Evidence map›Paper›PMID 23224554›Full record

ArticleScience (New York, N.Y.)2012

Identity and function of a large gene network underlying mutagenic repair of DNA breaks.

Abu Amar M Al Mamun, Mary-Jane Lombardo, Chandan Shee, Andreas M Lisewski, Caleb Gonzalez, Dongxu Lin, Ralf B Nehring, Claude Saint-Ruf, Janet L Gibson, Ryan L Frisch and 3 more

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers.

0numbers the graph read from it
0cells of the map it votes in
137citing 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

137 citing papers in PubMed.

  1. Article
  2. Article
  3. Systematic CRISPRi screening reveals genetic modulators ofbioRxiv : the preprint server for biology · 2026
    Article
  4. Article
  5. "Excluded phenotypes" restrict genetic paths toward adaptation in declining populations.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Review
  15. Review
  16. Article
  17. Bacterial persisters: molecular mechanisms and therapeutic development.Signal transduction and targeted therapy · 2024
    Review
  18. Article
  19. Article
  20. Article

77 more citing papers are in PubMed but not listed here.

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

13 authors.

Abu Amar M Al MamunDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA.
Mary-Jane Lombardo
Chandan Shee
Andreas M Lisewski
Caleb Gonzalez
Dongxu Lin
Ralf B Nehring
Claude Saint-Ruf
Janet L Gibson
Ryan L Frisch
Olivier Lichtarge
P J Hastings
Susan M Rosenberg

Funding

Initiative for Maximizing Student Development (IMSD) ProgramR25GM056929 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI PEREIRA, FRED A · 1998 to 2023
$12.4M
Functional Determinnats in G Protein-coupled ReceptorsR01GM066099 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI LICHTARGE, OLIVIER · 2003 to 2022
$7.5M
MOLECULAR MECHANISMS /STRESS-INDUCED MUTATION /E. COLIR01GM053158 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI ROSENBERG, SUSAN M · 1997 to 2014
$7.4M
Comparative genomics of protein structure and functionR01GM079656 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI LICHTARGE, OLIVIER · 2007 to 2019
$4.3M
Mechanisms of Adaptive AmplificationR01GM064022 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI HASTINGS, PHILIP JOHN · 2001 to 2010
$2.3M
Forward Genomics of Damage Control: An Undiscovered Class of Cancer GenesDP1CA174424 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ROSENBERG, SUSAN M · 2012 to 2013
$1.5M
Molecular basis of stress-induced mutagenesisF32GM095267 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI FRISCH, RYAN LEWIS · 2012 to 2012
$52k
CONTROL OF HYPERMUTATION IN STATIONARY-PHASE E COLIF32GM019909 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI LOMBARDO, MARY J · 1999 to 2000
$43k
NCI NIH HHS DP1 CA174424NCI NIH HHS DP1-CA174424NIGMS NIH HHS F32 GM019909NIGMS NIH HHS F32 GM095267NIGMS NIH HHS F32-GM095267NIGMS NIH HHS F32-GM19909NIGMS NIH HHS GM66099NIGMS NIH HHS GM79656NIGMS NIH HHS R01 GM053158NIGMS NIH HHS R01 GM064022NIGMS NIH HHS R01 GM066099NIGMS NIH HHS R01 GM079656NIGMS NIH HHS R01-GM53158NIGMS NIH HHS R01-GM64022NIGMS NIH HHS R25 GM056929
6 · The paper itself

Abstract

Mechanisms of DNA repair and mutagenesis are defined on the basis of relatively few proteins acting on DNA, yet the identities and functions of all proteins required are unknown. Here, we identify the network that underlies mutagenic repair of DNA breaks in stressed Escherichia coli and define functions for much of it. Using a comprehensive screen, we identified a network of ≥93 genes that function in mutation. Most operate upstream of activation of three required stress responses (RpoS, RpoE, and SOS, key network hubs), apparently sensing stress. The results reveal how a network integrates mutagenic repair into the biology of the cell, show specific pathways of environmental sensing, demonstrate the centrality of stress responses, and imply that these responses are attractive as potential drug targets for blocking the evolution of pathogens.

Indexed as

DNA Breaks, Double-StrandedGene Expression Regulation, BacterialGene Regulatory NetworksBacterial ProteinsDNA RepairEscherichia coliMutagenesisSigma FactorSOS Response, GeneticsStress, PhysiologicalBacterial ProteinsSigma Factorsigma factor KatF protein, Bacteriasporulation-specific sigma factors

Identifiers

PMID23224554
PMCPMC3782309

What OpenQuestion holds

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Registered trials

None linked

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.