Literature DB >> 35104846

Gradients in gene essentiality reshape antibacterial research.

Andrew M Hogan1, Silvia T Cardona1,2.   

Abstract

Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
© The Author(s) 2022. Published by Oxford University Press on behalf of FEMS.

Entities:  

Keywords:  CRISPRi; antibiotic discovery; conditional essentiality; cystic fibrosis; essential gene; genetic interaction; transposon mutagenesis

Mesh:

Substances:

Year:  2022        PMID: 35104846      PMCID: PMC9075587          DOI: 10.1093/femsre/fuac005

Source DB:  PubMed          Journal:  FEMS Microbiol Rev        ISSN: 0168-6445            Impact factor:   15.177


  253 in total

1.  Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA.

Authors:  Y Ji; B Zhang; S F Van; P Warren; G Woodnutt; M K Burnham; M Rosenberg
Journal:  Science       Date:  2001-09-21       Impact factor: 47.728

Review 2.  Emerging and evolving concepts in gene essentiality.

Authors:  Giulia Rancati; Jason Moffat; Athanasios Typas; Norman Pavelka
Journal:  Nat Rev Genet       Date:  2017-10-16       Impact factor: 53.242

3.  Chronic Stenotrophomonas maltophilia infection and mortality or lung transplantation in cystic fibrosis patients.

Authors:  Valerie Waters; Eshetu G Atenafu; Annie Lu; Yvonne Yau; Elizabeth Tullis; Felix Ratjen
Journal:  J Cyst Fibros       Date:  2013-01-05       Impact factor: 5.482

4.  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

5.  Global assessment of genomic regions required for growth in Mycobacterium tuberculosis.

Authors:  Yanjia J Zhang; Thomas R Ioerger; Curtis Huttenhower; Jarukit E Long; Christopher M Sassetti; James C Sacchettini; Eric J Rubin
Journal:  PLoS Pathog       Date:  2012-09-27       Impact factor: 6.823

6.  A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration.

Authors:  Apollo Stacy; Derek Fleming; Richard J Lamont; Kendra P Rumbaugh; Marvin Whiteley
Journal:  MBio       Date:  2016-06-28       Impact factor: 7.867

Review 7.  Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli.

Authors:  Enrique Martínez-Carranza; Hugo Barajas; Luis-David Alcaraz; Luis Servín-González; Gabriel-Yaxal Ponce-Soto; Gloria Soberón-Chávez
Journal:  Front Microbiol       Date:  2018-05-29       Impact factor: 5.640

8.  In Vitro Activity of the Ultrabroad-Spectrum Beta-Lactamase Inhibitor QPX7728 in Combination with Multiple Beta-Lactam Antibiotics against Pseudomonas aeruginosa.

Authors:  Olga Lomovskaya; Debora Rubio-Aparicio; Kirk Nelson; Dongxu Sun; Ruslan Tsivkovski; Mariana Castanheira; Jill Lindley; Jeffery Loutit; Michael Dudley
Journal:  Antimicrob Agents Chemother       Date:  2021-05-18       Impact factor: 5.191

9.  Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q.

Authors:  Jasper E Neggers; Brenton R Paolella; Adhana Asfaw; Michael V Rothberg; Thomas A Skipper; Annan Yang; Radha L Kalekar; John M Krill-Burger; Neekesh V Dharia; Guillaume Kugener; Jérémie Kalfon; Chen Yuan; Nancy Dumont; Alfredo Gonzalez; Mai Abdusamad; Yvonne Y Li; Liam F Spurr; Westley W Wu; Adam D Durbin; Brian M Wolpin; Federica Piccioni; David E Root; Jesse S Boehm; Andrew D Cherniack; Aviad Tsherniak; Andrew L Hong; William C Hahn; Kimberly Stegmaier; Todd R Golub; Francisca Vazquez; Andrew J Aguirre
Journal:  Cell Rep       Date:  2020-12-15       Impact factor: 9.423

10.  CRISPR RNA-guided activation of endogenous human genes.

Authors:  Morgan L Maeder; Samantha J Linder; Vincent M Cascio; Yanfang Fu; Quan H Ho; J Keith Joung
Journal:  Nat Methods       Date:  2013-07-25       Impact factor: 28.547

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