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Chang S, Laureti L, Thrall ES, Kay MS, Philippin G, Jergic S, Pagès V, Loparo JJ. A bipartite interaction with the processivity clamp potentiates Pol IV-mediated TLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596738. [PMID: 38853898 PMCID: PMC11160790 DOI: 10.1101/2024.05.30.596738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Processivity clamps mediate polymerase switching for translesion synthesis (TLS). All three E. coli TLS polymerases interact with the β2 processivity clamp through a conserved clamp-binding motif (CBM), which is indispensable for TLS. Notably, Pol IV also makes a unique secondary contact with the clamp through non-CBM residues. However, the role of this "rim contact" in Pol IV-mediated TLS remains poorly understood. Here we show that the rim contact is critical for TLS past strong replication blocks. In in vitro reconstituted Pol IV-mediated TLS, ablating the rim contact compromises TLS past 3-methyl dA, a strong block, while barely affecting TLS past N2-furfuryl dG, a weak block. Similar observations are also made in E. coli cells bearing a single copy of these lesions in the genome. Within lesion-stalled replication forks, the rim interaction and ssDNA binding protein cooperatively poise Pol IV to better compete with Pol III for binding to a cleft through its CBM. We propose that this bipartite clamp interaction enables Pol IV to rapidly resolve lesion-stalled replication through TLS at the fork, which reduces damage induced mutagenesis.
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Affiliation(s)
- Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Luisa Laureti
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Elizabeth S. Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marguerite S Kay
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gaëlle Philippin
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Slobodan Jergic
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, NSW, Australia
| | - Vincent Pagès
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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2
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Simonsen S, Søgaard CK, Olsen JG, Otterlei M, Kragelund BB. The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery. Cell Mol Life Sci 2024; 81:245. [PMID: 38814467 PMCID: PMC11139829 DOI: 10.1007/s00018-024-05252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.
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Affiliation(s)
- Signe Simonsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Johan G Olsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Birthe B Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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3
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Zein U, Turgimbayeva A, Abeldenov S. Biochemical Assessment of the Mutant Sliding β-Clamp on Stimulation of Endonuclease IV from Staphylococcus aureus. Indian J Microbiol 2024; 64:165-174. [PMID: 38468727 PMCID: PMC10924856 DOI: 10.1007/s12088-023-01148-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/13/2023] [Indexed: 03/13/2024] Open
Abstract
Staphylococcus aureus is a pathogenic bacterium that causes various infections in humans. The emergence of methicillin-resistant Staphylococcus aureus makes treatment more challenging. Recent research has shown that bacterial β-clamp is not only a processivity factor but can also stimulate the activity of other enzymes of DNA metabolism. This article examines the interaction between apurinic/apyrimidinic (AP) endonuclease IV (Nfo) and β-clamp from Staphylococcus aureus, which has not been previously researched. Recombinant DNA repair enzymes, beta-clamp, were cloned, expressed, and purified. Biochemical methods were employed to assess the stimulation of beta-clamp-activated AP endonuclease activity of Nfo. We demonstrated that mutations in the C-terminal conserved region led to disruption of stimulation of Nfo AP endonuclease activity. The study provides evidence of a specific interaction between Nfo and β-clamp, which suggests that β-clamp may play a more direct role in DNA repair processes than previously thought. These findings have important implications for understanding the mechanism of DNA repair, particularly in relation to the role of β-clamp. Understanding the underlying mechanisms of interaction between DNA metabolism enzymes can aid in predicting new drug targets for antibiotic resistance battle. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01148-8.
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Affiliation(s)
- Ulan Zein
- National Center for Biotechnology, Astana, 010000 Kazakhstan
- L. N. Gumilyov Eurasian National University, Astana, 010000 Kazakhstan
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4
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McHenry CS. Life at the replication fork: A scientific and personal journey. J Biol Chem 2024; 300:105658. [PMID: 38219819 PMCID: PMC10850973 DOI: 10.1016/j.jbc.2024.105658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 01/16/2024] Open
Affiliation(s)
- Charles S McHenry
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA.
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5
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Tashjian TF, Chien P. Clamp Loader Processing Is Important during DNA Replication Stress. J Bacteriol 2023; 205:e0043722. [PMID: 36728506 PMCID: PMC9945568 DOI: 10.1128/jb.00437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
The DNA clamp loader is critical to the processivity of the DNA polymerase and coordinating synthesis on the leading and lagging strands. In bacteria, the major subunit of the clamp loader, DnaX, has two forms: the essential full-length τ form and shorter γ form. These are conserved across bacterial species, and three distinct mechanisms have been found to create them: ribosomal frameshift, transcriptional slippage, and, in Caulobacter crescentus, partial proteolysis. This conservation suggests that DnaX processing is evolutionarily important, but its role remains unknown. Here we find a bias against switching from expression of a wild-type dnaX to a nonprocessable τ-only allele in Caulobacter. Despite this bias, cells are able to adapt to the τ-only allele with little effect on growth or morphology and only minor defects during DNA damage. Motivated by transposon sequencing, we find that loss of the gene sidA in the τ-only strain slows growth and increases filamentation. Even in the absence of exogenous DNA damage treatment, the ΔsidA τ-only double mutant shows induction of and dependence on recA, likely due to a defect in resolution of DNA damage or replication fork stalling. We find that some of the phenotypes of the ΔsidA τ-only mutant can be complemented by expression of γ but that an overabundance of τ-only dnaX is also detrimental. The data presented here suggest that DnaX processing is important during resolution of DNA damage events during DNA replication stress. Although the presence of DnaX τ and γ forms is conserved across bacteria, different species have developed different mechanisms to make these forms. This conservation and independent evolution of mechanisms suggest that having two forms of DnaX is important. Despite having been discovered more than 30 years ago, the purpose of expressing both τ and γ is still unclear. Here, we present evidence that expressing two forms of DnaX and controlling the abundance and/or ratio of the forms are important during the resolution of DNA replication stress. IMPORTANCE Though the presence of DnaX τ and γ forms is conserved across bacteria, different species have developed different mechanisms to make these forms. This conservation and independent evolution of mechanisms suggest that having two forms of DnaX is important. Despite having been discovered more than 30 years ago, the purpose of expressing both τ and γ is still unclear. Here, we present evidence that expressing two forms of DnaX and controlling the abundance and/or ratio of the forms is important during the resolution of DNA replication stress.
