The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG

Area of Science:

• Molecular Biology
• Microbiology
• Genetics

Background:

• RNA polymerase (RNAP) requires accessory factors for efficient synthesis of long RNA molecules.
• The precise molecular mechanisms by which these factors enhance RNAP processivity, by reducing pausing and termination, are not fully understood.

Purpose of the Study:

• To identify the specific RNA polymerase elements involved in the antipausing activity of the bacterial virulence factor RfaH.
• To elucidate the molecular mechanism by which RfaH and related factors increase RNA polymerase processivity.

Main Methods:

• Investigated the role of the RNAP β gate loop in RfaH-mediated antipausing activity.
• Differentiated between RfaH binding mechanisms and antipausing functions.

Main Results:

• The β gate loop of RNAP is essential for the antipausing activity of RfaH.
• RfaH interaction with the β gate loop, but not the β' clamp helices, is required for suppressing RNAP pausing and termination.
• Contacts with the β gate loop are also necessary for the antipausing function of NusG.

Conclusions:

• RfaH likely bridges the DNA channel via interactions with the clamp helices and gate loop, stabilizing RNAP and preventing pausing.
• Most NusG family homologs are proposed to utilize similar mechanisms involving the β gate loop to enhance RNAP processivity.