The secret to 6S: regulating RNA polymerase by ribo-sequestration

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Transcription regulation is crucial for organism adaptation to changing environments.
• In Escherichia coli, the transition from exponential to stationary growth involves significant transcriptional reprogramming.
• Sigma 70 (σ70) is a key specificity subunit of RNA polymerase essential for exponential growth transcription.

Purpose of the Study:

• To investigate the molecular interactions between 6S RNA and the Eσ70 holoenzyme.
• To clarify the mechanism by which 6S RNA regulates σ70-dependent transcription during growth phase transitions.
• To determine if 6S RNA binding to Eσ70 mimics promoter DNA binding.

Main Methods:

• Detailed biochemical and structural analyses of 6S RNA and Eσ70 complexes.
• Mutational analysis of σ70 region 4 residues involved in 6S RNA interaction.
• Comparison of interaction interfaces between 6S RNA/Eσ70 and promoter DNA/Eσ70.

Main Results:

• 6S RNA binding to Eσ70 involves distinct contacts compared to promoter DNA binding.
• Specific residues in σ70 region 4 interact differently with 6S RNA than with promoter DNA.
• Several 6S RNA interaction residues in σ70 are also known to interact with protein activators.

Conclusions:

• 6S RNA actively regulates Eσ70 activity through specific molecular interactions, not just mimicry.
• These interactions modulate σ70-dependent transcription, facilitating the shift to stationary phase growth.
• 6S RNA represents a significant regulatory factor influencing Eσ70 by binding to region 4.