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-Structure paper
Title | Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli. |
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Journal, issue, pages | J Biol Chem, Vol. 297, Issue 6, Page 101404, Year 2021 |
Publish date | Nov 12, 2021 |
Authors | M Zuhaib Qayyum / Vadim Molodtsov / Andrew Renda / Katsuhiko S Murakami / |
PubMed Abstract | 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 ...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 links | J Biol Chem / PubMed:34774797 / PubMed Central |
Methods | EM (single particle) |
Resolution | 3.15 - 4.8 Å |
Structure data | EMDB-23900, PDB-7mkn: EMDB-23901, PDB-7mko: EMDB-23902, PDB-7mkp: EMDB-23903, PDB-7mkq: |
Chemicals | ChemComp-MG: ChemComp-ZN: ChemComp-2TM: |
Source |
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Keywords | TRANSCRIPTION/DNA/RNA / RNAP recycling / RapA / Post-Termination Complex / PTC / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex |