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Abstract
I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
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Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
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2
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Lee JB, Hite RK, Hamdan SM, Xie XS, Richardson CC, van Oijen AM. DNA primase acts as a molecular brake in DNA replication. Nature 2006; 439:621-4. [PMID: 16452983 DOI: 10.1038/nature04317] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 10/13/2005] [Indexed: 11/09/2022]
Abstract
A hallmark feature of DNA replication is the coordination between the continuous polymerization of nucleotides on the leading strand and the discontinuous synthesis of DNA on the lagging strand. This synchronization requires a precisely timed series of enzymatic steps that control the synthesis of an RNA primer, the recycling of the lagging-strand DNA polymerase, and the production of an Okazaki fragment. Primases synthesize RNA primers at a rate that is orders of magnitude lower than the rate of DNA synthesis by the DNA polymerases at the fork. Furthermore, the recycling of the lagging-strand DNA polymerase from a finished Okazaki fragment to a new primer is inherently slower than the rate of nucleotide polymerization. Different models have been put forward to explain how these slow enzymatic steps can take place at the lagging strand without losing coordination with the continuous and fast leading-strand synthesis. Nonetheless, a clear picture remains elusive. Here we use single-molecule techniques to study the kinetics of a multiprotein replication complex from bacteriophage T7 and to characterize the effect of primase activity on fork progression. We observe the synthesis of primers on the lagging strand to cause transient pausing of the highly processive leading-strand synthesis. In the presence of both leading- and lagging-strand synthesis, we observe the formation and release of a replication loop on the lagging strand. Before loop formation, the primase acts as a molecular brake and transiently halts progression of the replication fork. This observation suggests a mechanism that prevents leading-strand synthesis from outpacing lagging-strand synthesis during the slow enzymatic steps on the lagging strand.
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Affiliation(s)
- Jong-Bong Lee
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, Massachusetts 02115, USA
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Chowdhury K, Tabor S, Richardson CC. A unique loop in the DNA-binding crevice of bacteriophage T7 DNA polymerase influences primer utilization. Proc Natl Acad Sci U S A 2000; 97:12469-74. [PMID: 11050188 PMCID: PMC18787 DOI: 10.1073/pnas.230448397] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional structure of bacteriophage T7 DNA polymerase reveals the presence of a loop of 4 aa (residues 401-404) within the DNA-binding groove; this loop is not present in other members of the DNA polymerase I family. A genetically altered T7 DNA polymerase, T7 polDelta401-404, lacking these residues, has been characterized biochemically. The polymerase activity of T7 polDelta401-404 on primed M13 single-stranded DNA template is one-third of the wild-type enzyme and has a 3'-to-5' exonuclease activity indistinguishable from that of wild-type T7 DNA polymerase. T7 polDelta401-404 polymerizes nucleotides processively on a primed M13 single-stranded DNA template. T7 DNA polymerase cannot initiate de novo DNA synthesis; it requires tetraribonucleotides synthesized by the primase activity of the T7 gene 4 protein to serve as primers. T7 primase-dependent DNA synthesis on single-stranded DNA is 3- to 6-fold less with T7 polDelta401-404 compared with the wild-type enzyme. Furthermore, the altered polymerase is defective (10-fold) in its ability to use preformed tetraribonucleotides to initiate DNA synthesis in the presence of gene 4 protein. The location of the loop places it in precisely the position to interact with the tetraribonucleotide primer and, presumably, with the T7 gene 4 primase. Gene 4 protein also provides helicase activity for the replication of duplex DNA. T7 polDelta401-404 and T7 gene 4 protein catalyze strand-displacement DNA synthesis at nearly the same rate as does wild-type polymerase and T7 gene 4 protein, suggesting that the coupling of helicase and polymerase activities is unaffected.
