Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters.

Area of Science:

• Microbiology
• Molecular Biology
• Genomics

Background:

• Transcription factors (TFs) primarily regulate bacterial transcription by binding to promoter regions.
• The role and mechanisms of TFs binding within coding sequences (CDS) in prokaryotes are largely unknown.

Purpose of the Study:

• To investigate the binding patterns and regulatory functions of bacterial TFs within coding sequences (CDS).
• To elucidate novel mechanisms by which CDS-bound TFs influence gene transcription and expression.

Main Methods:

• Analysis of 409 bacterial TF datasets, including ChIP-seq and SELEX assays across seven model bacteria.
• Biochemical and genetic experiments to validate TF binding and regulatory effects.
• Strand-specific RNA sequencing and ChIP-seq/Ribo-seq co-analysis to identify regulatory targets and mechanisms.

Main Results:

• Bacterial TFs exhibit similar binding capabilities in both coding and intergenic/promoter regions.
• Identified three distinct regulatory mechanisms for CDS-bound TFs: regulation of adjacent genes, cryptic promoter activation leading to antisense RNA, and interference with transcriptional elongation.
• TF RhpR was shown to affect translational efficiency of bound genes.

Conclusions:

• Bacterial TFs can bind and regulate genes within coding sequences, challenging the traditional promoter-centric view.
• The study reveals novel regulatory roles for CDS-bound TFs, highlighting the complexity of bacterial transcriptomes and the prevalence of internal cryptic promoters.