1
|
Morcinek-Orłowska J, Zdrojewska K, Węgrzyn A. Bacteriophage-Encoded DNA Polymerases-Beyond the Traditional View of Polymerase Activities. Int J Mol Sci 2022; 23:635. [PMID: 35054821 PMCID: PMC8775771 DOI: 10.3390/ijms23020635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA polymerases are enzymes capable of synthesizing DNA. They are involved in replication of genomes of all cellular organisms as well as in processes of DNA repair and genetic recombination. However, DNA polymerases can also be encoded by viruses, including bacteriophages, and such enzymes are involved in viral DNA replication. DNA synthesizing enzymes are grouped in several families according to their structures and functions. Nevertheless, there are examples of bacteriophage-encoded DNA polymerases which are significantly different from other known enzymes capable of catalyzing synthesis of DNA. These differences are both structural and functional, indicating a huge biodiversity of bacteriophages and specific properties of their enzymes which had to evolve under certain conditions, selecting unusual properties of the enzymes which are nonetheless crucial for survival of these viruses, propagating as special kinds of obligatory parasites. In this review, we present a brief overview on DNA polymerases, and then we discuss unusual properties of different bacteriophage-encoded enzymes, such as those able to initiate DNA synthesis using the protein-priming mechanisms or even start this process without any primer, as well as able to incorporate untypical nucleotides. Apart from being extremely interesting examples of biochemical biodiversity, bacteriophage-encoded DNA polymerases can also be useful tools in genetic engineering and biotechnology.
Collapse
Affiliation(s)
- Joanna Morcinek-Orłowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland
| |
Collapse
|
2
|
λ Recombineering Used to Engineer the Genome of Phage T7. Antibiotics (Basel) 2020; 9:antibiotics9110805. [PMID: 33202746 PMCID: PMC7697293 DOI: 10.3390/antibiotics9110805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage T7 and T7-like bacteriophages are valuable genetic models for lytic phage biology that have heretofore been intractable with in vivo genetic engineering methods. This manuscript describes that the presence of λ Red recombination proteins makes in vivo recombineering of T7 possible, so that single base changes and whole gene replacements on the T7 genome can be made. Red recombination functions also increase the efficiency of T7 genome DNA transfection of cells by ~100-fold. Likewise, Red function enables two other T7-like bacteriophages that do not normally propagate in E. coli to be recovered following genome transfection. These results constitute major technical advances in the speed and efficiency of bacteriophage T7 engineering and will aid in the rapid development of new phage variants for a variety of applications.
Collapse
|
3
|
Brieba LG. Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System. PLANTS 2019; 8:plants8120533. [PMID: 31766564 PMCID: PMC6963530 DOI: 10.3390/plants8120533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.
Collapse
Affiliation(s)
- Luis Gabriel Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato C.P. 36821, Mexico
| |
Collapse
|
4
|
Hürtgen D, Mascarenhas J, Heymann M, Murray SM, Schwille P, Sourjik V. Reconstitution and Coupling of DNA Replication and Segregation in a Biomimetic System. Chembiochem 2019; 20:2633-2642. [PMID: 31344304 PMCID: PMC6899551 DOI: 10.1002/cbic.201900299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/20/2019] [Indexed: 12/30/2022]
Abstract
A biomimetic system capable of replication and segregation of genetic material constitutes an essential component for the future design of a minimal synthetic cell. Here we have used the simple T7 bacteriophage system and the plasmid-derived ParMRC system to establish in vitro DNA replication and DNA segregation, respectively. These processes were incorporated into biomimetic compartments providing an enclosed reaction space. The functional lifetime of the encapsulated segregation system could be prolonged by equipping it with ATP-regenerating and oxygen-scavenging systems. Finally, we showed that DNA replication and segregation processes could be coupled in vitro by using condensed DNA nanoparticles resulting from DNA replication. ParM spindles extended over tens of micrometers and could thus be used for segregation in compartments that are significantly longer than bacterial cell size. Overall, this work demonstrates the successful bottom-up assembly and coupling of molecular machines that mediate replication and segregation, thus providing an important step towards the development of a fully functional minimal cell.
Collapse
Affiliation(s)
- Daniel Hürtgen
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Judita Mascarenhas
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Michael Heymann
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Seán M. Murray
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Petra Schwille
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| |
Collapse
|
5
|
Ramachandran A, Nandakumar D, Deshpande AP, Lucas TP, R-Bhojappa R, Tang GQ, Raney K, Yin YW, Patel SS. The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA. J Biol Chem 2016; 291:16828-39. [PMID: 27311715 DOI: 10.1074/jbc.m116.740282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 01/12/2023] Open
Abstract
Primases use single-stranded (ss) DNAs as templates to synthesize short oligoribonucleotide primers that initiate lagging strand DNA synthesis or reprime DNA synthesis after replication fork collapse, but the origin of this activity in the mitochondria remains unclear. Herein, we show that the Saccharomyces cerevisiae mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) is an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. However, the ssDNA-binding protein Rim1 severely inhibits the RNA synthesis activity of Rpo41, but not the Rpo41-Mtf1 complex, which continues to prime DNA synthesis efficiently in the presence of Rim1. We show that RNAs as short as 10-12 nt serve as primers for DNA synthesis. Characterization of the RNA-DNA products shows that Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. However, both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3 Based on our studies, we propose that Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA.
