Regulation of Single-stranded DNA Binding by the C Termini of Escherichia coli Single-stranded DNA-binding (SSB) Protein

Alexander G Kozlov,Michael M Cox,Timothy M Lohman

doi:10.1074/jbc.m110.118273

Abstract

The homotetrameric Escherichia coli single-stranded DNA-binding (SSB) protein plays a central role in DNA replication, repair, and recombination. In addition to its essential activity of binding to transiently formed single-stranded (ss) DNA, SSB also binds an array of partner proteins and recruits them to their sites of action using its four intrinsically disordered C-terminal tails. Here we show that the binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. We examined the energetics of ssDNA binding to short oligodeoxynucleotides and find that at moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits. The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites. This inhibition and its relief by ssDNA binding suggest a mechanism that enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA.

Highlights

SsDNA Wrapping around the ssDNA binding modes identified are denoted (SSB) Tetramer in Its (SSB)65 Mode Is Unaffected by the C-terminal Tail— The C-terminal tails of E. coli SSB
Appears to be unaffected by removal of the C-terminal tails of Deletion of the Last 8 Amino Acids in the C-terminal Tail Enhances SSB Binding to ssDNA at Moderate [NaCl]—At [NaCl] Ն0.2 M, E. coli SSB tetramers can bind two molecules of35 but with a negative cooperativity that increases with decreasing salt concentration [40, 42, 46]
In addition to the ability to interact with a variety of metabolic proteins involved in genome maintenance [4], the SSB C termini can influence SSB binding to ssDNA

Summary

EXPERIMENTAL PROCEDURES

Reagents and Buffers—All buffers were prepared with reagent grade chemicals and distilled water that was subsequently treated with a Milli-Q (Millipore, Bedford, MA) water purification system. The concentrations of wtSSB and its C-terminal deletion fragments were determined spectrophotometrically in Tris buffer (pH 8.1, 0.2 M NaCl) using an extinction coefficient of ⑀280 ϭ 1.13 ϫ 105 MϪ1 (tetramer) cmϪ1 [12]. All ssDNA concentrations were determined spectrophotometrically in buffer T (pH 8.1), 100 mM NaCl using the extinction coefficient ⑀260 ϭ 8.1 ϫ 103 MϪ1 (nucleotide) cmϪ1 for oligo(dT) and poly(dT) [35] and ⑀260 ϭ 9.65 ϫ 103 MϪ1 (nucleotide) cmϪ1 for (dA)35 [36, 37]. All DNA and protein samples were dialyzed extensively versus the particular buffer containing the indicated salt concentration that was used in the fluorescence or isothermal titration calorimetry (ITC) titration experiments. The concentration of free DNA, D, was determined from Equation 2, Dtot ϭ

Dbound ϭ

RESULTS

Temperature SSB

DISCUSSION