Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• Transcriptional pausing is a critical step for termination in gene expression.
• Rho factor-dependent termination is a key mechanism in bacteria for regulating gene expression.

Purpose of the Study:

• To investigate the interplay and efficiencies of the three known Rho-dependent termination routes.
• To elucidate the role of transcriptional pause duration in Rho-dependent termination efficiency.
• To understand how factors like NusA/NusG, competitor RNAs, and crowding agents affect termination.

Main Methods:

• Single-molecule studies were employed to analyze bacterial Rho factor-dependent terminators.
• Investigated the dynamics of Rho factor binding to nascent RNA and RNA polymerase (RNAP).
• Examined the release of transcript RNA and template DNA from RNAP under various conditions.

Main Results:

• All three Rho-dependent termination routes can operate simultaneously within a single terminator.
• Termination efficiencies are unexpectedly dependent on transcriptional pause duration.
• The stand-by Rho route's efficiency positively correlates with pause duration, unlike the catch-up Rho routes.

Conclusions:

• Long transcriptional pauses are not essential for catch-up Rho termination but benefit the stand-by Rho route.
• Rho-dependent termination of specific riboswitches (mgtA and ribB) is primarily modulated by the stand-by route.
• Findings challenge long-standing assumptions about the role of pause duration in Rho-dependent termination.