1
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Evans GW, Craggs T, Kapanidis AN. The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. J Mol Biol 2022; 434:167410. [PMID: 34929202 PMCID: PMC8783057 DOI: 10.1016/j.jmb.2021.167410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/12/2021] [Indexed: 12/03/2022]
Abstract
DNA polymerases maintain genomic integrity by copying DNA with high fidelity, part of which relies on the polymerase fingers opening-closing transition, a series of conformational changes during the DNA synthesis reaction cycle. Fingers opening and closing has been challenging to study, mainly due to the need to synchronise molecular ensembles. We previously studied fingers opening-closing on single polymerase-DNA complexes using single-molecule FRET; however, our work was limited to pre-chemistry reaction steps. Here, we advance our analysis to extensible substrates, and observe DNA polymerase (Pol) conformational changes across the entire DNA polymerisation reaction in real-time, gaining direct access to an elusive post-chemistry step rate-limiting for DNA synthesis. Our results showed that Pol adopts the fingers-closed conformation during polymerisation, and that the post-chemistry rate-limiting step occurs in the fingers-closed conformation. We found that fingers-opening in the Pol-DNA binary complex in the absence of polymerisation is slow (∼5.3 s-1), and comparable to the rate of fingers-opening after polymerisation (3.4 s-1); this indicates that the fingers-opening step itself could be largely responsible for the slow post-chemistry step, with the residual rate potentially accounted for by pyrophosphase release. We also observed that DNA chain-termination of the 3' end of the primer increases substantially the rate of fingers-opening in the Pol-DNA binary complex (5.3 → 29 s-1), demonstrating that the 3'-OH residue is important for the kinetics of fingers conformational changes. Our observations offer mechanistic insight and tools to offer mechanistic insight for all nucleic acid polymerases.
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Affiliation(s)
- Geraint W Evans
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom. https://twitter.com/geraintwe
| | - Timothy Craggs
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom; Sheffield Institute for Nucleic Acids, Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom. https://twitter.com/Craggs_Lab
| | - Achillefs N Kapanidis
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom.
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2
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Dilmore C, DeStefano JJ. HIV Reverse Transcriptase Pre-Steady-State Kinetic Analysis of Chain Terminators and Translocation Inhibitors Reveals Interactions between Magnesium and Nucleotide 3'-OH. ACS OMEGA 2021; 6:14621-14628. [PMID: 34124485 PMCID: PMC8190884 DOI: 10.1021/acsomega.1c01742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 05/06/2023]
Abstract
Deoxythymidine triphosphate analogues with various 3' substituents in the sugar ring (-OH (dTTP)), -H, -N3, -NH2, -F, -O-CH3, no group (2',3'-didehydro-2',3'-dideoxythymidine triphosphate (d4TTP)), and those retaining the 3'-OH but with 4' additions (4'-C-methyl, 4'-C-ethyl) or sugar ring modifications (d-carba dTTP) were evaluated using pre-steady-state kinetics in low (0.5 mM) and high (6 mM) Mg2+ with HIV reverse transcriptase (RT). Analogues showed diminished observed incorporation rate constants (k obs) compared to dTTP ranging from about 2-fold (3'-H, -N3, and d4TTP with high Mg2+) to >10-fold (3'-NH2 and 3'-F with low Mg2+), while 3'-O-CH3 dTTP incorporated much slower than other analogues. Illustrating the importance of interactions between Mg2+ and the 3'-OH, k obs using 5 μM dTTP and 0.5 mM Mg2+ was only modestly slower (1.6-fold) than with 6 mM Mg2+, while analogues with 3' alterations incorporated 2.8-5.1-fold slower in 0.5 mM Mg2+. In contrast, 4'-C-methyl and d-carba dTTP, which retain the 3'-OH, were not significantly affected by Mg2+. Consistent with these results, analogues with 3' modifications were better inhibitors in 6 versus 0.5 mM Mg2+. Equilibrium dissociation constant (K D) and maximum incorporation rate (k pol) determinations for dTTP and analogues lacking a 3'-OH indicated that low Mg2+ caused a several-fold greater reduction in k pol with the analogues but did not significantly affect K D, results consistent with a role for 3'-OH/Mg2+ interactions in catalysis rather than nucleotide binding. Overall, results emphasize the importance of previously unreported interactions between Mg2+ and the 3'-OH of the incoming nucleotide and suggest that inhibitors with 3'-OH groups may have advantages in low free Mg2+ in physiological settings.
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Affiliation(s)
- Christopher
R. Dilmore
- Cell
Biology and Molecular Genetics, 3130 Bioscience Research
Building, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffrey J. DeStefano
- Cell
Biology and Molecular Genetics, 3130 Bioscience Research
Building, University of Maryland, College Park, Maryland 20742, United States
- Maryland
Pathogen Research Institute, College
Park, Maryland 20742, United States
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3
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Zahn KE, Jensen RB, Wood RD, Doublié S. RETRACTED: Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair. Mol Cell 2021; 81:1534-1547.e4. [PMID: 33577776 PMCID: PMC8231307 DOI: 10.1016/j.molcel.2021.01.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Cancers with hereditary defects in homologous recombination rely on DNA polymerase θ (pol θ) for repair of DNA double-strand breaks. During end joining, pol θ aligns microhomology tracts internal to 5'-resected broken ends. An unidentified nuclease trims the 3' ends before synthesis can occur. Here we report that a nuclease activity, which differs from the proofreading activity often associated with DNA polymerases, is intrinsic to the polymerase domain of pol θ. Like the DNA synthesis activity, the nuclease activity requires conserved metal-binding residues, metal ions, and dNTPs and is inhibited by ddNTPs or chain-terminated DNA. Our data indicate that pol θ repurposes metal ions in the polymerase active site for endonucleolytic cleavage and that the polymerase-active and end-trimming conformations of the enzyme are distinct. We reveal a nimble strategy of substrate processing that allows pol θ to trim or extend DNA depending on the DNA repair context.
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Affiliation(s)
- Karl E Zahn
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA; Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 78957, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA.
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4
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Ji J, Day A. Construction of a highly error-prone DNA polymerase for developing organelle mutation systems. Nucleic Acids Res 2020; 48:11868-11879. [PMID: 33135056 PMCID: PMC7708058 DOI: 10.1093/nar/gkaa929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation of 3'-5' exonuclease function resulted in a modest 5-8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.
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MESH Headings
- Amino Acid Sequence
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/metabolism
- Binding Sites
- Chloroplasts/genetics
- Chloroplasts/metabolism
- Cloning, Molecular
- DNA Polymerase gamma/chemistry
- DNA Polymerase gamma/genetics
- DNA Polymerase gamma/metabolism
- DNA Replication
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Molecular
- Mutation
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymorphism, Single Nucleotide
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Selection, Genetic
- Sequence Alignment
- Sequence Homology, Amino Acid
- Nicotiana/classification
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- Junwei Ji
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Anil Day
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
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5
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Johnson MK, Kottur J, Nair DT. A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res 2020; 47:10693-10705. [PMID: 31544946 PMCID: PMC6846668 DOI: 10.1093/nar/gkz792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2’-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4–Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.
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Affiliation(s)
- Mary K Johnson
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Jithesh Kottur
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
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6
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Abstract
Life on Earth depends on polymerases. These enzymes copy genetic information to produce the DNA and RNA strands at the core of the central dogma. Polymerases act by forming phosphodiester linkages to produce polynucleotide strands. While synthetic chemistry can generate a broad range of alternative genetic materials with unnatural linkages, polymerases have so far been limited to forming O-P bonds. Here, we show that, in fact, unnatural N-P bonds can also be formed by a modified DNA polymerase. This template-directed activity generates complementary strands linked by phosphoramidate (NP) esters, an alternative backbone linkage only known to exist in the laboratory. The emergence of NP-DNA polymerase activity implies the biochemical plausibility of alternative central dogmas for cellular life. All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3′-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3′-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3′→P5′ phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3′-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca2+ rather than Mg2+, the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3′-amino-2′,3′-dideoxynucleoside 5′-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA.
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7
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Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE. Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton. Front Microbiol 2018; 9:3053. [PMID: 30619142 PMCID: PMC6302109 DOI: 10.3389/fmicb.2018.03053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components.