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Affiliation(s)
- Tommy F. Tashjian
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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6
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Elevated Levels of the Escherichia coli nrdAB-Encoded Ribonucleotide Reductase Counteract the Toxicity Caused by an Increased Abundance of the β Clamp. J Bacteriol 2021; 203:e0030421. [PMID: 34543109 DOI: 10.1128/jb.00304-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Expression of the Escherichia coli dnaN-encoded β clamp at ≥10-fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. A mutant clamp (βE202K bearing a glutamic acid-to-lysine substitution at residue 202) binds to DNA polymerase III (Pol III) with higher affinity than the wild-type clamp, suggesting that its failure to impede growth is independent of its ability to sequester Pol III away from the replication fork. Our results demonstrate that the dnaNE202K strain underinitiates DNA replication due to insufficient levels of DnaA-ATP and expresses several DnaA-regulated genes at altered levels, including nrdAB, that encode the class 1a ribonucleotide reductase (RNR). Elevated expression of nrdAB was dependent on hda function. As the β clamp-Hda complex regulates the activity of DnaA by stimulating its intrinsic ATPase activity, this finding suggests that the dnaNE202K allele supports an elevated level of Hda activity in vivo compared with the wild-type strain. In contrast, using an in vitro assay reconstituted with purified components the βE202K and wild-type clamp proteins supported comparable levels of Hda activity. Nevertheless, co-overexpression of the nrdAB-encoded RNR relieved the growth defect caused by elevated levels of the β clamp. These results support a model in which increased cellular levels of DNA precursors relieve the ability of elevated β clamp levels to impede growth and suggest either that multiple effects stemming from the dnaNE202K mutation contribute to elevated nrdAB levels or that Hda plays a noncatalytic role in regulating DnaA-ATP by sequestering it to reduce its availability. IMPORTANCE DnaA bound to ATP acts in initiation of DNA replication and regulates the expression of several genes whose products act in DNA metabolism. The state of the ATP bound to DnaA is regulated in part by the β clamp-Hda complex. The dnaNE202K allele was identified by virtue of its inability to impede growth when expressed ≥10-fold higher than chromosomally expressed levels. While the dnaNE202K strain exhibits several phenotypes consistent with heightened Hda activity, the wild-type and βE202K clamp proteins support equivalent levels of Hda activity in vitro. Taken together, these results suggest that βE202K-Hda plays a noncatalytic role in regulating DnaA-ATP. This, as well as alternative models, is discussed.
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7
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The Mutant β E202K Sliding Clamp Protein Impairs DNA Polymerase III Replication Activity. J Bacteriol 2021; 203:e0030321. [PMID: 34543108 DOI: 10.1128/jb.00303-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Expression of the Escherichia coli dnaN-encoded β clamp at ≥10-fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. We hypothesized that the excess β clamp sequesters the replicative DNA polymerase III (Pol III) to inhibit replication. As a test of this hypothesis, we obtained eight mutant clamps with an inability to impede growth and measured their ability to stimulate Pol III replication in vitro. Compared with the wild-type clamp, seven of the mutants were defective, consistent with their elevated cellular levels failing to sequester Pol III. However, the βE202K mutant that bears a glutamic acid-to-lysine substitution at residue 202 displayed an increased affinity for Pol IIIα and Pol III core (Pol IIIαεθ), suggesting that it could still sequester Pol III effectively. Of interest, βE202K supported in vitro DNA replication by Pol II and Pol IV but was defective with Pol III. Genetic experiments indicated that the dnaNE202K strain remained proficient in DNA damage-induced mutagenesis but was induced modestly for SOS and displayed sensitivity to UV light and methyl methanesulfonate. These results correlate an impaired ability of the mutant βE202K clamp to support Pol III replication in vivo with its in vitro defect in DNA replication. Taken together, our results (i) support the model that sequestration of Pol III contributes to growth inhibition, (ii) argue for the existence of an additional mechanism that contributes to lethality, and (iii) suggest that physical and functional interactions of the β clamp with Pol III are more extensive than appreciated currently. IMPORTANCE The β clamp plays critically important roles in managing the actions of multiple proteins at the replication fork. However, we lack a molecular understanding of both how the clamp interacts with these different partners and the mechanisms by which it manages their respective actions. We previously exploited the finding that an elevated cellular level of the β clamp impedes Escherichia coli growth by interfering with DNA replication. Using a genetic selection method, we obtained novel mutant β clamps that fail to inhibit growth. Their analysis revealed that βE202K is unique among them. Our work offers new insights into how the β clamp interacts with and manages the actions of E. coli DNA polymerases II, III, and IV.
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8
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Spinks RR, Spenkelink LM, Stratmann SA, Xu ZQ, Stamford NPJ, Brown SE, Dixon NE, Jergic S, van Oijen AM. DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies. Nucleic Acids Res 2021; 49:6804-6816. [PMID: 34139009 PMCID: PMC8266626 DOI: 10.1093/nar/gkab493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 01/09/2023] Open
Abstract
In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Sarah A Stratmann
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - N Patrick J Stamford
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Susan E Brown
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
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9
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Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O'Shea VL, Berger JM, Dixon NE, van Oijen AM. A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome. Mol Cell 2020; 79:140-154.e7. [PMID: 32464091 DOI: 10.1016/j.molcel.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly found plasticity lies in the 500-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747, the Netherlands
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Valerie L O'Shea
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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10
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A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes. Proc Natl Acad Sci U S A 2019; 116:25591-25601. [PMID: 31796591 DOI: 10.1073/pnas.1914485116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA lesions stall the replisome and proper resolution of these obstructions is critical for genome stability. Replisomes can directly replicate past a lesion by error-prone translesion synthesis. Alternatively, replisomes can reprime DNA synthesis downstream of the lesion, creating a single-stranded DNA gap that is repaired primarily in an error-free, homology-directed manner. Here we demonstrate how structural changes within the Escherichia coli replisome determine the resolution pathway of lesion-stalled replisomes. This pathway selection is controlled by a dynamic interaction between the proofreading subunit of the replicative polymerase and the processivity clamp, which sets a kinetic barrier to restrict access of translesion synthesis (TLS) polymerases to the primer/template junction. Failure of TLS polymerases to overcome this barrier leads to repriming, which competes kinetically with TLS. Our results demonstrate that independent of its exonuclease activity, the proofreading subunit of the replisome acts as a gatekeeper and influences replication fidelity during the resolution of lesion-stalled replisomes.
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11
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Jiang X, Zhang L, An J, Wang M, Teng M, Guo Q, Li X. Caulobacter crescentus β sliding clamp employs a noncanonical regulatory model of DNA replication. FEBS J 2019; 287:2292-2311. [PMID: 31725950 DOI: 10.1111/febs.15138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/23/2019] [Accepted: 11/12/2019] [Indexed: 01/19/2023]
Abstract
The eubacterial β sliding clamp (DnaN) plays a crucial role in DNA metabolism through direct interactions with DNA, polymerases, and a variety of protein factors. A canonical protein-DnaN interaction has been identified in Escherichia coli and some other species, during which protein partners are tethered into the conserved canonical hydrophobic crevice of DnaN via the consensus β-binding motif. Caulobacter crescentus is an excellent research model for use in the investigation of DNA replication and cell-cycle regulation due to its unique asymmetric cell division pattern with restricted replication initiation; however, little is known about the specific features of C. crescentus DnaN (CcDnaN). Here, we report a significant divergence in the association of CcDnaN with proteins based on docking analysis and crystal structures that show that the β-binding motifs of its protein partners bind a novel pocket instead of the canonical site. Pull-down and isothermal titration calorimetry results revealed that mutations within the novel pocket disrupt protein-CcDnaN interactions. It was also shown by replication and regulatory inactivation of DnaA assays that mediation of protein interaction by the novel pocket is closely related to the performance of CcDnaN during replication and the DnaN-mediated regulation process. Moreover, assessments of clamp competition showed that DNA does not compete with protein partners when binding to the novel pocket. Overall, our structural and biochemical analyses provide strong evidence that CcDnaN employs a noncanonical protein association pattern.
