Rewiring the specificity of extracytoplasmic function sigma factors

Area of Science:

• Bacterial genomics
• Molecular biology
• Systems biology

Background:

• Bacterial genome sequencing is advancing rapidly, but understanding gene regulation is lagging.
• Deciphering transcriptional wiring is crucial for discovering new biological insights from genomic data.
• Accurate prediction of DNA-binding sites for regulators is essential for de novo determination of regulatory interactions.

Purpose of the Study:

• To solve the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs).
• To predict the regulons (sets of genes regulated) for ECF σs.
• To develop a framework for deciphering bacterial gene regulatory networks.

Main Methods:

• Leveraged autoregulation of ECF σs for promoter discovery to create aligned collections of ECF σs and their promoters.
• Analyzed conserved amino acid-nucleotide interactions to determine promoter specificity.
• Combined specificity predictions with phylogenetic footprinting using precomputed orthologs to identify direct gene targets.

Main Results:

• Successfully predicted the DNA-specificity code for ECF σs.
• Identified and characterized conserved interactions determining promoter specificity.
• Predicted direct targets for approximately 67% of ECF σs, revealing both global and local regulatory roles.
• Discovered that some ECF σs act as conserved global regulators, while others are species-specific local regulators.

Conclusions:

• The study provides a conceptual and computational framework for deciphering bacterial gene regulatory networks.
• Reveals fundamental organizing principles of bacterial gene regulation.
• Enables de novo prediction of ECF σ specificity and target genes, advancing our understanding of bacterial biology.