1
|
Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
Collapse
|
2
|
Yeom T, Lee J, Lee S, Kang S, Kim KR, Han B, Lee HS, Jo K. Mass spectrometric investigation of the role of the linking polypeptide chain in DNA polymerase I. Analyst 2015; 139:2432-9. [PMID: 24695614 DOI: 10.1039/c4an00107a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerase I offers great promise for a wide range of biotechnological applications due to its capability to add labeled nucleotides into double-stranded large DNA molecules by using both polymerase and nuclease domains. Accordingly, it is crucially important to thoroughly characterize this enzyme for further developments. Although the enzyme has been thus far characterized using mainly traditional analytical instruments, here we utilized an advanced and convenient means of mass spectrometry to elucidate enzymatic functions and mechanisms by measuring DNA oligomers generated by polymerase and nuclease reactions. Our analysis revealed several novel enzymatic features, including the observation that polymerase readily dissociates from the DNA molecules containing a wide single-stranded section. From this finding, we reasoned a serious situation of DNA break because polymerase domains cannot efficiently repair the wide single-stranded section, which is susceptible to DNA breaks. Furthermore, we deduced a plausible explanation for a paradoxical question as to why two domains of polymerase and 5'-nuclease are linked by a small and flexible polypeptide in polymerase I. The polypeptide link seems to prevent a 5'-nuclease from causing DNA breaks by locating a polymerase domain closely for immediate repair reaction. Here we present experimental evidence to prove our hypothesis via a set of mass spectrometric analyses as well as single DNA molecule observation and bacterial cell growth assay. Consequently, mass spectrometric analysis for DNA polymerase I provides a meaningful biological insight that a polypeptide link can be a molecular leash to control an aggressive domain in order to prevent unmanageable damages.
Collapse
Affiliation(s)
- Taeho Yeom
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.
| | | | | | | | | | | | | | | |
Collapse
|
3
|
Abstract
The native T7 DNA polymerase is a fast and highly processive enzyme that can be used for in situ detection of apoptosis and various types of DNA breaks. The technique is quick and simple, and was shown to label earlier stages of apoptosis compared to the terminal transferase technique. The in situ labeling applications of T7 DNA polymerase are presented and summarized from the DNA damage detection standpoint. The detailed protocols are provided together with the discussion of their advantages and limitations.
Collapse
Affiliation(s)
- Vladimir V Didenko
- Departments of Neurosurgery and Molecular & Cellular Biology, Baylor College of Medicine, and Michael E DeBakey VA Medical Center, Houston, TX, USA.
| |
Collapse
|
4
|
Viikov K, Väljamäe P, Sedman J. Yeast mitochondrial DNA polymerase is a highly processive single-subunit enzyme. Mitochondrion 2010; 11:119-26. [PMID: 20807588 DOI: 10.1016/j.mito.2010.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/30/2010] [Accepted: 08/20/2010] [Indexed: 10/19/2022]
Abstract
Polymerase γ is solely responsible for fast and faithful replication of the mitochondrial genome. High processivity of the polymerase γ is often achieved by association of the catalytic subunit with accessory factors that enhance its catalytic activity and/or DNA binding. Here we characterize the intrinsic catalytic activity and processivity of the recombinant catalytic subunit of yeast polymerase γ, the Mip1 protein. We demonstrate that Mip1 can efficiently synthesize DNA stretches of up to several thousand nucleotides without dissociation from the template. Furthermore, we show that Mip1 can perform DNA synthesis on double-stranded templates utilizing a strand displacement mechanism. Our observations confirm that in contrast to its homologues in other organisms, Mip1 can function as a single-subunit replicative polymerase.
