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Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

https://doi.org/10.1101/749887
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471142727.mb0117s79openalex-snapshot
E. coli Genome Manipulation by P1 Transduction
inferredcites →https://doi.org/10.1002/0471250953.bi1107s32openalex-snapshot
Aligning Short Sequencing Reads with Bowtie
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Two regulatory fim genes, fimB and fimE, control the phase variation of type 1 fimbriae in Escherichia coli.
inferredcites →https://doi.org/10.1006/abbi.1999.1518openalex-snapshot
Iron and Oxidative Stress in Bacteria
inferredcites →https://doi.org/10.1007/978-1-4939-0554-6_12openalex-snapshot
Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq
inferredcites →https://doi.org/10.1007/bf00331127openalex-snapshot
Amber suppression relaxes stringent control by elongating stringent factor
inferredcites →https://doi.org/10.1016/0378-4274(95)03532-xopenalex-snapshot
Toxicity of iron and hydrogen peroxide: the Fenton reaction
inferredcites →https://doi.org/10.1016/b0-08-043748-6/08214-1openalex-snapshot
Iron–Sulfur Clusters in Enzyme Catalysis
inferredcites →https://doi.org/10.1016/j.bbabio.2013.05.001openalex-snapshot
Reprint of: Iron/sulfur proteins biogenesis in prokaryotes: Formation, regulation and diversity
inferredcites →https://doi.org/10.1016/j.cell.2007.06.049openalex-snapshot
A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics
inferredcites →https://doi.org/10.1016/j.celrep.2015.07.043openalex-snapshot
Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
inferredcites →https://doi.org/10.1016/j.mib.2015.01.004openalex-snapshot
Diagnosing oxidative stress in bacteria: not as easy as you might think
inferredcites →https://doi.org/10.1016/s0378-1097(00)00148-8openalex-snapshot
The role of antioxidant enzymes in response of Escherichia coli to osmotic upshift
inferredcites →https://doi.org/10.1021/bi3003204openalex-snapshot
Characterization of the [2Fe-2S] Cluster of Escherichia coli Transcription Factor IscR
inferredcites →https://doi.org/10.1038/286524a0openalex-snapshot
Prevalence of amber suppressor-containing coliforms in the natural environment
inferredcites →https://doi.org/10.1038/msb4100050openalex-snapshot
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
inferredcites →https://doi.org/10.1038/ncomms12984openalex-snapshot
Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nsmb.2568openalex-snapshot
Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity
inferredcites →https://doi.org/10.1073/pnas.0911586107openalex-snapshot
A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life
inferredcites →https://doi.org/10.1073/pnas.251550898openalex-snapshot
IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins
inferredcites →https://doi.org/10.1073/pnas.96.24.13703openalex-snapshot
Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm
inferredcites →https://doi.org/10.1074/jbc.m406487200openalex-snapshot
Repair of Oxidized Iron-Sulfur Clusters in Escherichia coli
inferredcites →https://doi.org/10.1074/jbc.m408754200openalex-snapshot
Are Respiratory Enzymes the Primary Sources of Intracellular Hydrogen Peroxide?
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/genetics/165.2.455openalex-snapshot
Why Are Suppressors of Amber Mutations So Frequent Among Escherichia coli K12 Strains?: A Plausible Explanation for a Long-Lasting Puzzle
inferredcites →https://doi.org/10.1093/nar/gky983openalex-snapshot
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation
inferredcites →https://doi.org/10.1097/wox.0b013e3182439613openalex-snapshot
Oxidative Stress and Antioxidant Defense
inferredcites →https://doi.org/10.1099/mic.0.2007/010363-0openalex-snapshot
Comparative analysis of FimB and FimE recombinase activity
inferredcites →https://doi.org/10.1101/536201openalex-snapshot
Escherichia coli O157:H7 responds to phosphate starvation by modifying LPS involved in biofilm formation
inferredcites →https://doi.org/10.1101/575134openalex-snapshot
Non-lethal exposure to H 2 O 2 boosts bacterial survival and evolvability against oxidative stress
inferredcites →https://doi.org/10.1101/cshperspect.a012559openalex-snapshot
DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation
inferredcites →https://doi.org/10.1111/j.1365-2958.2006.05028.xopenalex-snapshot
Iron‐sulphur clusters and the problem with oxygen
inferredcites →https://doi.org/10.1111/j.1365-2958.2011.07593.xopenalex-snapshot
The alternative aerobic ribonucleotide reductase of Escherichia coli , NrdEF, is a manganese‐dependent enzyme that enables cell replication during periods of iron starvation
inferredcites →https://doi.org/10.1111/j.1365-2958.2011.07594.xopenalex-snapshot
Making DNA without iron – induction of a manganese‐dependent ribonucleotide reductase in response to iron starvation
inferredcites →https://doi.org/10.1128/aem.01015-12openalex-snapshot
