Evidence map›Paper›PMID 36279294›Full record

ArticlePLoS genetics2022

Intracellular acidification is a hallmark of thymineless death in E. coli.

Alexandra Ketcham, Lydia Freddolino, Saeed Tavazoie

Open access · goldAbstract read
In one paragraph

Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
1.7field-weighted citation impact, top 15% of its field
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

7 citing papers in PubMed, 9 citations in OpenAlex.

  1. Article
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  7. Regulation of phosphate starvation-specific responses inMicrobiology (Reading, England) · 2023
    Review
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

3 authors at 1 institution in 1 country.

Alexandra KetchamDepartment of Biological Sciences, Columbia University, New York, New York, United States of America.ORCID 0000-0003-1822-5577
Lydia FreddolinoDepartment of Systems Biology, Columbia University, New York, New York, United States of America.ORCID 0000-0002-5821-4226
Saeed TavazoieDepartment of Biological Sciences, Columbia University, New York, New York, United States of America.ORCID 0000-0003-2183-4162
Columbia University · US

Funding

Systems biological interrogation of bacterial persistenceR01AI077562 · NIAID · PRINCETON UNIVERSITY · PI TAVAZOIE, SAEED F · 2010 to 2024
$6.4M
Building a unified framework for understanding bacterial gene regulation and chromosomal architectureR35GM128637 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Lydia Petra Freddolino · 2018 to 2026
$3.6M
Evolutionary paths toward intrinsic antibiotic resistanceF31GM108419 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI KETCHAM, ALEXANDRA NOGUEIRA · 2013 to 2016
$172k
NIAID NIH HHS R01 AI077562NIGMS NIH HHS F31 GM108419NIGMS NIH HHS R35 GM128637
6 · The paper itself

Abstract

Thymidine starvation causes rapid cell death. This enigmatic process known as thymineless death (TLD) is the underlying killing mechanism of diverse antimicrobial and antineoplastic drugs. Despite decades of investigation, we still lack a mechanistic understanding of the causal sequence of events that culminate in TLD. Here, we used a diverse set of unbiased approaches to systematically determine the genetic and regulatory underpinnings of TLD in Escherichia coli. In addition to discovering novel genes in previously implicated pathways, our studies revealed a critical and previously unknown role for intracellular acidification in TLD. We observed that a decrease in cytoplasmic pH is a robust early event in TLD across different genetic backgrounds. Furthermore, we show that acidification is a causal event in the death process, as chemical and genetic perturbations that increase intracellular pH substantially reduce killing. We also observe a decrease in intracellular pH in response to exposure to the antibiotic gentamicin, suggesting that intracellular acidification may be a common mechanistic step in the bactericidal effects of other antibiotics.

Indexed as

Escherichia coliThymineDNA, BacterialHydrogen-Ion ConcentrationMicrobial ViabilityRecombination, GeneticDNA, BacterialThymine

Identifiers

PMID36279294
PMCPMC9632930
OpenAlexW4307171522

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.