51
|
McInerney P, Johnson A, Katz F, O'Donnell M. Characterization of a triple DNA polymerase replisome. Mol Cell 2007; 27:527-38. [PMID: 17707226 DOI: 10.1016/j.molcel.2007.06.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 05/15/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022]
Abstract
The replicase of all cells is thought to utilize two DNA polymerases for coordinated synthesis of leading and lagging strands. The DNA polymerases are held to DNA by circular sliding clamps. We demonstrate here that the E. coli DNA polymerase III holoenzyme assembles into a particle that contains three DNA polymerases. The three polymerases appear capable of simultaneous activity. Furthermore, the trimeric replicase is fully functional at a replication fork with helicase, primase, and sliding clamps; it produces slightly shorter Okazaki fragments than replisomes containing two DNA polymerases. We propose that two polymerases can function on the lagging strand and that the third DNA polymerase can act as a reserve enzyme to overcome certain types of obstacles to the replication fork.
Collapse
Affiliation(s)
- Peter McInerney
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
| | | | | | | |
Collapse
|
52
|
Abstract
Our view of DNA replication has been of two coupled DNA polymerases anchored to the replication fork helicase in a "replisome" complex, synthesizing leading and lagging strands simultaneously. New evidence suggests that three DNA polymerases can be accommodated into the replisome and that polymerases and repair factors are dynamically recruited and engaged without dismantling of the replisome.
Collapse
Affiliation(s)
- Susan T Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Institute, MS029, Brandeis University, Waltham, MA 02454-9110, USA.
| |
Collapse
|
53
|
Griep MA, Blood S, Larson MA, Koepsell SA, Hinrichs SH. Myricetin inhibits Escherichia coli DnaB helicase but not primase. Bioorg Med Chem 2007; 15:7203-8. [PMID: 17851081 DOI: 10.1016/j.bmc.2007.07.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/29/2007] [Accepted: 07/03/2007] [Indexed: 10/22/2022]
Abstract
Primase and DnaB helicase play central roles during DNA replication initiation and elongation. Both enzymes are drug targets because they are essential, persistent among bacterial genomes, and have different sequences than their eukaryotic equivalents. Myricetin is a ubiquitous natural product in plants that is known to inhibit a variety of DNA polymerases, RNA polymerases, reverse transcriptases, and telomerases in addition being able to inhibit kinases and helicases. We have shown that myricetin inhibits Escherichia coli DnaB helicase according to a mechanism dominated by noncompetitive behavior with a K(i) of 10.0+/-0.5 microM. At physiological ATP concentration, myricetin inhibits E. coli DnaB helicase with an inhibitory concentration at 50% maximal (IC(50)) of 11.3+/-1.6 microM. In contrast, myricetin inhibited E. coli primase at least 60-fold weaker than DnaB helicase and far weaker than any other polymerase.
Collapse
Affiliation(s)
- Mark A Griep
- Department of Chemistry, University of Nebraska-Lincoln, 614 Hamilton Hall, Lincoln, NE 68588-0304, USA.
| | | | | | | | | |
Collapse
|
54
|
Su XC, Jergic S, Keniry MA, Dixon NE, Otting G. Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit. Nucleic Acids Res 2007; 35:2825-32. [PMID: 17452361 PMCID: PMC1888800 DOI: 10.1093/nar/gkm080] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τC16), and domains shortened at the C-terminus by 11 and 18 residues, respectively. The only interacting residues were found in the C-terminal 30-residue segment of τ, most of which is structurally disordered in free τC16. Since the N- and C-termini of the structured core of τC16 are located close to each other, this limits the possible distance between α and the pentameric δτ2γδ′ clamp–loader complex and, hence, between the two α subunits involved in leading- and lagging-strand DNA synthesis. Analysis of an N-terminally extended construct (τC22) showed that τC14 presents the only part of Domains IVa and V of τ which comprises a globular fold in the absence of other interaction partners.
