Carboxyl-terminal domain III of the delta' subunit of the DNA polymerase III holoenzyme binds delta

The delta and delta' subunits are essential components of the DNA polymerase III holoenzyme, required for assembly and function of the DnaX-complex clamp loader (tau2gammadeltadelta'chipsi). The x-ray crystal structure of delta' contains three structural domains (Guenther, B., Onrust, R., Sali, A., O'Donnell, M., and Kuriyan, J. (1997) Cell 91, 335-345). In this study, we localize the delta-binding domain of delta' to a carboxyl-terminal domain III by quantifying the interaction of delta with a series of delta' fusion proteins lacking specific domains. Purification and immobilization of the fusion proteins were facilitated by the inclusion of a tag containing hexahistidine and a short biotinylation sequence. Both NH2- and COOH-terminal-tagged full-length delta' were soluble and had specific activities comparable with that of native delta'. delta and delta' form a 1:1 heterodimer with a dissociation constant (K(D)) of 5 x 10(-7) m determined by equilibrium sedimentation. The K(D) determined by surface plasmon resonance was comparable. Domain III alone bound delta at an affinity comparable to that of wild type delta', whereas proteins lacking domain III did not bind delta. Using a panel of domain-specific anti-delta' monoclonal antibodies, we found that two of the domain III-specific monoclonal antibodies interfered with delta-delta' interaction and abolished the replication activity of DNA polymerase-III holoenzyme.

A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of deltadelta' with DnaX(4) forms DnaX(3)deltadelta'

We have constructed a plasmid-borne artificial operon that expresses the six subunits of the DnaX complex of Escherichia coli DNA polymerase III holoenzyme: tau, gamma, delta, delta', chi and psi. Induction of this operon followed by assembly in vivo produced two taugamma mixed DnaX complexes with stoichiometries of tau(1)gamma(2)deltadelta'chipsi and tau(2)gamma(1)deltadelta'chipsi rather than the expected gamma(2)tau(2)deltadelta'chipsi. We observed the same heterogeneity when taugamma mixed DnaX complexes were reconstituted in vitro. Re-examination of homomeric DnaX tau and gamma complexes assembled either in vitro or in vivo also revealed a stoichiometry of DnaX(3)deltadelta'chipsi. Equilibrium sedimentation analysis showed that free DnaX is a tetramer in equilibrium with a free monomer. An assembly mechanism, in which the association of heterologous subunits with a homomeric complex alters the stoichiometry of the homomeric assembly, is without precedent. The significance of our findings to the architecture of the holoenzyme and the clamp-assembly apparatus of all other organisms is discussed.

Characterization of the unique C terminus of the Escherichia coli tau DnaX protein. Monomeric C-tau binds alpha AND DnaB and can partially replace tau in reconstituted replication forks

A contact between the dimeric tau subunit within the DNA polymerase III holoenzyme and the DnaB helicase is required for replication fork propagation at physiologically-relevant rates (Kim, S., Dallmann, H. G., McHenry, C. S., and Marians, K. J. (1996) Cell 84, 643-650). In this report, we exploit the OmpT protease to generate C-tau, a protein containing only the unique C-terminal sequences of tau, free of the sequences shared with the alternative gamma frameshifting product of dnaX. We have established that C-tau is a monomer by sedimentation equilibrium and sedimentation velocity ultracentrifugation. Monomeric C-tau binds the alpha catalytic subunit of DNA polymerase III with a 1:1 stoichiometry. C-tau also binds DnaB, revealed by a coupled immunoblotting method. C-tau restores the rapid replication rate of inefficient forks reconstituted with only the gamma dnaX gene product. The acceleration of the DnaB helicase can be observed in the absence of primase, when only leading-strand replication occurs. This indicates that C-tau, bound only to the leading-strand polymerase, can trigger the conformational change necessary for DnaB to assume the fast, physiologically relevant form.

