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Structure paper

TitleStructural and mechanistic basis of reiterative transcription initiation.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 5, Year 2022
Publish dateFeb 1, 2022
AuthorsYu Liu / Libing Yu / Chirangini Pukhrambam / Jared T Winkelman / Emre Firlar / Jason T Kaelber / Yu Zhang / Bryce E Nickels / Richard H Ebright /
PubMed AbstractReiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5' sequences noncomplementary to the ...Reiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5' sequences noncomplementary to the DNA template. Here, using crystallography and cryoelectron microscopy to define structures, protein-DNA photocrosslinking to map positions of RNAP leading and trailing edges relative to DNA, and single-molecule DNA nanomanipulation to assess RNA polymerase (RNAP)-dependent DNA unwinding, we show that RNA extension in reiterative transcription initiation 1) occurs without DNA scrunching; 2) involves a short, 2- to 3-bp, RNA-DNA hybrid; and 3) generates RNA that exits RNAP through the portal by which scrunched nontemplate-strand DNA exits RNAP in standard transcription initiation. The results establish that, whereas RNA extension in standard transcription initiation proceeds through a scrunching mechanism, RNA extension in reiterative transcription initiation proceeds through a slippage mechanism, with slipping of RNA relative to DNA within a short RNA-DNA hybrid, and with extrusion of RNA from RNAP through an alternative RNA exit.
External linksProc Natl Acad Sci U S A / PubMed:35082149 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.0 - 3.75 Å
Structure data

24424

7rdq

EMDB-24424, PDB-7rdq:
Cryo-EM structure of Thermus thermophilus reiterative transcription complex with 11nt oligo-G RNA
Method: EM (single particle) / Resolution: 3.0 Å

PDB-7mlb:
Crystal structure of Thermus thermophilus transcription initiation complex with 5nt RNA
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-7mli:
Crystal structure of Thermus thermophilus reiterative transcription complex with 5nt oligo-C RNA
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-7mlj:
Crystal structure of Thermus thermophilus reiterative transcription complex with 4nt oligo-G RNA
Method: X-RAY DIFFRACTION / Resolution: 3.75 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • thermus thermophilus hb8 (bacteria)
  • synthetic construct (others)
  • thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (bacteria)
KeywordsTRANSCRIPTION / Thermus thermophilus / transcription initiation

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