Collapse
Affiliation(s)
| | | | | | | | - Gottfried Otting
- *To whom correspondence should be addressed. +61-2-61256507+61-2-61250750
| |
Collapse
|
55
|
Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Nucleic Acids Res 2007; 35:2813-24. [PMID: 17355988 PMCID: PMC1888804 DOI: 10.1093/nar/gkm079] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for the α−τC16Δ7 complex. Low-level expression of the genes encoding τC16 and τC16▵7, but not τC16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τC16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τC24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τC16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.
Collapse
Affiliation(s)
- Slobodan Jergic
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Kiyoshi Ozawa
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Neal K. Williams
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Daniel D. Scott
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Samir M. Hamdan
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Jeffrey A. Crowther
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
- *To whom correspondence should be addressed. +61 2 42214346+61 2 42214287
| |
Collapse
|
56
|
Neylon C, Kralicek AV, Hill TM, Dixon NE. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol Mol Biol Rev 2005; 69:501-26. [PMID: 16148308 PMCID: PMC1197808 DOI: 10.1128/mmbr.69.3.501-526.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the Tus-Ter complex itself is sufficient to block the helicase in a polar manner, without the need for specific protein-protein interactions. This review integrates three decades of experimental information on the action of the Tus-Ter complex with information available from the Tus-TerA crystal structure. We conclude that while it is possible to explain polar fork arrest by a mechanism involving only the Tus-Ter interaction, there are also strong indications of a role for specific Tus-DnaB interactions. The evidence suggests, therefore, that the termination system is more subtle and complex than may have been assumed. We describe some further experiments and insights that may assist in unraveling the details of this fascinating process.
Collapse
Affiliation(s)
- Cameron Neylon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
| | | | | | | |
Collapse
|
57
|
Degnan PH, Lazarus AB, Wernegreen JJ. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res 2005; 15:1023-33. [PMID: 16077009 PMCID: PMC1182215 DOI: 10.1101/gr.3771305] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The distinct lifestyle of obligately intracellular bacteria can alter fundamental forces that drive and constrain genome change. In this study, sequencing the 792-kb genome of Blochmannia pennsylvanicus, an obligate endosymbiont of Camponotus pennsylvanicus, enabled us to trace evolutionary changes that occurred in the context of a bacterial-ant association. Comparison to the genome of Blochmannia floridanus reveals differential loss of genes involved in cofactor biosynthesis, the composition and structure of the cell wall and membrane, gene regulation, and DNA replication. However, the two Blochmannia species show complete conservation in the order and strand orientation of shared genes. This finding of extreme stasis in genome architecture, also reported previously for the aphid endosymbiont Buchnera, suggests that genome stability characterizes long-term bacterial mutualists of insects and constrains their evolutionary potential. Genome-wide analyses of protein divergences reveal 10- to 50-fold faster amino acid substitution rates in Blochmannia compared to related bacteria. Despite these varying features of genome evolution, a striking correlation in the relative divergences of proteins indicates parallel functional constraints on gene functions across ecologically distinct bacterial groups. Furthermore, the increased rates of amino acid substitution and gene loss in Blochmannia have occurred in a lineage-specific fashion, which may reflect life history differences of their ant hosts.
Collapse
Affiliation(s)
- Patrick H Degnan
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | | | | |
Collapse
|
58
|
Abstract
DNA replicases are multicomponent machines that have evolved clever strategies to perform their function. Although the structure of DNA is elegant in its simplicity, the job of duplicating it is far from simple. At the heart of the replicase machinery is a heteropentameric AAA+ clamp-loading machine that couples ATP hydrolysis to load circular clamp proteins onto DNA. The clamps encircle DNA and hold polymerases to the template for processive action. Clamp-loader and sliding clamp structures have been solved in both prokaryotic and eukaryotic systems. The heteropentameric clamp loaders are circular oligomers, reflecting the circular shape of their respective clamp substrates. Clamps and clamp loaders also function in other DNA metabolic processes, including repair, checkpoint mechanisms, and cell cycle progression. Twin polymerases and clamps coordinate their actions with a clamp loader and yet other proteins to form a replisome machine that advances the replication fork.