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Affiliation(s)
- Daniel J Nasko
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jessica Chopyk
- School of Public Health, University of Maryland, College Park, MD, United States
| | - Eric G Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Barbra D Ferrell
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Shawn W Polson
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
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8
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Raper AT, Suo Z. Investigation of Intradomain Motions of a Y-Family DNA Polymerase during Substrate Binding and Catalysis. Biochemistry 2016; 55:5832-5844. [PMID: 27685341 DOI: 10.1021/acs.biochem.6b00878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA polymerases catalyze DNA synthesis through a stepwise kinetic mechanism that begins with binding to DNA, followed by selection, binding, and incorporation of a nucleotide into an elongating primer. It is hypothesized that subtle active site adjustments in a polymerase to align reactive moieties limit the rate of correct nucleotide incorporation. DNA damage can impede this process for many DNA polymerases, causing replication fork stalling, genetic mutations, and potentially cell death. However, specialized Y-family DNA polymerases are structurally evolved to efficiently bypass DNA damage in vivo, albeit at the expense of replication fidelity. Dpo4, a model Y-family polymerase from Sulfolobus solfataricus, has been well-studied kinetically, structurally, and computationally, which yielded a mechanistic understanding of how the Y-family DNA polymerases achieve their unique catalytic properties. We previously employed a real-time Förster resonance energy transfer (FRET) technique to characterize the global conformational motions of Dpo4 during DNA binding as well as nucleotide binding and incorporation by monitoring changes in distance between sites on the polymerase and DNA, and even between domains of Dpo4. Here, we extend the utility of our FRET methodology to observe conformational transitions within individual domains of Dpo4 during DNA binding and nucleotide incorporation. The results of this novel, intradomain FRET approach unify findings from many studies to fully clarify the complex DNA binding mechanism of Dpo4. Furthermore, intradomain motions in the Finger domain during nucleotide binding and incorporation, for the first time, report on the rate-limiting step of a single-nucleotide addition catalyzed by Dpo4.
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Affiliation(s)
- Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
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9
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A mathematical model of recombinase polymerase amplification under continuously stirred conditions. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Meli M, Sustarsic M, Craggs TD, Kapanidis AN, Colombo G. DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Front Mol Biosci 2016; 3:20. [PMID: 27303671 PMCID: PMC4882331 DOI: 10.3389/fmolb.2016.00020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/10/2016] [Indexed: 12/11/2022] Open
Abstract
Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD) simulations that cover a total timespan of ~5 ms. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (de)stabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed toward open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics, and function of DNA polymerase I at the atomistic level.
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Affiliation(s)
- Massimiliano Meli
- Computational Biochemistry Group, Istituto di Chimica del Riconoscimento Molecolare, National Research Council of Italy Milano, Italy
| | - Marko Sustarsic
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Timothy D Craggs
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Achillefs N Kapanidis
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Giorgio Colombo
- Computational Biochemistry Group, Istituto di Chimica del Riconoscimento Molecolare, National Research Council of Italy Milano, Italy
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11
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Szymanski MR, Kuznetsov VB, Shumate C, Meng Q, Lee YS, Patel G, Patel S, Yin YW. Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase. EMBO J 2015; 34:1959-70. [PMID: 26056153 DOI: 10.15252/embj.201591520] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/18/2015] [Indexed: 11/09/2022] Open
Abstract
The human DNA polymerase gamma (Pol γ) is responsible for DNA replication in mitochondria. Pol γ is particularly susceptible to inhibition by dideoxynucleoside-based inhibitors designed to fight viral infection. Here, we report crystal structures of the replicating Pol γ-DNA complex bound to either substrate or zalcitabine, an inhibitor used for HIV reverse transcriptase. The structures reveal that zalcitabine binds to the Pol γ active site almost identically to the substrate dCTP, providing a structural basis for Pol γ-mediated drug toxicity. When compared to the apo form, Pol γ undergoes intra- and inter-subunit conformational changes upon formation of the ternary complex with primer/template DNA and substrate. We also find that the accessory subunit Pol γB, which lacks intrinsic enzymatic activity and does not contact the primer/template DNA directly, serves as an allosteric regulator of holoenzyme activities. The structures presented here suggest a mechanism for processivity of the holoenzyme and provide a model for understanding the deleterious effects of Pol γ mutations in human disease. Crystal structures of the mitochondrial DNA polymerase, Pol γ, in complex with substrate or antiviral inhibitor zalcitabine provide a basis for understanding Pol γ-mediated drug toxicity.
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Affiliation(s)
- Michal R Szymanski
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vladmir B Kuznetsov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Christie Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Qingchao Meng
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Young-Sam Lee
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gayatri Patel
- Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Smita Patel
- Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Y Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
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12
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Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB. A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase. Biochemistry 2015; 54:881-9. [PMID: 25537790 PMCID: PMC4310628 DOI: 10.1021/bi501198f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5'-to-3' exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E-DNA-ddNTP) and binary (E-DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5'-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.
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Affiliation(s)
- Eugene Y Wu
- Department of Biology and ‡Department of Chemistry, University of Richmond , Richmond, Virginia 23173, United States
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13
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Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley NDF, Joyce CM, Kapanidis AN. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nat Commun 2014; 4:2131. [PMID: 23831915 PMCID: PMC3715850 DOI: 10.1038/ncomms3131] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 06/11/2013] [Indexed: 01/04/2023] Open
Abstract
The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the conformational transitions and free-energy landscape that underlie fidelity decisions in DNA synthesis. Ternary complexes of high fidelity derivatives with complementary dNTPs adopt mainly a fully closed conformation, whereas a conformation with a FRET value between those of open and closed is sparsely populated. This intermediate-FRET state, which we attribute to a partially closed conformation, is also predominant in ternary complexes with incorrect nucleotides and, strikingly, in most ternary complexes of low-fidelity derivatives for both correct and incorrect nucleotides. The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection. The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint.
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Affiliation(s)
- Johannes Hohlbein
- Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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14
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Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME JOURNAL 2013; 8:103-14. [PMID: 23985748 DOI: 10.1038/ismej.2013.124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 06/07/2013] [Accepted: 06/18/2013] [Indexed: 02/07/2023]
Abstract
Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.
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Affiliation(s)
- Helen F Schmidt
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Eric G Sakowski
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | | | - Shawn W Polson
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - K Eric Wommack
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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15
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Bermek O, Grindley NDF, Joyce CM. Prechemistry nucleotide selection checkpoints in the reaction pathway of DNA polymerase I and roles of glu710 and tyr766. Biochemistry 2013; 52:6258-74. [PMID: 23937394 PMCID: PMC3770053 DOI: 10.1021/bi400837k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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The accuracy of high-fidelity DNA
polymerases such as DNA polymerase
I (Klenow fragment) is governed by conformational changes early in
the reaction pathway that serve as fidelity checkpoints, identifying
inappropriate template–nucleotide pairings. The fingers-closing
transition (detected by a fluorescence resonance energy transfer-based
assay) is the unique outcome of binding a correct incoming nucleotide,
both complementary to the templating base and with a deoxyribose (rather
than ribose) sugar structure. Complexes with mispaired dNTPs or complementary
rNTPs are arrested at an earlier stage, corresponding to a partially
closed fingers conformation, in which weak binding of DNA and nucleotide
promote dissociation and resampling of the substrate pool. A 2-aminopurine
fluorescence probe on the DNA template provides further information
about the steps preceding fingers closing. A characteristic 2-aminopurine
signal is observed on binding a complementary nucleotide, regardless
of whether the sugar is deoxyribose or ribose. However, mispaired
dNTPs show entirely different behavior. Thus, a fidelity checkpoint
ahead of fingers closing is responsible for distinguishing complementary
from noncomplementary nucleotides and routing them toward different
outcomes. The E710A mutator polymerase has a defect in the early fidelity
checkpoint such that some complementary dNTPs are treated as if they
were mispaired. In the Y766A mutant, the early checkpoint functions
normally, but some correctly paired dNTPs do not efficiently undergo
fingers closing. Thus, both mutator alleles cause a blurring of the
distinction between correct and incorrect base pairs and result in
a larger fraction of errors passing through the prechemistry fidelity
checkpoints.
