Escherichia coli replicative helicase PriA protein-single-stranded DNA complex. Stoichiometries, free energy of binding, and cooperativities

Characterization of Streptococcus pneumoniae PriA helicase and its ATPase and unwinding activities in DNA replication restart

DNA replication forks often encounter template DNA lesions that can stall their progression. The PriA-dependent pathway is the major replication restart mechanism in Gram-positive bacteria, and it requires several primosome proteins. Among them, PriA protein - a 3' to 5' superfamily-2 DNA helicase - is the key factor in recognizing DNA lesions and it also recruits other proteins. Here, we investigated the ATPase and helicase activities of Streptococcus pneumoniae PriA (SpPriA) through biochemical and kinetic analyses. By comparing various DNA substrates, we observed that SpPriA is unable to unwind duplex DNA with high GC content. We constructed a deletion mutant protein (SpPriAdeloop) from which the loop area of the DNA-binding domain of PriA had been removed. Functional assays on SpPriAdeloop revealed that the loop area is important in endowing DNA-binding properties on the helicase. We also show that the presence of DnaD loader protein is important for enhancing SpPriA ATPase and DNA unwinding activities.

Deinococcus radiodurans PriA is a Pseudohelicase

Reactivation of repaired DNA replication forks in bacteria is catalyzed by PriA helicase. This broadly-conserved bacterial enzyme can remodel the structure of DNA at a repaired DNA replication fork by unwinding small portions of duplex DNA to prepare the fork for replisome reloading. While PriA's helicase activity is not strictly required for cell viability in E. coli, the sequence motifs that confer helicase activity upon PriA are well-conserved among sequenced bacterial priA genes, suggesting that PriA's duplex DNA unwinding activity confers a selective advantage upon cells. However, these helicase sequence motifs are not well-conserved among priA genes from the Deinococcus-Thermus phylum. Here, we show that PriA from a highly radiation-resistant member of that phylum, Deinococcus radiodurans, lacks the ability to hydrolyze ATP and unwind duplex DNA, thus qualifying D. radiodurans PriA as a pseudohelicase. Despite the lack of helicase activity, D. radiodurans PriA has retained the DNA binding activity expected of a typical PriA helicase, and we present evidence for a physical interaction between D. radiodurans PriA and its cognate replicative helicase, DnaB. This suggests that PriA has retained a role in replisome reloading onto repaired DNA replication forks in D. radiodurans despite its lack of helicase activity.

Monomeric nature of dengue virus NS3 helicase and thermodynamic analysis of the interaction with single-stranded RNA

Dengue virus nonstructural protein 3 (NS3) is a multifunctional protein formed by a superfamily-2 RNA helicase linked to a protease domain. In this work, we report results from in vitro experiments designed to determine the oligomeric state of dengue virus NS3 helicase (NS3h) and to characterize fundamental properties of the interaction with single-stranded (ss)RNA. Pulsed field gradient-NMR spectroscopy was used to determine the effective hydrodynamic radius of NS3h, which was constant over a wide range of protein concentrations in the absence and presence of ssRNA. Size exclusion chromatography-static light scattering experiments showed that NS3h eluted as a monomeric molecule even in the presence of ssRNA. Binding of NS3h to ssRNA was studied by quantitative fluorescence titrations using fluorescein-labeled and unlabeled ssRNA oligonucleotides of different lengths, and the effect of the fluorescein label on the interaction parameters was also analyzed. Experimental results were well described by a statistical thermodynamic model based on the theory of non-specific interactions of large ligands to a one-dimensional lattice. We found that binding of NS3h to ssRNA oligonucleotides and to poly(A) is characterized by minimum and occluded binding site sizes both of 10 nucleotides and by a weak positive cooperativity between adjacent proteins.

The Escherichia coli primosomal DnaT protein exists in solution as a monomer-trimer equilibrium system

The oligomerization reaction of the Escherichia coli DnaT protein has been quantitatively examined using fluorescence anisotropy and analytical ultracentrifugation methods. In solution, DnaT exists as a monomer-trimer equilibrium system. At the estimated concentration in the E. coli cell, DnaT forms a mixture of the monomer and trimer states with a 3:1 molar ratio. In spite of the modest affinity, the trimerization is a highly cooperative process, without the detectable presence of the intervening dimer. The DnaT monomer consists of a large N-terminal core domain and a small C-terminal region. The removal of the C-terminal region dramatically affects the oligomerization process. The isolated N-terminal domain forms a dimer instead of the trimer. These results indicate that the DnaT monomer possesses two structurally different, interacting sites. One site is located on the N-terminal domain, and two monomers, in the trimer, are associated through their binding sites located on that domain. The C-terminal region forms the other interacting site. The third monomer is engaged through the C-terminal regions. Surprisingly, the high affinity of the N-terminal domain dimer indicates that the DnaT monomer undergoes a conformational transition upon oligomerization, involving the C-terminal region. These data and the high specificity of the trimerization reaction, i.e., lack of any oligomers higher than a trimer, indicate that each monomer in the trimer is in contact with the two remaining monomers. A model of the global structure of the DnaT trimer based on the thermodynamic and hydrodynamic data is discussed.