Collapse
Affiliation(s)
- Aparna Ramachandran
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Divya Nandakumar
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Aishwarya P Deshpande
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Thomas P Lucas
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, and
| | - Ramanagouda R-Bhojappa
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Guo-Qing Tang
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Kevin Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Y Whitney Yin
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, and
| | - Smita S Patel
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854,
| |
Collapse
|
6
|
|
7
|
Sanchez-Sandoval E, Diaz-Quezada C, Velazquez G, Arroyo-Navarro LF, Almanza-Martinez N, Trasviña-Arenas CH, Brieba LG. Yeast mitochondrial RNA polymerase primes mitochondrial DNA polymerase at origins of replication and promoter sequences. Mitochondrion 2015; 24:22-31. [PMID: 26184436 DOI: 10.1016/j.mito.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 11/15/2022]
Abstract
Three proteins phylogenetically grouped with proteins from the T7 replisome localize to yeast mitochondria: DNA polymerase γ (Mip1), mitochondrial RNA polymerase (Rpo41), and a single-stranded binding protein (Rim1). Human and T7 bacteriophage RNA polymerases synthesize primers for their corresponding DNA polymerases. In contrast, DNA replication in yeast mitochondria is explained by two models: a transcription-dependent model in which Rpo41 primes Mip1 and a model in which double stranded breaks create free 3' OHs that are extended by Mip1. Herein we found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA. In contrast to human mitochondrial RNA polymerase, which primes DNA polymerase γ using transcripts from the light-strand and heavy-strand origins of replication, Rpo41 primes Mip1 at replication origins and promoter sequences in vitro. Our results suggest that in ori1, short transcripts serve as primers, whereas in ori5 an RNA transcript longer than 29 nucleotides is used as primer.
Collapse
Affiliation(s)
- Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Gilberto Velazquez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Luis F Arroyo-Navarro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Norineli Almanza-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico.
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
| |
Collapse
|
9
|
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
|
10
|
Pham XH, Farge G, Shi Y, Gaspari M, Gustafsson CM, Falkenberg M. Conserved Sequence Box II Directs Transcription Termination and Primer Formation in Mitochondria. J Biol Chem 2006; 281:24647-52. [PMID: 16790426 DOI: 10.1074/jbc.m602429200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human mitochondrial transcription machinery generates the RNA primers needed for initiation of heavy strand DNA synthesis. Most DNA replication events from the heavy strand origin are prematurely terminated, forming a persistent RNA-DNA hybrid, which remains annealed to the parental DNA strand. This triple-stranded structure is called the D-loop and encompasses the conserved sequence box II, a DNA element required for proper primer formation. We here use a purified recombinant mitochondrial transcription system and demonstrate that conserved sequence box II is a sequence-dependent transcription termination element in vitro. Transcription from the light strand promoter is prematurely terminated at positions 300-282 in the mitochondrial genome, which coincide with the major RNA-DNA transition points in the D-loop of human mitochondria. Based on our findings, we propose a model for primer formation at the origin of heavy strand DNA replication.
Collapse
Affiliation(s)
- Xuan Hoi Pham
- Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Bacteriophages (prokaryotic viruses) are favourite model systems to study DNA replication in prokaryotes, and provide examples for every theoretically possible replication mechanism. In addition, the elucidation of the intricate interplay of phage-encoded replication factors with 'host' factors has always advanced the understanding of DNA replication in general. Here we review bacteriophage replication based on the long-standing observation that in most known phage genomes the replication genes are arranged as modules. This allows us to discuss established model systems--f1/fd, phiX174, P2, P4, lambda, SPP1, N15, phi29, T7 and T4--along with those numerous phages that have been sequenced but not studied experimentally. The review of bacteriophage replication mechanisms and modules is accompanied by a compendium of replication origins and replication/recombination proteins (available as supplementary material online).
Collapse
|
12
|
Scholl D, Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J Bacteriol 2006; 187:8499-503. [PMID: 16321955 PMCID: PMC1317022 DOI: 10.1128/jb.187.24.8499-8503.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage K1F specifically infects Escherichia coli strains that produce the K1 polysaccharide capsule. Like several other K1 capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase) that is part of the tail structure which allows the phage to recognize and degrade the polysaccharide capsule. The complete nucleotide sequence of the K1F genome reveals that it is closely related to bacteriophage T7 in both genome organization and sequence similarity. The most striking difference between the two phages is that K1F encodes the endosialidase in the analogous position to the T7 tail fiber gene. This is in contrast with bacteriophage K1-5, another K1-specific phage, which encodes a very similar endosialidase which is part of a tail gene "module" at the end of the phage genome. It appears that diverse phages have acquired endosialidase genes by horizontal gene transfer and that these genes or gene products have adapted to different genome and virion architectures.
