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NusA interaction with the ? subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition.

ABSTRACT: Elongating Escherichia coli RNAP is modulated by NusA protein. The C-terminal domain (CTD) of the RNAP ? subunit (?CTD) interacts with the acidic CTD 2 (AR2) of NusA, releasing the autoinhibitory blockade of the NusA S1-KH1-KH2 motif and allowing NusA to bind nascent nut spacer RNA. We determined the solution conformation of the AR2:?CTD complex. The ?CTD residues that interface with AR2 are identical to those that recognize UP promoter elements A nusA-?AR2 mutation does not affect UP-dependent rrnH transcription initiation in vivo. Instead, the mutation inhibits Rho-dependent transcription termination at phage ?tR1, which lies adjacent to the ?nutR sequence. The Rho-dependent ?timm terminator, which is not preceded by a ?nut sequence, is fully functional. We propose that constitutive binding of NusA-?AR2 to ?nutR occludes Rho. In addition, the mutation confers a dominant defect in exiting stationary phase.

SUBMITTER: Schweimer K

PROVIDER: S-EPMC3134791 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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NusA interaction with the α subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition.

Schweimer Kristian K Prasch Stefan S Sujatha Pagadala Santhanam PS Bubunenko Mikhail M Gottesman Max E ME Rösch Paul P

Structure (London, England : 1993) 20110701 7

Elongating Escherichia coli RNAP is modulated by NusA protein. The C-terminal domain (CTD) of the RNAP α subunit (αCTD) interacts with the acidic CTD 2 (AR2) of NusA, releasing the autoinhibitory blockade of the NusA S1-KH1-KH2 motif and allowing NusA to bind nascent nut spacer RNA. We determined the solution conformation of the AR2:αCTD complex. The αCTD residues that interface with AR2 are identical to those that recognize UP promoter elements A nusA-ΔAR2 mutation does not affect UP-dependent ...[more]

PMID: 21742261

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Project description:Strict regulation of replisome components is essential to ensure the accurate transmission of the genome to the next generation. The sliding clamp processivity factors play a central role in this regulation, interacting with both DNA polymerases and multiple DNA processing and repair proteins. Clamp binding partners share a common peptide binding motif, the nature of which is essentially conserved from phage through to humans. Given the degree of conservation of these motifs, much research effort has focussed on understanding how the temporal and spatial regulation of multiple clamp binding partners is managed. The bacterial sliding clamps have come under scrutiny as potential targets for rational drug design and comprehensive understanding of the structural basis of their interactions is crucial for success.In this study we describe the crystal structure of a complex of the E. coli ?-clamp with a 12-mer peptide from the UmuC protein. UmuC is the catalytic subunit of the translesion DNA polymerase, Pol V (UmuD'?C). Due to its potentially mutagenic action, Pol V is tightly regulated in the cell to limit access to the replication fork. Atypically for the translesion polymerases, both bacterial and eukaryotic, Pol V is heterotrimeric and its ?-clamp binding motif (³??QLNLF³?¹) is internal to the protein, rather than at the more usual C-terminal position. Our structure shows that the UmuC peptide follows the overall disposition of previously characterised structures with respect to the highly conserved glutamine residue. Despite good agreement with the consensus ?-clamp binding motif, distinct variation is shown within the hydrophobic binding pocket. While UmuC Leu-360 interacts as noted in other structures, Phe-361 does not penetrate the pocket at all, sitting above the surface.Although the ?-clamp binding motif of UmuC conforms to the consensus sequence, variation in its mode of clamp binding is observed compared to related structures, presumably dictated by the proximal aspartate residues that act as linker to the poorly characterised, unique C-terminal domain of UmuC. Additionally, interactions between Asn-359 of UmuC and Arg-152 on the clamp surface may compensate for the reduced interaction of Phe-361.

Dataset Information

NusA interaction with the ? subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition.

Publications

NusA interaction with the α subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition.

Similar Datasets

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