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Affiliation(s)
- Oya Bermek
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520, United States
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16
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Wang H, Hurt N, Dunbar WB. Measuring and modeling the kinetics of individual DNA-DNA polymerase complexes on a nanopore. ACS NANO 2013; 7:3876-3886. [PMID: 23565679 PMCID: PMC3682681 DOI: 10.1021/nn401180j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The assembly of a DNA-DNA polymerase binary complex is the precursory step in genome replication, in which the enzyme binds to the 3' junction created when a primer binds to its complementary substrate. In this study, we use an active control method for observing the binding interaction between Klenow fragment (exo-) (KF) in the bulk-phase chamber above an α-hemolysin (α-HL) nanopore and a single DNA molecule tethered noncovalently in the nanopore. Specifically, the control method regulates the temporal availability of the primer-template DNA to KF binding and unbinding above the nanopore, on millisecond-to-second time scales. Our nanopore measurements support a model that incorporates two mutually exclusive binding states of KF to DNA at the primer-template junction site, termed "weakly bound" and "strongly bound" states. The composite binding affinity constant, the equilibrium constant between the weak and strong states, and the unbound-to-strong association rate are quantified from the data using derived modeling analysis. The results support that the strong state is in the nucleotide incorporation pathway, consistent with other nanopore assays. Surprisingly, the measured unbound-to-strong association process does not fit a model that admits binding of only free (unbound) KF to the tethered DNA but does fit an association rate that is proportional to the total (unbound and DNA-bound) KF concentration in the chamber above the nanopore. Our method provides a tool for measuring pre-equilibrium kinetics one molecule at a time, serially and for tens of thousands of single-molecule events, and can be used for other polynucleotide-binding enzymes.
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Affiliation(s)
- Hongyun Wang
- Department of Applied Mathematics and Statistics, University of California, Santa Cruz, 95064
| | - Nicholas Hurt
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 95064
| | - William B. Dunbar
- Department of Computer Engineering, University of California, Santa Cruz, 95064
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17
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Wang W, Wu EY, Hellinga HW, Beese LS. Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J Biol Chem 2012; 287:28215-26. [PMID: 22648417 PMCID: PMC3436578 DOI: 10.1074/jbc.m112.366609] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/15/2012] [Indexed: 12/20/2022] Open
Abstract
In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2'-hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base pair discrimination.
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Affiliation(s)
- Weina Wang
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Eugene Y. Wu
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Homme W. Hellinga
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Lorena S. Beese
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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18
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Cağlayan M, Bilgin N. Temperature dependence of accuracy of DNA polymerase I from Geobacillus anatolicus. Biochimie 2012; 94:1968-73. [PMID: 22652043 DOI: 10.1016/j.biochi.2012.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 05/21/2012] [Indexed: 11/30/2022]
Abstract
Klenow-like DNA polymerase I fragment from Geobacillus anatolicus (GF) was cloned and purified. The accuracy of GF was measured in vitro at three different temperatures under single turnover conditions as well as using a forward mutation assay. In pre-steady-state kinetic measurements, when temperature was raised from 22 °C to 50 °C, the rate (k(pol)) for cognate dTTP and non-cognate dATP nucleotide incorporations increased six- and four-fold, respectively, whereas the K(d) for both nucleotide incorporations changed only slightly. As a result, the error frequency was remained constant (∼4 × 10(-4)) over this temperature range. The accuracy of GF was also measured using a forward mutation assay during a single cycle of DNA synthesis of the lacZα complementation gene in M13mp2 DNA. In this assay, which scores various types of replication errors, mutant frequency of GF was 5 × 10(-3) at 72 °C which is four-fold higher than that of 37 °C.
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Affiliation(s)
- Melike Cağlayan
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Istanbul, Turkey
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19
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Gardner AF, Wang J, Wu W, Karouby J, Li H, Stupi BP, Jack WE, Hersh MN, Metzker ML. Rapid incorporation kinetics and improved fidelity of a novel class of 3'-OH unblocked reversible terminators. Nucleic Acids Res 2012; 40:7404-15. [PMID: 22570423 PMCID: PMC3424534 DOI: 10.1093/nar/gks330] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent developments of unique nucleotide probes have expanded our understanding of DNA polymerase function, providing many benefits to techniques involving next-generation sequencing (NGS) technologies. The cyclic reversible termination (CRT) method depends on efficient base-selective incorporation of reversible terminators by DNA polymerases. Most terminators are designed with 3′-O-blocking groups but are incorporated with low efficiency and fidelity. We have developed a novel class of 3′-OH unblocked nucleotides, called Lightning Terminators™, which have a terminating 2-nitrobenzyl moiety attached to hydroxymethylated nucleobases. A key structural feature of this photocleavable group displays a ‘molecular tuning’ effect with respect to single-base termination and improved nucleotide fidelity. Using Therminator™ DNA polymerase, we demonstrate that these 3′-OH unblocked terminators exhibit superior enzymatic performance compared to two other reversible terminators, 3′-O-amino-TTP and 3′-O-azidomethyl-TTP. Lightning Terminators™ show maximum incorporation rates (kpol) that range from 35 to 45 nt/s, comparable to the fastest NGS chemistries, yet with catalytic efficiencies (kpol/KD) comparable to natural nucleotides. Pre-steady-state kinetic studies of thymidine analogs revealed that the major determinant for improved nucleotide selectivity is a significant reduction in kpol by >1000-fold over TTP misincorporation. These studies highlight the importance of structure–function relationships of modified nucleotides in dictating polymerase performance.
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20
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Arana ME, Potapova O, Kunkel TA, Joyce CM. Kinetic analysis of the unique error signature of human DNA polymerase ν. Biochemistry 2011; 50:10126-35. [PMID: 22008035 DOI: 10.1021/bi201197p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The fidelity of DNA synthesis by A-family DNA polymerases ranges from very accurate for bacterial, bacteriophage, and mitochondrial family members to very low for certain eukaryotic homologues. The latter include DNA polymerase ν (Pol ν) which, among all A-family polymerases, is uniquely prone to misincorporating dTTP opposite template G in a highly sequence-dependent manner. Here we present a kinetic analysis of this unusual error specificity, in four different sequence contexts and in comparison to Pol ν's more accurate A-family homologue, the Klenow fragment of Escherichia coli DNA polymerase I. The kinetic data strongly correlate with rates of stable misincorporation during gap-filling DNA synthesis. The lower fidelity of Pol ν compared to that of Klenow fragment can be attributed primarily to a much lower catalytic efficiency for correct dNTP incorporation, whereas both enzymes have similar kinetic parameters for G-dTTP misinsertion. The major contributor to sequence-dependent differences in Pol ν error rates is the reaction rate, k(pol). In the sequence context where fidelity is highest, k(pol) for correct G-dCTP incorporation by Pol ν is ~15-fold faster than k(pol) for G-dTTP misinsertion. However, in sequence contexts where the error rate is higher, k(pol) is the same for both correct and mismatched dNTPs, implying that the transition state does not provide additional discrimination against misinsertion. The results suggest that Pol ν may be fine-tuned to function when high enzyme activity is not a priority and may even be disadvantageous and that the relaxed active-site specificity toward the G-dTTP mispair may be associated with its cellular function(s).
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Affiliation(s)
- Mercedes E Arana
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA
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21
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Yoshimine H, Kojima T, Furusawa H, Okahata Y. Small Mass-Change Detectable Quartz Crystal Microbalance and Its Application to Enzymatic One-Base Elongation on DNA. Anal Chem 2011; 83:8741-7. [DOI: 10.1021/ac202224d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroshi Yoshimine
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Taisuke Kojima
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Furusawa
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
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22
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Kasiviswanathan R, Copeland WC. Ribonucleotide discrimination and reverse transcription by the human mitochondrial DNA polymerase. J Biol Chem 2011; 286:31490-500. [PMID: 21778232 DOI: 10.1074/jbc.m111.252460] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
During DNA synthesis, DNA polymerases must select against ribonucleotides, present at much higher levels compared with deoxyribonucleotides. Most DNA polymerases are equipped to exclude ribonucleotides from their active site through a bulky side chain residue that can sterically block the 2'-hydroxyl group of the ribose ring. However, many nuclear replicative and repair DNA polymerases incorporate ribonucleotides into DNA, suggesting that the exclusion mechanism is not perfect. In this study, we show that the human mitochondrial DNA polymerase γ discriminates ribonucleotides efficiently but differentially based on the base identity. Whereas UTP is discriminated by 77,000-fold compared with dTTP, the discrimination drops to 1,100-fold for GTP versus dGTP. In addition, the efficiency of the enzyme was reduced 3-14-fold, depending on the identity of the incoming nucleotide, when it extended from a primer containing a 3'-terminal ribonucleotide. DNA polymerase γ is also proficient in performing single-nucleotide reverse transcription reactions from both DNA and RNA primer terminus, although its bypass efficiency is significantly diminished with increasing stretches of ribonucleotides in template DNA. Furthermore, we show that the E895A mutant enzyme is compromised in its ability to discriminate ribonucleotides, mainly due to its defects in deoxyribonucleoside triphosphate binding, and is also a poor reverse transcriptase. The potential biochemical defects of a patient harboring a disease mutation in the same amino acid (E895G) are discussed.