Collapse
Affiliation(s)
- Aaron Johnson
- Howard Hughes Medical Institute, New York City, New York 10021-6399, USA.
| | | |
Collapse
|
59
|
Abstract
Replication of genomic DNA is a universal process that proceeds in distinct stages, from initiation to elongation and finally to termination. Each stage involves multiple stable or transient interactions between protein subunits with functions that are more or less conserved in all organisms. In Escherichia coli, initiation of bidirectional replication at the origin (oriC) occurs through the concerted actions of the DnaA replication initiator protein, the hexameric DnaB helicase, the DnaC?helicase loading partner and the DnaG primase, leading to establishment of two replication forks. Elongation of RNA primers at each fork proceeds simultaneously on both strands by actions of the multimeric replicase, DNA polymerase III holoenzyme. The fork that arrives first in the terminus region is halted by its encounter with a correctly-oriented complex of the Tus replication terminator protein bound at one of several Ter sites, where it is trapped until the other fork arrives. We summarize current understanding of interactions among the various proteins that act in the different stages of replication of the chromosome of E. coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7.
Collapse
Affiliation(s)
- Patrick M Schaeffer
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | | |
Collapse
|
60
|
Hamdan SM, Marintcheva B, Cook T, Lee SJ, Tabor S, Richardson CC. A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor. Proc Natl Acad Sci U S A 2005; 102:5096-101. [PMID: 15795374 PMCID: PMC556000 DOI: 10.1073/pnas.0501637102] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage T7 DNA polymerase (gene 5 protein, gp5) interacts with its processivity factor, Escherichia coli thioredoxin, via a unique loop at the tip of the thumb subdomain. We find that this thioredoxin-binding domain is also the site of interaction of the phage-encoded helicase/primase (gp4) and ssDNA binding protein (gp2.5). Thioredoxin itself interacts only weakly with gp4 and gp2.5 but drastically enhances their binding to gp5. The acidic C termini of gp4 and gp2.5 are critical for this interaction in the absence of DNA. However, the C-terminal tail of gp4 is not required for binding to gp5 when the latter is bound to a primer/template. We propose that the thioredoxin-binding domain is a molecular switch that regulates the interaction of T7 DNA polymerase with other proteins of the replisome.
Collapse
Affiliation(s)
- Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
61
|
Sherratt DJ, Søballe B, Barre FX, Filipe S, Lau I, Massey T, Yates J. Recombination and chromosome segregation. Philos Trans R Soc Lond B Biol Sci 2004; 359:61-9. [PMID: 15065657 PMCID: PMC1693297 DOI: 10.1098/rstb.2003.1365] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site-specific recombination system. Dimer resolution also requires FtsK, a division septum-located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination-associated proteins, RecQ and RarA, and specific genes within living Escherichia coli cells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated.
Collapse
Affiliation(s)
- David J Sherratt
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | | | | | | | | | | | | |
Collapse
|
62
|
Haroniti A, Anderson C, Doddridge Z, Gardiner L, Roberts CJ, Allen S, Soultanas P. The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus. J Mol Biol 2004; 336:381-93. [PMID: 14757052 PMCID: PMC3034218 DOI: 10.1016/j.jmb.2003.12.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The clamp-loader-helicase interaction is an important feature of the replisome. Although significant biochemical and structural work has been carried out on the clamp-loader-clamp-DNA polymerase alpha interactions in Escherichia coli, the clamp-loader-helicase interaction is poorly understood by comparison. The tau subunit of the clamp-loader mediates the interaction with DnaB. We have recently characterised this interaction in the Bacillus system and established a tau(5)-DnaB(6) stoichiometry. Here, we have obtained atomic force microscopy images of the tau-DnaB complex that reveal the first structural insight into its architecture. We show that despite the reported absence of the shorter gamma version in Bacillus, tau has a domain organisation similar to its E.coli counterpart and possesses an equivalent C-terminal domain that interacts with DnaB. The interaction interface of DnaB is also localised in its C-terminal domain. The combined data contribute towards our understanding of the bacterial replisome.
