ArticleProceedings of the National Academy of Sciences of the United States of America2020
Rewiring the specificity of extracytoplasmic function sigma factors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 25 citations in OpenAlex.
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- Article
- The N-Terminal Domain of LIC12756 Is the Key Determinant of This Protein's Anti-Sigma Activity Toward LIC12757 in PathogenicPathogens (Basel, Switzerland) · 2026Article
- Physiological roles of anmBio · 2025Article
- Peering into the Bacterial Cell: From Transcription to Functional Genomics.Journal of molecular biology · 2025Review
- Synthetic biology design principles enable efficient bioproduction of Heparosan with low molecular weight and low polydispersion index for the biomedical industry.Synthetic biology (Oxford, England) · 2025Article
- Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σJournal of computer-aided molecular design · 2024Article
- Physiological Roles of anbioRxiv : the preprint server for biology · 2024Article
- σCommunications biology · 2024Article
- A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis.Biodesign research · 2024Article
- Critical role of the RpoE stress response pathway in polymyxin resistance of Escherichia coli.The Journal of antimicrobial chemotherapy · 2023Article
- RNA-activated protein cleavage with a CRISPR-associated endopeptidase.Science (New York, N.Y.) · 2022Article
- Novel switchable ECF sigma factor transcription system for improving thaxtomin A production inSynthetic and systems biotechnology · 2022Article
- Intelligent host engineering for metabolic flux optimisation in biotechnology.The Biochemical journal · 2021Review
- Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses.International journal of molecular sciences · 2021Review
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Extracellular haem utilization by the opportunistic pathogen Pseudomonas aeruginosa and its role in virulence and pathogenesis.Advances in microbial physiology · 2021Article
- Multi-Omic Analyses Reveal Habitat Adaptation of Marine CyanobacteriumFrontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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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.