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Affiliation(s)
- Rajesh Kasiviswanathan
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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23
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Kennedy EM, Daddacha W, Slater R, Gavegnano C, Fromentin E, Schinazi RF, Kim B. Abundant non-canonical dUTP found in primary human macrophages drives its frequent incorporation by HIV-1 reverse transcriptase. J Biol Chem 2011; 286:25047-55. [PMID: 21454906 PMCID: PMC3137078 DOI: 10.1074/jbc.m111.234047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 03/29/2011] [Indexed: 01/21/2023] Open
Abstract
Terminally differentiated/non-dividing macrophages contain extremely low cellular dNTP concentrations (20-40 nm), compared with activated CD4(+) T cells (2-5 μm). However, our LC-MS/MS study revealed that the non-canonical dUTP concentration (2.9 μm) is ∼60 times higher than TTP in macrophages, whereas the concentrations of dUTP and TTP in dividing human primary lymphocytes are very similar. Specifically, we evaluated the contribution of HIV-1 reverse transcriptase to proviral DNA uracilation under the physiological conditions found in HIV-1 target cells. Indeed, biochemical simulation of HIV-1 reverse transcription demonstrates that HIV-1 RT efficiently incorporates dUTP in the macrophage nucleotide pools but not in the T cell nucleotide pools. Measurement of both pre-steady state and steady state kinetic parameters of dUTP incorporation reveals minimal selectivity of HIV-1 RT for TTP over dUTP, implying that the cellular dUTP/TTP ratio determines the frequency of HIV-1 RT-mediated dUTP incorporation. The RT of another lentivirus, simian immunodeficiency virus, also displays efficient dUTP incorporation in the dNTP/dUTP pools found in macrophages but not in T cells. Finally, 2',3'-dideoxyuridine was inhibitory to HIV-1 proviral DNA synthesis in macrophages but not in T cells. The data presented demonstrates that the non-canonical dUTP was abundant relative to TTP, and efficiently incorporated during HIV-1 reverse transcription, particularly in non-dividing macrophages.
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Affiliation(s)
- Edward M. Kennedy
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Waaqo Daddacha
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Rebecca Slater
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Christina Gavegnano
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Emilie Fromentin
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Raymond F. Schinazi
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Baek Kim
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
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24
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Wu EY, Beese LS. The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J Biol Chem 2011; 286:19758-67. [PMID: 21454515 DOI: 10.1074/jbc.m110.191130] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established "open" and "closed" states. In this "ajar" conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.
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Affiliation(s)
- Eugene Y Wu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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25
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Olasagasti F, Lieberman KR, Benner S, Cherf GM, Dahl JM, Deamer DW, Akeson M. Replication of individual DNA molecules under electronic control using a protein nanopore. NATURE NANOTECHNOLOGY 2010; 5:798-806. [PMID: 20871614 PMCID: PMC3711841 DOI: 10.1038/nnano.2010.177] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 08/04/2010] [Indexed: 05/20/2023]
Abstract
Nanopores can be used to analyse DNA by monitoring ion currents as individual strands are captured and driven through the pore in single file by an applied voltage. Here, we show that serial replication of individual DNA templates can be achieved by DNA polymerases held at the α-haemolysin nanopore orifice. Replication is blocked in the bulk phase, and is initiated only after the DNA is captured by the nanopore. We used this method, in concert with active voltage control, to observe DNA replication catalysed by bacteriophage T7 DNA polymerase (T7DNAP) and by the Klenow fragment of DNA polymerase I (KF). T7DNAP advanced on a DNA template against an 80-mV load applied across the nanopore, and single nucleotide additions were measured on the millisecond timescale for hundreds of individual DNA molecules in series. Replication by KF was not observed when this enzyme was held on top of the nanopore orifice at an applied potential of 80 mV. Sequential nucleotide additions by KF were observed upon applying controlled voltage reversals.
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Affiliation(s)
- Felix Olasagasti
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - Kate R. Lieberman
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - Seico Benner
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - Gerald M. Cherf
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - Joseph M. Dahl
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - David W. Deamer
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
| | - Mark Akeson
- Department of Biomolecular Engineering Baskin School of Engineering MS SOE2 University of California Santa Cruz, CA 95064
- Correspondence and requests for materials should be addressed to [MA].
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A nuclear family A DNA polymerase from Entamoeba histolytica bypasses thymine glycol. PLoS Negl Trop Dis 2010; 4:e786. [PMID: 20706627 PMCID: PMC2919377 DOI: 10.1371/journal.pntd.0000786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 07/12/2010] [Indexed: 01/26/2023] Open
Abstract
Background Eukaryotic family A DNA polymerases are involved in mitochondrial DNA replication or translesion DNA synthesis. Here, we present evidence that the sole family A DNA polymerase from the parasite protozoan E. histolytica (EhDNApolA) localizes to the nucleus and that its biochemical properties indicate that this DNA polymerase may be involved in translesion DNA synthesis. Methodology and Results EhDNApolA is the sole family A DNA polymerase in E. histolytica. An in silico analysis places family A DNA polymerases from the genus Entamoeba in a separate branch of a family A DNA polymerases phylogenetic tree. Biochemical studies of a purified recombinant EhDNApolA demonstrated that this polymerase is active in primer elongation, is poorly processive, displays moderate strand displacement, and does not contain 3′–5′ exonuclease or editing activity. Importantly, EhDNApolA bypasses thymine glycol lesions with high fidelity, and confocal microscopy demonstrates that this polymerase is translocated into the nucleus. These data suggest a putative role of EhDNApolA in translesion DNA synthesis in E. histolytica. Conclusion This is the first report of the biochemical characterization of a DNA polymerase from E. histolytica. EhDNApolA is a family A DNA polymerase that is grouped into a new subfamily of DNA polymerases with translesion DNA synthesis capabilities similar to DNA polymerases from subfamily ν. Genotoxic agents like ultraviolet radiation, alkylating compounds and reactive oxidative species have the potential to originate DNA lesions that are not bypassed by replicative DNA polymerases. Eukaryotic organisms contain a specialized subset of DNA polymerases capable of translesion DNA synthesis. These DNA polymerases belong to DNA polymerases from families A, B, and Y. In this work, we characterized the sole family A DNA polymerase of the parasitic protozoa E. histolytica, EhDNApolA. The biochemical characterization of recombinant EhDNApolA indicates that this protein is an active DNA polymerase able to primer extension and moderate strand displacement. The ability of EhDNApolA to faithfully incorporate dATP opposite thymine glycol, and its nuclear localization indicates that this polymerase may have a role in translesion DNA synthesis. E. histolytica is exposed to oxidative stress during tissue invasion by phagocytes. Understanding DNA metabolism in E. histolytica is important because this parasite has shaped some metabolic pathways by horizontal gene transfer, infects approximately 50 million people annually, and is the second leading cause of death among protozoan diseases.