Collapse
Affiliation(s)
- Anna Haroniti
- School of Chemistry University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Christopher Anderson
- Laboratory of Biophysics and Surface Analysis School of Pharmacy University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Zara Doddridge
- School of Chemistry University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Laurence Gardiner
- School of Chemistry University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Clive J. Roberts
- Laboratory of Biophysics and Surface Analysis School of Pharmacy University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Stephanie Allen
- Laboratory of Biophysics and Surface Analysis School of Pharmacy University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Panos Soultanas
- School of Chemistry University of Nottingham University Park, Nottingham NG7 2RD, UK
- Corresponding author
| |
Collapse
|
63
|
Gulbis JM, Kazmirski SL, Finkelstein J, Kelman Z, O'Donnell M, Kuriyan J. Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex. ACTA ACUST UNITED AC 2004; 271:439-49. [PMID: 14717711 DOI: 10.1046/j.1432-1033.2003.03944.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The chi (chi) and psi (psi) subunits of Escherichia coli DNA polymerase III form a heterodimer that is associated with the ATP-dependent clamp-loader machinery. In E. coli, the chi:psi heterodimer serves as a bridge between the clamp-loader complex and the single-stranded DNA-binding protein. We determined the crystal structure of the chi:psi heterodimer at 2.1 A resolution. Although neither chi (147 residues) nor psi (137 residues) bind to nucleotides, the fold of each protein is similar to the folds of mononucleotide-(chi) or dinucleotide-(psi) binding proteins, without marked similarity to the structures of the clamp-loader subunits. Genes encoding chi and psi proteins are found to be readily identifiable in several bacterial genomes and sequence alignments showed that residues at the chi:psi interface are highly conserved in both proteins, suggesting that the heterodimeric interaction is of functional significance. The conservation of surface-exposed residues is restricted to the interfacial region and to just two other regions in the chi:psi complex. One of the conserved regions was found to be located on chi, distal to the psi interaction region, and we identified this as the binding site for a C-terminal segment of the single-stranded DNA-binding protein. The other region of sequence conservation is localized to an N-terminal segment of psi (26 residues) that is disordered in the crystal structure. We speculate that psi is linked to the clamp-loader complex by this flexible, but conserved, N-terminal segment, and that the chi:psi unit is linked to the single-stranded DNA-binding protein via the distal surface of chi. The base of the clamp-loader complex has an open C-shaped structure, and the shape of the chi:psi complex is suggestive of a loose docking within the crevice formed by the open faces of the delta and delta' subunits of the clamp-loader.
Collapse
Affiliation(s)
- Jacqueline M Gulbis
- Laboratory of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | | | | | | | | |
Collapse
|
64
|
Kaufmann G, Nethanel T. Did an early version of the eukaryal replisome enable the emergence of chromatin? PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 77:173-209. [PMID: 15196893 DOI: 10.1016/s0079-6603(04)77005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Gabriel Kaufmann
- Biochemistry Department, Tel Aviv University, Ramat Aviv 69978, Israel
| | | |
Collapse
|
65
|
López de Saro FJ, Georgescu RE, O'Donnell M. A peptide switch regulates DNA polymerase processivity. Proc Natl Acad Sci U S A 2003; 100:14689-94. [PMID: 14630952 PMCID: PMC299760 DOI: 10.1073/pnas.2435454100] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromosomal DNA polymerases are tethered to DNA by a circular sliding clamp for high processivity. However, lagging strand synthesis requires the polymerase to rapidly dissociate on finishing each Okazaki fragment. The Escherichia coli replicase contains a subunit (tau) that promotes separation of polymerase from its clamp on finishing DNA segments. This report reveals the mechanism of this process. We find that tau binds the C-terminal residues of the DNA polymerase. Surprisingly, this same C-terminal "tail" of the polymerase interacts with the beta clamp, and tau competes with beta for this sequence. Moreover, tau acts as a DNA sensor. On binding primed DNA, tau releases the polymerase tail, allowing polymerase to bind beta for processive synthesis. But on sensing the DNA is complete (duplex), tau sequesters the polymerase tail from beta, disengaging polymerase from DNA. Therefore, DNA sensing by tau switches the polymerase peptide tail on and off the clamp and coordinates the dynamic turnover of polymerase during lagging strand synthesis.