Collapse
Affiliation(s)
- Katrin Viikov
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Vanemuise 46, Tartu 51014, Estonia
| | | | | |
Collapse
|
5
|
García-Villada L, Drake JW. Mutational clusters generated by non-processive polymerases: A case study using DNA polymerase betain vitro. DNA Repair (Amst) 2010; 9:871-8. [PMID: 20627824 DOI: 10.1016/j.dnarep.2010.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 05/03/2010] [Indexed: 11/28/2022]
Abstract
Available DNA mutational spectra reveal that the number of mutants with multiple mutations ("multiples") is usually greater than expected from a random distribution of mutations among mutants. These overloads imply the occurrence of non-random clusters of mutations, probably generated during episodes of low-fidelity DNA synthesis. Excess multiples have been reported not only for viruses, bacteria, and eukaryotic cells but also for the DNA polymerases of phages T4 and RB69 in vitro. In the simplest case of a purified polymerase, non-random clusters may be generated by a subfraction of phenotypic variants able to introduce more errors per cycle of DNA synthesis than the normal enzyme. According to this hypothesis, excess multiples are not expected with non-processive polymerases even if they harbor rare mutator variants. DNA polymerase beta (Pol beta) is a mammalian DNA-repair polymerase with very low processivity. Although several Pol beta mutational spectra have been described, there is conflicting evidence on whether or not excess multiples occur, with spectra based on the HSV-tk system tending to show excess multiples. Excess multiples generated by Pol beta or any of its mutants might imply that the excesses of multiples observed in numerous other systems, especially those with processive polymerases, could be artifactual. Here, the distributions of mutations generated by native and recombinant rat Pol beta and by the Pol beta(Y265C) mutator were analyzed in the M13mp2 lacZalpha system. Our results present no evidence for a significant excess of multiples over the expected numbers with any of the Pol beta enzymes tested in this system. The reported excess of Pol beta-generated multiples in the HSV-tk system may reflect a reduced efficiency of detection of base substitutions that cause weak phenotypes, which in turn may artifactually increase the frequency of multiples.
Collapse
Affiliation(s)
- Libertad García-Villada
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| | | |
Collapse
|
6
|
Abstract
Replisomes are the protein assemblies that replicate DNA. They function as molecular motors to catalyze template-mediated polymerization of nucleotides, unwinding of DNA, the synthesis of RNA primers, and the assembly of proteins on DNA. The replisome of bacteriophage T7 contains a minimum of proteins, thus facilitating its study. This review describes the molecular motors and coordination of their activities, with emphasis on the T7 replisome. Nucleotide selection, movement of the polymerase, binding of the processivity factor, unwinding of DNA, and RNA primer synthesis all require conformational changes and protein contacts. Lagging-strand synthesis is mediated via a replication loop whose formation and resolution is dictated by switches to yield Okazaki fragments of discrete size. Both strands are synthesized at identical rates, controlled by a molecular brake that halts leading-strand synthesis during primer synthesis. The helicase serves as a reservoir for polymerases that can initiate DNA synthesis at the replication fork. We comment on the differences in other systems where applicable.
Collapse
Affiliation(s)
- Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | | |
Collapse
|
7
|
Mizrahi V, Benkovic SJ. The dynamics of DNA polymerase-catalyzed reactions. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 61:437-57. [PMID: 2833078 DOI: 10.1002/9780470123072.ch8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V Mizrahi
- Department of Chemistry, Pennsylvania State University, University Park 16802
| | | |
Collapse
|
8
|
Andraos N, Tabor S, Richardson CC. The highly processive DNA polymerase of bacteriophage T5. Role of the unique N and C termini. J Biol Chem 2004; 279:50609-18. [PMID: 15377656 DOI: 10.1074/jbc.m408428200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA polymerase encoded by bacteriophage T5 has been reported previously to be processive and to catalyze extensive strand displacement synthesis. The enzyme, purified from phage-infected cells, did not require accessory proteins for these activities. Although T5 DNA polymerase shares extensive sequence homology with Escherichia coli DNA polymerase I and T7 DNA polymerase, it contains unique regions of 130 and 71 residues at its N and C termini, respectively. We cloned the gene encoding wild-type T5 DNA polymerase and characterized the overproduced protein. We also examined the effect of N- and C-terminal deletions on processivity and strand displacement synthesis. T5 DNA polymerase lacking its N-terminal 30 residues resembled the wild-type enzyme albeit with a 2-fold reduction in polymerase activity. Deletion of 24 residues at the C terminus resulted in a 30-fold reduction in polymerase activity on primed circular DNA, had dramatically reduced processivity, and was unable to carry out strand displacement synthesis. Deletion of 63 residues at the C terminus resulted in a 20,000-fold reduction in polymerase activity. The 3' to 5' double-stranded DNA exonuclease activity associated with T5 DNA polymerase was reduced by a factor of 5 in the polymerase truncated at the N terminus but was stimulated by a factor of 7 in the polymerase truncated at the C terminus. We propose a model in which the C terminus increases the affinity of the DNA for the polymerase active site, thus increasing processivity and decreasing the accessibility of the DNA to the exonuclease active site.
