Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase

Abstract

Gene transcription is catalyzed by DNA-dependent RNA polymerases (RNAPs) in a multistep regulated process (1)(2)(3)(4). Multi-subunit and single-subunit RNAPs catalyze transcription initiation by a series of events -(i) promoter-specific recognition, (ii) formation of a transcription bubble, (iii) RNA synthesis accompanied by DNA scrunching, and (iv) aborted synthesis of short RNA transcripts or transition to the elongation phase with promoter release. Understanding the mechanism of transcription initiation requires capturing key intermediate states of RNAP complexes and characterizing them biochemically and structurally. Mitochondrial DNA is transcribed by single-subunit RNAPs (mtRNAP), which unlike their phage counterparts, depend on one or more transcription factors for promoter-specific transcription initiation. Much of our understanding of mitochondrial DNA transcription comes from studies of yeast (S. cerevisiae) and human mtRNAPs (2,3,5). The yeast mtRNAP transcription initiation complex (y-mtIC) is comprised of the catalytic subunit RPO41 and a transcription factor MTF1. The human mtRNAP transcription initiation complex (h-mtIC) comprises of POLRMT and two transcription factors. The h-mtIC has been structurally characterized by crystallography (6), but the structure was captured in an inactive fingersclenched state with a major part of the transcription bubble disordered. Hence, the structural basis for promoter melting, DNA scrunching, and transcription initiation remains largely unknown for the mtRNAPs. RPO41 (∆N100) and MTF1 were assembled on a pre-melted promoter (-21 to +12, 15S yeast mtDNA promoter; Fig. 1A) to generate the yeast mitochondrial transcription preinitiation complex (y-mtPIC) (Fig. S1). The y-mtPIC was incubated with pppGpG RNA and a . CC-BY-NC: bioRxiv preprint 4 non-hydrolysable UTPaS to generate the y-mtIC poised to incorporate the +3 NTP. Singleparticle cryo-EM data analysis of the quinary y-mtIC revealed a surprising coexistence of PIC and IC states in equilibrium (Fig. S2). The y-mtIC structure had bound RNA and NTP, and y-mtPIC structure had no RNA or NTP. Another dataset collected from a PIC-only grid extends the resolution to 3.1 Å. Key steps guiding transcription initiation are revealed from the 3.1 Å y-mtPIC and 3.7 Å y-mtIC structures.In y-mtPIC structure ( Fig. 1B & C), the MTF1 is traced from 2 to 336 out of 341 amino acid residues, RPO41 is traced from 386 to the end residue 1351 with few disordered regions, and unambiguously traced DNA (Fig. S3A). A stable transcription core is composed of RPO41, MTF1, and transcription bubble (Fig. 1C). RPO41 interacts with MTF1 at multiple locations. Two RPO41 b-hairpins -the intercalating hairpin (ICH) and the MTF1supporting hairpin (K613-P632) form a crescent-shaped platform that accommodates the C-terminal domain of MTF1 (252-325) (Fig. 1D). The N-terminal domain of MTF1 (2-251) contacts the tip of the RPO41 thumb helix (Fig. 1E); biochemically, we show the interaction stabilizes RPO41-MTF1 complex ( Fig. S3C-D)(7). The MTF1-supp...

Structure, mechanism, and regulation of mitochondrial DNA transcription initiation

“…The recent cryo-EM structures of y-mtRNAP and MTF1 show base-specific interactions of MTF1 with the conserved nonanucleotide promoter sequence from position −8 to +1 ( Fig. 4 , C and D ) ( 36 ). The structure did not resolve the NTE in y-mtRNAP; hence, it is not clear whether y-mtRNAP has the equivalent PPR domains present in h-mtRNAP.…”

“…The CTD's basic structure resembles the classic “right hand” shape composed of the thumb, palm, and fingers domains ( Fig. 2 C ) ( 34 , 35 , 36 , 37 , 38 , 39 ). The palm domain and fingers domain contain the polymerase active site responsible for catalyzing nucleotide incorporation, and the thumb domain is essential for DNA binding ( 40 ).…”

“…Promoter bending is necessary for generating a productive initiation complex ( Fig. 2 C ) and is a conserved feature observed in all single-subunit RNAPs ( 35 , 36 , 37 ).…”

“…The CTD insertion in y-mtRNAP interacts with the downstream DNA around +11 bp. The CTD insertion interactions stabilize the bent conformation of the DNA around the initiation site, whereas MTF1 stabilizes the DNA at the opposite end ( 36 ). Perhaps due to these additional promoter contacts with downstream DNA, y-mtRNAP does not need ABF2, the TFAM homolog.…”

“…MTF1 shows several contact points with the y-mtRNAP; the CTD of MTF1 interacts with a prominent hairpin in y-mtRNAP adjacent to the intercalating hairpin (MTF1-hairpin equivalent to the TFB2M-loop in h-mtRNAP), and the NTD of MTF1 contacts the thumb domain of y-mtRNAP ( 36 , 73 ). The thumb domain in h-mtRNAP is projected toward TFB2M, suggesting interactions like in y-mtRNAP ( Fig.…”