tau couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork

Synthesis of an Okazaki fragment occurs once every 1 or 2 s at the Escherichia coli replication fork. To account for the rapid recycling required of the lagging-strand polymerase, it has been proposed that it is held at the replication fork by protein-protein interactions with the leading-strand polymerase as part of a dimeric polymerase assembly. Solution studies showed that the replicative polymerase, the DNA polymerase III holoenzyme, was indeed a dimer with two catalytic cores held together by the tau subunit. However, the functionality of this arrangement at the replication fork has never been demonstrated. We showed previously that the lagging-strand polymerase acted processively during multiple rounds of Okazaki fragment synthesis, i.e. the same polymerase core assembly synthesized each and every fragment made by the fork. Using extreme dilution of active replication forks and the isolation of protein-DNA complexes capable of supporting coupled leading- and lagging-strand synthesis, we demonstrate here that this coupling of leading- and lagging-strand synthesis is, in fact, mediated by the tau subunit of the holoenzyme acting as a physical bridge between the core assemblies synthesizing the leading and lagging strands.

In vivo assembly of the tau-complex of the DNA polymerase III holoenzyme expressed from a five-gene artificial operon. Cleavage of the tau-complex to form a mixed gamma-tau-complex by the OmpT protease

A plasmid was constructed that encodes all five subunits of the Escherichia coli tau-complex on a single artificially constructed operon under the control of an inducible promoter. The proteins tau, delta, delta , chi, and psi overproduced from this artificial operon assemble efficiently in vivo, providing an efficient source of homogeneous tau-complex. The gamma subunit is a truncated form of tau that is produced by a translational frameshift. When protein expression was induced in bacterial strains containing the outer membrane protein T (OmpT) protease, tau was proteolyzed after lysis to a gamma-like protein, gammaP, and a peptide, C-tau, corresponding to the C terminus of tau. N-terminal sequencing of C-tau revealed a cleavage site between two lysines at positions 429 and 430 of tau. The deduced sequence of gammaP is, therefore, only two amino acids shorter than natural gamma. The proteolysis by OmpT was also shown directly by using purified OmpT and tau-complex in an in vitro reaction. A gammaP-complex and a mixed tau-gammaP-complex were purified from ompT+ cells. When the tau-complex proteins were overexpressed in ompT- bacteria, intact tau-complex lacking gammaP could be purified.

Coupling of a replicative polymerase and helicase: a tau-DnaB interaction mediates rapid replication fork movement

The E. coli replication fork synthesizes DNA at the rate of nearly 1000 nt/s. We show here that an interaction between the tau subunit of the replicative polymerase (the DNA polymerase III holoenzyme) and the replication fork DNA helicase (DnaB) is required to mediate this high rate of replication fork movement. In the absence of this interaction, the polymerase follows behind the helicase at a rate equal to the slow (approximately 35 nt/s) unwinding rate of the helicase alone, whereas upon establishing a tau-DnaB contact, DnaB becomes a more effective helicase, increasing its translocation rate by more than 10-fold. This finding establishes the existence of both a physical and communications link between the two major replication machines in the replisome: the DNA polymerase and the primosome.

Tau protects beta in the leading-strand polymerase complex at the replication fork

Replication forks formed in the absence of the tau subunit of the DNA polymerase III holoenzyme produce shorter leading and lagging strands than when tau is present. We show that one reason for this is that in the absence of tau, but in the presence of the gamma-complex, leading-strand synthesis is no longer highly processive. In the absence of tau, the size of the leading strand becomes proportional to the concentration of beta and inversely proportional to the concentration of the gamma-complex. In addition, the beta in the leading-strand complex is no longer resistant to challenge by either anti-beta antibodies or poly(dA):oligo(dT). Thus, tau is required to cement a processive leading-strand complex, presumably by preventing removal of beta catalyzed by the gamma-complex.

DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Physical characterization of the DnaX subunits and complexes