Energetics of the Escherichia coli DnaT protein trimerization reaction

Thermodynamic and structural characteristics of the Escherichia coli DnaT protein trimerization reaction have been quantitatively examined using fluorescence anisotropy and analytical ultracentrifugation methods. Binding of magnesium to the DnaT monomers regulates the intrinsic affinity of the DnaT trimerization reaction. Comparison between the DnaT trimer and the isolated N-terminal core domain suggests that magnesium binds to the N-terminal domain but does not associate with the C-terminal region of the protein. The magnesium binding process is complex and involves approximately three Mg(2+) cations per protein monomer. The observed effect seems to be specific for Mg(2+). In the examined salt concentration range, monovalent cations and anions do not affect the trimer assembly process. However, magnesium affects neither the cooperativity of the trimerization reaction nor the GnHCl-induced trimer dissociation, strongly indicating that Mg(2+) indirectly stabilizes the trimer through the induced changes in the monomer structures. Nevertheless, formation of the trimer also involves specific conformational changes of the monomers, which are independent of the presence of magnesium. Binding of Mg(2+) cations dramatically changes the thermodynamic functions of the DnaT trimerization, transforming the reaction from a temperature-dependent to temperature-independent process. Highly cooperative dissociation of the trimer by GnHCl indicates that both interacting sites of the monomer, located on the N-terminal core domain and formed by the small C-terminal region, are intimately integrated with the entire protein structure. In the intact protein, the C-terminal region most probably interacts with the corresponding binding site on the N-terminal domain of the monomer. Functional implications of these findings are discussed.

Identification of a small molecule PriA helicase inhibitor

PriA helicase catalyzes the initial steps of replisome reloading onto repaired DNA replication forks in bacterial DNA replication restart pathways. We have used a high-throughput screen to identify a small molecule inhibitor of PriA-catalyzed duplex DNA unwinding. The compound, CGS 15943, targets Neisseria gonorrhoeae PriA helicase with an IC(50) of 114 ± 24 μM. The PriA helicase of Escherichia coli is also inhibited, although to a lesser extent than N. gonorrhoeae PriA. CGS 15943 decreases rates of PriA-catalyzed ATP hydrolysis and reduces the affinity with which PriA binds DNA. Steady-state kinetic data indicate that CGS 15943 inhibits PriA through a mixed mode of inhibition with respect to ATP and with respect to DNA, indicating that it binds to a site on PriA that participates in both substrate binding and catalysis. Inhibitor binding constants derived from steady-state kinetic experiments reveal that CGS 15943 has the highest binding affinity for the PriA·PriB·ATP complex, intermediate binding affinity for the PriA·PriB·DNA complex, and the lowest binding affinity for the PriA·PriB·DNA·ATP complex, suggesting that PriA assumes different conformations in each of these complexes. We propose that CGS 15943 binds to PriA at a site distinct from the DNA and primary ATP binding sites, perhaps at PriA's weak nucleotide binding site, and induces a conformational change in PriA that renders it less catalytically proficient or prevents conformational changes in PriA that are necessary for ATP hydrolysis and duplex DNA unwinding.

Equilibrium binding and kinetic characterization of putative tetracycline repressor family transcription regulator Fad35R from Mycobacterium tuberculosis

Fatty acids play critical role in the survival and virulence of Mycobacterium tuberculosis (Mtb). Activation of fatty acids by acyl-CoA synthetases (Fad) into fatty acyl-CoA is the first and one of the crucial steps in fatty acid metabolism. Mtb possesses 36 fatty acyl-CoA synthetases, unlike Escherichia coli, which has single enzyme. However, the mechanisms by which the expression of these multiple Fad genes is regulated remain uncharacterized. We characterized the DNA- and ligand-binding properties of a putative tetracycline repressor family regulator, named Fad35R, located upstream of the Fad35 gene and ScoA-citE operon. We identified a palindromic regulatory motif upstream of Fad35 and characterized the binding of Fad35R to this motif. Equilibrium binding studies show that Fad35R binds to this motif with high affinity (K(d) ∼ 0.033 μm) and the specificity of binding was confirmed by an electromobility gel shift assay. Kinetic studies indicate that faster association (k(a,avg) ∼ 5.4 × 10(4) m(-1) · s(-1)) and slower dissociation rates (k(d,avg) ∼ 5.84 × 10(-4) s(-1)) confer higher affinity. The affinity for the promoter is maximum at 300 mm NaCl but decreases rapidly beyond this range. Ligand-binding studies indicate that Fad35R binds specifically to tetracycline and also binds to fatty acid derivatives. The promoter-binding affinity is decreased significantly in the presence of palmityl-CoA, suggesting that Fad35R can sense the levels of activated fatty acids and alter its DNA-binding activity. Our results suggest that Fad35R may be the functional homologue of FadR and controls the expression of genes in a metabolite-dependent manner.

The N-terminal domain of the Escherichia coli PriA helicase contains both the DNA- and nucleotide-binding sites. Energetics of domain--DNA interactions and allosteric effect of the nucleotide cofactors

Functional interactions of the Escherichia coli PriA helicase 181N-terminal domain with the DNA and nucleotide cofactors have been quantitatively examined. The isolated 181N-terminal domain forms a stable dimer in solution, most probably reflecting the involvement of the domain in specific cooperative interactions of the intact PriA protein--double-stranded DNA (dsDNA) complex. Only one monomer of the domain dimer binds the DNA; i.e., the dimer has one effective DNA-binding site. Although the total site size of the dimer--single-stranded DNA (ssDNA) complex is ~13 nucleotides, the DNA-binding subsite engages in direct interactions with approximately five nucleotides. A small number of interacting nucleotides indicates that the DNA-binding subsites of the PriA helicase, i.e., the strong subsite on the helicase domain and the weak subsite on the N-terminal domain, are spatially separated in the intact enzyme. Contrary to current views, the subsite has an only slight preference for the 3'-end OH group of the ssDNA and lacks any significant base specificity, although it has a significant dsDNA affinity. Unlike the intact helicase, the DNA-binding subsite of the isolated domain is in an open conformation, indicating the presence of the direct helicase domain--N-terminal domain interactions. The discovery that the 181N-terminal domain possesses a nucleotide-binding site places the allosteric, weak nucleotide-binding site of the intact PriA on the N-terminal domain. The specific effect of ADP on the domain DNA-binding subsite indicates that in the intact helicase, the bound ADP not only opens the DNA-binding subsite but also increases its intrinsic DNA affinity.