Collapse
Affiliation(s)
- Nathalie Andraos
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | |
Collapse
|
9
|
Bebenek A, Carver GT, Dressman HK, Kadyrov FA, Haseman JK, Petrov V, Konigsberg WH, Karam JD, Drake JW. Dissecting the fidelity of bacteriophage RB69 DNA polymerase: site-specific modulation of fidelity by polymerase accessory proteins. Genetics 2002; 162:1003-18. [PMID: 12454051 PMCID: PMC1462346 DOI: 10.1093/genetics/162.3.1003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriophage RB69 encodes a replicative B-family DNA polymerase (RB69 gp43) with an associated proofreading 3' exonuclease. Crystal structures have been determined for this enzyme with and without DNA substrates. We previously described the mutation rates and kinds of mutations produced in vivo by the wild-type (Pol(+) Exo(+)) enzyme, an exonuclease-deficient mutator variant (Pol(+) Exo(-)), mutator variants with substitutions at Tyr(567) in the polymerase active site (Pol(M) Exo(+)), and the double mutator Pol(M) Exo(-). Comparing the mutational spectra of the Pol(+) Exo(-) and Pol(+) Exo(+) enzymes revealed the patterns and efficiencies of proofreading, while Tyr(567) was identified as an important determinant of base-selection fidelity. Here, we sought to determine how well the fidelities of the same enzymes are reflected in vitro. Compared to their behavior in vivo, the three mutator polymerases exhibited modestly higher mutation rates in vitro and their mutational predilections were also somewhat different. Although the RB69 gp43 accessory proteins exerted little or no effect on total mutation rates in vitro, they strongly affected mutation rates at many specific sites, increasing some rates and decreasing others.
Collapse
Affiliation(s)
- Anna Bebenek
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Yang XM, Richardson CC. Amino acid changes in a unique sequence of bacteriophage T7 DNA polymerase alter the processivity of nucleotide polymerization. J Biol Chem 1997; 272:6599-606. [PMID: 9045689 DOI: 10.1074/jbc.272.10.6599] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
T7 gene 5 DNA polymerase forms a complex with Escherichia coli thioredoxin (its processivity factor), and a 76-amino acid sequence (residues 258-334), unique to gene 5 protein, has been implicated in this interaction. We have examined the effect of amino acid substitution(s) in this region on T7 phage growth and on the interaction of the polymerase with thioredoxin. Among the mutations in gene 5, we found that a substitution of either Glu or Ala for Lys-302 yielded a protein that could not complement T7 phage lacking gene 5 (T7Delta5) to grow on E. coli having reduced thioredoxin levels. One triple mutant (K300E,K302E,K304E) could not support the growth of T7Delta5 even in wild type cells. This altered polymerase is stimulated 4-fold less by thioredoxin than is the wild type enzyme and the polymerase-thioredoxin complex has reduced processivity. The exonuclease activity of the altered polymerase is not stimulated to the same extent as that of the wild type enzyme by thioredoxin. The observed dissociation constant of the gene 5 protein K(300,302,304)E-thioredoxin complex is 7-fold higher than that of the wild type complex. The altered polymerase also has a lower binding affinity for double-stranded DNA.
