A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems

The interaction between DNA polymerases and sliding clamp proteins confers processivity in DNA synthesis. This interaction is critical for most DNA re plication machines from viruses and prokaryotes to higher eukaryotes. The c lamp proteins also participate in a variety of dynamic and competing protei n-protein interactions. However, clamp-protein binding sequences have not s o far been identified in the eubacteria. Here we show from three lines of e vidence, bioinformatics, yeast two-hybrid analysis, and inhibition of prote in-protein interaction by modified peptides, that variants of a pentapeptid e motif (consensus QL[SD]LF) are sufficient to enable interaction of a numb er of proteins with an archetypal eubacterial sliding clamp (the beta subun it of Escherichia coli DNA polymerase III holoenzyme). Representatives of t his motif are present in most sequenced members of the eubacterial DnaE, Po lC, PolB, DinB, and UmuC families of DNA polymerases and the MutS1 mismatch repair protein family. The component tripeptide DLF inhibits the binding o f the a (DnaE) subunit of E. coli DNA polymerase III to beta at muM concent ration, identifying key residues. Comparison of the eubacterial, eukaryotic , and archaeal sliding clamp binding motifs suggests that the basic interac tions have been conserved across the evolutionary landscape.