Full-length Dengue virus RNA-dependent RNA polymerase-RNA/DNA complexes: stoichiometries, intrinsic affinities, cooperativities, base, and conformational specificities

Fundamental aspects of interactions of the Dengue virus type 3 full-length polymerase with the single-stranded and double-stranded RNA and DNA have been quantitatively addressed. The polymerase exists as a monomer with an elongated shape in solution. In the absence of magnesium, the total site size of the polymerase-ssRNA complex is 26 ± 2 nucleotides. In the presence of Mg(2+), the site size increases to 29 ± 2 nucleotides, indicating that magnesium affects the enzyme global conformation. The enzyme shows a preference for the homopyrimidine ssRNAs. Positive cooperativity in the binding to homopurine ssRNAs indicates that the type of nucleic acid base dramatically affects the enzyme orientation in the complex. Both the intrinsic affinity and the cooperative interactions are accompanied by a net ion release. The polymerase binds the dsDNA with an affinity comparable with the ssRNAs affinity, indicating that the binding site has an open conformation in solution. The lack of detectable dsRNA or dsRNA-DNA hybrid affinities indicates that the entry to the binding site is specific for the sugar-phosphate backbone and/or conformation of the duplex.

A bacterial PriB with weak single-stranded DNA binding activity can stimulate the DNA unwinding activity of its cognate PriA helicase

Background

Bacterial DNA replication restart pathways facilitate reinitiation of DNA replication following disruptive encounters of a replisome with DNA damage, thereby allowing complete and faithful duplication of the genome. In Neisseria gonorrhoeae, the primosome proteins that catalyze DNA replication restart differ from the well-studied primosome proteins of E. coli with respect to the number of proteins involved and the affinities of their physical interactions: the PriA:PriB interaction is weak in E. coli, but strong in N. gonorrhoeae, and the PriB:DNA interaction is strong in E. coli, but weak in N. gonorrhoeae. In this study, we investigated the functional consequences of this affinity reversal.

Results

We report that N. gonorrhoeae PriA's DNA binding and unwinding activities are similar to those of E. coli PriA, and N. gonorrhoeae PriA's helicase activity is stimulated by its cognate PriB, as it is in E. coli. This finding is significant because N. gonorrhoeae PriB's single-stranded DNA binding activity is weak relative to that of E. coli PriB, and in E. coli, PriB's single-stranded DNA binding activity is important for PriB stimulation of PriA helicase. Furthermore, a N. gonorrhoeae PriB variant defective for binding single-stranded DNA can stimulate PriA's helicase activity, suggesting that DNA binding by PriB might not be important for PriB stimulation of PriA helicase in N. gonorrhoeae. We also demonstrate that N. gonorrhoeae PriB stimulates ATP hydrolysis catalyzed by its cognate PriA. This activity of PriB has not been observed in E. coli, and could be important for PriB stimulation of PriA helicase in N. gonorrhoeae.

Conclusions

The results of this study demonstrate that a bacterial PriB homolog with weak single-stranded DNA binding activity can stimulate the DNA unwinding activity of its cognate PriA helicase. While it remains unclear if N. gonorrhoeae PriB's weak DNA binding activity is required for PriB stimulation of PriA helicase, the ability of PriB to stimulate PriA-catalyzed ATP hydrolysis could play an important role. Thus, the weak interaction between N. gonorrhoeae PriB and DNA might be compensated for by the strong interaction between PriB and PriA, which could result in allosteric activation of PriA's ATPase activity.

Functional characterization of the multidomain F plasmid TraI relaxase-helicase

TraI, a bifunctional enzyme containing relaxase and helicase activities, initiates and drives the conjugative transfer of the Escherichia coli F plasmid. Here, we examined the structure and function of the TraI helicase. We show that TraI binds to single-stranded DNA (ssDNA) with a site size of ∼25 nucleotides, which is significantly longer than the site size of other known superfamily I helicases. Low cooperativity was observed with the binding of TraI to ssDNA, and a double-stranded DNA-binding site was identified within the N-terminal region of TraI 1-858, outside the core helicase motifs of TraI. We have revealed that the affinity of TraI for DNA is negatively correlated with the ionic strength of the solution. The binding of AMPPNP or ADP results in a 3-fold increase in the affinity of TraI for ssDNA. Moreover, TraI prefers to bind ssDNA oligomers containing a single type of base. Finally, we elucidated the solution structure of TraI using small angle x-ray scattering. TraI exhibits an ellipsoidal shape in solution with four domains aligning along one axis. Taken together, these data result in the assembly of a model for the multidomain helicase activity of TraI.

Size-independent and noncooperative recognition of dsRNA by the Rice stripe virus RNA silencing suppressor NS3

Plant and animal viruses employ diverse suppressor proteins to thwart the host antiviral reaction of RNA silencing. Many suppressors bind dsRNA with different size specificity. Here, we examine the dsRNA recognition mechanism of the Rice stripe virus NS3 suppressor using quantitative biochemical approaches, as well as mutagenesis and suppression activity analyses in plants. We show that dimeric NS3 is a size-independent, rather than small interfering RNA-specific, dsRNA-binding protein that recognizes a minimum of 9 bp and can bind to long dsRNA with two or more copies. Global analysis using a combinatorial approach reveals that NS3 dimer has an occluded site size of ∼ 13 bp on dsRNA, an intrinsic binding constant of 1 × 10(8) M(-1), and virtually no binding cooperativity. This lack of cooperativity suggests that NS3 is not geared to target long dsRNA. The larger site size of NS3, compared with its interacting size, indicates that the NS3 structure has a border region that has no direct contact with dsRNA but occludes a ∼ 4-bp region from binding. We also develop a method to correct the border effect of ligand by extending the lattice length. In addition, we find that NS3 recognizes the helical structure and 2'-hydroxyl group of dsRNA with moderate specificity. Analysis of dsRNA-binding mutants suggests that silencing of the suppression activity of NS3 is mechanistically related to its dsRNA binding ability.