Collapse
Affiliation(s)
- X M Yang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
11
|
Bedford E, Tabor S, Richardson CC. The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Proc Natl Acad Sci U S A 1997; 94:479-84. [PMID: 9012809 PMCID: PMC19538 DOI: 10.1073/pnas.94.2.479] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Bacteriophage T7 DNA polymerase shares extensive sequence homology with Escherichia coli DNA polymerase I. However, in vivo, E. coli DNA polymerase I is involved primarily in the repair of DNA whereas T7 DNA polymerase is responsible for the replication of the viral genome. In accord with these roles, T7 DNA polymerase is highly processive while E. coli DNA polymerase I has low processivity. The high processivity of T7 DNA polymerase is achieved through tight binding to its processivity factor, E. coli thioredoxin. We have identified a unique 76-residue domain in T7 DNA polymerase responsible for this interaction. Insertion of this domain into the homologous site in E. coli DNA polymerase I results in a dramatic increase in the processivity of the chimeric DNA polymerase, a phenomenon that is dependent upon its binding to thioredoxin.
Collapse
Affiliation(s)
- E Bedford
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
12
|
Himawan JS, Richardson CC. Amino acid residues critical for the interaction between bacteriophage T7 DNA polymerase and Escherichia coli thioredoxin. J Biol Chem 1996; 271:19999-20008. [PMID: 8702717 DOI: 10.1074/jbc.271.33.19999] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Upon infection of Escherichia coli, bacteriophage T7 annexes a host protein, thioredoxin, to serve as a processivity factor for its DNA polymerase, T7 gene 5 protein. In a previous communication (Himawan, J., and Richardson, C. C. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 9774-9778), we reported that an E. coli strain encoding a Gly-74 to Asp-74 (G74D) thioredoxin mutation could not support wild-type T7 growth and that in vivo, six mutations in T7 gene 5 could individually suppress this G74D thioredoxin defect. In the present study, we report the purification and biochemical characterization of the G74D thioredoxin mutant and two suppressor gene 5 proteins, a Glu-319 to Lys-319 (E319K) mutant of gene 5 protein and an Ala-45 to Thr-45 (A45T) mutant. The suppressor E319K mutation, positioned within the DNA polymerization domain of gene 5 protein, appears to suppress the parental thioredoxin mutation by compensating for the binding defect that was caused by the G74D alteration. We suggest that the Glu-319 residue of T7 gene 5 protein and the Gly-74 residue of E. coli thioredoxin define a contact point or site of interaction between the two proteins. In contrast, the A45T mutation in gene 5 protein, located within the 3' to 5' exonuclease domain, does not suppress the G74D thioredoxin mutation by simple restoration of binding affinity. Based upon our understanding of the mechanisms of suppression, we propose a model for the T7 gene 5 protein-E. coli thioredoxin interaction.
Collapse
Affiliation(s)
- J S Himawan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
13
|
Esteban J, Soengas M, Salas M, Blanco L. 3‘–>5‘ exonuclease active site of phi 29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)31787-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
14
|
Processivity of mitochondrial DNA polymerase from Drosophila embryos. Effects of reaction conditions and enzyme purity. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74543-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
15
|
Bambara RA, Jessee CB. Properties of DNA polymerases delta and epsilon, and their roles in eukaryotic DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1088:11-24. [PMID: 1846563 DOI: 10.1016/0167-4781(91)90147-e] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R A Bambara
- Department of Biochemistry, University of Rochester, NY
| | | |
Collapse
|
16
|
Chatterjee DK, Fujimura RK, Campbell JH, Gerard GF. Cloning and overexpression of the gene encoding bacteriophage T5 DNA polymerase. Gene 1991; 97:13-9. [PMID: 1995424 DOI: 10.1016/0378-1119(91)90004-u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
T5 DNA polymerase (T5Pol), an essential enzyme for bacteriophage T5 DNA replication, is unusual because of its high processivity and strand-displacing ability. These two properties in a single polypeptide make T5Pol an ideal candidate for structural and functional analysis. Therefore, the structural gene encoding the DNA polymerase of bacteriophage T5 (T5pol) has been cloned and overexpressed in Escherichia coli. Elimination of sequences upstream from the 5' end of the T5pol by exonuclease III digestion was necessary to obtain stable clones containing a full-length structural gene. Determination of the nucleotide (nt) sequence of the region deleted during clone construction revealed the presence of a promoter sequence having extensive homology with known T5 phage 'early' promoters. By primer extension of mRNA isolated from T5 phage-infected cells, two successive G residues located 6 and 7 nt downstream from the -10 region of this promoter were identified as the initiating nt at the 5' end of T5pol mRNA. T5Pol produced in E. coli from the cloned gene under control of a tac or phage lambda pL promoter represented as much as 40% of total cell protein. The majority of the T5Pol present in extracts of E. coli was insoluble. The amount of active enzyme present was estimated to be a maximum of tenfold higher than that found in extracts of T5 phage-infected cells.
