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Structure paper

TitleStructural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
Journal, issue, pagesJ Biol Chem, Vol. 297, Issue 6, Page 101404, Year 2021
Publish dateNov 12, 2021
AuthorsM Zuhaib Qayyum / Vadim Molodtsov / Andrew Renda / Katsuhiko S Murakami /
PubMed AbstractAfter transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and ...After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and subsequently leading to inefficient transcription. In Escherichia coli, a Swi2/Snf2 family of ATPase called RapA is known to be involved in countering such inefficiency through RNAP recycling; however, the precise mechanism of this recycling is unclear. To better understand its mechanism, here we determined the structures of two sets of E. coli RapA-RNAP complexes, along with the RNAP core enzyme and the elongation complex, using cryo-EM. These structures revealed the large conformational changes of RNAP and RapA upon their association that has been implicated in the hindrance of PTC formation. Our results along with DNA-binding assays reveal that although RapA binds RNAP away from the DNA-binding main channel, its binding can allosterically close the RNAP clamp, thereby preventing its nonspecific DNA binding and PTC formation. Taken together, we propose that RapA acts as a guardian of RNAP by which RapA prevents nonspecific DNA binding of RNAP without affecting the binding of promoter DNA recognition σ factor, thereby enhancing RNAP recycling.
External linksJ Biol Chem / PubMed:34774797 / PubMed Central
MethodsEM (single particle)
Resolution3.15 - 4.8 Å
Structure data

23900

7mkn

EMDB-23900, PDB-7mkn:
Escherichia coli RNA polymerase and RapA elongation complex
Method: EM (single particle) / Resolution: 3.3 Å

23901

7mko

EMDB-23901, PDB-7mko:
Escherichia coli RNA polymerase elongation complex
Method: EM (single particle) / Resolution: 3.15 Å

23902

7mkp

EMDB-23902, PDB-7mkp:
Escherichia coli RNA polymerase core enzyme
Method: EM (single particle) / Resolution: 3.41 Å

23903

7mkq

EMDB-23903, PDB-7mkq:
Escherichia coli RNA polymerase and RapA binary complex
Method: EM (single particle) / Resolution: 4.8 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-2TM:
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine

Source
  • escherichia coli k-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSCRIPTION/DNA/RNA / RNAP recycling / RapA / Post-Termination Complex / PTC / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex

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