Crystallization of single-strand DNA-binding protein

A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria

The crystal structure of the DNA-binding domain of E. coli SSB (EcoSSB) has been determined to a resolution of 2.5 A. This is the first reported structure of a prokaryotic SSB. The structure of the DNA-binding domain of the E. coli protein is compared to that of the human mitochondrial SSB (HsmtSSB). In spite of the relatively low sequence identity between them, the two proteins display a high degree of structural similarity. EcoSSB crystallises with two dimers in the asymmetric unit, unlike HsmtSSB which contains only a dimer. This is probably a consequence of the different polypeptide chain lengths in the EcoSSB heterotetramer. Crucial differences in the dimer-dimer interface of EcoSSB may account for the inability of EcoSSB and HsmtSSB to form cross-species heterotetramers, in contrast to many bacterial SSBs.

Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution

The crystal structure of the tetrameric DNA-binding domain of the single-stranded DNA binding protein from Escherichia coli was determined at a resolution of 2.9 A using multiwavelength anomalous dispersion. Each monomer in the tetramer is topologically similar to an oligomer-binding fold. Two monomers each contribute three beta-strands to a single six-stranded beta-sheet to form a dimer. Two dimer-dimer interfaces are observed within the crystal. One of these stabilizes the tetramer in solution. The other interface promotes a superhelical structure within the crystal that may reflect tetramer-tetramer interactions involved in the positive cooperative binding of the single-stranded DNA-binding protein to single-stranded DNA.

Stability of Escherichia coli single-stranded DNA binding protein (EcoSSB)

Conformation and stability of EcoSSB, a single-stranded DNA binding protein encoded by Escherichia coli, were analyzed by circular dichroism and fluorescence measurements. From CD measurements at pH 7.5, EcoSSB can be classified as a protein with high alpha-helix and beta-sheet content. The hydrophobicity of the environment of the tryptophan residues of the native protein is only marginally increased in comparison to the unfolded protein. The GdnHCl induced unfolding curves measured by CD and fluorescence are coincident and sigmoidal and show a monophasic transition. The stability of EcoSSB is concentration dependent and the unfolding behavior can be described as a two-state transition from the folded tetrameter to unfolded monomers. The mean values of free energy of dissociation and unfolding delta GH2O mu are between 173 and 177 kJ.mol-1 and the mean half concentration c1/2 of GdnHCl of the transition curves are about 1.5 M and 1.7 M for protein concentrations of 0.1 mg.ml-1 and 0.5 mg.ml-1, respectively.

Amino acid 55 plays a central role in tetramerization and function of Escherichia coli single-stranded DNA binding protein

The histidine at position 55 of the amino acid sequence of the Escherichia coli single-stranded DNA binding protein was replaced by tyrosine, glutamic acid, lysine, phenylalanine, and isoleucine. The properties of the mutant proteins were determined using analytical ultracentrifugation, NMR spectroscopy, gel filtration, and fluorimetric detection of their single-stranded DNA binding ability. While the phenylalanine and isoleucine substitutions did not change the properties of the protein measurably, tyrosine and lysine mutants dissociate into subunits and loose some of their binding affinity for poly(dT). For the lysine mutant we show by electron microscopy that the protein, although fully dissociated and possibly denatured in the free state, binds to poly(dT) as a tetramer indistinguishable from the wild-type protein. The process of tetramerization as observed via single-stranded DNA binding ability is composed of a variety of steps ranging in time from some milliseconds to several hours; it probably involves several forms of dissociated and non-native protein.

The single-stranded DNA-binding protein of Escherichia coli

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.

Modulation of the affinity of the single-stranded DNA-binding protein of Escherichia coli (E. coli SSB) to poly(dT) by site-directed mutagenesis

A vector for site-directed mutagenesis and overproduction of the Escherichia coli single-stranded-DNA-binding protein (E. coli SSB) was constructed. An E. coli strain carrying this vector produces up to 400 mg pure protein from 25 g wet cells. The vector was used to mutate specifically the Phe60 residue of E. coli SSB. Phe60 had been proposed to be located near the single-stranded-DNA-binding site. Substitution of the Phe60 residue by Val, Ser, Leu, His, Tyr and Trp gave proteins with no or only minor conformational changes, as detected by NMR spectroscopy. The affinity of the mutant E. coli SSB proteins for single-stranded DNA decreased in the order Trp greater than Phe (wild-type) greater than Tyr greater than Leu greater than His greater than Val greater than Ser, leading to the conclusion that position 60 is a site of hydrophobic interaction of the protein with DNA.