Collapse
Affiliation(s)
- D K Chatterjee
- Molecular Biology Research and Development, Bethesda Research Laboratory, Life Technologies, Inc., Gaithersburg, MD 20877
| | | | | | | |
Collapse
|
17
|
How DNA Travels between the Separate Polymerase and 3′-5′-Exonuclease Sites of DNA Polymerase I (Klenow Fragment). J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81699-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
18
|
Burgers PM. Eukaryotic DNA polymerases alpha and delta: conserved properties and interactions, from yeast to mammalian cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:235-80. [PMID: 2505329 DOI: 10.1016/s0079-6603(08)60700-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
19
|
Kaguni LS, Lehman IR. Eukaryotic DNA polymerase-primase: structure, mechanism and function. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 950:87-101. [PMID: 3289619 DOI: 10.1016/0167-4781(88)90001-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- L S Kaguni
- Department of Biochemistry, Michigan State University, East Lansing
| | | |
Collapse
|
20
|
Tabor S, Huber HE, Richardson CC. Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47718-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
21
|
Tubo RA, Martelli AM, Berezney R. Enhanced processivity of nuclear matrix bound DNA polymerase alpha from regenerating rat liver. Biochemistry 1987; 26:5710-8. [PMID: 3676280 DOI: 10.1021/bi00392a020] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Translocation of DNA during in vitro DNA synthesis on nuclear matrix bound replicational assemblies from regenerating rat liver was determined by measuring the processivity (average number of nucleotides added following one productive binding event of the polymerase to the DNA template) of nuclear matrix bound DNA polymerase alpha with poly(dT).oligo(A)10 as template primer. The matrix-bound polymerase had an average processivity (28.4 nucleotides) that was severalfold higher than the bulk nuclear DNA polymerase alpha activity extracted during nuclear matrix preparation (8.9 nucleotides). ATP at 1 mM markedly enhanced the activity and processivity of the matrix-bound polymerase but not the corresponding salt-soluble enzyme. The majority of the ATP-dependent activity and processivity enhancement was completed by 100 microM ATP and included products ranging up to full template length (1000-1200 nucleotides). Average processivity of the net ATP-stimulated polymerase activity exceeded 80 nucleotides with virtually all the DNA products greater than 50 nucleotides. Release of nuclear matrix bound DNA polymerase alpha by sonication resulted in a loss of ATP stimulation of activity and a corresponding decrease in processivity to a level similar to that of the salt-soluble polymerase (6.8 nucleotides). All nucleoside di- and triphosphates were as effective as ATP. Stimulation of both activity and processivity by the nonhydrolyzable ATP analogues adenosine 5'-O-(3-thiotriphosphate), 5'-adenylyl imidodiphosphate, and adenosine 5'-O-(1-thiotriphosphate) further suggested that the hydrolysis of ATP is not required for enhancement to occur.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- R A Tubo
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo 14260
| | | | | |
Collapse
|
22
|
Robinson N, Clark J, Wood H. Polyphosphate kinase from Propionibacterium shermanii. Demonstration that polyphosphates are primers and determination of the size of the synthesized polyphosphate. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61176-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
23
|
Pepin C, Wood H. The mechanism of utilization of polyphosphate by polyphosphate glucokinase from Propionibacterium shermanii. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61177-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
24
|
Brody RS, Doherty KG, Zimmerman PD. Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)38366-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
25
|
Loeb LA, Liu PK, Fry M. DNA polymerase-alpha: enzymology, function, fidelity, and mutagenesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1986; 33:57-110. [PMID: 3797680 DOI: 10.1016/s0079-6603(08)60020-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
26
|
DNA primase-DNA polymerase alpha from simian cells. Modulation of RNA primer synthesis by ribonucleoside triphosphates. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88965-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
27
|
Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 1985; 313:762-6. [PMID: 3883192 DOI: 10.1038/313762a0] [Citation(s) in RCA: 703] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most striking feature of the larger domain is a deep crevice of the appropriate size and shape for binding double-stranded B-DNA. A flexible subdomain may allow the enzyme to surround completely the DNA substrate, thereby allowing processive nucleotide polymerization without enzyme dissociation.