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Affiliation(s)
- Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Linjuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Jiancheng An
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Qiong Guo
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
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12
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Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A. Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic Acids Res 2019; 47:4831-4842. [PMID: 30916336 PMCID: PMC6511837 DOI: 10.1093/nar/gkz115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 11/15/2022] Open
Abstract
The β-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the β-clamp harbor a conserved clamp-binding motif that is often found in extended regions. Therefore, clamp interactions have -almost exclusively- been studied using short peptides recapitulating the binding motif. This approach has revealed the molecular determinants that mediate the binding but cannot describe how proteins with clamp-binding motifs embedded in structured domains are recognized. The mismatch repair protein MutL has an internal clamp-binding motif, but its interaction with the β-clamp has different roles depending on the organism. In Bacillus subtilis, the interaction stimulates the endonuclease activity of MutL and it is critical for DNA mismatch repair. Conversely, disrupting the interaction between Escherichia coli MutL and the β-clamp only causes a mild mutator phenotype. Here, we determined the structures of the regulatory domains of E. coli and B. subtilis MutL bound to their respective β-clamps. The structures reveal different binding modes consistent with the binding to the β-clamp being a two-step process. Functional characterization indicates that, within the regulatory domain, only the clamp binding motif is required for the interaction between the two proteins. However, additional motifs beyond the regulatory domain may stabilize the interaction. We propose a model for the activation of the endonuclease activity of MutL in organisms lacking methyl-directed mismatch repair.
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Affiliation(s)
- Ahmad W Almawi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Michelle K Scotland
- Department of Biochemistry, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Witebsky Center for Microbial Pathogenesis and Immunology, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Justin R Randall
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Linda Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Heather K Martin
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lauralicia Sacre
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Yao Shen
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Monica C Pillon
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Lyle A Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Mark D Sutton
- Department of Biochemistry, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Witebsky Center for Microbial Pathogenesis and Immunology, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics and Bioinformatics Program, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
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13
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André C, Martiel I, Wolff P, Landolfo M, Lorber B, Silva da Veiga C, Dejaegere A, Dumas P, Guichard G, Oliéric V, Wagner J, Burnouf DY. Interaction of a Model Peptide on Gram Negative and Gram Positive Bacterial Sliding Clamps. ACS Infect Dis 2019; 5:1022-1034. [PMID: 30912430 DOI: 10.1021/acsinfecdis.9b00089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, EcS346 and EcM362, and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography, and biochemical analyses. EcM362 and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. EcS346 has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive-specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets, but the complex stability varies according to a pocket-specific network of interactions.
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Affiliation(s)
- Christophe André
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, CBMN, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Isabelle Martiel
- Swiss Light Source (SLS), Paul-Scherrer-Institute (PSI), 5232 Villigen, Switzerland
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67000 Strasbourg, France
| | - Marie Landolfo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67000 Strasbourg, France
| | - Bernard Lorber
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67000 Strasbourg, France
| | - Cyrielle Silva da Veiga
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67000 Strasbourg, France
| | - Annick Dejaegere
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale et Génomique, 1 rue Laurent Fries, BP10142, 67404 Illkirch, France
| | - Philippe Dumas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale et Génomique, 1 rue Laurent Fries, BP10142, 67404 Illkirch, France
| | - Gilles Guichard
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, CBMN, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Vincent Oliéric
- Swiss Light Source (SLS), Paul-Scherrer-Institute (PSI), 5232 Villigen, Switzerland
| | - Jérôme Wagner
- Biologie et Signalisation Cellulaire, ESBS, UMR7242 CNRS/Université de Strasbourg, Bld S. Brant, 67412 Illkirch Cedex, France
| | - Dominique Y. Burnouf
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67000 Strasbourg, France
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14
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In vivo demonstration of enhanced binding between β-clamp and DnaE of pol III bearing consensus i-CBM. Genes Genomics 2019; 41:613-619. [PMID: 30929144 DOI: 10.1007/s13258-019-00796-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Among several key protein-protein and protein-DNA interactions within the replisome, the interaction between β-clamp and the DNA polymerase (Pol) III is of crucial importance. This interaction is mediated by a five or six-residue conserved sequence of the DnaE subunit of Pol III, referred to as the Clamp Binding Motif (CBM). In E. coli, DnaE contains two CBMs designated as e-CBM and i-CBM. A consensus sequence (QL[S/D]LF) for the CBMs has previously been proposed and studies involving mutagenesis of both the CBMs have evaluated their protein-binding properties. Surface Plasmon Resonance has been used to show that replacing i-CBM in DnaE with the consensus sequence enhances its binding to β-clamp 120-fold. OBJECTIVE The current study was aimed to evaluate in vivo interaction between DnaE bearing the consensus i-CBM and β-clamp. METHOD The C-terminal 405 residues of DnaE, bearing either the consensus i-CBM or the WT i-CBM, with β-clamp were co-expressed in E. coli followed by co-purification of the protein complexes. The interaction was assessed by the ability of the co-expressed proteins to form stable complexes during both affinity and gel filtration chromatography. RESULT The interaction of β-clamp with DnaEΔ755M containing the consensus i-CBM was found to be more stable than with WT DnaEΔ755, consistent with the in vitro data previously reported. CONCLUSION The presence of the pieces of sheared DNA generated during sonication promote the interaction of DnaEΔ755M with β-clamp by binding the OB-fold of DnaEΔ755M and β-clamp and serves as a bridge between them.
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15
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Patoli AA, Patoli BB. The N-Terminal 6×His Tag on β-Clamp Processivity Factor Occludes Gly66 and Affects the Growth of Escherichia coli B834 (DE3) Cells. Mol Biol 2019. [DOI: 10.1134/s0026893319010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Zhao G, Gleave ES, Lamers MH. Single-molecule studies contrast ordered DNA replication with stochastic translesion synthesis. eLife 2017; 6:32177. [PMID: 29210356 PMCID: PMC5731819 DOI: 10.7554/elife.32177] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
High fidelity replicative DNA polymerases are unable to synthesize past DNA adducts that result from diverse chemicals, reactive oxygen species or UV light. To bypass these replication blocks, cells utilize specialized translesion DNA polymerases that are intrinsically error prone and associated with mutagenesis, drug resistance, and cancer. How untimely access of translesion polymerases to DNA is prevented is poorly understood. Here we use co-localization single-molecule spectroscopy (CoSMoS) to follow the exchange of the E. coli replicative DNA polymerase Pol IIIcore with the translesion polymerases Pol II and Pol IV. We find that in contrast to the toolbelt model, the replicative and translesion polymerases do not form a stable complex on one clamp but alternate their binding. Furthermore, while the loading of clamp and Pol IIIcore is highly organized, the exchange with the translesion polymerases is stochastic and is not determined by lesion-recognition but instead a concentration-dependent competition between the polymerases.
