Evidence map›Paper›PMID 38456318›Full record

ArticleG3 (Bethesda, Md.)2024

A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth.

Richard S Pollenz, Kaylee Barnhill, Abbigail Biggs, Jackson Bland, Victoria Carter, Michael Chase, Hayley Clark, Caitlyn Coleman, Marshall Daffner, Caitlyn Deam and 22 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors.

Richard S PollenzDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.ORCID 0000-0001-8891-6053
Kaylee BarnhillDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Abbigail BiggsDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Jackson BlandDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Victoria CarterDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Michael ChaseDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Hayley ClarkDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Caitlyn ColemanDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Marshall DaffnerDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Caitlyn DeamDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Alyssa FinocchiaroDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Vanessa FrancoDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Thomas FullerDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Juan Gallardo PineraDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Mae HorneDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Zoe HowardDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Olivia KanahanDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Christopher MiklaszewskiDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Sydney MillerDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Ryan MorganDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Oluwatobi OnalajaDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Louis OteroDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Shivani PadhyeDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Emily RaineyDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Fareed RasulDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Kobe RobichauxDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Alexandra RodierDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Sydni SchlosserDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Ava SciacchitanoDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Emma StewartDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Rajvi ThakkarDepartment of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Danielle M HellerCenter for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA.ORCID 0000-0002-6581-1256

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.

Indexed as

Genome, ViralMycobacteriophagesMycobacterium smegmatisViral ProteinsViral ProteinscytotoxicitymycobacteriophagesMycobacterium smegmatisphage–host interactions

Identifiers

PMID38456318
PMCPMC11075535

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.