Collapse
|
28
|
Lee YH, Fang SC, Wei RD. The effects of Penicillium roqueforti toxin on the activity of rat hepatic DNA polymerases. Toxicology 1984; 33:43-57. [PMID: 6495345 DOI: 10.1016/0300-483x(84)90015-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
PR toxin, a mycotoxin from cultures of Penicillium roqueforti, inhibited the in vitro activities of rat liver DNA polymerase alpha, beta, and gamma irrespectively of the nature of template-primer used. The concentration required for 50% inhibition of DNA polymerase alpha was 5-6 X 10(-6) M, while those for DNA polymerase beta and gamma were several times higher. By using DNA polymerase beta as a model, and based on the enzyme and template-primer concentration effects and also from the kinetic analysis on PR toxin inhibition, we concluded that two action mechanisms of PR toxin inhibition on in vitro DNA synthesis are operative. Inhibition of the in vitro DNA synthesis directed by DNA template was mediated primarily through alteration of the enzyme itself, whereas in the DNA synthesis reaction directed by RNA template DNA primer, the impairment of template or primer function due to PR toxin treatment probably had occurred. The inhibition of DNA polymerase by PR toxin persisted even after exhaustive dialysis. Addition of PR toxin to an ongoing reaction also inhibited DNA synthesis. Inactivation of DNA polymerase activity of PR toxin likely involved some essential amino acid residues other than sulfhydryl groups.
Collapse
|
29
|
Abstract
Three different methods have been used to determine the rate at which an individual bacteriophage T4 DNA polymerase molecule moves when synthesizing DNA on a single-stranded DNA template chain. These methods agree in suggesting an in vitro rate for this enzyme of about 250 nucleotides per second at 37 degrees C. This rate is close to the rate at which bacteriophage T4 replication forks move in vivo (about 500 nucleotides per second). Comparison with the overall amount of DNA synthesis seen in in vitro reactions reveals that only a small fraction of the T4 DNA polymerase molecules present are synthesizing DNA at any one time. This is explicable in terms of the limited processivity of the enzyme in these reactions, along with its capacity for non-productive DNA binding to the DNA template molecules.
