopez-Isidro; Duncan A Proctor; Guillermo Najarro; Carolina Arias
Journal:  Viruses       Date:  2021-04-28       Impact factor: 5.048

Review 3.  Gradients in gene essentiality reshape antibacterial research.

Authors:  Andrew M Hogan; Silvia T Cardona
Journal:  FEMS Microbiol Rev       Date:  2022-05-06       Impact factor: 15.177

Review 4.  Next-generation microbiology: from comparative genomics to gene function.

Authors:  Carolin M Kobras; Andrew K Fenton; Samuel K Sheppard
Journal:  Genome Biol       Date:  2021-04-29       Impact factor: 13.583

5.  Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p-coumarate.

Authors:  Jacob A Fenster; Allison Z Werner; Jian Wei Tay; Matthew Gillen; Leo Schirokauer; Nicholas C Hill; Audrey Watson; Kelsey J Ramirez; Christopher W Johnson; Gregg T Beckham; Jeffrey C Cameron; Carrie A Eckert
Journal:  Metab Eng Commun       Date:  2022-08-28

6.  Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum.

Authors:  Ye Liu; Ruoyu Wang; Jiahui Liu; Hui Lu; Haoran Li; Yu Wang; Xiaomeng Ni; Junwei Li; Yanmei Guo; Hongwu Ma; Xiaoping Liao; Meng Wang
Journal:  Sci Adv       Date:  2022-08-31       Impact factor: 14.957

7.  Development and validation of a CRISPR interference system for gene regulation in Campylobacter jejuni.

Authors:  Ruby Costigan; Emily Stoakes; R Andres Floto; Julian Parkhill; Andrew J Grant
Journal:  BMC Microbiol       Date:  2022-10-05       Impact factor: 4.465

8.  Improved Dynamic Range of a Rhamnose-Inducible Promoter for Gene Expression in Burkholderia spp.

Authors:  Andrew M Hogan; Kevin R Jeffers; Armando Palacios; Silvia T Cardona
Journal:  Appl Environ Microbiol       Date:  2021-08-26       Impact factor: 4.792

9.  Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system.

Authors:  Dandan Jiang; Dandan Zhang; Shengnan Li; Yueting Liang; Qianwei Zhang; Xu Qin; Jinlan Gao; Jin-Long Qiu
Journal:  Mol Plant Pathol       Date:  2021-12-26       Impact factor: 5.663
  9 in total

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