ArticleNucleic acids research2021
Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 52 citations in OpenAlex.
- Transcriptional landscape of metal-resistantJournal of bacteriology · 2026Article
- How mutagenesis and laboratory conditions affect the genome of the metal-resistant bacteriumJournal of bacteriology · 2026Article
- A Hanks-type bacterial kinase, PknS, directly phosphorylates the alternative sigma factor EcfK to promote resistance to protist predation.The FEBS journal · 2026Article
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- Article
- Structural basis of pausing during transcription initiation in mycobacterium tuberculosis.Nature communications · 2026Article
- Alternative Sigma Factors of RNA Polymerase as Master Regulators in the Pathogenic SpirochaetePathogens (Basel, Switzerland) · 2025Review
- Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning.Nucleic acids research · 2025Article
- Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.Scientific reports · 2025Article
- Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes.Nucleic acids research · 2025Article
- Structural basis for regulation of a CBASS-CRISPR-Cas defense island by a transmembrane anti-σ factor and its ECF σ partner.Science advances · 2024Article
- The modular architecture of sigma factors in cyanobacteria: a framework to assess their diversity and understand their evolution.BMC genomics · 2024Article
- MiST 4.0: a new release of the microbial signal transduction database, now with a metagenomic component.Nucleic acids research · 2024Article
- A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis.Biodesign research · 2024Article
- From regulation to ruin: a rogue sigma factor causes cell death inJournal of bacteriology · 2023Article
- Structure of the transcription open complex of distinct σNature communications · 2023Article
- Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria.Microorganisms · 2023Review
- Immunoreactivity of a Putative ECF σ Factor, LIC_10559, fromPathogens (Basel, Switzerland) · 2023Article
- RNA-activated protein cleavage with a CRISPR-associated endopeptidase.Science (New York, N.Y.) · 2022Article
- Expanding the genetic toolkit helps dissect a global stress response in the early-branching speciesProceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 4 countries.
Funding
Abstract
Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As a result, we identified an average of ∼10 ECFs per bacterial genome and 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands previous classification efforts ∼50-fold, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences and an openly accessible data repository called 'ECF Hub' (https://www.computational.bio.uni-giessen.de/ecfhub), will serve as a powerful hypothesis-generator to guide future research in the field.
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Registered trials
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.