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Affiliation(s)
- Gengjing Zhao
- MRC laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Emma S Gleave
- MRC laboratory of Molecular Biology, Cambridge, United Kingdom
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17
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Park J, Jergic S, Jeon Y, Cho WK, Lee R, Dixon NE, Lee JB. Dynamics of Proofreading by the E. coli Pol III Replicase. Cell Chem Biol 2017; 25:57-66.e4. [PMID: 29104063 DOI: 10.1016/j.chembiol.2017.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/09/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023]
Abstract
The αɛθ core of Escherichia coli DNA polymerase III (Pol III) associates with the β2 sliding clamp to processively synthesize DNA and remove misincorporated nucleotides. The α subunit is the polymerase while ɛ is the 3' to 5' proofreading exonuclease. In contrast to the polymerase activity of Pol III, dynamic features of proofreading are poorly understood. We used single-molecule assays to determine the excision rate and processivity of the β2-associated Pol III core, and observed that both properties are enhanced by mutational strengthening of the interaction between ɛ and β2. Thus, the ɛ-β2 contact is maintained in both the synthesis and proofreading modes. Remarkably, single-molecule real-time fluorescence imaging revealed the dynamics of transfer of primer-template DNA between the polymerase and proofreading sites, showing that it does not involve breaking of the physical interaction between ɛ and β2.
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Affiliation(s)
- Jonghyun Park
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong & Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Yongmoon Jeon
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Won-Ki Cho
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Ryanggeun Lee
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong & Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea; School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 37673, Korea.
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18
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Pandey P, Tarique KF, Mazumder M, Rehman SAA, Kumari N, Gourinath S. Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori. Sci Rep 2016; 6:31181. [PMID: 27499105 PMCID: PMC4976356 DOI: 10.1038/srep31181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/14/2016] [Indexed: 12/30/2022] Open
Abstract
Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of β-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of β-clamp binding regions in them and validated by SPR studies. Hpβ-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of β-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with β-clamp.
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Affiliation(s)
- Preeti Pandey
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India
| | | | - Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Nilima Kumari
- Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India
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19
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Abstract
DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the β2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads β2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.
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Affiliation(s)
- J S Lewis
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - S Jergic
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N E Dixon
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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20
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Gu S, Li W, Zhang H, Fleming J, Yang W, Wang S, Wei W, Zhou J, Zhu G, Deng J, Hou J, Zhou Y, Lin S, Zhang XE, Bi L. The β2 clamp in the Mycobacterium tuberculosis DNA polymerase III αβ2ε replicase promotes polymerization and reduces exonuclease activity. Sci Rep 2016; 6:18418. [PMID: 26822057 PMCID: PMC4731781 DOI: 10.1038/srep18418] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022] Open
Abstract
DNA polymerase III (DNA pol III) is a multi-subunit replication machine responsible for the accurate and rapid replication of bacterial genomes, however, how it functions in Mycobacterium tuberculosis (Mtb) requires further investigation. We have reconstituted the leading-strand replication process of the Mtb DNA pol III holoenzyme in vitro, and investigated the physical and functional relationships between its key components. We verify the presence of an αβ2ε polymerase-clamp-exonuclease replicase complex by biochemical methods and protein-protein interaction assays in vitro and in vivo and confirm that, in addition to the polymerase activity of its α subunit, Mtb DNA pol III has two potential proofreading subunits; the α and ε subunits. During DNA replication, the presence of the β2 clamp strongly promotes the polymerization of the αβ2ε replicase and reduces its exonuclease activity. Our work provides a foundation for further research on the mechanism by which the replication machinery switches between replication and proofreading and provides an experimental platform for the selection of antimicrobials targeting DNA replication in Mtb.
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Affiliation(s)
- Shoujin Gu
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Li
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Joy Fleming
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiqiang Yang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenjing Wei
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhou
- The Fourth People's Hospital, Foshan 528000, China
| | - Guofeng Zhu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jian Hou
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Zhou
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shiqiang Lin
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijun Bi
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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21
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Dohrmann PR, Correa R, Frisch RL, Rosenberg SM, McHenry CS. The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase. Nucleic Acids Res 2016; 44:1285-97. [PMID: 26786318 PMCID: PMC4756838 DOI: 10.1093/nar/gkv1510] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX3δδ’χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-Ctag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-Ctag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III2τ2 γδδ’χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F’ episome.
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Affiliation(s)
- Paul R Dohrmann
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Raul Correa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
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22
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Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res 2015; 44:1681-90. [PMID: 26657641 PMCID: PMC4770218 DOI: 10.1093/nar/gkv1375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli has three DNA polymerases implicated in the bypass of DNA damage, a process called translesion synthesis (TLS) that alleviates replication stalling. Although these polymerases are specialized for different DNA lesions, it is unclear if they interact differently with the replication machinery. Of the three, DNA polymerase (Pol) II remains the most enigmatic. Here we report a stable ternary complex of Pol II, the replicative polymerase Pol III core complex and the dimeric processivity clamp, β. Single-molecule experiments reveal that the interactions of Pol II and Pol III with β allow for rapid exchange during DNA synthesis. As with another TLS polymerase, Pol IV, increasing concentrations of Pol II displace the Pol III core during DNA synthesis in a minimal reconstitution of primer extension. However, in contrast to Pol IV, Pol II is inefficient at disrupting rolling-circle synthesis by the fully reconstituted Pol III replisome. Together, these data suggest a β-mediated mechanism of exchange between Pol II and Pol III that occurs outside the replication fork.
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Affiliation(s)
- James E Kath
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle K Scotland
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Johannes H Wilbertz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Slobodan Jergic
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Mark D Sutton
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Genetics, Genomics and Bioinformatics Program, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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23
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Fernandez-Leiro R, Conrad J, Scheres SH, Lamers MH. cryo-EM structures of the E. coli replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and τ. eLife 2015; 4. [PMID: 26499492 PMCID: PMC4703070 DOI: 10.7554/elife.11134] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/23/2015] [Indexed: 11/13/2022] Open
Abstract
The replicative DNA polymerase PolIIIα from Escherichia coli is a uniquely fast and processive enzyme. For its activity it relies on the DNA sliding clamp β, the proofreading exonuclease ε and the C-terminal domain of the clamp loader subunit τ. Due to the dynamic nature of the four-protein complex it has long been refractory to structural characterization. Here we present the 8 Å resolution cryo-electron microscopy structures of DNA-bound and DNA-free states of the PolIII-clamp-exonuclease-τc complex. The structures show how the polymerase is tethered to the DNA through multiple contacts with the clamp and exonuclease. A novel contact between the polymerase and clamp is made in the DNA bound state, facilitated by a large movement of the polymerase tail domain and τc. These structures provide crucial insights into the organization of the catalytic core of the replisome and form an important step towards determining the structure of the complete holoenzyme.