The Escherichia coli PriA helicase-double-stranded DNA complex: location of the strong DNA-binding subsite on the helicase domain of the protein and the affinity control by the two nucleotide-binding sites of the enzyme

The Escherichia coli PriA helicase complex with the double-stranded DNA (dsDNA), the location of the strong DNA-binding subsite, and the effect of the nucleotide cofactors, bound to the strong and weak nucleotide-binding site of the enzyme on the dsDNA affinity, have been analyzed using the fluorescence titration, analytical ultracentrifugation, and photo-cross-linking techniques. The total site size of the PriA-dsDNA complex is only 5±1 bp, that is, dramatically lower than 20±3 nucleotides occluded in the enzyme-single-stranded DNA (ssDNA) complex. The helicase associates with the dsDNA using its strong ssDNA-binding subsite in an orientation very different from the complex with the ssDNA. The strong DNA-binding subsite of the enzyme is located on the helicase domain of the PriA protein. The dsDNA intrinsic affinity is considerably higher than the ssDNA affinity and the binding process is accompanied by a significant positive cooperativity. Association of cofactors with strong and weak nucleotide-binding sites of the protein profoundly affects the intrinsic affinity and the cooperativity, without affecting the stoichiometry. ATP analog binding to either site diminishes the intrinsic affinity but preserves the cooperativity. ADP binding to the strong site leads to a dramatic increase of the cooperativity and only slightly affects the affinity, while saturation of both sites with ADP strongly increases the affinity and eliminates the cooperativity. Thus, the coordinated action of both nucleotide-binding sites on the PriA-dsDNA interactions depends on the structure of the phosphate group. The significance of these results for the enzyme activities in recognizing primosome assembly sites or the ssDNA gaps is discussed.

Binding specificity of Escherichia coli single-stranded DNA binding protein for the chi subunit of DNA pol III holoenzyme and PriA helicase

The Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA metabolism through its high affinity interactions with ssDNA, as well as its interactions with numerous other proteins via its unstructured C-termini. Although SSB interacts with at least 14 other proteins, it is not understood how SSB might recruit one protein over another for a particular metabolic role. To probe the specificity of these interactions, we have used isothermal titration calorimetry to examine the thermodynamics of binding of SSB to two E. coli proteins important for DNA replication, the chi subunit of DNA polymerase III holoenzyme and the PriA helicase. We find that an SSB tetramer can bind up to four molecules of either protein primarily via interactions with the last approximately 9 amino acids in the conserved SSB C-terminal tails (SSB-Ct). We observe intrinsic specificity for the binding of an isolated SSB-Ct peptide to PriA over chi due primarily to a more favorable enthalpic component. PriA and chi also bind with weaker affinity to SSB (in the absence of ssDNA) than to isolated SSB-Ct peptides, indicating an inhibitory effect of the SSB protein core. Although the binding affinity of SSB for both chi and PriA is enhanced if SSB is prebound to ssDNA, this effect is larger with PriA indicating a further enhancement of SSB specificity for PriA. These results also suggest that DNA binding proteins such as PriA, which also interact with SSB, could use this interaction to gain access to ssDNA by first interacting with the SSB C-termini.

Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities

Quantitative analysis of the interactions of the Escherichia coli primosomal PriB protein with a single-stranded DNA was done using quantitative fluorescence titration, photocrosslinking, and analytical ultracentrifugation techniques. Stoichiometry studies were done with a series of etheno-derivatives of single-stranded (ss) DNA oligomers. Interactions with the unmodified nucleic acids were studied, using the macromolecular competition titration (MCT) method. The total site-size of the PriB dimer-ssDNA complex, i.e. the maximum number of nucleotides occluded by the PriB dimer in the complex, is 12+/-1 nt. The protein has a single DNA-binding site, which is located centrally within the dimer and has a functionally homogeneous structure. The stoichiometry and photocrosslinking data show that only a single monomer of the PriB dimer engages in interactions with the nucleic acid. The analysis of the PriB binding to long oligomers was done using a statistical thermodynamic model that takes into account the overlap of potential binding sites and cooperative interactions. The PriB dimer binds the ssDNA with strong positive cooperativity. Both the intrinsic affinity and cooperative interactions are accompanied by a net ion release, with anions participating in the ion exchange process. The intrinsic binding process is an entropy-driven reaction, suggesting strongly that the DNA association induces a large conformational change in the protein. The PriB protein shows a dramatically strong preference for the homo-pyrimidine oligomers with an intrinsic affinity higher by about three orders of magnitude, as compared to the homo-purine oligomers. The significance of these results for PriB protein activity is discussed.

The Escherichia coli PriA helicase specifically recognizes gapped DNA substrates: effect of the two nucleotide-binding sites of the enzyme on the recognition process

Energetics and specificity of interactions between the Escherichia coli PriA helicase and the gapped DNAs have been studied, using the quantitative fluorescence titration and analytical ultracentrifugation methods. The gap complex has a surprisingly low minimum total site size, corresponding to approximately 7 nucleotides of the single-stranded DNA (ssDNA), as compared with the site size of approximately 20 nucleotides of the enzyme-ssDNA complex. The dramatic difference in stoichiometries indicates that the enzyme predominantly engages the strong DNA-binding subsite in interactions with the gap and assumes a very different orientation in the gap complex, as compared with the complex with the ssDNA. The helicase binds the ssDNA gaps with 4-5 nucleotides with the highest affinity, which is approximately 3 and approximately 2 orders of magnitude larger than the affinities for the ssDNA and double-stranded DNA, respectively. In the gap complex, the protein does not engage in cooperative interactions with the enzyme predominantly associated with the surrounding dsDNA. Binding of nucleoside triphosphate to the strong and weak nucleotide-binding sites of the helicase eliminates the selectivity of the enzyme for the size of the gap, whereas saturation of both sites with ADP leads to amplified affinity for the ssDNA gap containing 5 nucleotides and engagement of an additional protein area in interactions with the nucleic acid.

Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF1010: analyses using fluorescence stopped-flow intensity and anisotropy methods

The kinetic mechanism of the single-stranded DNA (ssDNA) recognition by the RepA hexameric replicative helicase of the plasmid RSF1010 and the nature of formed intermediates, in the presence of the ATP nonhydrolyzable analog, beta,gamma-imidoadenosine-5'-triphosphate (AMP-PNP), have been examined, using the fluorescence intensity and anisotropy stopped-flow and analytical ultracentrifugation methods. Association of the RepA hexamer with the ssDNA oligomers that engage the total DNA-binding site and exclusively the strong DNA-binding subsite is a minimum four-step mechanism [formula: see text]. Extreme stability of the RepA hexamer precludes any disintegration of its structure, and the sequential character of the mechanism indicates that the enzyme exists in a predominantly single conformation prior to the association with the nucleic acid. Moreover, the hexameric helicase possesses a DNA-binding site located outside its cross channel. The reaction steps have dramatically different dynamics, with rate constants differing by 2-3 orders of magnitude. Such behavior indicates a very diverse nature of the observed transitions, which comprises binding steps and large conformational transitions of the helicase, including local opening of the hexameric structure. Steady-state fluorescence anisotropies of intermediates indicate that the entry of the DNA into the cross channel is initiated from the 5' end of the bound nucleic acid. The global structure of the tertiary complex RepA-ssDNA-AMP-PNP is very different from the structure of the binary complex RepA-AMP-PNP, indicating that, in equilibrium, the RepA hexamer-ssDNA-AMP-PNP complex exists as a mixture of partially open states.

Thermodynamic analysis of the structure-function relationship in the total DNA-binding site of enzyme-DNA complexes

Both helicases and polymerases perform their activities when bound to the nucleic acids, that is, the enzymes possess a nucleic acid-binding site. Functional complexity of the helicase or the polymerase action is reflected in the intricate structure of the total nucleic acid-binding site, which allows the enzymes to control and change their nucleic acid affinities during the catalysis. Understanding the fundamental aspects of the functional heterogeneity of the total nucleic acid-binding site of a polymerase or helicase can be achieved through quantitative thermodynamic analysis of the enzyme binding to the nucleic acids oligomers, which differ in their length. Such an analysis allows the experimenter to assess the presence of areas with strong and weak affinity for the nucleic acid, that is, the presence of the strong and the weak nucleic acid-binding subsites, determine the number of the nucleotide occlude by each subsite, and estimate their intrinsic free energies of interactions.

Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins

S. cerevisiae ribosome biogenesis is a highly ordered and dynamic process that involves over 100 accessory proteins, including 18 DExD/H-box proteins that act at discrete steps in the pathway. Although often termed RNA helicases, the biochemical functions of individual DExD/H-box proteins appear to vary considerably. Four DExD/H-box proteins, Dbp3p, Dbp4p, Rok1p, and Rrp3p, involved in yeast ribosome assembly were expressed in E. coli, and all were found to be active RNA-dependent ATPases with k(cat) values ranging from 13 to 170 min(-1) and K(M)(ATP) values ranging from 0.24 to 2.3 mM. All four proteins are activated by single-stranded oligonucleotides, but they require different chain lengths for maximal ATPase activity, ranging from 10 to >40 residues. None of the four proteins shows significant specificity for yeast rRNA, compared to nonspecific control RNAs since these large RNAs contain multiple binding sites that appear to be catalytically similar. This systematic comparison of four members of the DExD/H-box family demonstrates a range of biochemical properties and lays the foundation for relating the activities of proteins to their biological functions.

Multiple global conformational states of the hexameric RepA helicase of plasmid RSF1010 with different ssDNA-binding capabilities are induced by different numbers of bound nucleotides. Analytical ultracentrifugation and dynamic light scattering studies

Global conformational transitions of the hexameric RepA helicase of plasmid RSF1010, induced by the nucleoside tri and di-phosphate binding, have been examined using analytical ultracentrifugation and dynamic light scattering techniques. The global structure of the RepA hexamer in solution, modeled as an oblate ellipsoid of revolution, is very different from its crystal structure, with the axial ratio of the ellipsoid being approximately 4.5 as compared to only approximately 2.4 in the crystal structure. The large axial ratio and the experimentally determined partial specific volume strongly suggest that, in solution, the diameter of the cross-channel of the hexamer is larger than approximately 17 A seen in the crystal. The global conformation of the helicase is modulated by a specific number of bound nucleotides. The enzyme exists in at least four conformational states, occurring sequentially as a function of the number of bound cofactors. These conformational states are different for ADP, as compared to beta,gamma-imidoadenosine 5'-triphosphate (AMP-PNP). Modulation of the global structure is separated into two phases, different for complexes with up to three bound nucleotides, from the effect observed at the saturating level of cofactors. This heterogeneity indicates different functional roles of the two modulation processes. Nucleotide control of helicase - single-stranded (ss)DNA interactions occurs through affecting the enzyme structure and the ssDNA affinity prior to DNA binding. Only one conformational state of the helicase, with two AMP-PNP molecules bound, has dramatically higher ssDNA-affinities than the complexes with ADP. Moreover the same state also has an increased site-size of the enzyme - ssDNA complexes. The implications of these findings for functional activities of a hexameric helicase are discussed.

Interactions of the DNA polymerase X from African swine fever virus with gapped DNA substrates. Quantitative analysis of functional structures of the formed complexes

Energetics and specificity of interactions between the African swine fever virus polymerase X and gapped DNA substrates have been studied, using the quantitative fluorescence titration technique. Stoichiometries of pol X complexes, with the DNA substrates, are higher than suggested by NMR studies. This can be understood in the context of the functionally heterogeneous organization of the total DNA-binding site of pol X, which is composed of two DNA-binding subsites. The enzyme forms two different complexes with the gapped DNAs, differing dramatically in affinities. In the high-affinity complex, pol X engages the total DNA-binding site, forming the gap complex, while in the low-affinity the enzyme binds to the dsDNA parts of the gapped DNA, using only one of the DNA-binding subsites. As a result, the net number of ions released in the gap complex formation is significantly larger than in the binding of the dsDNA part. In the presence of Mg+2, pol X shows a strong preference for the ssDNA gaps having one and two nucleotides. Recognition of the short gaps already occurs in the ground state of the enzyme-DNA complex. Surprisingly, the specific structure necessary to recognize the short gaps is induced by magnesium binding to the enzyme. In the absence of Mg+2, pol X looses its selectivity for short ssDNA gaps. Pol X binds gapped DNAs with considerable cooperative interactions, which increase with the decreasing gap size. The functional implications of these findings for ASFV pol X activities are discussed.

