Human replication protein A binds single-stranded DNA in two distinct complexes.

Abstract

Human replication protein A, a single-stranded DNA (ssDNA)-binding protein, is a required factor in eukaryotic DNA replication and DNA repair systems and has been suggested to function during DNA recombination. The protein is also a target of interaction for a variety of proteins that control replication, transcription, and cell growth. To understand the role of hRPA in these processes, we examined the binding of hRPA to defined ssDNA molecules. Employing gel shift assays that "titrated" the length of ssDNA, hRPA was found to form distinct multimeric complexes that could be detected by glutaraldehyde cross-linking. Within these complexes, monomers of hRPA utilized a minimum binding site size on ssDNA of 8 to 10 nucleotides (the hRPA8_10t complex) and appeared to bind ssDNA cooperatively. Intriguingly, alteration of gel shift conditions revealed the formation of a second, distinctly different complex that bound ssDNA in roughly 30-nucleotide steps (the hRPA30t complex), a complex similar to that described by Kim et al. (C. Kim, R. 0. Snyder, and M. S. Wold, Mol. Cell. Biol. 12:3050-3059, 1992). Both the hRPA8_l10t and hRPA30t complexes can coexist in solution. We speculate that the role of hRPA in DNA metabolism may be modulated through the ability of hRPA to bind ssDNA in these two modes.The replication, recombination, and repair of the cellular genetic information entail interconversion of DNA between the duplex and single-stranded forms. Study of nucleic acid enzymology has shown that single-stranded DNA (ssDNA) generated within cells is invariably associated with protein factors, often ssDNA-binding proteins (SSBs). SSBs combine with the ssDNA to form protein-DNA complexes that maintain the unwound state and are more active as substrates, for example, in DNA replication (12). A clear understanding of the architecture of SSB-ssDNA complexes is required to comprehend the function of SSB in DNA metabolism and determine how these processes are regulated within the cell.Eukaryotic SSBs with defined roles in DNA enzymology have recently been isolated, one of which, from human cells, is termed human replication protein A (hRPA). hRPA, a heterotrimer with subunits of 68, 29, and 14 kDa, was initially isolated as a factor from primate cells required to support simian virus 40 (SV40) DNA replication in vitro (24,42,43). The factor was identified as an SSB by various criteria including the high affinity of hRPA for ssDNA (24,42,43) and ability to stimulate human DNA polymerase a, an essential eukaryotic replication factor (22, 31). hRPA is phosphorylated in a cell-cycle specific manner, suggesting that DNA replication and other hRPA-mediated events may be modulated through regulation of hRPA activity (18,21,25). Moreover, recent studies have shown that hRPA specifically interacts with a number of transcription factors, suggesting that these factors regulate DNA replication, in part, through hRPA (20, 27, 35). In addition to its defined role in SV40 DNA replication, hRPA is also a required factor in an in vitro system...

Saccharomyces cerevisiae Replication Protein A Binds to Single-Stranded DNA in Multiple Salt-Dependent Modes

“…In both cases two or more titrations were performed at different scRPA concentrations and the titrations were analyzed using the model independent binding density function analysis (59) to determine the relationship between the average fluorescence quenching signal and the average extent of (dT) L binding per scRPA. The results, plotted in Figure 6B (for (dT) 28 ) and Figure 6D (for (dT) 20 ), demonstrate that the average quenching increases linearly with the average extent of binding. Furthermore, a linear extrapolation of this line to the maximum fluorescence quenching observed at saturation (Q max ) (plateau values in Figure 6A and 6C) indicates a 1:1 stoichiometry of binding.…”

“…The ssDNA binding properties of RPA have previously been characterized using a variety of approaches (25)(26)(27)(28)(29). As is true for most SSB proteins, RPA binds with high affinity to ssDNA with no apparent sequence specificity (26,(29)(30)(31)(32), although it does display a preference for polypyrimidines (26).…”

“…Recall that the occluded site size, n, determined with poly(dT) is 26−28 nucleotides under these conditions (see Table 2). The results of scRPA titrations with (dT) 28 and (dT) 20 are shown in Figure 6A and 6C, respectively. In both cases two or more titrations were performed at different scRPA concentrations and the titrations were analyzed using the model independent binding density function analysis (59) to determine the relationship between the average fluorescence quenching signal and the average extent of (dT) L binding per scRPA.…”

“…There appears to be general agreement for the binding site size of human RPA (hRPA) on ssDNA (30 nucleotides) (25,28), although a less stable mode involving interactions with only 8−10 nucleotides of ssDNA, that is observable only upon cross-linking, has also been reported (28). A site size of 22 nucleotides has been reported for D. melanogaster (dm) RPA (32); 20 −25 nucleotides for calf thymus RPA (30) and 20−30 nucleotides for RPA from primates (47).…”

“…Each OB-fold within RPA could potentially provide a site for ssDNA binding (21)(22)(23)(24). Four OB-folds are located within RPA70, referred to as F, A, B and C, (see Figure 1), a fifth OB-fold (D) is contained within the RPA32 subunit, and a sixth OB-fold (E) is contained within RPA14.The ssDNA binding properties of RPA have previously been characterized using a variety of approaches (25)(26)(27)(28)(29). As is true for most SSB proteins, RPA binds with high affinity to ssDNA with no apparent sequence specificity (26,(29)(30)(31)(32), although it does display a preference for polypyrimidines (26).…”