Elucidating the mechanism of RNA G-quadruplex mediated mitochondrial RNA polymerase pausing

Authors

• A Kaminski
• W Peele
• E Derose
• LC Pedersen
• MJ Borgnia
• G Mueller
• JA Watts

Abstract

This project studies the contribution of nucleic acid folding in the regulation of RNA polymerase pausing. In a previous study, we found the mitochondrial RNA polymerase (mtRNAP) pauses at hundreds of locations when transcribing the mitochondrial DNA, and these pauses are associated with sequences which form quadruplexes in the nascent RNA. While it has been shown DNA quadruplexes that form ahead of the polymerase can act as a barrier to elongation, it is less clear how RNA quadruplexes behind the mtRNAP can contribute to pausing. In this study, we used a structural biology approach to characterize the mechanism of RNA quadruplex mediated mtRNAP pausing. First, using a G4 forming sequence in the MT-CO1 gene (MT-CO1-G4) which is associated with paused mtRNAP, we showed the sequence forms a quadruplex in RNA, but not DNA, and regulates transcription by mtRNAP. We then designed an RNA-DNA template using the MT-CO1-G4 sequence and confirmed quadruplex folding through gel-based and spectroscopic assays. Next, we cloned and purified a truncated version of the mtRNAP protein. After evaluating its functional activity, we used cryo electron microscopy (Cryo-EM) to solve the apo structure of mtRNAP. With a functional RNA-DNA template and purified mtRNAP protein we are poised to solve the structure of a mtRNAP paused by an RNA G4 by Cryo-EM and X-ray crystallography. In this presentation I will discuss the implications of RNA G4 mediated mtRNAP pausing in the regulation of mitochondrial function.

Scientific Focus Area: RNA Biology

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