Collapse
|
30
|
Pritchard CG, Weaver DT, Baril EF, DePamphilis ML. DNA polymerase alpha cofactors C1C2 function as primer recognition proteins. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44570-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
31
|
Sega GA, Kelley MR, Owens JG, Carricarte VC. Caffeine pretreatment enhances the unscheduled DNA synthesis in spermatids of mice exposed to methyl methanesulfonate. Mutat Res 1983; 108:345-58. [PMID: 6682172 DOI: 10.1016/0027-5107(83)90131-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
32
|
Hübscher U. DNA polymerases in prokaryotes and eukaryotes: mode of action and biological implications. EXPERIENTIA 1983; 39:1-25. [PMID: 6297955 DOI: 10.1007/bf01960616] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
33
|
Bacteriophage T4 gene 44/62 and gene 45 polymerase accessory proteins stimulate hydrolysis of duplex DNA by T4 DNA polymerase. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33732-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
34
|
Yagura T, Kozu T, Seno T. Mouse DNA replicase. DNA polymerase associated with a novel RNA polymerase activity to synthesize initiator RNA of strict size. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33941-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
35
|
Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Chain termination and modulation by polynucleotides. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34139-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
36
|
Akiyoshi H. Conversion of dNTP to dNMP dependent on DNA synthesis in isolated Yoshida sarcoma nuclei. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 696:332-9. [PMID: 7066329 DOI: 10.1016/0167-4781(82)90065-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nuclei isolated from Yoshida sarcoma cells had activity for conversion of dGTP dependent on DNA synthesis. The ratio of nucleotide generation/generation + incorporation was 0.4 +/0- 0.1, indicating that approx. 40% of the incorporated dGMP was excised. Two lines of evidence indicated the dependence of this activity on DNA synthesis. (1) The activity was observed only in the presence of ATP, which is essential for nuclear DNA synthesis. (2) Inhibitors of DNA synthesis, such as N-ethylmaleimide, aphidicolin, spermine and KCl, also inhibited ATP- or DNA synthesis-dependent dGMP generation. Although nuclei contain nucleoside triphosphatase (N-nucleotidase), this enzyme was not involved appreciably in DNA synthesis-dependent dGMP generation. The reason for this was explained by the following findings. (a) Inhibitors did not decrease dGMP production in the complete absence of DNA synthesis. (b) Inhibitors did not inactivate N-nucleotidase to the same degree as they inhibited DNA synthesis-dependent dGMP generation. (c) Addition of ATP reduced dGMP hydrolysis catalyzed by N-nucleotidase. (d) GDP has no appreciable effect on DNA synthesis-dependent dGMP generation, but had a diluting effect on dGMP production catalyzed by N-nucleotidase. These results show that the pathway of dGMP generation in isolated nuclei was switched on addition of ATP from a N-nucleotidase-catalyzed one to a DNA polymerase-exonuclease-catalyzed one.
Collapse
|
37
|
Abstract
Captan inhibits DNA polymerases of both eukaryotic and prokaryotic sources. When polymerases were employed in assays with various nucleotides as template-primer, no specificity in the base sequence of polynucleotide was required for inhibition. Sucrose gradient centrifugation and preincubation studies showed the inhibition was caused by an irreversible alteration of the polymerase. Captan and DNA compete for the same site on the polymerase, thus DNA can serve a protective role in the elimination of captan's action. The pyrophosphate exchange activity associated with the polymerase is not inhibited by captan and the fidelity with which DNa polymerase I copies the DNA template also is not altered by captan treatment.
Collapse
|
38
|
Roth A, Nossal N, Englund P. Rapid hydrolysis of deoxynucleoside triphosphates accompanies DNA synthesis by T4 DNA polymerase and T4 accessory proteins 44/62 and 45. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68186-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
39
|
Clough W, McMahon J. Characterization of the Epstein-Barr virion-associated DNA polymerase as isolated from superinfected and drug-stimulated cells. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 656:76-85. [PMID: 6272863 DOI: 10.1016/0005-2787(81)90029-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We reported previously that Epstein-Barr (EB) virions and detergent-treated nucleocapsids co-purified with significant amounts of DNA polymerase activity that did not resemble other known host or viral polymerases. We report here that this species of DNA polymerase activity is present at early times after infection in lymphocytes abortively lytically infected (superinfected) with EB virus. However, studies with [35S]methionine labeling suggest de novo synthesis of enzyme has not occurred. Conversely, drug-stimulated lymphocytes that synthesize EB viral late proteins and virions contain this species of polymerase to the virtual exclusion of all others. This EB viral polymerase shows a marked preference for nicked and gapped double-stranded rather than primed single-stranded DNA templates. Its processiveness as measured on primed theta X174 phage DNA template is lower than that of lymphocyte beta polymerase. The data reported here are consistent with the hypothesis that the EB virion-associated DNA polymerase is synthesized at late times in the viral life cycle as are other structural proteins but it plays an important role early after viral infection. It is known that mature herpes virion DNA (including that of EB virus) is nicked and gapped and we propose that virion polymerase repairs the viral DNA at an early stage in infection before viral DNA replication begins.