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Cavanaugh NA, Beard WA, Wilson SH. DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. J Biol Chem 2010; 285:24457-65. [PMID: 20519499 DOI: 10.1074/jbc.m110.132407] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA polymerases must select nucleotides that preserve Watson-Crick base pairing rules and choose substrates with the correct (deoxyribose) sugar. Sugar discrimination represents a great challenge because ribonucleotide triphosphates are present at much higher cellular concentrations than their deoxy-counterparts. Although DNA polymerases discriminate against ribonucleotides, many therapeutic nucleotide analogs that target polymerases have sugar modifications, and their efficacy depends on their ability to be incorporated into DNA. Here, we investigate the ability of DNA polymerase beta to utilize nucleotides with modified sugars. DNA polymerase beta readily inserts dideoxynucleoside triphosphates but inserts ribonucleotides nearly 4 orders of magnitude less efficiently than natural deoxynucleotides. The efficiency of ribonucleotide insertion is similar to that reported for other DNA polymerases. The poor polymerase-dependent insertion represents a key step in discriminating against ribonucleotides because, once inserted, a ribonucleotide is easily extended. Likewise, a templating ribonucleotide has little effect on insertion efficiency or fidelity. In contrast to insertion and extension of a ribonucleotide, the chemotherapeutic drug arabinofuranosylcytosine triphosphate is efficiently inserted but poorly extended. These results suggest that the sugar pucker at the primer terminus plays a crucial role in DNA synthesis; a 3'-endo sugar pucker facilitates nucleotide insertion, whereas a 2'-endo conformation inhibits insertion.
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Affiliation(s)
- Nisha A Cavanaugh
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
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28
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Bailey CM, Anderson KS. A mechanistic view of human mitochondrial DNA polymerase gamma: providing insight into drug toxicity and mitochondrial disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1213-22. [PMID: 20083238 DOI: 10.1016/j.bbapap.2010.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 12/30/2009] [Accepted: 01/04/2010] [Indexed: 02/08/2023]
Abstract
Mitochondrial DNA polymerase gamma (Pol gamma) is the sole polymerase responsible for replication of the mitochondrial genome. The study of human Pol gamma is of key importance to clinically relevant issues such as nucleoside analog toxicity and mitochondrial disorders such as progressive external ophthalmoplegia. The development of a recombinant form of the human Pol gamma holoenzyme provided an essential tool in understanding the mechanism of these clinically relevant phenomena using kinetic methodologies. This review will provide a brief history on the discovery and characterization of human mitochondrial DNA polymerase gamma, focusing on kinetic analyses of the polymerase and mechanistic data illustrating structure-function relationships to explain drug toxicity and mitochondrial disease.
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Affiliation(s)
- Christopher M Bailey
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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29
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Johnson KA. The kinetic and chemical mechanism of high-fidelity DNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1041-8. [PMID: 20079883 DOI: 10.1016/j.bbapap.2010.01.006] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 12/15/2009] [Accepted: 01/04/2010] [Indexed: 10/19/2022]
Abstract
This review summarizes our current understanding of the structural, kinetic and thermodynamic basis for the extraordinary accuracy of high-fidelity DNA polymerases. High-fidelity DNA polymerases, such as the enzyme responsible for the replication of bacteriophage T7 DNA, discriminate against similar substrates with an accuracy that approaches one error in a million base pairs while copying DNA at a rate of approximately 300 base pairs per second. When the polymerase does make an error, it stalls, giving time for the slower proofreading exonuclease to remove the mismatch so that the overall error frequency approaches one in a billion. Structural analysis reveals a large change in conformation after nucleotide binding from an open to a closed state. Kinetic analysis has shown that the substrate-induced structural change plays a key role in the discrimination between correct and incorrect base pairs by governing whether a nucleotide will be retained and incorporated or rapidly released.
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Affiliation(s)
- Kenneth A Johnson
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, Austin, TX 78712, USA.
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30
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Williams AA, Darwanto A, Theruvathu JA, Burdzy A, Neidigh JW, Sowers LC. Impact of sugar pucker on base pair and mispair stability. Biochemistry 2009; 48:11994-2004. [PMID: 19899814 PMCID: PMC2814217 DOI: 10.1021/bi9014133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The selection of nucleoside triphosphates by a polymerase is controlled by several energetic and structural features, including base pairing geometry as well as sugar structure and conformation. Whereas base pairing has been considered exhaustively, substantially less is known about the role of sugar modifications for both nucleotide incorporation and primer extension. In this study, we synthesized oligonucleotides containing 2'-fluoro-modified nucleosides with constrained sugar pucker in an internucleotide position and, for the first time, at a primer 3'-end. The thermodynamic stability of these duplexes was examined. The nucleoside 2'-deoxy-2'-fluoroarabinofuranosyluracil [U(2'F(ara))] favors the 2'-endo conformation (DNA-like), while 2'-deoxy-2'-fluororibofuranosyluracil [U(2'F(ribo))] favors the 3'-endo conformation (RNA-like). Oligonucleotides containing U(2'F(ara)) have slightly higher melting temperatures (T(m)) than those containing U(2'F(ribo)) when located in internucleotide positions or at the 3'-end and when correctly paired with adenine or mispaired with guanine. However, both modifications decrease the magnitude of DeltaH degrees and DeltaS degrees for duplex formation in all sequence contexts. In examining the thermodynamic properties for this set of oligonucleotides, we find entropy-enthalpy compensation is apparent. Our thermodynamic findings led to a series of experiments with DNA ligase that reveal, contrary to expectation based upon observed T(m) values, that the duplex containing the U(2'F(ribo)) analogue is more easily ligated. The 2'-fluoro-2'-deoxynucleosides examined here are valuable probes of the impact of sugar constraint and are also members of an important class of antitumor and antiviral agents. The data reported here may facilitate an understanding of the biological properties of these agents, as well as the contribution of sugar conformation to replication fidelity.
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Affiliation(s)
- Adides A. Williams
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Agus Darwanto
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jacob A. Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Artur Burdzy
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jonathan W. Neidigh
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Lawrence C. Sowers
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
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31
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Kennedy EM, Hergott C, Dewhurst S, Kim B. The mechanistic architecture of thermostable Pyrococcus furiosus family B DNA polymerase motif A and its interaction with the dNTP substrate. Biochemistry 2009; 48:11161-8. [PMID: 19817489 DOI: 10.1021/bi9010122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thermostable DNA polymerases isolated from archaeal organisms have not been completely characterized kinetically and require further study if we are to understand both their dNTP binding mechanism and their role within the organism. Here, we demonstrate that the thermostable family B DNA polymerase from Pyrococcus furiosus (Pfu Pol) contains sensitive determinants of both dNTP binding and replicational fidelity within the highly conserved motif A. Site-directed mutagenesis of the motif A SYLP region revealed that small shifts in side chain volume result in significant changes in the dNTP binding affinity, steady state kinetics, and fidelity of the enzyme. Mutants of Y410 show high fidelity in both misincorporation assays and forward mutation assays, but display a substantially higher K(m) than the wild type. In contrast, mutations of upstream residue L409 result in a drastically reduced affinity for the correct dNTP, a much higher efficiency of both misincorporation and mismatch extension, and substantially lower fidelity as demonstrated by a PCR-based forward mutation assay. The A408S mutant, however, displayed a significant increase in both dNTP binding affinity and fidelity. In summary, these data show that modulation of motif A can greatly shift both the steady and pre-steady state kinetics of the enzyme as well as the fidelity of Pfu Pol.
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Affiliation(s)
- Edward M Kennedy
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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32
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Single molecule measurement of the "speed limit" of DNA polymerase. Proc Natl Acad Sci U S A 2009; 106:20294-9. [PMID: 19906998 DOI: 10.1073/pnas.0907404106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although DNA replication is often imagined as a regular and continuous process, the DNA polymerase enzyme is a complicated machine and can pause upon encountering physical and chemical barriers. We used single molecule measurements to make a detailed characterization of this behavior as a function of the template's secondary structure and the sequence context. Strand displacement replication through a DNA hairpin by single DNA polymerase molecules was measured in real time with near single base resolution and physiological concentrations of nucleotides. These data enabled the measurement of the intrinsic "speed limit" of DNA polymerase by separating the burst synthesis rate from pausing events. The strand displacement burst synthesis rate for Escherichia coli DNA Polymerase I (KF) was found to be an order of magnitude faster than the reported bulk strand displacement rate, a discrepancy that can be accounted for by to sequence specific pausing. The ability to follow trajectories of single molecules revealed that the burst synthesis rate is also highly stochastic and varies up to 50-fold from molecule to molecule. Surprisingly, our results allow a unified explanation of strand displacement and single strand primer extension synthesis rates.
