Persistence and plasticity in bacterial gene regulation.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transcription factors (TFs) regulate gene expression, but their target genes are largely uncharacterized across many species.
• Understanding TF-target gene interactions is crucial for deciphering cellular functions and regulatory networks.

Purpose of the Study:

• To develop and apply a high-throughput method for genome-wide characterization of TF-target gene interactions across diverse bacterial species.
• To investigate the evolutionary dynamics and functional significance of transcriptional regulatory modules.

Main Methods:

• A high-throughput approach was employed to generate genome-wide binding maps for 354 transcription factors across 48 bacterial species.
• Phenotypic data was integrated to define functional regulatory modules and pathways.
• TF DNA-binding motifs were identified and analyzed for conservation.

Main Results:

• Generated 17,000 genome-wide binding maps, revealing ancient conservation and rapid evolution of regulatory modules.
• Observed regulatory rewiring where TF function is conserved but target genes diverge, leading to new functions.
• Identified 242 new TF DNA-binding motifs, significantly increasing known motifs for *Escherichia coli* and annotating motifs in *Pseudomonas simiae*.

Conclusions:

• The developed method is a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.
• The study provides insights into the evolution of transcriptional regulation and bacterial promoter architecture.
• The findings expand the understanding of TF-mediated gene regulation and its role in functional diversification.