A physical characterization of the tau and gamma subunits of the Escherichia coli DNA polymerase III holoenzyme and their complexes with the delta, delta', chi, and psi subunits is presented. The native molecular mass of the tau and gamma subunits was determined to be 255,000 and 189,000 Da, respectively, by sedimentation equilibrium analytical ultracentrifugation. Both values indicate a tetrameric quaternary structure. The tau and gamma complexes were reconstituted and purified using two different methods. Both complexes assembled readily and were reconstituted at subunit concentrations approaching physiological levels. The stoichiometries of the tau and gamma complexes, as determined by quantitative densitometry of SDS-polyacrylamide gels, were found to be tau 4 delta 1 delta' 1 chi 1 psi 1 and gamma 4 delta 1 delta' 1 chi 1 psi 1. BIAcore analysis demonstrated that the formation of large multiprotein complexes of holoenzyme subunits depends on the presence of the tau subunit; gamma could not substitute. We present a model for a gamma-less form of DNA polymerase III holoenzyme that has asymmetrical structural features that may be responsible for the functional asymmetry observed in holoenzyme. The stoichiometry of the reconstituted DNA polymerase III* component of holoenzyme in this model is (alpha epsilon theta)2DnaX4 delta 1 delta' 1 chi 1 psi 1.

DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Central role of tau in initiation complex assembly and in determining the functional asymmetry of holoenzyme

The alternative forms of the DnaX protein found in Escherichia coli DNA polymerase III holoenzyme, tau and gamma, were purified from extracts of strains carrying overexpressing plasmids mutated in their frameshifting sequences such that they produced only one subunit or the other. The purified subunits were used to reconstitute the tau and gamma complexes which were characterized by functional assays. The gamma complex-reconstituted holoenzyme required a stoichiometric excess of DNA polymerase III core, beyond physiological levels, for activity. The tau subunit stimulated the gamma complex 2-fold, but could not be used to reconstitute a holoenzyme with gamma complex and stoichiometric quantities of core. In the presence of adenosine 5'-O-(3'-thiotriphospate) (ATP gamma S), the DNA polymerase III holoenzyme behaves as an asymmetric dimer; it can form only initiation complexes with primed DNA in one-half of the enzyme (Johanson, K. O., and McHenry, C. S. (1984) J. Biol. Chem. 259, 4589-4595). An asymmetric distribution of two products of the dnaX gene, gamma and tau, has been postulated to underlie the asymmetry of holoenzyme. To provide a direct test for this hypothesis, we reconstituted holoenzyme containing only the gamma or tau DnaX proteins. We observed that, although gamma could function in the presence of ATP and high concentrations of DNA polymerase III core, it was nearly inert in the presence of ATP gamma S. In contrast, tau-containing holoenzyme behaved exactly like native holoenzyme in the presence of ATP gamma S. These results implicate tau as a key component required to reconstitute holoenzyme with native behavior and show that tau plays a key role in initiation complex formation. These results also show that gamma is not a necessary component, since all of the known properties of native holoenzyme can be reproduced with a 9-subunit tau-holoenzyme.

DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range

An artificial operon that contains tandem holC-holD genes was used to overproduce a complex of the chi and psi subunits of the DNA polymerase III holoenzyme. Normally insoluble by itself, psi forms a tight soluble complex with chi. A purification procedure that yields pure, active chi psi complex in 100-mg quantities suitable for biophysical studies is reported. Sedimentation equilibrium studies demonstrate that chi psi is a 1:1 heterodimer. The presence of chi psi dramatically lowers the level of delta.delta' required to reconstitute holoenzyme to levels expected in vivo. That chi psi accomplishes this by binding to gamma or tau and increasing their affinity for delta.delta' was demonstrated by surface plasmon resonance using a Pharmacia BIA-core instrument. In the absence of delta.delta', chi psi binds to either the gamma or tau DnaX protein with Kd = 2 nM.

Translation through an uncDC mRNA secondary structure governs the level of uncC expression in Escherichia coli

Escherichia coli expresses the beta and epsilon subunits of F1F0-ATP synthase at relative levels consistent with the 3:1 (beta/epsilon) stoichiometry in the holoenzyme. The mechanism of translational control of expression of the uncC gene (epsilon subunit) relative to the immediately 5' uncD gene (beta subunit) was examined. Previous expression studies and a computer analysis suggested the presence of an RNA secondary structure including the 3' end of uncD, the uncDC intergenic region, and the uncC Shine-Dalgarno sequence (S. D. Dunn and H. G. Dallmann, J. Bacteriol. 172:2782-2784, 1990). Analysis of in vitro-transcribed RNA by cleavage with RNases T1, V1, and CL3 and by chemical modification with dimethyl sulfate and diethyl pyrocarbonate confirmed a predicted structure. Introduction of premature uncD stop codons inserted 5' of the secondary structure strongly reduced epsilon expression, whereas stop codons inserted at positions within the secondary structure showed smaller effects, indicating that translational control of epsilon synthesis involves partial coupling to beta synthesis. Possible mechanisms by which the RNA secondary structure and the unfolding of this structure by translation of uncD may govern the level of uncC expression are discussed.