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33
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Loakes D, Gallego J, Pinheiro VB, Kool ET, Holliger P. Evolving a polymerase for hydrophobic base analogues. J Am Chem Soc 2009; 131:14827-37. [PMID: 19778048 PMCID: PMC2762193 DOI: 10.1021/ja9039696] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.
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Affiliation(s)
- David Loakes
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - José Gallego
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Vitor B. Pinheiro
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Eric T. Kool
- Stanford University, Department of Chemistry, Stanford, CA 94305, USA
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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34
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Loakes D, Holliger P. Polymerase engineering: towards the encoded synthesis of unnatural biopolymers. Chem Commun (Camb) 2009:4619-31. [PMID: 19641798 DOI: 10.1039/b903307f] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA is not only a repository of genetic information for life, it is also a unique polymer with remarkable properties: it associates according to well-defined rules, it can be assembled into diverse nanostructures of defined geometry, it can be evolved to bind ligands and catalyse chemical reactions and it can serve as a supramolecular scaffold to arrange chemical groups in space. However, its chemical makeup is rather uniform and the physicochemical properties of the four canonical bases only span a narrow range. Much wider chemical diversity is accessible through solid-phase synthesis but oligomers are limited to <100 nucleotides and variations in chemistry can usually not be replicated and thus are not amenable to evolution. Recent advances in nucleic acid chemistry and polymerase engineering promise to bring the synthesis, replication and ultimately evolution of nucleic acid polymers with greatly expanded chemical diversity within our reach.
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Affiliation(s)
- David Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, Cambridgeshire, UKCB2 0QH
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35
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Gyarfas B, Olasagasti F, Benner S, Garalde D, Lieberman KR, Akeson M. Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution. ACS NANO 2009; 3:1457-1466. [PMID: 19489560 DOI: 10.1021/nn900303g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA polymerases are molecular motors that catalyze template-dependent DNA replication, advancing along template DNA by one nucleotide with each catalytic cycle. Nanopore-based measurements have emerged as a single molecule technique for the study of these enzymes. Using the alpha-hemolysin nanopore, we determined the position of DNA templates bearing inserts of abasic (1',2'-dideoxy) residues, bound to the Klenow fragment of Escherichia coli DNA polymerase I (KF) or to bacteriophage T7 DNA polymerase. Hundreds of individual polymerase complexes were analyzed at 5 A precision within minutes. We generated a map of current amplitudes for DNA-KF-deoxynucleoside triphosphate (dNTP) ternary complexes, using a series of templates bearing blocks of three abasic residues that were displaced by approximately 5 A in the nanopore lumen. Plotted as a function of the distance of the abasic insert from n = 0 in the active site of the enzyme held atop the pore, this map has a single peak. The map is similar when the primer length, the DNA sequences flanking the abasic insert, and the DNA sequences in the vicinity of the KF active site are varied. Primer extension catalyzed by KF using a three abasic template in the presence of a mixture of dNTPs and 2',3'-dideoxynucleoside triphosphates resulted in a ladder of ternary complexes with discrete amplitudes that closely corresponded to this map. An ionic current map measured in the presence of 0.15 M KCl mirrored the map obtained with 0.3 M KCl, permitting experiments with a broader range of mesophilic DNA and RNA processing enzymes. We used the abasic templates to show that capture of complexes with the KF homologue, T7 DNA polymerase, yields an amplitude map nearly indistinguishable from the KF map.
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Affiliation(s)
- Brett Gyarfas
- Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
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36
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A new DNA polymerase I from Geobacillus caldoxylosilyticus TK4: cloning, characterization, and mutational analysis of two aromatic residues. Appl Microbiol Biotechnol 2009; 84:105-17. [PMID: 19365630 DOI: 10.1007/s00253-009-1962-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 03/11/2009] [Accepted: 03/11/2009] [Indexed: 10/20/2022]
Abstract
DNA polymerase I gene was cloned and sequenced from the thermophilic bacterium Geobacillus caldoxylosilyticus TK4. The gene is 2,634 bp long and encodes a protein of 878 amino acids in length. The enzyme has a molecular mass of 99 kDa and shows sequence homology with DNA polymerase I from Bacillus species (89% identity). The gene was overexpressed in Escherichia coli and the purified enzyme was biochemically characterized. It has all of the primary structural elements necessary for DNA polymerase and 5' --> 3' exonuclease activity, but lacks the motifs required for 3' --> 5' exonuclease activity. 5' nuclease and 3' --> 5' exonuclease assays confirmed that Gca polymerase I has a double-stranded DNA-dependent 5' --> 3' nuclease activity but no 3' --> 5' exonuclease activity. Its specific activity was observed to be 495,000 U/mg protein, and K (D) (DNA) , K (D) (dNTP) , and K (pol) were found to be 0.19 nM, 22.64 microM, and 24.99 nucleotides(-1), respectively. The enzyme showed significant reverse-transcriptase activity (RT) with Mn(2+), but very little RT activity with Mg(2+). Its error rate was found to be 2.5 x 10(-5) which is comparable to that of the previously reported error rate for the E. coli DNA polymerase I. Two aromatic residues required for dideoxyribonucleotide triphosphate sensitivity (F712Y) and strand displacement activity (Y721F) were identified.
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37
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R964C mutation of DNA polymerase gamma imparts increased stavudine toxicity by decreasing nucleoside analog discrimination and impairing polymerase activity. Antimicrob Agents Chemother 2009; 53:2610-2. [PMID: 19364868 DOI: 10.1128/aac.01659-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The R964C mutation of human DNA polymerase gamma was recently linked to stavudine (d4T)-mediated mitochondrial toxicity. We utilized pre-steady-state kinetics to determine the effect of this mutation on incorporation of natural substrate dTTP and the active metabolite of d4T (d4TTP). The R964C polymerase gamma holoenzyme demonstrated a 33% decrease in dTTP incorporation efficiency and a threefold-lower d4TTP discrimination relative to that of the wild-type polymerase gamma, providing a mechanistic basis for genetic predisposition to nucleoside reverse transcriptase inhibitor toxicity.
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38
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Abstract
The lysogenic bacteriophage APSE infects "Candidatus Hamiltonella defensa," a facultative endosymbiont of aphids and other sap-feeding insects. This endosymbiont has established a beneficial association with aphids, increasing survivorship following attack by parasitoid wasps. Although APSE and "Ca. Hamiltonella defensa" are effectively maternally transmitted between aphid generations, they can also be horizontally transferred among insect hosts, which results in genetically distinct "Ca. Hamiltonella defensa" strains infecting the same aphid species and sporadic distributions of both APSE and "Ca. Hamiltonella defensa" among hosts. Aphids infected only with "Ca. Hamiltonella defensa" have significantly less protection than those infected with both "Ca. Hamiltonella defensa" and APSE. This protection has been proposed to be connected to eukaryote-targeted toxins previously discovered in the genomes of two characterized APSE strains. In this study, we have sequenced partial genomes from seven additional APSE strains to address the evolution and extent of toxin variation in this phage. The APSE lysis region has been a hot spot for nonhomologous recombination of novel virulence cassettes. We identified four new toxins from three protein families, Shiga-like toxin, cytolethal distending toxin, and YD-repeat toxins. These recombination events have also resulted in reassortment of the downstream lysozyme and holin genes. Analysis of the conserved APSE genes flanking the variable toxin cassettes reveals a close phylogenetic association with phage sequences from two other facultative endosymbionts of insects. Thus, phage may act as a conduit for ongoing gene exchange among heritable endosymbionts.
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39
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Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A. Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc 2008; 130:10748-57. [PMID: 18627154 DOI: 10.1021/ja8028284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerase selectivity is crucial for the survival of any living species, yet varies significantly among different DNA polymerases. Errors within DNA polymerase-catalyzed DNA synthesis result from the insertion of noncanonical nucleotides and extension of misaligned DNA substrates. The substrate binding characteristics among DNA polymerases are believed to vary in properties such as shape and tightness of the binding pocket, which might account for the observed differences in fidelity. Here, we employed 4'-alkylated nucleotides and primer strands bearing 4'-alkylated nucleotides at the 3'-terminal position as steric probes to investigate differential active site properties of human DNA polymerase beta (Pol beta) and the 3'-->5'-exonuclease-deficient Klenow fragment of E. coli DNA polymerase I (KF(exo-)). Transient kinetic measurements indicate that both enzymes vary significantly in active site tightness at both positions. While small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected. Just the opposite was observed for KF(exo-). Here, incorporation of the modified nucleotides is only slightly reduced, whereas size augmentation of the 3'-terminal nucleotide in the primer reduces the catalytic efficiency by more than 7000- and 260,000-fold, respectively. NMR studies support the notion that the observed effects derive from enzyme substrate interactions rather than inherent properties of the modified substrates. These findings are consistent with the observed differential capability of the investigated DNA polymerases in fidelity such as processing misaligned DNA substrates. The results presented provide direct evidence for the involvement of varied steric effects among different DNA polymerases on their fidelity.
