Modulation of protein activity by small RNA base pairing internal to coding sequences.

Area of Science:

• Bacterial regulatory RNAs
• Gene expression regulation
• RNA-RNA interactions

Background:

• Bacterial small RNAs (sRNAs) typically regulate translation initiation or mRNA decay.
• RNA-RNA interactome approaches reveal sRNA binding within coding sequences.

Purpose of the Study:

• Investigate the functional consequences of sRNA pairing within mRNA coding sequences.
• Determine the impact of sRNA overexpression on target protein levels and activity.

Main Methods:

• Overexpression of a specific sRNA (ArcZ) targeting seven different mRNAs.
• Analysis of target protein levels.
• Detailed examination of ArcZ-ligA and ArcZ-hemK interactions.
• Site-directed mutagenesis to disrupt sRNA-mRNA pairing.

Main Results:

• sRNA overexpression decreased target protein levels for two out of seven targets.
• ArcZ binding to ligA and hemK mRNAs caused translation pausing and increased protein activity.
• A ligA mutation disrupting ArcZ pairing led to increased DNA damage sensitivity.

Conclusions:

• Regulatory RNA pairing within coding sequences can slow translation elongation.
• This localized slowing impacts co-translational protein folding and cofactor incorporation.
• sRNA regulation in coding regions has significant physiological implications, as demonstrated by ligA regulation.