Structure of the tertiary complex of the RepA hexameric helicase of plasmid RSF1010 with the ssDNA and nucleotide cofactors in solution

The structure of the complex of the hexameric replicative helicase RepA protein of plasmid RSF1010 with ssDNA has been examined using the fluorescence energy transfer and analytical ultracentrifugation methods. We utilized the fact that the RepA monomer contains a single, natural cysteine residue. The cysteine residue has been modified with a fluorescent marker, which serves as the donor to the acceptor placed in different locations on the DNA. Using the two independent fluorescence donor-acceptor pairs and different DNA oligomers, we provide direct evidence that, in the complex with the enzyme, the ssDNA passes through the inner channel of the RepA hexamer. In the stationary complex, the RepA hexamer assumes a strictly single orientation with respect to the polarity of the sugar-phosphate backbone of the nucleic acid, with the large domain of protomers facing the 3' end of the bound DNA. Interactions with the helicase induce profound changes in the structure of the bound DNA, and these changes are predominantly localized in the proper DNA-binding site. The heterogeneity of the structure of the bound DNA reflects the heterogeneous structure of the total RepA helicase DNA-binding site. This is in excellent agreement with the thermodynamic data. The structure of the RepA hexamer, in solution, differs considerably from the crystal structure of the enzyme. Both fluorescence energy transfer and analytical ultracentrifugation data indicate a significant conformational flexibility of the RepA hexamer. Implications of these results for the mechanism of interactions of the hexameric helicase with the DNA are discussed.

Interactions of the DNA polymerase X of African swine fever virus with double-stranded DNA. Functional structure of the complex

Interactions of the polymerase X of African swine fever virus with the double-stranded DNA (dsDNA) have been studied with fluorescent dsDNA oligomers, using quantitative fluorescence titrations, analytical ultracentrifugation, and fluorescence energy transfer techniques. Studies with unmodified dsDNAs were performed, using competition titration method. ASV pol X binds the dsDNA with a site-size of n=10(+/-2) base-pairs, which is significantly shorter than the total site-size of 16(+/-2) nucleotides of the enzyme-ssDNA complex. The small site size indicates that the enzyme binds the dsDNA exclusively using the proper DNA-binding subsite. Fluorescence energy transfer studies between the tryptophan residue W92 and the acceptor, located at the 5' or 3' end of the dsDNA, suggest strongly that the proper DNA-binding subsite is located on the non-catalytic C-terminal domain. Moreover, intrinsic interactions with the dsDNA 10-mer or 20-mer are accompanied by the same net number of ions released, independent of the length of the DNA, indicating the same length of the DNA engaged in the complex. The dsDNA intrinsic affinity is about two orders of magnitude higher than the ssDNA affinity, indicating that the proper DNA-binding subsite is, in fact, the specific dsDNA-binding site. Surprisingly, ASFV pol X binds the dsDNA with significant positive cooperativity, which results from protein-protein interactions. Cooperative interactions are accompanied by the net ion release, with anions participating in the ion-exchange process. The significance of these results for ASFV pol X activity in the recognition of damaged DNA is discussed.

Allosteric interactions between the nucleotide-binding sites and the ssDNA-binding site in the PriA helicase-ssDNA complex. 3

Allosteric interactions between the strong and weak nucleotide-binding sites and the total and proper single-stranded (ss)DNA-binding sites of the Escherichia coli PriA helicase have been analyzed using the fluorescence titration technique. Binding of the DNA exclusively to the proper DNA-binding site of the helicase, profoundly affects the intrinsic affinities of both nucleotide-binding sites, indicating a direct communication between the nucleotide-binding sites and the proper DNA-binding site. The communication involves conformational changes of the entire protein molecule. Nevertheless, the bound DNA differently affects the structures of the strong and weak nucleotide-binding sites. While the polarity of the strong site is moderately diminished, the polarity of the weak site is dramatically increased, indicating an intimate involvement of the weak site in controlling the helicase interactions with the DNA. The strong site does not directly control the DNA affinity of the enzyme. Only when the helicase has both nucleotide-binding sites saturated with ADP but not with ATP analogues does the enzyme have an increased affinity for the ssDNA, indicating that the control of ssDNA affinity involves a coordinated action of both nucleotide-binding sites and depends upon the phosphate group of the bound cofactor. A dramatic increase of the DNA affinity, when the DNA encompasses the total DNA-binding site of the enzyme, with both nucleotide-binding sites saturated with ADP or NDP, indicates that an additional area of the protein within the total DNA-binding site becomes engaged in interactions with the DNA. The significance of these results for the enzyme activities in the DNA unwinding and recognition is discussed.