Limited co-operativity in protein-nucleic acid interactions. A thermodynamic model for the interactions of Escherichia coli single strand binding protein with single-stranded nucleic acids in the "beaded", (SSB)65 mode

We present a statistical thermodynamic model ("tetramer/octamer" model) that describes the equilibrium binding of the Escherichia coli single strand binding (SSB) protein to single-stranded nucleic acids in its "beaded" binding mode, which seems to be equivalent to the high site size, (SSB)65 binding mode. The method of sequence-generating functions is used to derive the model, which accounts for the observation that clustering of bound SSB tetramers is limited to the formation of octamers, which have been observed as "beads" in the electron microscope. The model also accounts for the overlap of potential protein binding sites on the nucleic acid. The "tetramer/octamer" model is fully described by only three parameters: the site size, n; the intrinsic equilibrium constant, K; and the co-operativity parameter, omega, and we obtain exact, closed form expressions for the binding isotherm as well as the distribution of DNA-bound SSB tetramers and octamers. The closed form expressions allow one to calculate easily average binding properties and analyze experimental binding isotherms to obtain estimates of K and omega. In order to test the tetramer/octamer model, we have determined the equilibrium binding isotherm for the E. coli SSB protein-poly(U) interaction in 0.2 M-NaCl over a wide range of binding densities. These are conditions in which the low co-operativity (SSB)65 binding mode solely exists. The tetramer/octamer model provides a much better description of the experimental isotherm over the entire binding density range than a model that assumes the formation of clusters of unlimited size. A co-operativity parameter of omega = 420 +/- 80 provides a good fit to data for SSB binding to poly(dA) and poly(U), corresponding to an interaction free energy of -3.6 kcal/mol of SSB octamer formed. On the basis of this moderate value of omega, the tetramer/octamer model predicts that at low to intermediate binding densities, a significant fraction of bound SSB exists in the form of tetramers co-existing with octamers. In the case of E. coli SSB protein binding in the "beaded", (SSB)65 mode this model provides a significant improvement over previous treatments which assume unlimited nearest-neighbor interactions, since the binding parameters, K and omega, represent physically meaningful interaction constants rather than fitting parameters.

Salt-dependent changes in the DNA binding co-operativity of Escherichia coli single strand binding protein

The co-operative nature of the binding of the Escherichia coli single strand binding protein (SSB) to single-stranded nucleic acids has been examined over a range of salt concentrations (NaCl and MgCl2) to determine if different degrees of binding co-operativity are associated with the two SSB binding modes that have been identified recently. Quantitative estimates of the binding properties, including the co-operativity parameter, omega, of SSB to single-stranded DNA and RNA homopolynucleotides have been obtained from equilibrium binding isotherms, at high salt (greater than or equal to 0.2 M-NaCl), by monitoring the fluorescence quenching of the SSB upon binding. Under these high salt conditions, where only the high site size SSB binding mode exists (65 +/- 5 nucleotides per tetramer), we find only moderate co-operativity for SSB binding to both DNA and RNA, (omega = 50 +/- 10), independent of the concentration of salt. This value for omega is much lower than most previous estimates. At lower concentrations of NaCl, where the low site size SSB binding mode (33 +/- 3 nucleotides/tetramer) exists, but where SSB affinity for single-stranded DNA is too high to estimate co-operativity from classical binding isotherms, we have used an agarose gel electrophoresis technique to qualitatively examine SSB co-operativity with single-stranded (ss) M13 phage DNA. The apparent binding co-operativity increases dramatically below 0.20 M-NaCl, as judged by the extremely non-random distribution of SSB among the ssM13 DNA population at low SSB to DNA ratios. However, the highly co-operative complexes are not at equilibrium at low SSB/DNA binding densities, but are formed only transiently when SSB and ssDNA are directly mixed at low concentrations of NaCl. The conversions of these metastable, highly co-operative SSB-ssDNA complexes to their equilibrium, low co-operativity form is very slow at low concentrations of NaCl. At equilibrium, the SSB-ssDNA complexes seem to possess the same low degree of co-operativity (omega = 50 +/- 10) under all conditions tested. However, the highly co-operative mode of SSB binding, although metastable, may be important during non-equilibrium processes such as DNA replication. The possible relation between the two SSB binding modes, which differ in site size by a factor of two, and the high and low co-operativity complexes, which we report here, is discussed.