Collapse
Affiliation(s)
- Francisco J López de Saro
- Howard Hughes Medical Institute and Laboratory of DNA Replication, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA
| | | | | |
Collapse
|
66
|
Williams CR, Snyder AK, Kuzmic P, O'Donnell M, Bloom LB. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the gamma complex. J Biol Chem 2003; 279:4376-85. [PMID: 14610067 DOI: 10.1074/jbc.m310429200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli DNA polymerase III gamma complex loads the beta clamp onto DNA, and the clamp tethers the core polymerase to DNA to increase the processivity of synthesis. ATP binding and hydrolysis promote conformational changes within the gamma complex that modulate its affinity for the clamp and DNA, allowing it to accomplish the mechanical task of assembling clamps on DNA. This is the first of two reports (Snyder, A. K., Williams, C. R., Johnson, A., O'Donnell, M., and Bloom, L. B. (2004) J. Biol. Chem. 279, 4386-4393) addressing the question of how ATP binding and hydrolysis modulate specific interactions with DNA and beta. Pre-steady-state rates of ATP hydrolysis were slower when reactions were initiated by addition of ATP than when the gamma complex was equilibrated with ATP and were limited by the rate of an intramolecular reaction, possibly ATP-induced conformational changes. Kinetic modeling of assays in which the gamma complex was incubated with ATP for different periods of time prior to adding DNA to trigger hydrolysis suggests a mechanism in which a relatively slow conformational change step (kforward = 6.5 s(-1)) produces a species of the gamma complex that is activated for DNA (and beta) binding. In the absence of beta, 2 of the 3 molecules of ATP are hydrolyzed rapidly prior to releasing DNA, and the 3rd molecule is hydrolyzed slowly. In the presence of beta, all 3 molecules of ATP are hydrolyzed rapidly. These results suggest that hydrolysis of 2 molecules of ATP may be coupled to conformational changes that reduce interactions with DNA, whereas hydrolysis of the 3rd is coupled to changes that result in release of beta.
Collapse
Affiliation(s)
- Christopher R Williams
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610-0245, USA
| | | | | | | | | |
Collapse
|
67
|
Haroniti A, Till R, Smith MCM, Soultanas P. Clamp-loader-helicase interaction in Bacillus. Leucine 381 is critical for pentamerization and helicase binding of the Bacillus tau protein. Biochemistry 2003; 42:10955-64. [PMID: 12974630 PMCID: PMC3034353 DOI: 10.1021/bi034955g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we revealed the architecture of the clamp-loader-helicase (tau-DnaB) complex in Bacillus by atomic force microscopy imaging and constructed a structural model, whereby a pentameric clamp-loader interacts with the hexameric helicase. Crucial to this model is the assumption that the clamp-loader forms a pentamer in the absence of other components of the clamp-loader complex such as deltadelta'. Here, we show that the Bacillus subtilis tau protein, even in the absence of deltadelta', interacts as a pentamer with the hexameric DnaB and that the L381 of tau is critical for the integrity of the tau oligomer and interaction with DnaB. The effects of the L381A mutation were confirmed by gel filtration, ultracentrifugation, circular dichroism, cross-linking studies, and genetic replacement of the dnaX gene with a mutant L381A dnaX gene in vivo. The L381A protein is able to support growth in vivo only when expressed in high quantities. Finally, despite the fact that a mutation at P465 has been reported to result in a thermosensitive gene in vivo, a P465L mutant protein interacts with DnaB in vitro suggesting that this defect is not a result of a defective tau-DnaB interaction.