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Affiliation(s)
| | - Julian Conrad
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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24
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Abstract
This review describes the components of the Escherichia coli replisome and the dynamic process in which they function and interact under normal conditions. It also briefly describes the behavior of the replisome during situations in which normal replication fork movement is disturbed, such as when the replication fork collides with sites of DNA damage. E. coli DNA Pol III was isolated first from a polA mutant E. coli strain that lacked the relatively abundant DNA Pol I activity. Further biochemical studies, and the use of double mutant strains, revealed Pol III to be the replicative DNA polymerase essential to cell viability. In a replisome, DnaG primase must interact with DnaB for activity, and this constraint ensures that new RNA primers localize to the replication fork. The leading strand polymerase continually synthesizes DNA in the direction of the replication fork, whereas the lagging-strand polymerase synthesizes short, discontinuous Okazaki fragments in the opposite direction. Discontinuous lagging-strand synthesis requires that the polymerase rapidly dissociate from each new completed Okazaki fragment in order to begin the extension of a new RNA primer. Lesion bypass can be thought of as a two-step reaction that starts with the incorporation of a nucleotide opposite the lesion, followed by the extension of the resulting distorted primer terminus. A remarkable property of E. coli, and many other eubacterial organisms, is the speed at which it propagates. Rapid cell division requires the presence of an extremely efficient replication machinery for the rapid and faithful duplication of the genome.
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25
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A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis. PLoS Genet 2015; 11:e1005507. [PMID: 26352807 PMCID: PMC4564189 DOI: 10.1371/journal.pgen.1005507] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/14/2015] [Indexed: 11/19/2022] Open
Abstract
Translesion DNA synthesis (TLS) by specialized DNA polymerases (Pols) is a conserved mechanism for tolerating replication blocking DNA lesions. The actions of TLS Pols are managed in part by ring-shaped sliding clamp proteins. In addition to catalyzing TLS, altered expression of TLS Pols impedes cellular growth. The goal of this study was to define the relationship between the physiological function of Escherichia coli Pol IV in TLS and its ability to impede growth when overproduced. To this end, 13 novel Pol IV mutants were identified that failed to impede growth. Subsequent analysis of these mutants suggest that overproduced levels of Pol IV inhibit E. coli growth by gaining inappropriate access to the replication fork via a Pol III-Pol IV switch that is mechanistically similar to that used under physiological conditions to coordinate Pol IV-catalyzed TLS with Pol III-catalyzed replication. Detailed analysis of one mutant, Pol IV-T120P, and two previously described Pol IV mutants impaired for interaction with either the rim (Pol IVR) or the cleft (Pol IVC) of the β sliding clamp revealed novel insights into the mechanism of the Pol III-Pol IV switch. Specifically, Pol IV-T120P retained complete catalytic activity in vitro but, like Pol IVR and Pol IVC, failed to support Pol IV TLS function in vivo. Notably, the T120P mutation abrogated a biochemical interaction of Pol IV with Pol III that was required for Pol III-Pol IV switching. Taken together, these results support a model in which Pol III-Pol IV switching involves interaction of Pol IV with Pol III, as well as the β clamp rim and cleft. Moreover, they provide strong support for the view that Pol III-Pol IV switching represents a vitally important mechanism for regulating TLS in vivo by managing access of Pol IV to the DNA. Bacterial DNA polymerase IV (Pol IV) is capable of replicating damaged DNA via a process termed translesion DNA synthesis (TLS). Pol IV-mediated TLS can be accurate or error-prone, depending on the type of DNA damage. Errors made by Pol IV contribute to antibiotic resistance and adaptation of bacterial pathogens. In addition to catalyzing TLS, overproduction of Escherichia coli Pol IV impedes growth. In the current work, we demonstrate that both of these functions rely on the ability of Pol IV to bind the β sliding processivity clamp and switch places on DNA with the replicative Pol, Pol III. This switch requires that Pol IV contact both Pol III as well as two discrete sites on the β clamp protein. Taken together, these results provide a deeper understanding of how E. coli manages the actions of Pol III and Pol IV to coordinate high fidelity replication with potentially error-prone TLS.
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Kling A, Lukat P, Almeida DV, Bauer A, Fontaine E, Sordello S, Zaburannyi N, Herrmann J, Wenzel SC, König C, Ammerman NC, Barrio MB, Borchers K, Bordon-Pallier F, Brönstrup M, Courtemanche G, Gerlitz M, Geslin M, Hammann P, Heinz DW, Hoffmann H, Klieber S, Kohlmann M, Kurz M, Lair C, Matter H, Nuermberger E, Tyagi S, Fraisse L, Grosset JH, Lagrange S, Müller R. Antibiotics. Targeting DnaN for tuberculosis therapy using novel griselimycins. Science 2015; 348:1106-12. [PMID: 26045430 DOI: 10.1126/science.aaa4690] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of Streptomyces-produced streptomycin founded the age of tuberculosis therapy. Despite the subsequent development of a curative regimen for this disease, tuberculosis remains a worldwide problem, and the emergence of multidrug-resistant Mycobacterium tuberculosis has prioritized the need for new drugs. Here we show that new optimized derivatives from Streptomyces-derived griselimycin are highly active against M. tuberculosis, both in vitro and in vivo, by inhibiting the DNA polymerase sliding clamp DnaN. We discovered that resistance to griselimycins, occurring at very low frequency, is associated with amplification of a chromosomal segment containing dnaN, as well as the ori site. Our results demonstrate that griselimycins have high translational potential for tuberculosis treatment, validate DnaN as an antimicrobial target, and capture the process of antibiotic pressure-induced gene amplification.
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Affiliation(s)
- Angela Kling
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Peer Lukat
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany. Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Deepak V Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - Armin Bauer
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Evelyne Fontaine
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Sylvie Sordello
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Nestor Zaburannyi
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Silke C Wenzel
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Claudia König
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Nicole C Ammerman
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - María Belén Barrio
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Kai Borchers
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Florence Bordon-Pallier
- Sanofi-Aventis R&D, Strategy, Science Policy & External Innovation (S&I), 75008 Paris, France
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany. Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Gilles Courtemanche
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Martin Gerlitz
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Michel Geslin
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Peter Hammann
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 65926 Frankfurt, Germany
| | - Dirk W Heinz
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany. Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Holger Hoffmann
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Sylvie Klieber
- Sanofi-Aventis R&D, Disposition Safety and Animal Research, 34184 Montpellier, France
| | - Markus Kohlmann
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Michael Kurz
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Christine Lair
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Hans Matter
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Sandeep Tyagi
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Laurent Fraisse
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Jacques H Grosset
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - Sophie Lagrange
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany.
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Lindow JC, Dohrmann PR, McHenry CS. DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection. J Biol Chem 2015; 290:16851-60. [PMID: 25987558 DOI: 10.1074/jbc.m115.661090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Indexed: 11/06/2022] Open
Abstract
Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized.
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Affiliation(s)
- Janet C Lindow
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Paul R Dohrmann
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Charles S McHenry
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
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28
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Khanam T, Rai N, Ramachandran R. Mycobacterium tuberculosis class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β-clamp. Mol Microbiol 2015; 98:46-68. [PMID: 26103519 DOI: 10.1111/mmi.13102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 11/30/2022]
Abstract
The class-II AP-endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239 QLRFPKK245 motif in the DNA-binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of β-clamp located on different domains interact with XthA. The β-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β-clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β-clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
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29
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Yin Z, Whittell LR, Wang Y, Jergic S, Ma C, Lewis PJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J Med Chem 2015; 58:4693-702. [PMID: 25970224 DOI: 10.1021/acs.jmedchem.5b00232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.
