Structural basis of que pause in the pre$Q_1$-I riboswitch-bound RNA polymerase elongation complex

Abstract

Riboswitch is a non-coding RNA element that modulates transcription or translation. It attracts much attention because it offers clues about the regulation of RNA polymerases and the development of antibiotic drugs. Pre$Q_1$-I riboswitch regulates transcription of operons related to queuosine biosynthesis. Previous structural studies show that it forms a pseudoknot fold by itself. However, the structure of the pre$Q_1$-I riboswitch bound to RNA polymerase is still unknown. Here, we report its structure determined using single-particle electron cryo-electron microscopy. Our cryo-EM structure reveals that a single-stranded RNA is located on the RNA exit channel and no nucleic acids protrude through the secondary channel. Furthermore, the polymerase in the riboswitch complex shows a swiveling movement related to the elongation complex's pausing mechanism. These results are distinct from those of hairpin pause or the backtracking pause. Our structural study will help a deeper understanding of prokaryotic gene regulation by riboswitches.