Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli

• Published in: The Journal of biological chemistry Vol. 297; no. 6; p. 101404
• Main Authors: Qayyum, M. Zuhaib, Molodtsov, Vadim, Renda, Andrew, Murakami, Katsuhiko S.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2021; American Society for Biochemistry and Molecular Biology
• Subjects: Adenosine Triphosphatases - chemistry; Adenosine Triphosphatases - metabolism; cryo-EM; Cryoelectron Microscopy; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; DNA, Bacterial - ultrastructure; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Escherichia coli - chemistry; Escherichia coli - metabolism; Escherichia coli - ultrastructure; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Multienzyme Complexes - chemistry; Multienzyme Complexes - metabolism; Multienzyme Complexes - ultrastructure; post-termination complex; RapA; RNAP recycling; AMPPNP; RapA; CMPCPP; RNAP recycling; RNAP; PDB; CTF; NCI; post-termination complex; cryo-EM; ZBD; EC; PTC; NTD
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/j.jbc.2021.101404

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.