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Structure paper

TitleIn transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 33, Page e2205278119, Year 2022
Publish dateAug 16, 2022
AuthorsZhou Yin / Jeremy G Bird / Jason T Kaelber / Bryce E Nickels / Richard H Ebright /
PubMed AbstractLambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP ...Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
External linksProc Natl Acad Sci U S A / PubMed:35951650 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.46 - 3.36 Å
Structure data

EMDB-26438, PDB-7ubm:
Transcription antitermination complex: "pre-engaged" Qlambda-loading complex
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-26439, PDB-7ubn:
Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
Method: EM (single particle) / Resolution: 3.36 Å

PDB-7ubj:
Transcription antitermination factor Qlambda, type-I crystal
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-7ubk:
Transcription antitermination factor Qlambda, type-II crystal
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7ubl:
Transcription antitermination factor Qlambda in complex with Q-lambda-binding-element DNA
Method: X-RAY DIFFRACTION / Resolution: 2.177 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-HOH:
WATER / Water

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
  • escherichia phage lambda (virus)
KeywordsGENE REGULATION / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor / GENE REGULATION/DNA / GENE REGULATION-DNA complex / TRANSFERASE/DNA/RNA / TRANSFERASE-DNA-RNA complex

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