Nucleic Acid Sequence Determinants of Transcriptional Pausing by the Human Mitochondrial RNA Polymerase (POLRMT)

Transcription by RNA polymerase (RNAP) lies at the heart of gene expression in all organisms. The speed with which RNAPs produce RNA is tuned, in part, by signals in the transcribed nucleic acid sequences, which temporarily arrange RNAPs into a paused conformation that is unable to extend the RNA. In turn, the altered transcription kinetics of paused RNAPs determine the three-dimensional shape into which RNA ultimately folds and promote or inhibit cotranscriptional events. While pause sequence determinants have been characterized for multisubunit RNAPs in bacteria and in eukaryotic nuclei, this information is lacking for the single-subunit, T-odd phage-like RNAP of human mitochondria, POLRMT. Here, we developed a robust nucleic acid scaffold system to reconstitute POLRMT transcription in vitro and identified multiple transcriptional pause sites on the human mitochondrial DNA (mtDNA). Using one of the pause sequences as a representative, we performed a suite of mutational studies to pinpoint the nucleic acid elements that enhance, weaken, or completely abolish POLRMT pausing. Based on these mutational results, we constructed a consensus pause motif expected to cause strong pausing for POLRMT: 5′-R–10NNNNNNNGT–1G+1-3′, where −1 is the 3′ nascent RNA nucleotide in the POLRMT active site, +1 is the incoming NTP to be added to the nascent RNA, R is A or G, and N is any base. Strikingly, most of the consensus pause elements in this motif are the same for multisubunit prokaryotic and nuclear RNAPs, hinting at potentially shared features of the pausing mechanism despite the structural differences between polymerases. Finally, a search of the human mtDNA for this pause motif revealed multiple predicted pause sites with potential roles in mitochondrial cotranscriptional processes.