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Affiliation(s)
- K Chowdhury
- Department of Biological Chemistry and Molecular Pharmacology, Harvard University Medical School, Boston, MA 02115, USA
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Yong Y, Romano LJ. Nucleotide and DNA-induced conformational changes in the bacteriophage T7 gene 4 protein. J Biol Chem 1995; 270:24509-17. [PMID: 7592668 DOI: 10.1074/jbc.270.41.24509] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The bacteriophage T7 gene 4 protein is a multifunctional enzyme that has DNA helicase, primase, and deoxyribonucleotide 5'-triphosphatase activities. Prior studies have shown that in the presence of dTTP or dTDP the gene 4 protein assembles into a functionally active hexamer prior to binding to single-stranded DNA. In this study, we have examined the effects of different nucleotide cofactors on the conformation of the gene 4 protein in the presence and absence of DNA. Gel retardation analysis, partial protease digestion, and DNA footprinting all suggest that the gene 4 protein undergoes a conformational change when dTTP is hydrolyzed to dTTP and that in the presence of dTDP the complex with DNA is more open or extended. We have also found that the dissociation constant of the gene 4 protein.DNA complex in the presence of dTDP was 10-fold lower than that determined in the presence of dTTP, further suggesting that these cofactors exerts different allosteric effects on the DNA-binding site of the gene 4 protein.
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Affiliation(s)
- Y Yong
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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Debyser Z, Tabor S, Richardson CC. Coordination of leading and lagging strand DNA synthesis at the replication fork of bacteriophage T7. Cell 1994; 77:157-66. [PMID: 8156591 DOI: 10.1016/0092-8674(94)90243-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have used the T7 DNA replication system to examine coordination of leading and lagging strand synthesis at a replication fork. The 63 kd gene 4 protein provides both helicase and primase activities; we demonstrate that primer synthesis inhibits helicase activity on a synthetic replication fork. Lagging strand DNA synthesis by a complex of gene 4 protein and T7 DNA polymerase decreases the rate of leading strand synthesis. Both leading and lagging strand synthesis are resistant to dilution of the replication proteins, and to challenge with heparin. Furthermore, dilution does not increase the average length of Okazaki fragments. We propose that leading and lagging strand synthesis at a T7 replication fork are coupled and that the replication proteins are recycled.
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Affiliation(s)
- Z Debyser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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Fuller CW, Richardson CC. Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins. Site and direction of initial DNA synthesis. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89490-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Matson SW, Richardson CC. Nucleotide-dependent binding of the gene 4 protein of bacteriophage T7 to single-stranded DNA. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89551-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Bäumel I, Meyer TF, Geider K. Functional aspects of Escherichia coli rep helicase in unwinding and replication of DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 138:247-51. [PMID: 6141940 DOI: 10.1111/j.1432-1033.1984.tb07908.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The gene for Escherichia coli rep helicase (rep protein) was subcloned in a pBR plasmid and the protein overproduced in cells transformed with the hybrid DNA. The effect of purified enzyme on strand unwinding and DNA replication was investigated by electron microscopy. The templates used were partial duplexes of viral DNA from bacteriophage fd::Tn5 and reannealed DNA from bacteriophage Mu. The experiments with the two DNA species show DNA unwinding uncoupled from replication. The single-stranded phage fd::Tn5 DNA with the inverted repeat of transposon Tn5 could be completely replicated in the presence of the E. coli enzymes rep helicase, DNA binding protein I, RNA polymerase and DNA polymerase III holoenzyme. A block in the unwinding step increases secondary initiation events in single-stranded parts of the template, as DNA polymerase III holoenzyme cannot switch across the stem structure of the transposon.
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Marians KJ. Enzymology of DNA in replication in prokaryotes. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1984; 17:153-215. [PMID: 6097404 DOI: 10.3109/10409238409113604] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This review stresses recent developments in the in vitro study of DNA replication in prokaryotes. New insights into the enzymological mechanisms of initiation and elongation of leading and lagging strand DNA synthesis in ongoing studies are emphasized. Data from newly developed systems, such as those replicating oriC containing DNA or which are dependent on the lambda, O, and P proteins, are presented and the information compared to existing mechanisms. Evidence bearing on the coupling of DNA synthesis on both parental strands through protein-protein interactions and on the turnover of the elongation systems are analyzed. The structure of replication origins, and how their tertiary structure affects recognition and interaction with the various replication proteins is discussed.
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Matson SW, Tabor S, Richardson CC. The gene 4 protein of bacteriophage T7. Characterization of helicase activity. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44018-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Matson SW, Richardson CC. DNA-dependent nucleoside 5'-triphosphatase activity of the gene 4 protein of bacteriophage T7. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44017-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
An attempt is made to survey ATPases with respect to features common to all or some of them and features peculiar to each individual enzyme of the group. Clues are presented for a tentative classification of ATPases and a simple system is suggested for the designation of interaction of ATPases with ions which is often used as the main feature of identification of individual ATPases.
