Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

Area of Science:

• Molecular Biology
• Genomics
• Transcriptional Regulation

Background:

• RNA polymerase (RNAP) interactions with RNA molecules play crucial roles in gene expression.
• Identifying specific RNA sequences that directly modulate RNAP activity is essential for understanding gene regulation.

Purpose of the Study:

• To identify and characterize RNA signals that directly interact with RNAP and modulate bacterial transcription.
• To investigate the function and mechanisms of these RNAP-binding RNAs (RAPs) in controlling gene expression.

Main Methods:

• Deep sequencing of an E. coli genomic library enriched for RNAP-binding RNAs.
• In vitro and in vivo experimental approaches to characterize identified RAPs.
• Analysis of RAPs' impact on transcription termination and gene expression under various conditions.

Main Results:

• Numerous natural RNAP-binding aptamers (RAPs) were identified across the E. coli genome, with over 60% of genes containing RAPs in their mRNA.
• A subset of inhibitory RAPs (iRAPs) was characterized, which promote Rho-dependent transcription termination.
• An iRAP in the essential nadD gene demonstrated significant reduction in transcriptional output during stationary phase and oxidative stress, highlighting environmental responsiveness.
• iRAPs function by uncoupling transcription and translation, facilitating Rho access to nascent RNA.
• Antisense strand-encoded iRAPs were found to enhance gene expression by mitigating transcriptional interference.

Conclusions:

• A broad class of cis-acting RNA signals (RAPs) that globally control bacterial transcription has been uncovered.
• These RAPs act as regulatory elements, modulating transcription through direct interaction with RNAP.
• iRAPs provide a mechanism for bacteria to dynamically regulate gene expression in response to environmental cues, influencing transcription termination and interference.