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Affiliation(s)
- Francesca Di Pasquale
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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40
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Kaminski PA, Dacher P, Dugué L, Pochet S. In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution. J Biol Chem 2008; 283:20053-9. [PMID: 18487606 DOI: 10.1074/jbc.m802706200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleoside 2'-deoxyribosyltransferases catalyze the transfer of 2-deoxyribose between bases and have been widely used as biocatalysts to synthesize a variety of nucleoside analogs. The genes encoding nucleoside 2'-deoxyribosyltransferase (ndt) from Lactobacillus leichmannii and Lactobacillus fermentum underwent random mutagenesis to select variants specialized for the synthesis of 2',3'-dideoxynucleosides. An Escherichia coli strain, auxotrophic for uracil and unable to use 2',3'-dideoxyuridine, cytosine, and 2',3'-dideoxycytidine as a source of uracil was constructed. Randomly mutated lactobacilli ndt libraries from two species, L. leichmannii and L. fermentum, were screened for the production of uracil with 2',3'-dideoxyuridine as a source of uracil. Several mutants suitable for the synthesis of 2',3'-dideoxynucleosides were isolated. The nucleotide sequence of the corresponding genes revealed a single mutation (G --> A transition) leading to the substitution of a small aliphatic amino acid by a nucleophilic one, A15T (L. fermentum) or G9S (L. leichmannii), respectively. We concluded that the "adaptation" of the nucleoside 2'-deoxyribosyltransferase activity to 2,3-dideoxyribosyl transfer requires an additional hydroxyl group on a key amino acid side chain of the protein to overcome the absence of such a group in the corresponding substrate. The evolved proteins also display significantly improved nucleoside 2',3'-didehydro-2',3'-dideoxyribosyltransferase activity.
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41
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Joyce CM, Potapova O, Delucia AM, Huang X, Basu VP, Grindley NDF. Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 2008; 47:6103-16. [PMID: 18473481 DOI: 10.1021/bi7021848] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have developed a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP and have used this and other fluorescence assays to place the fingers-closing step within the reaction pathway. Because the rate of fingers-closing was substantially faster than the rate of nucleotide incorporation measured in chemical quench experiments, fingers-closing cannot be the rate-limiting prechemistry step defined by earlier kinetic studies. Experiments using Ca (2+) instead of Mg (2+) as the metal cofactor suggest instead that the prechemistry step may involve a change in metal ion occupancy at the polymerase active site. The use of ribonucleotide substrates shows there is a base discriminating step that precedes fingers-closing. This earlier step, detected by 2-AP fluorescence, is promoted by complementary nucleotides (ribo- as well as deoxyribo-) but is blocked by mismatches. The complementary rNTP blocks the subsequent fingers-closing step. Thus, discrimination against rNTPs occurs during the transition from open to closed conformations, whereas selection against mismatched bases is initiated earlier in the pathway, in the open complex. Mismatched dNTPs accelerate DNA release from the polymerase, suggesting the existence of an early intermediate in which DNA binding is destabilized relative to the binary complex; this could correspond to a conformation that allows an incoming dNTP to preview the template base. The early kinetic checkpoints identified by this study provide an efficient mechanism for the rejection of mismatched bases and ribose sugars and thus enhance polymerase throughput.
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Affiliation(s)
- Catherine M Joyce
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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42
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Moriyama T, Terasawa K, Fujiwara M, Sato N. Purification and characterization of organellar DNA polymerases in the red alga Cyanidioschyzon merolae. FEBS J 2008; 275:2899-918. [PMID: 18430024 DOI: 10.1111/j.1742-4658.2008.06426.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerase gamma, a mitochondrial replication enzyme of yeasts and animals, is not present in photosynthetic eukaryotes. Recently, DNA polymerases with distant homology to bacterial DNA polymerase I were reported in rice, Arabidopsis, and tobacco, and they were localized to both plastids and mitochondria. We call them plant organellar DNA polymerases (POPs). However, POPs have never been purified in the native form from plant tissues. The unicellular thermotrophic red alga Cyanidioschyzon merolae contains two genes encoding proteins related to Escherichia coli DNA polymerase I (PolA and PolB). Phylogenetic analysis revealed that PolB is an ortholog of POPs. Nonphotosynthetic eukaryotes also have POPs, which suggested that POPs have an ancient origin before eukaryotic photosynthesis. PolA is a homolog of bacterial DNA polymerase I and is distinct from POPs. PolB was purified from the C. merolae cells by a series of column chromatography steps. Recombinant protein of PolA was also purified. Sensitivity to inhibitors of DNA synthesis was different in PolA, PolB, and E. coli DNA polymerase I. Immunoblot analysis and targeting studies with green fluorescent protein fusion proteins demonstrated that PolA was localized in the plastids, whereas PolB was present in both plastids and mitochondria. The expression of PolB was regulated by the cell cycle. The available results suggest that PolB is involved in the replication of plastids and mitochondria.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Japan
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43
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Henry AA, Romesberg FE. The evolution of DNA polymerases with novel activities. Curr Opin Biotechnol 2007; 16:370-7. [PMID: 16006114 DOI: 10.1016/j.copbio.2005.06.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 06/01/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
DNA and RNA polymerases have evolved in nature to function in specific environments with specific substrates. Thus, although the commercial availability of these enzymes has revolutionized the biotechnology industry, their applications are limited. The availability of polymerases that have unnatural properties would be of even greater utility. Towards this goal, several activity-based screening and selection approaches have been developed. Using these techniques, polymerases that synthesize a variety of different polymers, including those containing 2'-O-methyl-modified nucleotides or unnatural base pairs, have been evolved. These results suggest that polymerases tailored for any specific application could soon be available.
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Affiliation(s)
- Allison A Henry
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, USA
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44
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Lone S, Romano LJ. The role of specific amino acid residues in the active site of Escherichia coli DNA polymerase I on translesion DNA synthesis across from and past an N-2-aminofluorene adduct. Biochemistry 2007; 46:2599-607. [PMID: 17305316 DOI: 10.1021/bi061324o] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding how carcinogenic DNA adducts compromise accurate DNA replication is an important goal in cancer research. A central part of these studies is to determine the molecular mechanism that allows a DNA polymerase to incorporate a nucleotide across from and past a bulky adduct in a DNA template. To address the importance of polymerase architecture on replication across from this type of bulky DNA adduct, three active-site mutants of Escherichia coli DNA polymerase I (Klenow fragment) were used to study DNA synthesis on DNA modified with the carcinogen N-2-aminofluorene (AF). Running-start synthesis studies showed that full-length synthesis past the AF adduct was inhibited for all of the mutants, but that this inhibition was substantially less for the F762A mutant. Single nucleotide extension and steady-state kinetic experiments showed that the Y766S mutant displayed higher rates of insertion of each incorrect nucleotide relative to WT across from the dG-AF adduct. This effect was not observed for F762A or E710A mutants. Similar experiments that measured synthesis one nucleotide past the dG-AF adduct revealed an enhanced preference by the F762A mutant for dG opposite the T at this position. Finally, synthesis at the +1 and +2 positions was inhibited to a greater extent for the Y766S and E710A mutants compared with both the WT and F762A mutants. Taken together, this work is consistent with the model that polymerase geometry plays a crucial role in both the insertion and extension steps during replication across from bulky DNA lesions.