Collapse
Affiliation(s)
| | | | | | - P. Soultanas
- Corresponding author. Tel.: (+44)-(0)-115-9513525. Fax: (+44)-(0)-115-9513564.
| |
Collapse
|
68
|
McHenry CS. Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences. Mol Microbiol 2003; 49:1157-65. [PMID: 12940977 DOI: 10.1046/j.1365-2958.2003.03645.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Studies of the DNA polymerase III holoenzyme of Escherichia coli support a model in which both the leading and lagging strand polymerases are held together in a complex with the replicative helicase and priming activities, allowing two identical alpha catalytic subunits to assume different functions on the two strands of the replication fork. Creation of distinct functions for each of the two polymerases within the holoenzyme depends on the asymmetric character of the entire complex. The asymmetry of the holoenzyme is created by the DnaX complex, a heptamer that includes tau and gamma products of the dnaX gene. tau and gamma perform unique functions in the DnaX complex, and the interaction between alpha and tau appears to dictate the catalytic subunit's role in the replicative reaction. This review considers the properties of the DnaX complex including both tau and gamma, with the goal of understanding the properties of the replicase and its function in vivo. Recent studies in eukaryotic and other prokaryotic systems suggest that an asymmetric dimeric replicase may be universal. The leading and lagging strand polymerases may be distinct in some systems. For example, Pol e and Pol delta may function as distinct leading and lagging strand polymerases in eukaryotes, and PolC and DnaE may function as distinct leading and lagging strand polymerases in low GC content Gram-positive bacteria.
Collapse
Affiliation(s)
- Charles S McHenry
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262, USA.
| |
Collapse
|
69
|
Boshoff HIM, Reed MB, Barry CE, Mizrahi V. DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 2003; 113:183-93. [PMID: 12705867 DOI: 10.1016/s0092-8674(03)00270-8] [Citation(s) in RCA: 313] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The presence of multiple copies of the major replicative DNA polymerase (DnaE) in some organisms, including important pathogens and symbionts, has remained an unresolved enigma. We postulated that one copy might participate in error-prone DNA repair synthesis. We found that UV irradiation of Mycobacterium tuberculosis results in increased mutation frequency in the surviving fraction. We identified dnaE2 as a gene that is upregulated in vitro by several DNA damaging agents, as well as during infection of mice. Loss of this protein reduces both survival of the bacillus after UV irradiation and the virulence of the organism in mice. Our data suggest that DnaE2, and not a member of the Y family of error-prone DNA polymerases, is the primary mediator of survival through inducible mutagenesis and can contribute directly to the emergence of drug resistance in vivo. These results may indicate a potential new target for therapeutic intervention.
Collapse
Affiliation(s)
- Helena I M Boshoff
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II, 12441 Parklawn Drive, Rockville, MD 20852, USA
| | | | | | | |
Collapse
|
70
|
Leu FP, Georgescu R, O'Donnell M. Mechanism of the E. coli tau processivity switch during lagging-strand synthesis. Mol Cell 2003; 11:315-27. [PMID: 12620221 DOI: 10.1016/s1097-2765(03)00042-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The E. coli replication machinery employs a beta clamp that tethers the polymerase to DNA, thus ensuring high processivity. The replicase also contains a processivity switch that dissociates the polymerase from its beta clamp. The switch requires the tau subunit of the clamp loader and is regulated by different DNA structures. At a primed site, the switch is "off." When the replicase reaches the downstream primer to form a nick, the switch is flipped, and tau ejects the polymerase from beta. This switch has high fidelity for completed synthesis, remaining "off" until just prior to incorporation of the last nucleotide and turning "on" only after addition of the last dNTP. These actions of tau are confined to its C-terminal region, which is located outside the clamp loading apparatus. Thus, this highly processive replication machine has evolved a mechanism to specifically counteract processivity at a defined time in the lagging-strand cycle.
Collapse
Affiliation(s)
- Frank P Leu
- Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | | | |
Collapse
|
71
|
Martínez-Jiménez MI, Mesa P, Alonso JC. Bacillus subtilis tau subunit of DNA polymerase III interacts with bacteriophage SPP1 replicative DNA helicase G40P. Nucleic Acids Res 2002; 30:5056-64. [PMID: 12466528 PMCID: PMC137964 DOI: 10.1093/nar/gkf650] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic evidence suggests that the Bacillus subtilis dnaX gene only encodes for the tau subunit of both DNA polymerases III (Pol IIIs). The B.subtilis full-length protein and their mutant derivatives tau(373- 563) (lacking the N-terminal, domains I-III or amino acid residues 1-372) and tau(1-372) (lacking the C-terminal region or amino acids 373-563) have been purified. The tau protein forms tetramers, tau(373- 563) forms dimers, whereas tau(1-372), depending on the ionic strength, forms trimers or tetramers in solution. In the absence of single-stranded (ss) DNA and a nucleotide cofactor, tau interacts with the SPP1 hexameric replicative G40P DNA helicase in solution or with G40P-ATP bound to ssDNA, with a 1:1 stoichiometry. G40P(109-442), lacking the N-terminal amino acid residues 1-108, interacts with the C-terminal moiety of tau. The data indicate that the interaction of G40P with the tau subunit of Pol III, is relevant for the loading of the Pol IIIs into the SPP1 G38P-promoted open complex.