Determination of the 1-ethyl-3-[(3-dimethylamino)propyl]-carbodiimide- induced cross-link between the beta and epsilon subunits of Escherichia coli F1-ATPase

The zero-length cross-link between the inhibitory epsilon subunit and one of three catalytic beta subunits of Escherichia coli F1-ATPase (alpha 3 beta 3 gamma delta epsilon), induced by a water-soluble carbodiimide, 1-ethyl-3-[(3-dimethylamino) propyl]-carbodiimide (EDC), has been determined at the amino acid level. Lability of cross-linked beta-epsilon to base suggested an ester cross-link rather than the expected amide. A 10-kDa cross-linked CNBr fragment derived from beta-epsilon was identified by electrophoresis on high percentage polyacrylamide gels. Sequence analysis of this peptide revealed the constituent peptides to be Asp-380 to Met-431 of beta and Glu-96 to Met-138 of epsilon. Glu-381 of beta was absent from cycle 2 indicating that it was one of the cross-linked residues, but no potential cross-linked residue in epsilon was identified in this analysis. A form of epsilon containing a methionine residue in place of Val-112 (epsilon V112M) was produced by site-directed mutagenesis. epsilon V112M was incorporated into F1-ATPase which was then cross-linked with EDC. An 8-kDa cross-linked CNBr fragment of beta-epsilon V112M was shown to contain the peptide of epsilon between residues Glu-96 and Met-112 and the peptide of beta between residues Asp-380 and Met-431. Again residue Glu-381 of beta was notably reduced and no missing residue from the epsilon peptide could be identified, but the peptide sequence limited the possible choices to Ser-106, Ser-107, or Ser-108. Furthermore, an epsilon mutant in which Ser-108 was replaced by cysteine could no longer be cross-linked to a beta subunit in F1-ATPase by EDC. Both mutant forms of epsilon supported growth of an uncC-deficient E. coli strain and inhibited F1-ATPase. These results indicate that the EDC-induced cross-link between the beta and epsilon subunits of F1-ATPase is an ester linkage between beta-Glu-381 and, likely, epsilon-Ser-108. As these residues must be located immediately adjacent to one another in F1-ATPase, our results define a site of subunit-subunit contact between beta and epsilon.

The Escherichia coli unc transcription terminator enhances expression of uncC, encoding the epsilon subunit of F1-ATPase, from plasmids by stabilizing the transcript

The effect of the unc transcription terminator on expression of uncC, encoding the epsilon subunit of Escherichia coli F1-ATPase, from plasmids was studied. The cloned sequence in pTK1 included the uncC ribosome binding site, the uncC structural gene, and the unc transcription terminator. The cloned region in pSD37 was similar, but lacked the unc transcription terminator. Transformants carrying pTK1 produced the epsilon subunit of F1-ATPase, encoded by uncC, in 10-fold greater abundance than transformants carrying pSD37. Northern blots revealed similar differences in the steady-state uncC mRNA levels. The half-life of the message transcribed from pTK1 was 90-100 seconds, while that from pSD37 was 25-30 seconds. These studies indicate the importance of message stabilization through features at the 3' end of the transcript in ensuring adequate production of epsilon. We have exploited this stabilization to develop a simple, efficient, and gentle method of purifying the overproduced epsilon subunit.

An upstream uncD sequence modulates translation of Escherichia coli uncC

The effect of upstream uncD sequences on expression of the Escherichia coli uncC gene, encoding the epsilon subunit of F1-ATPase, was studied. uncC expression was reduced severalfold in plasmid constructs bearing, in addition to uncC, a region of uncD located between 85 and 119 bases upstream from the uncC initiation codon. This reduction was independent of in-frame translation of the uncD sequences. An mRNA stem-loop structure in which sequences located within the inhibitory region of uncD base pair with the uncDC intercistronic region is suggested to function in modulating uncC expression.