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Affiliation(s)
- Samer Lone
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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45
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Warren JJ, Forsberg LJ, Beese LS. The structural basis for the mutagenicity of O(6)-methyl-guanine lesions. Proc Natl Acad Sci U S A 2006; 103:19701-6. [PMID: 17179038 PMCID: PMC1750904 DOI: 10.1073/pnas.0609580103] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Indexed: 11/18/2022] Open
Abstract
Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine with similar efficiency opposite O(6)-methyl-guanine (O6MeG). We combined pre-steady-state kinetic analysis and a series of nine x-ray crystal structures to contrast the reaction pathways of accurate and mutagenic replication of O6MeG in a high-fidelity DNA polymerase from Bacillus stearothermophilus. Polymerases achieve substrate specificity by selecting for nucleotides with shape and hydrogen-bonding patterns that complement a canonical DNA template. Our structures reveal that both thymine and cytosine O6MeG base pairs evade proofreading by mimicking the essential molecular features of canonical substrates. The steric mimicry depends on stabilization of a rare cytosine tautomer in C.O6MeG-polymerase complexes. An unusual electrostatic interaction between O-methyl protons and a thymine carbonyl oxygen helps stabilize T.O6MeG pairs bound to DNA polymerase. Because DNA methylators constitute an important class of chemotherapeutic agents, the molecular mechanisms of replication of these DNA lesions are important for our understanding of both the genesis and treatment of cancer.
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Affiliation(s)
- Joshua J. Warren
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
| | - Lawrence J. Forsberg
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
| | - Lorena S. Beese
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
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46
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Ong JL, Loakes D, Jaroslawski S, Too K, Holliger P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J Mol Biol 2006; 361:537-50. [PMID: 16859707 DOI: 10.1016/j.jmb.2006.06.050] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 06/13/2006] [Accepted: 06/21/2006] [Indexed: 11/19/2022]
Abstract
DNA polymerases enable key technologies in modern biology but for many applications, native polymerases are limited by their stringent substrate recognition. Here we describe short-patch compartmentalized self-replication (spCSR), a novel strategy to expand the substrate spectrum of polymerases in a targeted way. spCSR is based on the previously described CSR, but unlike CSR only a short region (a "patch") of the gene under investigation is diversified and replicated. This allows the selection of polymerases under conditions where catalytic activity and processivity are compromised to the extent that full self-replication is inefficient. We targeted two specific motifs involved in substrate recognition in the active site of DNA polymerase I from Thermus aquaticus (Taq) and selected for incorporation of both ribonucleotide- (NTP) and deoxyribonucleotide-triphosphates (dNTPs) using spCSR. This allowed the isolation of multiple variants of Taq with apparent dual substrate specificity. They were able to synthesize RNA, while still retaining essentially wild-type (wt) DNA polymerase activity as judged by PCR. One such mutant (AA40: E602V, A608V, I614M, E615G) was able to incorporate both NTPs and dNTPs with the same catalytic efficiency as the wt enzyme incorporates dNTPs. AA40 allowed the generation of mixed RNA-DNA amplification products in PCR demonstrating DNA polymerase, RNA polymerase as well as reverse transcriptase activity within the same polypeptide. Furthermore, AA40 displayed an expanded substrate spectrum towards other 2'-substituted nucleotides and was able to synthesize nucleic acid polymers in which each base bore a different 2'-substituent. Our results suggest that spCSR will be a powerful strategy for the generation of polymerases with altered substrate specificity for applications in nano- and biotechnology and in the enzymatic synthesis of antisense and RNAi probes.
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Affiliation(s)
- Jennifer L Ong
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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47
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Smith RA, Anderson DJ, Preston BD. Hypersusceptibility to substrate analogs conferred by mutations in human immunodeficiency virus type 1 reverse transcriptase. J Virol 2006; 80:7169-78. [PMID: 16809322 PMCID: PMC1489025 DOI: 10.1128/jvi.00322-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 04/29/2006] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) contains four structural motifs (A, B, C, and D) that are conserved in polymerases from diverse organisms. Motif B interacts with the incoming nucleotide, the template strand, and key active-site residues from other motifs, suggesting that motif B is an important determinant of substrate specificity. To examine the functional role of this region, we performed "random scanning mutagenesis" of 11 motif B residues and screened replication-competent mutants for altered substrate analog sensitivity in culture. Single amino acid replacements throughout the targeted region conferred resistance to lamivudine and/or hypersusceptibility to zidovudine (AZT). Substitutions at residue Q151 increased the sensitivity of HIV-1 to multiple nucleoside analogs, and a subset of these Q151 variants was also hypersusceptible to the pyrophosphate analog phosphonoformic acid (PFA). Other AZT-hypersusceptible mutants were resistant to PFA and are therefore phenotypically similar to PFA-resistant variants selected in vitro and in infected patients. Collectively, these data show that specific amino acid replacements in motif B confer broad-spectrum hypersusceptibility to substrate analog inhibitors. Our results suggest that motif B influences RT-deoxynucleoside triphosphate interactions at multiple steps in the catalytic cycle of polymerization.
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Affiliation(s)
- Robert A Smith
- Department of Pathology, University of Washington, K-084 HSB, Box 357705, 1959 NE Pacific St., Seattle, 98195, USA.
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48
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Potapova O, Chan C, DeLucia AM, Helquist SA, Kool ET, Grindley NDF, Joyce CM. DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics. Biochemistry 2006; 45:890-8. [PMID: 16411765 PMCID: PMC2567902 DOI: 10.1021/bi051792i] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen-bonding ability in the nascent pair, the efficiency (k(pol)/Kd) of the polymerase reaction is decreased by 30-fold, affecting the ground state (Kd) and transition state (k(pol)) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen-bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most of the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer-terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen-bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. In contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions and more dependent upon hydrogen bonding between base-paired partners.
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Affiliation(s)
- Olga Potapova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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49
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Mauger F, Jaunay O, Chamblain V, Reichert F, Bauer K, Gut IG, Gelfand DH. SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry. Nucleic Acids Res 2006; 34:e18. [PMID: 16473841 PMCID: PMC1369287 DOI: 10.1093/nar/gnj021] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.
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Affiliation(s)
| | | | | | - Fred Reichert
- Roche Molecular Systems Inc.1145 Atlantic Avenue, Alameda, CA 94501, USA
| | - Keith Bauer
- Roche Molecular Systems Inc.1145 Atlantic Avenue, Alameda, CA 94501, USA
| | - Ivo G. Gut
- To whom correspondence should be addressed. Tel: +33 160 87 84 00; Fax: +33 160 87 83 83;
| | - David H. Gelfand
- Roche Molecular Systems Inc.1145 Atlantic Avenue, Alameda, CA 94501, USA
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50
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Jamburuthugoda VK, Guo D, Wedekind JE, Kim B. Kinetic evidence for interaction of human immunodeficiency virus type 1 reverse transcriptase with the 3'-OH of the incoming dTTP substrate. Biochemistry 2005; 44:10635-43. [PMID: 16060672 DOI: 10.1021/bi050611+] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two previously identified human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) mutants, Q151N and V148I, are known to have reduced dNTP binding affinity but possess wild-type chemical catalysis rates. Structural modeling based on the crystal structure of the HIV-1 RT ternary complex with dTTP proposes that Q151N loses the interaction with the 3'-OH of the incoming dTTP and that V148I disrupts positioning of Q151 for this interaction. On the basis of this, we predicted that while wild-type (WT) HIV-1 RT would have decreased binding affinity to dTTP analogues lacking 3'-OH, compared to dTTP, the Q151N and V148I RT mutants should have decreased but similar affinity to both dTTP and dTTP analogues. Pre-steady-state kinetics on WT RT showed 14- and 53-fold higher K(d) values for the 3'-OH lacking ddTTP and acyTTP, compared to dTTP. In contrast, the Q151N and V148I mutants, which were predicted to have lost H-bonding interaction with the 3'-OH of dTTP, showed higher but similar K(d) values for dTTP, ddTTP, and acyTTP. Interestingly, the Q151N and V148I RTs bound to AZTTP approximately 12 and 18 times more tightly than to dTTP, respectively. Our structure modeling suggests that these RT mutants can interact with the azido moiety of AZTTP, which is 1.4 A longer than the 3'-OH of dTTP. The kinetic data presented in this report demonstrate the functional role of the Q151 residue in HIV-1 RT interaction with dTTP and its analogues containing chemical modifications at the 3'-C of the sugar moiety.
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Affiliation(s)
- Varuni K Jamburuthugoda
- Department of Biochemistry and Biophysics, University of Rochester, 601 Elmwood Avenue, Box 672, Rochester, New York 14642, USA
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