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Affiliation(s)
- Zhou Yin
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Louise R Whittell
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Yao Wang
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Cong Ma
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J Lewis
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas E Dixon
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jennifer L Beck
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael J Kelso
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Aaron J Oakley
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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30
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Yin Z, Whittell LR, Wang Y, Jergic S, Liu M, Harry EJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J Med Chem 2014; 57:2799-806. [PMID: 24592885 DOI: 10.1021/jm500122r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.
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Affiliation(s)
- Zhou Yin
- School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Yuan Q, McHenry CS. Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork. Nucleic Acids Res 2013; 42:1747-56. [PMID: 24234450 PMCID: PMC3919610 DOI: 10.1093/nar/gkt1098] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment—either collision with the 5′-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific perturbation of lagging strand elongation on minicircles with a highly asymmetric G:C distribution with ddGTP or dGDPNP yielded results that confirmed the signaling model and ruled out the collision model. We demonstrated that the presence of a primer, not primase per se, provides the signal that triggers cycling. Lagging strand synthesis proceeds much faster than leading strand synthesis, explaining why gaps between Okazaki fragments are not found under physiological conditions.
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Affiliation(s)
- Quan Yuan
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Timinskas K, Balvočiūtė M, Timinskas A, Venclovas Č. Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res 2013; 42:1393-413. [PMID: 24106089 PMCID: PMC3919608 DOI: 10.1093/nar/gkt900] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set.
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Affiliation(s)
- Kestutis Timinskas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
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Chaurasiya KR, Ruslie C, Silva MC, Voortman L, Nevin P, Lone S, Beuning PJ, Williams MC. Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA. Nucleic Acids Res 2013; 41:8959-68. [PMID: 23901012 PMCID: PMC3799427 DOI: 10.1093/nar/gkt648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.
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Affiliation(s)
- Kathy R. Chaurasiya
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Clarissa Ruslie
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Michelle C. Silva
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Lukas Voortman
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Philip Nevin
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Samer Lone
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Penny J. Beuning
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
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Patoli AA, Winter JA, Bunting KA. The UmuC subunit of the E. coli DNA polymerase V shows a unique interaction with the β-clamp processivity factor. BMC STRUCTURAL BIOLOGY 2013; 13:12. [PMID: 23822808 PMCID: PMC3716654 DOI: 10.1186/1472-6807-13-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 06/28/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Strict regulation of replisome components is essential to ensure the accurate transmission of the genome to the next generation. The sliding clamp processivity factors play a central role in this regulation, interacting with both DNA polymerases and multiple DNA processing and repair proteins. Clamp binding partners share a common peptide binding motif, the nature of which is essentially conserved from phage through to humans. Given the degree of conservation of these motifs, much research effort has focussed on understanding how the temporal and spatial regulation of multiple clamp binding partners is managed. The bacterial sliding clamps have come under scrutiny as potential targets for rational drug design and comprehensive understanding of the structural basis of their interactions is crucial for success. RESULTS In this study we describe the crystal structure of a complex of the E. coli β-clamp with a 12-mer peptide from the UmuC protein. UmuC is the catalytic subunit of the translesion DNA polymerase, Pol V (UmuD'₂C). Due to its potentially mutagenic action, Pol V is tightly regulated in the cell to limit access to the replication fork. Atypically for the translesion polymerases, both bacterial and eukaryotic, Pol V is heterotrimeric and its β-clamp binding motif (³⁵⁷QLNLF³⁶¹) is internal to the protein, rather than at the more usual C-terminal position. Our structure shows that the UmuC peptide follows the overall disposition of previously characterised structures with respect to the highly conserved glutamine residue. Despite good agreement with the consensus β-clamp binding motif, distinct variation is shown within the hydrophobic binding pocket. While UmuC Leu-360 interacts as noted in other structures, Phe-361 does not penetrate the pocket at all, sitting above the surface. CONCLUSION Although the β-clamp binding motif of UmuC conforms to the consensus sequence, variation in its mode of clamp binding is observed compared to related structures, presumably dictated by the proximal aspartate residues that act as linker to the poorly characterised, unique C-terminal domain of UmuC. Additionally, interactions between Asn-359 of UmuC and Arg-152 on the clamp surface may compensate for the reduced interaction of Phe-361.
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Affiliation(s)
- Atif A Patoli
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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35
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Ozawa K, Horan NP, Robinson A, Yagi H, Hill FR, Jergic S, Xu ZQ, Loscha KV, Li N, Tehei M, Oakley AJ, Otting G, Huber T, Dixon NE. Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain. Nucleic Acids Res 2013; 41:5354-67. [PMID: 23580545 PMCID: PMC3664792 DOI: 10.1093/nar/gkt162] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 11/24/2022] Open
Abstract
A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data.
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Affiliation(s)
- Kiyoshi Ozawa
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas P. Horan
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Andrew Robinson
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Hiromasa Yagi
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Flynn R. Hill
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Slobodan Jergic
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Zhi-Qiang Xu
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Karin V. Loscha
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nan Li
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Moeava Tehei
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Aaron J. Oakley
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Gottfried Otting
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Thomas Huber
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas E. Dixon
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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36
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Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J 2013; 32:1334-43. [PMID: 23549287 PMCID: PMC3642679 DOI: 10.1038/emboj.2013.68] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/27/2013] [Indexed: 11/08/2022] Open
Abstract
DNA polymerase III (Pol III) is the catalytic α subunit of the bacterial DNA Polymerase III holoenzyme. To reach maximum activity, Pol III binds to the DNA sliding clamp β and the exonuclease ε that provide processivity and proofreading, respectively. Here, we characterize the architecture of the Pol III-clamp-exonuclease complex by chemical crosslinking combined with mass spectrometry and biochemical methods, providing the first structural view of the trimeric complex. Our analysis reveals that the exonuclease is sandwiched between the polymerase and clamp and enhances the binding between the two proteins by providing a second, indirect, interaction between the polymerase and clamp. In addition, we show that the exonuclease binds the clamp via the canonical binding pocket and thus prevents binding of the translesion DNA polymerase IV to the clamp, providing a novel insight into the mechanism by which the replication machinery can switch between replication, proofreading, and translesion synthesis.
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Structure of the PolIIIα-τc-DNA complex suggests an atomic model of the replisome. Structure 2013; 21:658-64. [PMID: 23478062 PMCID: PMC3652607 DOI: 10.1016/j.str.2013.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/22/2013] [Accepted: 02/01/2013] [Indexed: 01/07/2023]
Abstract
The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3.2 Å resolution structure of Thermus aquaticus PolIIIα in complex with τc and a DNA substrate. The structure reveals that the CTD of τc interacts with the CTD of PolIIIα through its C-terminal helix and the adjacent loop. Additionally, in this complex PolIIIα displays an open conformation that includes the reorientations of the oligonucleotide-binding fold and the thumb domain, which may be an indirect result of crystal packing due to the presence of the τc. Nevertheless, the position of the τc on PolIIIα allows us to suggest an approximate model for how the PolIIIα is oriented and positioned on the DnaB helicase.