Phosphate Starvation Promotes Swarming Motility and Cytotoxicity of Pseudomonas aeruginosa
inferredcites →https://doi.org/10.1128/aem.02246-14openalex-snapshot
Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium
inferredcites →https://doi.org/10.1128/aem.69.6.3406-3411.2003openalex-snapshot
Increasing the Oxidative Stress Response AllowsEscherichia coliTo Overcome Inhibitory Effects of Condensed Tannins
inferredcites →https://doi.org/10.1128/iai.00801-12openalex-snapshot
YbcL of Uropathogenic Escherichia coli Suppresses Transepithelial Neutrophil Migration
inferredcites →https://doi.org/10.1128/iai.68.1.30-37.2000openalex-snapshot
Increased Expression of Periplasmic Cu,Zn Superoxide Dismutase Enhances Survival of Escherichia coli Invasive Strains within Nonphagocytic Cells
inferredcites →https://doi.org/10.1128/jb.00946-13openalex-snapshot
Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms
inferredcites →https://doi.org/10.1128/jb.01990-07openalex-snapshot
Genome-Wide Transcriptional Responses ofEscherichia coliK-12 to Continuous Osmotic and Heat Stresses
inferredcites →https://doi.org/10.1128/jb.06226-11openalex-snapshot
Evidence that the Folate-Dependent Proteins YgfZ and MnmEG Have Opposing Effects on Growth and on Activity of the Iron-Sulfur Enzyme MiaB
inferredcites →https://doi.org/10.1128/jb.131.2.505-511.1977openalex-snapshot
Two systems for the uptake of phosphate in Escherichia coli
inferredcites →https://doi.org/10.1128/jb.181.15.4639-4643.1999openalex-snapshot
OxyR and SoxRS Regulation of fur
inferredcites →https://doi.org/10.1128/jb.183.17.5008-5014.2001openalex-snapshot
Characterization of PitA and PitB from Escherichia coli
inferredcites →https://doi.org/10.1128/jb.185.7.2236-2242.2003openalex-snapshot
Differential Expression of the Escherichia coli Autoaggregation Factor Antigen 43
inferredcites →https://doi.org/10.1128/jb.186.21.7364-7368.2004openalex-snapshot
Diversion of the Metabolic Flux from Pyruvate Dehydrogenase to Pyruvate Oxidase Decreases Oxidative Stress during Glucose Metabolism in Nongrowing Escherichia coli Cells Incubated under Aerobic, Phosphate Starvation Conditions
inferredcites →https://doi.org/10.1128/jb.187.2.434-442.2005openalex-snapshot
Starvation for Different Nutrients in Escherichia coli Results in Differential Modulation of RpoS Levels and Stability
inferredcites →https://doi.org/10.1128/mmbr.00034-07openalex-snapshot
Fe-S Cluster Assembly Pathways in Bacteria
inferredcites →https://doi.org/10.1128/mmbr.52.3.354-374.1988openalex-snapshot
Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli
inferredcites →https://doi.org/10.1128/mr.55.4.561-585.1991openalex-snapshot
Oxidative stress responses in Escherichia coli and Salmonella typhimurium
inferredcites →https://doi.org/10.1186/1423-0127-17-84openalex-snapshot
A role of ygfZ in the Escherichia coli response to plumbagin challenge
inferredcites →https://doi.org/10.1186/1471-2164-9-568openalex-snapshot
Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant
inferredcites →https://doi.org/10.1186/1475-2859-10-39openalex-snapshot
Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition
inferredcites →https://doi.org/10.1186/1475-2859-12-23openalex-snapshot
Escherichia coli avoids high dissolved oxygen stress by activation of SoxRS and manganese-superoxide dismutase
inferredcites →https://doi.org/10.1186/1752-0509-4-122openalex-snapshot
A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress
inferredcites →https://doi.org/10.1186/s12859-017-1469-3openalex-snapshot
AfterQC: automatic filtering, trimming, error removing and quality control for fastq data
inferredcites →https://doi.org/10.1186/s12934-017-0819-1openalex-snapshot
Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pone.0007002openalex-snapshot
Design Parameters to Control Synthetic Gene Expression in Escherichia coli
inferredcites →https://doi.org/10.1371/journal.pone.0026172openalex-snapshot
Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli
inferredcites →https://doi.org/10.1371/journal.pone.0051179openalex-snapshot
Enhancing E. coli Tolerance towards Oxidative Stress via Engineering Its Global Regulator cAMP Receptor Protein (CRP)
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.2144/000114302openalex-snapshot
A Streamlined Ribosome Profiling Protocol for the Characterization of Microorganisms

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.lwt.2019.108787openalex-snapshot
Resistance of biofilm formation and formed-biofilm of Escherichia coli O157:H7 exposed to acid stress
inferred← citeshttps://doi.org/10.1101/2021.07.12.451780openalex-snapshot
Experimental evolution of Vibrio cholerae : Identification of genes involved in motility in presence of polymyxin B
inferred← citeshttps://doi.org/10.3389/fmicb.2022.932165openalex-snapshot
Experimental evolution of Vibrio cholerae identifies hypervesiculation as a way to increase motility in the presence of polymyxin B
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