Collapse
Affiliation(s)
- María I Martínez-Jiménez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, C.S.I.C., Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | | | | |
Collapse
|
72
|
Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
Collapse
Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
| | | |
Collapse
|
73
|
Bullard JM, Williams JC, Acker WK, Jacobi C, Janjic N, McHenry CS. DNA polymerase III holoenzyme from Thermus thermophilus identification, expression, purification of components, and use to reconstitute a processive replicase. J Biol Chem 2002; 277:13401-8. [PMID: 11823461 DOI: 10.1074/jbc.m110833200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA replication in bacteria is performed by a specialized multicomponent replicase, the DNA polymerase III holoenzyme, that consist of three essential components: a polymerase, the beta sliding clamp processivity factor, and the DnaX complex clamp-loader. We report here the assembly of the minimal functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme consists of alpha (pol III catalytic subunit), beta (sliding clamp processivity factor), and the essential DnaX (tau/gamma), delta and delta' components of the DnaX complex. We show with purified recombinant proteins that these five components are required for rapid and processive DNA synthesis on long single-stranded DNA templates. Subunit interactions known to occur in DNA polymerase III holoenzyme from mesophilic bacteria including delta-delta' interaction, deltadelta'-tau/gamma complex formation, and alpha-tau interaction, also occur within the Tth enzyme. As in mesophilic holoenzymes, in the presence of a primed DNA template, these subunits assemble into a stable initiation complex in an ATP-dependent manner. However, in contrast to replicative polymerases from mesophilic bacteria, Tth holoenzyme is efficient only at temperatures above 50 degrees C, both with regard to initiation complex formation and processive DNA synthesis. The minimal Tth DNA polymerase III holoenzyme displays an elongation rate of 350 bp/s at 72 degrees C and a processivity of greater than 8.6 kilobases, the length of the template that is fully replicated after a single association event.
Collapse
|
74
|
Bullard JM, Pritchard AE, Song MS, Glover BP, Wieczorek A, Chen J, Janjic N, McHenry CS. A three-domain structure for the delta subunit of the DNA polymerase III holoenzyme delta domain III binds delta' and assembles into the DnaX complex. J Biol Chem 2002; 277:13246-56. [PMID: 11809766 DOI: 10.1074/jbc.m108708200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using psi-BLAST, we have developed a method for identifying the poorly conserved delta subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting with Escherichia coli delta, leads not only to the identification of delta but also to the DnaX and delta' subunits of the DnaX complex and other AAA(+)-class ATPases. This suggests that, although not an ATPase, delta is related structurally to the other subunits of the DnaX complex that loads the beta sliding clamp processivity factor onto DNA. To test this prediction, we aligned delta sequences with those of delta' and, using the start of delta' Domain III established from its x-ray crystal structure, predicted the juncture between Domains II and III of delta. This putative delta Domain III could be expressed to high levels, consistent with the prediction that it folds independently. delta Domain III, like Domain III of DnaX and delta', assembles by itself into a complex with the other DnaX complex components. Cross-linking studies indicated a contact of delta with the DnaX subunits. These observations are consistent with a model where two tau subunits and one each of the gamma, delta', and delta subunits mutually interact to form a pentameric functional core for the DnaX complex.
Collapse
|
75
|
Abstract
During the expression of a certain genes standard decoding is over-ridden in a site or mRNA specific manner. This recoding occurs in response to special signals in mRNA and probably occurs in all organisms. This review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria.