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38
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Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JMH, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM, Dixon NE. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode. EMBO J 2013; 32:1322-33. [PMID: 23435564 DOI: 10.1038/emboj.2012.347] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/07/2012] [Indexed: 02/08/2023] Open
Abstract
Processive DNA synthesis by the αεθ core of the Escherichia coli Pol III replicase requires it to be bound to the β2 clamp via a site in the α polymerase subunit. How the ε proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of ε. Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in ε that, in conjunction with the site in α, maintains a closed state of the αεθ-β2 replicase in the polymerization mode of DNA synthesis. The ε-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states.
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Affiliation(s)
- Slobodan Jergic
- School of Chemistry, University of Wollongong, Wollongong, New South Wales, Australia
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39
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Escherichia coli DNA polymerase IV (Pol IV), but not Pol II, dynamically switches with a stalled Pol III* replicase. J Bacteriol 2012; 194:3589-600. [PMID: 22544274 DOI: 10.1128/jb.00520-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The dnaN159 allele encodes a temperature-sensitive mutant form of the β sliding clamp (β159). SOS-induced levels of DNA polymerase IV (Pol IV) confer UV sensitivity upon the dnaN159 strain, while levels of Pol IV ∼4-fold higher than those induced by the SOS response severely impede its growth. Here, we used mutations in Pol IV that disrupted specific interactions with the β clamp to test our hypothesis that these phenotypes were the result of Pol IV gaining inappropriate access to the replication fork via a Pol III*-Pol IV switch relying on both the rim and cleft of the clamp. Our results clearly demonstrate that Pol IV relied on both the clamp rim and cleft interactions for these phenotypes. In contrast to the case for Pol IV, elevated levels of the other Pols, including Pol II, which was expressed at levels ∼8-fold higher than the normal SOS-induced levels, failed to impede growth of the dnaN159 strain. These findings suggest that the mechanism used by Pol IV to switch with Pol III* is distinct from those used by the other Pols. Results of experiments utilizing purified components to reconstitute the Pol III*-Pol II switch in vitro indicated that Pol II switched equally well with both a stalled and an actively replicating Pol III* in a manner that was independent of the rim contact required by Pol IV. These results provide compelling support for the Pol III*-Pol IV two-step switch model and demonstrate important mechanistic differences in how Pol IV and Pol II switch with Pol III*.
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40
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Kelch BA, Makino DL, O'Donnell M, Kuriyan J. Clamp loader ATPases and the evolution of DNA replication machinery. BMC Biol 2012; 10:34. [PMID: 22520345 PMCID: PMC3331839 DOI: 10.1186/1741-7007-10-34] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 04/20/2012] [Indexed: 11/19/2022] Open
Abstract
Clamp loaders are pentameric ATPases of the AAA+ family that operate to ensure processive DNA replication. They do so by loading onto DNA the ring-shaped sliding clamps that tether the polymerase to the DNA. Structural and biochemical analysis of clamp loaders has shown how, despite differences in composition across different branches of life, all clamp loaders undergo the same concerted conformational transformations, which generate a binding surface for the open clamp and an internal spiral chamber into which the DNA at the replication fork can slide, triggering ATP hydrolysis, release of the clamp loader, and closure of the clamp round the DNA. We review here the current understanding of the clamp loader mechanism and discuss the implications of the differences between clamp loaders from the different branches of life.
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Affiliation(s)
- Brian A Kelch
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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41
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Silva MC, Nevin P, Ronayne EA, Beuning PJ. Selective disruption of the DNA polymerase III α-β complex by the umuD gene products. Nucleic Acids Res 2012; 40:5511-22. [PMID: 22406830 PMCID: PMC3384344 DOI: 10.1093/nar/gks229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, which are up-regulated during the SOS response, were previously shown to bind to the α, β and ε subunits of DNA pol III. Full-length UmuD inhibits DNA replication and prevents mutagenic TLS, while the cleaved form UmuD' facilitates mutagenesis. We show that α possesses two UmuD binding sites: at the N-terminus (residues 1-280) and the C-terminus (residues 956-975). The C-terminal site favors UmuD over UmuD'. We also find that UmuD, but not UmuD', disrupts the α-β complex. We propose that the interaction between α and UmuD contributes to the transition between replicative and TLS polymerases by removing α from the β clamp.
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Affiliation(s)
- Michelle C Silva
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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42
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Abstract
Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, polymerase III (Pol III), a β₂ processivity factor, and a DnaX complex ATPase that loads β₂ onto DNA and chaperones Pol III onto the newly loaded β₂. Bacterial replicases are highly processive, yet cycle rapidly during Okazaki fragment synthesis in a regulated way. Many bacteria encode both a full-length τ and a shorter γ form of DnaX by a variety of mechanisms. γ appears to be uniquely placed in a single position relative to two τ protomers in a pentameric ring. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to a prototypical ε Mg²⁺-dependent exonuclease, but also contains a second Zn²⁺-dependent proofreading exonuclease, at least in some bacteria. This review focuses on a critical evaluation of recent literature and concepts pertaining to the above issues and suggests specific areas that require further investigation.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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Dohrmann PR, Manhart CM, Downey CD, McHenry CS. The rate of polymerase release upon filling the gap between Okazaki fragments is inadequate to support cycling during lagging strand synthesis. J Mol Biol 2011; 414:15-27. [PMID: 21986197 DOI: 10.1016/j.jmb.2011.09.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/16/2011] [Accepted: 09/24/2011] [Indexed: 10/17/2022]
Abstract
Upon completion of synthesis of an Okazaki fragment, the lagging strand replicase must recycle to the next primer at the replication fork in under 0.1 s to sustain the physiological rate of DNA synthesis. We tested the collision model that posits that cycling is triggered by the polymerase encountering the 5'-end of the preceding Okazaki fragment. Probing with surface plasmon resonance, DNA polymerase III holoenzyme initiation complexes were formed on an immobilized gapped template. Initiation complexes exhibit a half-life of dissociation of approximately 15 min. Reduction in gap size to 1 nt increased the rate of dissociation 2.5-fold, and complete filling of the gap increased the off-rate an additional 3-fold (t(1/2)~2 min). An exogenous primed template and ATP accelerated dissociation an additional 4-fold in a reaction that required complete filling of the gap. Neither a 5'-triphosphate nor a 5'-RNA terminated oligonucleotide downstream of the polymerase accelerated dissociation further. Thus, the rate of polymerase release upon gap completion and collision with a downstream Okazaki fragment is 1000-fold too slow to support an adequate rate of cycling and likely provides a backup mechanism to enable polymerase release when the other cycling signals are absent. Kinetic measurements indicate that addition of the last nucleotide to fill the gap is not the rate-limiting step for polymerase release and cycling. Modest (approximately 7 nt) strand displacement is observed after the gap between model Okazaki fragments is filled. To determine the identity of the protein that senses gap filling to modulate affinity of the replicase for the template, we performed photo-cross-linking experiments with highly reactive and non-chemoselective diazirines. Only the α subunit cross-linked, indicating that it serves as the sensor.