Kinetic mechanisms of the nucleotide cofactor binding to the strong and weak nucleotide-binding site of the Escherichia coli PriA helicase. 2

Kinetics of the nucleotide binding to the strong (S) and weak (W) nucleotide-binding site of the Escherichia coli PriA helicase have been studied using the fluorescence stopped-flow technique. Experiments were performed with TNP-ADP and TNP-ATP analogues. Binding of the ADP analogue to the strong binding site is a four-step sequential reaction: (PriA)S + D (k1)<-->(k(-1)) + (S)1 (k2)<-->(k(-2)) (S)2 (k3)<-->(k(-3)) (S)3 (k4)<-->(k(-4)) (S)4. Association of TNP-ATP proceeds through an analogous three-step mechanism. The first two steps and intermediates are similar for both cofactors. However, the (S)3 intermediate is dramatically different for ADP and ATP analogues. Its emission is close to the emission of the free TNP-ADP, while it is by a factor of approximately 16 larger than the free TNP-ATP fluorescence. Thus, only the ADP analogue passes through an intermediate where it leaves the hydrophobic cleft of the site. This behavior corroborates with the fact that ADP leaves the ATPase site without undergoing a chemical change. The fast bimolecular step and the sequential mechanism indicate that the site is easily accessible to the cofactor, and it does not undergo an adjustment prior to binding. The subsequent step is also fast and stabilizes the complex. Magnesium profoundly affects the population of intermediates. The data indicate that the dominant (S)2 species is a part of the ATP catalytic cycle. ADP analogue binding to the weak nucleotide-binding site proceeds in a simpler two-step mechanism: (PriA)W + D (k1)<-->(k(-1)) (W)1 (k2)<-->(k(-2)) (W)2 with (W)1 being a dominant intermediate both in the presence and in the absence of Mg2+. The results indicate that the weak site is an allosteric control site in the functioning of the PriA helicase.

The Escherichia coli PriA helicase has two nucleotide-binding sites differing dramatically in their affinities for nucleotide cofactors. 1. Intrinsic affinities, cooperativities, and base specificity of nucleotide cofactor binding

Interactions of the Escherichia coli PriA helicase with nucleotide cofactors have been studied using the fluorescence titration and analytical ultracentrifugation techniques. Binding of unmodified cofactors was characterized by the fluorescence competition titration method. The obtained data establish that at saturation the PriA helicase binds two nucleotide molecules per protein monomer. This result corroborates with the primary structure of the protein, which contains sequence motifs implicated as putative nucleotide-binding sites. The intrinsic affinities of the binding sites differ by 2-4 orders of magnitude. Thus, the PriA helicase has a strong and a weak nucleotide-binding site. The binding sites differ dramatically in their properties. The strong site is highly specific for adenosine cofactors, while the weak site shows very modest base specificity. The affinities of the strong and weak binding sites for ATP are lower than the affinities for ADP, although both sites have similar affinity for the inorganic phosphate group. Unlike the weak site, the affinity of the strong site profoundly depends on the structure of the phosphate group of the ATP cofactor. Binding of unmodified nucleotides indicates the presence of positive cooperative interactions between bound cofactors (i.e., the existence of communication between the two sites). Magnesium cations are specifically involved in controlling the cofactor affinity for the strong site, while the affinity of the weak site is predominantly determined by interactions between the phosphate group and ribose regions of the cofactor and the protein matrix. The significance of these results for the activities of the PriA helicase is discussed.

DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex

Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligomers were carried out using the competition titration method. The total site-size of the pol X-ssDNA complex is 16(+/-1) nucleotide residues. The large total ssDNA-binding site has a complex heterogeneous structure. It contains the proper ssDNA-binding site that encompasses only 7(+/-1) residues. As the length of the ssDNA increases, the enzyme engages an additional binding area in interactions with the DNA, at a distance of approximately 7-8 nucleotides from the proper site, which is located asymmetrically within the polymerase molecule. As a result, the net ion release accompanying the interactions with the DNA, increases from approximately 1 for the proper DNA-binding site to approximately 6 for the total DNA-binding site. Unlike in the case of the mammalian polymerase beta that belongs to the same polymerase X family, the DNA-binding areas within the total DNA-binding site of pol X are not autonomous. Consequently, the enzyme does not form different binding modes with different numbers of occluded nucleotide residues, although the interacting areas are structurally separated. The statistical thermodynamic model that accounts for the engagement of the proper and the total DNA-binding site in interactions with the DNA provides an excellent description of the binding process. Pol X binds the ssDNA without detectable cooperativity and with very modest base specificity.

Interactions of the RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative analysis of stoichiometries, intrinsic affinities, cooperativities, and heterogeneity of the total ssDNA-binding site

Interactions between the replicative RepA helicase hexamer of plasmid RSF1010 with the single-stranded DNA (ssDNA) have been studied, using the quantitative fluorescence titration, analytical sedimentation velocity, and sedimentation equilibrium techniques. Experiments were performed with fluorescein-labeled ssDNA oligomers. Studies with unmodified ssDNA oligomers were accomplished using the macromolecular competition titration method. Analyses of RepA helicase interactions with a series of the ssDNA provide direct evidence that the total site-size of the RepA hexamer-ssDNA complex is 19 +/- 1 nucleotide residues. The total ssDNA-binding site of the hexamer has a heterogeneous structure. Part of the total binding site constitutes the proper ssDNA-binding site of the enzyme, an area that possesses strong ssDNA-binding capability and encompasses only 8 +/- 1 residues of the ssDNA. The statistical effect on the macroscopic binding constant for the proper ssDNA-binding site indicates that it is structurally separated from the remaining part of the total ssDNA-binding site. Engagement in interactions with the ssDNA is accompanied by net ion release. Moreover, the proper ssDNA-binding site shows little base specificity. On the other hand, with long ssDNA oligomers, the entire total ssDNA-binding site of the RepA hexamer engages in interactions with the ssDNA resulting in a dramatic change in the nature of interactions with the nucleic acid. The association includes an uptake of ions by the protein. Moreover, unlike the proper-ssDNA-binding site, the total binding site shows a significant preference for pyrimidine oligomers. In this aspect, the RepA helicase is different from the Escherichia coli DnaB hexamer that shows large preference for purine homo-oligomers. In similar solution conditions, the ssDNA intrinsic affinity of the RepA hexamer is similar to the intrinsic affinity of the DnaB helicase. The RepA helicase binds to ssDNA oligomers that can accept more than one RepA hexamer with significant positive cooperative interactions.

Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme

Kinetics of the Escherichia coli PriA helicase interactions with the ssDNA has been studied, using the fluorescence stopped-flow technique. Experiments have been performed with a series of fluorescent etheno derivatives of ssDNA adenosine oligomers, differing in the number of nucleotide residues. The PriA helicase binds the ssDNA in the sequential process defined by [reaction: see text]. In the first step, the enzyme associates fast with the ssDNA without inducing conformational changes in the DNA. The dependence of the partial equilibrium constant, characterizing the first step, upon the length of the ssDNA strictly reflects the statistical relationship between the size of the DNA-binding site and the number of potential binding sites on the ssDNA. Only the DNA-binding site that encompasses 6.3 +/- 1 residues is directly involved in interactions. The site is located on a structural domain allowing the enzyme to efficiently search and recognize small patches of the ssDNA. Intramolecular steps are independent of the ssDNA length and accompanied by changes in the DNA structure. Salt and glycerol effects on the studied kinetics indicate a very different nature of the intermediates. While the bimolecular step is characterized by net ion release and water uptake, net ion uptake and water release accompany intramolecular transitions. Specific ion binding stabilizes the helicase-ssDNA complex in (P)(2) and (P)(3) intermediates. However, magnesium and AMP-PNP do not affect the mechanism of enzyme-ssDNA interactions. The sequential character of the mechanism indicates that the enzyme does not exist in a preequilibrium conformational transition prior to the DNA binding.

A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks

Arrest of replication forks by various internal and external threats evokes a myriad of cellular reactions, collectively known as DNA replication checkpoint responses. In bacteria, PriA is essential for restoration of stalled replication forks and recombinational repair of double-stranded DNA breaks and is a candidate sensor protein that may recognize arrested forks. Here, we report that PriA protein specifically recognizes 3' termini of arrested nascent DNA chains at model stalled replication forks in vitro. Mutations in the putative "3' terminus binding pocket" present in the N-terminal segment of PriA result in reduced binding to stalled replication fork structures and loss of its biological functions. The results suggest a mechanism by which stalled replication forks are recognized by a sensor protein for checkpoint responses.

Characterization of simian virus 40 T-antigen double hexamers bound to a replication fork. The active form of the helicase

Large T-antigen (T-ag) is a viral helicase required for the initiation and elongation of simian virus 40 DNA replication. The unwinding activity of the helicase is powered by ATP hydrolysis and is critically dependent on the oligomeric state of the protein. We confirmed that the double hexamer is the active form of the helicase on synthetic replication forks. In contrast, the single hexamer cannot unwind synthetic forks and remains bound to the DNA as ATP is hydrolyzed. This inability of the T-ag single hexamer to release the DNA fork is the likely explanation for its poor helicase activity. We characterized the interactions of T-ag single and double hexamers with synthetic forks and single-stranded (ss) DNA. We demonstrated that DNA forks promote the formation of T-ag double hexamer. The lengths of the duplex region and the 3' tail of the synthetic forks are the critical factors in assembly of the double hexamer, which is bound to a single fork. We found that the cooperativity of T-ag binding to ss oligonucleotides increased with DNA length, suggesting that multiple consecutive subunits in the hexamer engage the ssDNA.

Helicase from hepatitis C virus, energetics of DNA binding

The ability of a helicase to bind single-stranded nucleic acid is critical for nucleic acid unwinding. The helicase from the hepatitis C virus, NS3 protein, binds to the 3'-DNA or the RNA strand during unwinding. As a step to understand the mechanism of unwinding, DNA binding properties of the helicase domain of NS3 (NS3h) were investigated by fluorimetric binding equilibrium titrations. The global analysis of the binding data by a combinatorial approach was done using MATLAB. NS3h interactions with single-stranded DNA (ssDNA) are 300-1000-fold tighter relative to duplex DNA. The NS3h protein binds to ssDNA less than 15 nt in length with a stoichiometry of one protein per DNA. The minimal ssDNA binding site of NS3h helicase was determined to be 8 nucleotides with the microscopic K(d) of 2-4 nm or an observed free energy of -50 kJ/mol. These NS3h-DNA interactions are highly sensitive to salt, and the K(d) increases 4 times when the NaCl concentration is doubled. Multiple HCV helicase proteins bind to ssDNA >15 nucleotides in length, with an apparent occluded site of 8-11 nucleotides. The DNA binding data indicate that the interactions of multiple NS3h protein molecules with long ssDNA are both noncooperative and sequence-independent. We discuss the DNA binding properties of HCV helicase in relation to other superfamily 1 and 2 helicases. These studies provide the basis to investigate the DNA binding interactions with the unwinding substrate and their modulation by the ATPase activity of HCV helicase.

Evidence for a functional monomeric form of the bacteriophage T4 DdA helicase. Dda does not form stable oligomeric structures

The active form of many helicases is oligomeric, possibly because oligomerization provides multiple DNA binding sites needed for unwinding of DNA. In order to understand the mechanism of the bacteriophage T4 Dda helicase, the potential requirement for oligomerization was investigated. Chemical cross-linking and high pressure gel filtration chromatography provided little evidence for the formation of an oligomeric species. The specific activity for ssDNA stimulated ATPase activity was independent of Dda concentration. Dda was mutated to produce an ATPase-deficient protein (K38A Dda) by altering a residue within a conserved, nucleotide binding loop. The helicase activity of K38A Dda was inactivated, although DNA binding properties were similar to Dda. In the presence of limiting DNA substrate, the rate of unwinding by Dda was not changed; however, the amplitude of product formation was reduced in the presence of increasing concentrations of K38A Dda. The reduction was between that expected for a monomeric or dimeric helicase based on simple competition for substrate binding. When unwinding of DNA was measured in the presence of excess DNA substrate, addition of K38A Dda caused no reduction in the observed rate for strand separation. Taken together, these results indicate that oligomerization of Dda is not required for DNA unwinding.