Caulobacter crescentus β sliding clamp employs a noncanonical regulatory model of DNA replication

Abstract

The eubacterial b sliding clamp (DnaN) plays a crucial role in DNA metabolism through direct interactions with DNA, polymerases, and a variety of protein factors. A canonical protein-DnaN interaction has been identified in Escherichia coli and some other species, during which protein partners are tethered into the conserved canonical hydrophobic crevice of DnaN via the consensus b-binding motif. Caulobacter crescentus is an excellent research model for use in the investigation of DNA replication and cell-cycle regulation due to its unique asymmetric cell division pattern with restricted replication initiation; however, little is known about the specific features of C. crescentus DnaN (CcDnaN). Here, we report a significant divergence in the association of CcDnaN with proteins based on docking analysis and crystal structures that show that the b-binding motifs of its protein partners bind a novel pocket instead of the canonical site. Pulldown and isothermal titration calorimetry results revealed that mutations within the novel pocket disrupt protein-CcDnaN interactions. It was also shown by replication and regulatory inactivation of DnaA assays that mediation of protein interaction by the novel pocket is closely related to the performance of CcDnaN during replication and the DnaN-mediated regulation process. Moreover, assessments of clamp competition showed that DNA does not compete with protein partners when binding to the novel pocket. Overall, our structural and biochemical analyses provide strong evidence that CcDnaN employs a noncanonical protein association pattern.Abbreviations C. crescentus, Caulobacter crescentus; DnaE, DNA polymerase III subunit alpha; DnaN, b clamp, DNA polymerase III beta sliding clamp subunit; Hda, DnaA regulatory inactivator Hda; HdaA, chromosome replication regulator protein HdaA; HolA, DNA polymerase III subunit delta; ITC, isothermal titration calorimetry; PDB, protein data bank; RIDA, regulatory inactivation of DnaA; b motif, b-binding motif, a consensus short peptide sequence motif for protein-DnaN interaction.

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