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Affiliation(s)
- Paul R Dohrmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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44
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McHenry CS. Bacterial replicases and related polymerases. Curr Opin Chem Biol 2011; 15:587-94. [PMID: 21855395 DOI: 10.1016/j.cbpa.2011.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/24/2022]
Abstract
Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, Pol III, a β(2) processivity factor and a DnaX complex ATPase that loads β(2) onto DNA and chaperones Pol III onto the newly loaded β(2). Many bacteria encode both a full length τ and a shorter γ form of DnaX by a variety of mechanisms. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to prototypical ɛ Mg(2+)-dependent exonuclease, but also contains a second Zn(2+)-dependent proofreading exonuclease, at least in some bacteria. Replication of the chromosomes of low GC Gram-positive bacteria require two Pol IIIs, one of which, DnaE, appears to extend RNA primers a only short distance before handing the product off to the major replicase, PolC. Other bacteria encode a second Pol III (ImuC) that apparently replaces Pol V, required for induced mutagenesis in E. coli. Approaches that permit simultaneous biochemical screening of all components of complex bacterial replicases promise inhibitors of specific protein targets and reaction stages.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309, USA.
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45
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Timinskas K, Venclovas Č. The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III τ subunit. FEBS J 2011; 278:3109-18. [DOI: 10.1111/j.1742-4658.2011.08236.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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46
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López de Saro FJ. Regulation of interactions with sliding clamps during DNA replication and repair. Curr Genomics 2011; 10:206-15. [PMID: 19881914 PMCID: PMC2705854 DOI: 10.2174/138920209788185234] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 03/09/2009] [Accepted: 03/16/2009] [Indexed: 01/12/2023] Open
Abstract
The molecular machines that replicate the genome consist of many interacting components. Essential to the organization of the replication machinery are ring-shaped proteins, like PCNA (Proliferating Cell Nuclear Antigen) or the β- clamp, collectively named sliding clamps. They encircle the DNA molecule and slide on it freely and bidirectionally. Sliding clamps are typically associated to DNA polymerases and provide these enzymes with the processivity required to synthesize large chromosomes. Additionally, they interact with a large array of proteins that perform enzymatic reactions on DNA, targeting and orchestrating their functions. In recent years there have been a large number of studies that have analyzed the structural details of how sliding clamps interact with their ligands. However, much remains to be learned in relation to how these interactions are regulated to occur coordinately and sequentially. Since sliding clamps participate in reactions in which many different enzymes bind and then release from the clamp in an orchestrated way, it is critical to analyze how these changes in affinity take place. In this review I focus the attention on the mechanisms by which various types of enzymes interact with sliding clamps and what is known about the regulation of this binding. Especially I describe emerging paradigms on how enzymes switch places on sliding clamps during DNA replication and repair of prokaryotic and eukaryotic genomes.
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Affiliation(s)
- Francisco J López de Saro
- Laboratorio de Ecología Molecular, Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain
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47
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Fang J, Engen JR, Beuning PJ. Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution. Biochemistry 2011; 50:5958-68. [PMID: 21657794 DOI: 10.1021/bi200580b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Escherichia coli DNA polymerase III is a highly processive replicase because of the presence of the β clamp protein that tethers DNA polymerases to DNA. The β clamp is a head-to-tail ring-shaped homodimer, in which each protomer contains three structurally similar domains. Although multiple studies have probed the functions of the β clamp, a detailed understanding of the conformational dynamics of the β clamp in solution is lacking. Here we used hydrogen exchange mass spectrometry to characterize the conformation and dynamics of the intact dimer β clamp and a variant form (I272A/L273A) with a weakened ability to dimerize in solution. Our data indicate that the β clamp is not a static closed ring but rather is dynamic in solution. The three domains exhibited different dynamics, though they share a highly similar tertiary structure. Domain I, which controls the opening of the clamp by dissociating from domain III, contained several highly flexible peptides that underwent partial cooperative unfolding (EX1 kinetics) with a half-life of ~4 h. The comparison between the β monomer variant and the wild-type β clamp showed that the β monomer was more dynamic. In the monomer, partial unfolding was much faster and additional regions of domain III also underwent partial unfolding with a half-life of ~1 h. Our results suggest that the δ subunit of the clamp loader may function as a "ring holder" to stabilize the transient opening of the β clamp, rather than as a "ring opener".
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Affiliation(s)
- Jing Fang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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48
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Wijffels G, Johnson WM, Oakley AJ, Turner K, Epa VC, Briscoe SJ, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple BP, Alewood PF, Jennings PA, Dixon NE, Winkler DA. Binding Inhibitors of the Bacterial Sliding Clamp by Design. J Med Chem 2011; 54:4831-8. [DOI: 10.1021/jm2004333] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gene Wijffels
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Wynona M. Johnson
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Aaron J. Oakley
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - Kathleen Turner
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - V. Chandana Epa
- CSIRO Material Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Susan J. Briscoe
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Mitchell Polley
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Andris J. Liepa
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Albert Hofmann
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Jens Buchardt
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Caspar Christensen
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Pavel Prosselkov
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Brian P. Dalrymple
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Paul F. Alewood
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Philip A. Jennings
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - David A. Winkler
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
- Monash Institute for Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria 3052, Australia
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49
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Chhabra G, Dixit A, C Garg L. DNA polymerase III α subunit from Mycobacterium tuberculosis H37Rv: Homology modeling and molecular docking of its inhibitor. Bioinformation 2011; 6:69-73. [PMID: 21544168 PMCID: PMC3082860 DOI: 10.6026/97320630006069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 03/16/2011] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The alpha subunit of Mycobacterial DNA polymerase III holo enzyme catalyzes the polymerization of both DNA strands. The present investigation reports three dimensional (3-D) structure model of DNA polymerase III α subunit of Mycobacterium tuberculosis H37Rv (MtbDnaE1) generated using homology modeling with the backbone structure of DNA polymerase III α of Thermus aquaticus as a template. The model was evaluated at various structure verification servers, which assess the stereo chemical parameters of the residues in the model, as well as structural and functional domains. Comparative analysis of MtbDnaE1 structure reveals the structure of its catalytic domain to be unrelated to that of the human. Successful docking of known inhibitor of bacterial DNA polymerases, 251D onto the modeled MtbDnaE1 was also performed. Therefore, the structure model of MtbDnaE1, a potential anti-mycobacterial target, opens a new avenue for structure-based drug designing against the pathogen. ABBREVIATIONS aa - amino acid(s), PolIIIα - DNA polymerase III alpha subunit, Taq Pol IIIα - Pol IIIα of Thermus aquaticus, MtbDnaE1 - PolIIIα of Mycobacterium tuberculosis.
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50
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Crystal structure of DNA polymerase III β sliding clamp from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2011; 405:272-7. [DOI: 10.1016/j.bbrc.2011.01.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 01/05/2011] [Indexed: 11/19/2022]
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