Collapse
Affiliation(s)
- Pavel V Baranov
- Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112-5330, USA
| | | | | |
Collapse
|
76
|
O'Donnell M, Jeruzalmi D, Kuriyan J. Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curr Biol 2001; 11:R935-46. [PMID: 11719243 DOI: 10.1016/s0960-9822(01)00559-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent determinations of the crystal structure of the Escherichia coli gamma complex and delta-beta assembly have shed light on the bacterial clamp loading reaction. In this review, we discuss the structures of delta-beta and the gamma(3)deltadelta' complex and its mechanism of action as a clamp loader of the E. coli beta sliding clamp. We also expand upon the implications of the structural findings to the structure and function of the eukaryotic clamp loader, RFC, and the structure of E. coli DNA polymerase III holoenzyme.
Collapse
Affiliation(s)
- M O'Donnell
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
| | | | | |
Collapse
|
77
|
Glover BP, Pritchard AE, McHenry CS. tau binds and organizes Escherichia coli replication proteins through distinct domains: domain III, shared by gamma and tau, oligomerizes DnaX. J Biol Chem 2001; 276:35842-6. [PMID: 11463787 DOI: 10.1074/jbc.m103719200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tau and gamma proteins of the DNA polymerase III holoenzyme DnaX complex are products of the dnaX gene with gamma being a truncated version of tau arising from ribosomal frameshifting. tau is comprised of five structural domains, the first three of which are shared by gamma (Gao, D., and McHenry, C. (2001) J. Biol. Chem. 276, 4433-4453). In the absence of the other holoenzyme subunits, DnaX exists as a tetramer. Association of delta, delta', chi, and psi with domain III of DnaX(4) results in a DnaX complex with a stoichiometry of DnaX(3)deltadelta'chipsi. To identify which domain facilitates DnaX self-association, we examined the properties of purified biotin-tagged DnaX fusion proteins containing domains I-II or III-V. Unlike domain I-II, treatment of domain III-V, gamma, and tau with the chemical cross-linking reagent BS3 resulted in the appearance of high molecular weight intramolecular cross-linked protein. Gel filtration of domains I-II and III-V demonstrated that domain I-II was monomeric, and domain III-V was an oligomer. Biotin-tagged domain III-V, and not domain I-II, was able to form a mixed DnaX complex by recruiting tau, delta, delta', chi, and psi onto streptavidin-agarose beads. Thus, domain III not only contains the delta, delta', chi, and psi binding interface, but also the region that enables DnaX to oligomerize.
Collapse
Affiliation(s)
- B P Glover
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
| | | | | |
Collapse
|
78
|
Pritchard AE, McHenry CS. Assembly of DNA polymerase III holoenzyme: co-assembly of gamma and tau is inhibited by DnaX complex accessory proteins but stimulated by DNA polymerase III core. J Biol Chem 2001; 276:35217-22. [PMID: 11463784 DOI: 10.1074/jbc.m102735200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the two alternative Escherichia coli dnaX gene products, tau and gamma, are found co-assembled in purified DNA polymerase III holoenzyme, the pathway of assembly is not well understood. When the 10 subunits of holoenzyme are simultaneously mixed, they rapidly form a nine-subunit assembly containing tau but not gamma. We developed a new assay based on the binding of complexes containing biotin-tagged tau to streptavidin-coated agarose beads to investigate the effects of various DNA polymerase III holoenzyme subunits on the kinetics of co-assembly of gamma and tau into the same complex. Auxiliary proteins in combination with delta' almost completely blocked co-assembly, whereas chipsi or delta' alone slowed the association only moderately compared with the interaction of tau with gamma alone. In contrast, DNA polymerase III core, in the absence of deltadelta' and chipsi, accelerated the co-assembly of tau and gamma, suggesting a role for DNA polymerase III' [tau(2)(pol III core)(2)] in the assembly pathway of holoenzyme.
Collapse
Affiliation(s)
- A E Pritchard
- Department of Biochemistry and Molecular Genetics and the Program in Molecular Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
| | | |
Collapse
|