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Structure paper

TitleStructural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from .
Journal, issue, pagesSci Adv, Vol. 9, Issue 6, Page eade7093, Year 2023
Publish dateFeb 10, 2023
AuthorsYuko Murayama / Haruhiko Ehara / Mari Aoki / Mie Goto / Takeshi Yokoyama / Shun-Ichi Sekine /
PubMed AbstractTranscription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the ...Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate-dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo-electron microscopy structure of the RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation.
External linksSci Adv / PubMed:36753546 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 5.8 Å
Structure data

34996

8hsg

EMDB-34996, PDB-8hsg:
Thermus thermophilus RNA polymerase elongation complex
Method: EM (single particle) / Resolution: 3.2 Å

34997

8hsh

EMDB-34997, PDB-8hsh:
Thermus thermophilus RNA polymerase coreenzyme
Method: EM (single particle) / Resolution: 3.4 Å

34999

8hsj

EMDB-34999, PDB-8hsj:
Thermus thermophilus transcription termination factor Rho bound with ADP-BeF3
Method: EM (single particle) / Resolution: 3.6 Å

35000

8hsl

EMDB-35000, PDB-8hsl:
Thermus thermophilus RNA polymerase bound with an inverted Rho hexamer
Method: EM (single particle) / Resolution: 5.8 Å

35004

8hsr

EMDB-35004, PDB-8hsr:
Thermus thermophilus Rho-engaged RNAP elongation complex
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-36744: Thermus thermophilus Rho-engaged RNAP elongation complex; EC part
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-36745: Thermus thermophilus Rho-engaged RNAP elongation complex; Rho part
Method: EM (single particle) / Resolution: 4.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • thermus thermophilus hb8 (bacteria)
  • dna molecule (others)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / Transcription elongation complex / RNA polymerase / RNA polymerase coreenzyme / Transcription termination / ATP-dependent RNA/DNA helicase/translocase / transcription termination factor Rho

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