NMR studies on the structures of bacterial replication-associated protein CNU and damaged DNA tolerance protein Rev1

Abstract

Cnu is a nucleoid protein that associates with oriC, the replication origin of the Escherichia coli, and shares a high degree of sequence homology with Hha/YmoA family proteins which bind to chromatin and regulate the expression of E. coli virulence genes in response to changes in temperature or ionic strength. Here, we characterize the solution structure of Cnu and the interaction between the Cnu and H-NS. Cnu consists of three a-helices which are similar to those of the Hha but it is very flexible at C-terminal region and lacks the fourth a-helix which is present in the Hha. The helices of Cnu are destabilized at elevated ionic strength in metal ion-dependent manner. Although Cnu and Hha share similar structures and comparable binding affinities for H-NS, the NMR characteristics observed for the Cnu-H-NS interaction are remarkably different from those of the Hha-H-NS interaction in binding dynamics or kinetics, which taken together with the structural differences may provide an insight into the functions of Cnu and Hha. Recently the C-terminal polymerase-binding domain of Rev1 was found to play a crucial role in the mutagenic DNA damage tolerance and be highly conserved among different organisms. Together with previous reports that this domain interacted with three other Y-family polymerase, kappa, eta and iota in both human and mouse, the C-terminal polymerase binding domain of Rev1 was proposed to play as the scaffold role in the translesional synthesis to recruit the different translesional DNA polymerases based on the different DNA damaged types. Despite its important biological function, little is known for the structural information on the polymerase binding domain of Rev1 and its related interaction with polymerase kappa, eta and iota. Here, we report the first solution structure on the polymerase binding domain of human Rev1 in the bound form with polymerase kappa. The overall structure shows that the polymerase binding domain of hRev1 consists of f...