Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.

Publication Type:

Journal Article


iScience, Volume 23, Issue 9, p.101445 (2020)


<p>In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the σ domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and σ-RNAP core separation to transition transcription from initiation to elongation.</p>

Coordinates and structure factor files have been deposited in the RCSB Protein DataBank under accession codes: 6UTW (STIC4, 4-nt RNA), 6UTX (SRPo, empty DNA bubble), 6UTY (SRPo soaked with CTP), 6UTZ (STIC4 soaked with CTP and UTP), 6UU0 (STIC4 soaked with GTP), 6UU1 (STIC4 soaked with CTP, GTP and ddTTP), 6UU2 (SRPo soaked with GTP and ATP), 6UU3 (SRPo soaked with GTP, ATP, CTP and ddTTP), 6UU4 (SRPo soaked with GTP and dinucleotide 5′-GA-3′), 6UU5 (SRPo soaked with GTP, UTP, CTP and dinucleotide 5′-GA-3′), 6UU6 (SRPo soaked with UTP, ddCTP and dinucleotide 5′-AG-3′), 6UU7 (SRPo soaked with UTP, CTP, ddGTP and dinucleotide 5′-AG-3′), 6UU8 (IGSA mutant STIC4 soaked with CTP, UTP and GTP), 6UU9 (IGSA mutant STIC4 soaked with CTP, UTP, GTP and ddATP), 6UUA (STIC4 soaked with CTP), 6UUB (STIC4 soaked with UTP), 6UUC (STIC4 soaked with ATP), 6UTV (STIC4 soaked with CTP, UTP, GTP and ddATP).