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6 Priming Enzymes. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Harth G, Bäumel I, Meyer TF, Geider K. Bacteriophage fd gene-2 protein. Processing of phage fd viral strands replicated by phage T7 enzymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 119:663-8. [PMID: 6975715 DOI: 10.1111/j.1432-1033.1981.tb05659.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacteriophage T7 gene 4 protein and DNA polymerase of the phage were used to study the viral strand synthesis of bacteriophage fd in vitro. Cleavage of supercoiled phage fd replicative form (RF) by fd gene 2 protein produced a nick at a specific site in the viral strand. The cleaved double-stranded DNA was unwound by T7 gene 4 protein and T7 DNA polymerase and the 3' end of the nicked strand simultaneously extended according to the rolling circle mechanism. After a complete round of DNA synthesis fd gene 2 protein cleaved the viral strand presumably at the same site, where the endonuclease cuts fd RF I, and subsequently sealed the single-stranded linear DNA into a circle. The reaction products were analyzed by velocity sedimentation, gel electrophoresis and electron microscopy. Most of the single-stranded DNA synthesized was circular. No host proteins were required for the formation of the single-stranded circles. Strand switching of the T7 DNA polymerase indicated by double-stranded tails of the rolling circle structures reduced the yield of viral single-stranded circles in this enzyme system.
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Fischer H, Hinkle D. Bacteriophage T7 DNA replication in vitro. Stimulation of DNA synthesis by T7 RNA polymerase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)43926-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Wang TS, Korn D. Reactivity of KB cell deoxyribonucleic acid polymerases alpha and beta with nicked and gapped deoxyribonucleic acid. Biochemistry 1980; 19:1782-90. [PMID: 6246934 DOI: 10.1021/bi00550a009] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Fujimura RK, Das SK. Replicative DNA polymerases and mechanisms at a replication fork. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1980; 24:87-107. [PMID: 6256822 DOI: 10.1016/s0079-6603(08)60672-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Deoxyribonucleic acid polymerase of bacteriophage T7. Purification and properties of the phage-encoded subunit, the gene 5 protein. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86526-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Romano L, Richardson C. Requirements for synthesis of ribonucleic acid primers during lagging strand synthesis by the DNA polymerase and gene 4 protein of bacteriophage T7. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86733-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Romano L, Richardson C. Characterization of the ribonucleic acid primers and the deoxyribonucleic acid product synthesized by the DNA polymerase and gene 4 protein of bacteriophage T7. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86734-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Wolfson J, Dressler D. Bacteriophage T7 DNA replication. An electron microscopic study of the growing point and the role of the T7 gene 4 protein in the formation of DNA fragments. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86735-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
A DNA-dependent ATPase has been purified from calf thymus. The enzyme hydrolyses ATP and dATP in the presence of heat-denatured DNA. It does not hydrolyse the corresponding nucleoside triphosphates of guanine, uridine and cytosine. The Km values for ATP and dATP are both 0.62 mM. The enzyme requires magnesium or manganese ions. Its sedimentation coefficient is about 4.4 S. The catalytic activity is inhibited by N-ethylmaleimide but is not sensitive to novobiocin and nalidixic acid which are potent inhibitors of bacterial DNA gyrase. In some cases, during purification, chromatographically distinct additional DNA-dependent ATPase activities were detected. Limited proteolysis or covalent modification of the enzyme in the tissues, or during the first steps of its extraction, are probably responsible for the appearance of these chromatographically distinct forms.
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Challberg M, Englund P. The effect of template secondary structure on vaccinia DNA polymerase. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)36020-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Nossal NG, Peterlin BM. DNA replication by bacteriophage T4 proteins. The T4 43, 32, 44–62, And 45 proteins are required for strand displacement synthesis at nicks in duplex DNA. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50515-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Kolodner R, Masamune Y, LeClerc J, Richardson C. Gene 4 protein of bacteriophage T7. Purification physical properties, and stimulation of T7 DNA polymerase during the elongation of polynucleotide chains. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38247-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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