Collapse
|
40
|
Studies on the mechanism of DNA polymerase alpha. Nascent chain elongation, steady state kinetics, and the initiation phase of DNA synthesis. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69081-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
41
|
Suzuki K, Miyaki M, Umeda M, Nishimura M, Ono T. Differential inactivation of DNA polymerases alpha and beta by aldehyde compounds. Biochem Biophys Res Commun 1981; 100:1626-33. [PMID: 7028034 DOI: 10.1016/0006-291x(81)90705-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
42
|
Huang C, Hearst J, Alberts B. Two types of replication proteins increase the rate at which T4 DNA polymerase traverses the helical regions in a single-stranded DNA template. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69569-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
43
|
Enzymological characterization of KB cell DNA polymerase-alpha. Regulation of template binding by nucleic acid base composition. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
44
|
Fujimura RK, Das SK, Allison DP, Roop BC. Replication of linear duplex DNA in vitro with bacteriophage T5 DNA polymerase. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1981; 26:49-62. [PMID: 7280264 DOI: 10.1016/s0079-6603(08)60394-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
45
|
Das S, Fujimura R. Mechanism of primer-template-dependent conversion of dNTP leads to dNMP by T5 DNA polymerase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(20)79678-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
46
|
Yagura T, Seno T. DNA synthesis in isolated chromatin. Nature of activities, and relationship to kinetics of DNA polymerase release from chromatin DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 608:277-86. [PMID: 7397186 DOI: 10.1016/0005-2787(80)90173-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromatin isolated from Ehrlich ascites tumor cells showed two DNA synthetic activities differing in sensitivity to N-ethylmaleimide. For studies on the nature of activities and relationship to kinetics of DNA polymerase, a new method was developed for detecting the activity of DNA polymerase released from chromatin DNA during DNA synthesis in vitro. The activity of DNA polymerase released was measured in a reaction mixture for DNA synthesis using exogenously added poly(dA-dT) as a template-primer in the presence of actinomycin D. Evidence that the DNA polymerase released was actually involved in DNA synthesis of chromatin was obtained in experiments using chromatin isolated from cells treated with various concentrations of 1-beta-D-arabinofuranosylcytosine and chromatin from adult mouse liver. The experiments showed that chromatin isolated from cells in which only small amount of DNA polymerase was engaged in DNA synthesis released a negligible amount of DNA polymerase, especially N-ethylmaleimide-sensitive polymerase. Kinetic analysis of DNA polymerase during chromatin DNA synthesis by the new method suggested that KCl at the optimal concentration (10-20 mM) for the N-ethylmaleimide-sensitive chromatin activity enhanced the binding of the N-ethylmaleimide-sensitive DNA polymerase to chromatin DNA. From the findings that addition of actinomycin D or omission of dNTPs from the preincubation mixture prevents this binding, it is suggested that the binding of DNA polymerase is followed by the DNA chain synthesis and that the DNA polymerase involved in this reaction is N-ethylmaleimide sensitive. Data on the effect of KCl on the rate of chromatin DNA synthesis and on the size of the DNA chain favor this assumption.
Collapse
|
47
|
Gregerson DS, Reid TW. Properties of the reverse transcription of synthetic and hamster retroviral RNA by avian and hamster viral polymerases. Biochem Biophys Res Commun 1980; 93:720-8. [PMID: 6155913 DOI: 10.1016/0006-291x(80)91137-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
48
|
Yagura T, Kozu T, Seno T. Partial purification and characterization of poly(dC)-dependent DNA polymerase and its stimulating factor. Biochem Biophys Res Commun 1980; 92:1289-96. [PMID: 7370036 DOI: 10.1016/0006-291x(80)90426-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
49
|
Phenylglyoxal as a template site-specific reagent for DNA and RNA polymerases. Selective inhibition of initiation. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)86120-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
50
|
|