Collapse
Affiliation(s)
- Dean Scholl
- National Institutes of Mental Health, National Institutes of Health, Building 49, Room B1B20, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | | |
Collapse
|
13
|
Belanger KG, Kreuzer KN. Bacteriophage T4 initiates bidirectional DNA replication through a two-step process. Mol Cell 1998; 2:693-701. [PMID: 9844641 DOI: 10.1016/s1097-2765(00)80167-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two-dimensional gel analysis of the bacteriophage T4 ori(uvsY) region revealed a novel "comet" on the Y arc. This comet contains simple Y molecules in which the branch points map to the ori(uvsY) transcript region. The comet depends on the the origin and DNA synthesis and is abolished by a mutation that reduces replication without affecting transcription. These results argue that the branched molecules are intermediates in replication initiation. A transcriptional terminator, cloned just downstream of the origin promoter, shortened the tail of the comet. Therefore, the location of the transcript determines the DNA branch points. We conclude that the comet DNA consists of intermediates in which unidirectional replication has been triggered by priming from the RNA of the origin R loop.
Collapse
MESH Headings
- Bacteriophage T4/genetics
- Bacteriophage T4/physiology
- Blotting, Northern
- Blotting, Southern
- DNA Helicases/metabolism
- DNA Replication/genetics
- DNA Replication/physiology
- DNA, Viral/biosynthesis
- DNA, Viral/isolation & purification
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- DNA-Directed DNA Polymerase
- Electrophoresis, Gel, Two-Dimensional
- Escherichia coli/virology
- Membrane Proteins/genetics
- Membrane Proteins/physiology
- Mutation
- Physical Chromosome Mapping
- RNA, Viral/metabolism
- Recombination, Genetic/physiology
- Replication Origin/genetics
- Replication Origin/physiology
- Ribonuclease H/genetics
- Ribonuclease H/physiology
- Terminator Regions, Genetic/genetics
- Transcription, Genetic/physiology
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Viral Proteins/physiology
- Virus Replication/genetics
- Virus Replication/physiology
Collapse
Affiliation(s)
- K G Belanger
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | |
Collapse
|
14
|
Yin Y, Carter CW. Incomplete factorial and response surface methods in experimental design: yield optimization of tRNA(Trp) from in vitro T7 RNA polymerase transcription. Nucleic Acids Res 1996; 24:1279-86. [PMID: 8614631 PMCID: PMC145796 DOI: 10.1093/nar/24.7.1279] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have studied the yield of Escherichia coli tRNA(Trp) obtained from in vitro T7 RNA polymerase transcription using incomplete factorial and response surface methods. Incomplete factorial experiments were first used to estimate the relative impact of six variables on the yield of tRNA(Trp). Fifteen trials were performed according to a balanced and randomized design. The correlation between observed yield and all experimental variables was identified by stepwise multiple linear regression analysis. The concentrations of T7 RNA polymerase, DNA template, NTP and MgCl2 proved to be significantly correlated with the yield of tRNA(Trp). We then optimized the yield with respect to each of these four variables simultaneously with a designed, response surface experiment based on the Hardin-Sloane minimum prediction variance algorithm. Twenty experiments were performed, in duplicate, to sample the quadratic surface relating the yield to the four significant variables. Coefficients of the quadratic function with all two-factor interactions were evaluated by stepwise regression using least squares, and significant coefficients were retained. Partial differentiation of the resulting quadratic model showed it to possess an optimum. Transcription performed at the corresponding conditions yielded 6-fold more tRNA(Trp) than the initial conditions, confirming the predictive value of the experimentally determined response surface.
Collapse
Affiliation(s)
- Y Yin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill 27599-7260, USA
| | | |
Collapse
|
15
|
Rigler MN, Romano LJ. Differences in the mechanism of stimulation of T7 DNA polymerase by two binding modes of Escherichia coli single-stranded DNA-binding protein. J Biol Chem 1995; 270:8910-9. [PMID: 7721799 DOI: 10.1074/jbc.270.15.8910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Escherichia coli single-stranded DNA-binding protein (Eco SSB) has been shown previously to display several DNA binding modes depending on the ionic conditions. To determine what effect these various binding modes have on DNA replication, we have studied DNA synthesis by the T7 DNA polymerase under ionic conditions where Eco SSB interacts with either 72 or 91 nucleotides of M13 DNA. These forms presumably correspond to the previously described (SSB)56 and (SSB)65 (Lohman and Ferrari, 1994) that were determined using the binding of SSB to homopolymers. Here we report the stimulation induced by (SSB)91 to be 4-fold greater than that produced by (SSB)72 under conditions where the template is in large excess. Surprisingly, when the polymerase level is raised so that it is in molecular excess, (SSB)91 no longer stimulates synthesis while (SSB)72 affords a 4-fold stimulation, which is the same level of stimulation as when the template was in excess. Both SSB forms increase the rate of DNA synthesis and were found to stimulate synthesis by relieving template secondary structures. However, (SSB)72 specifically increases strand displacement synthesis, while (SSB)91 stimulates synthesis by increasing the affinity of the polymerase for the template.
Collapse
Affiliation(s)
- M N Rigler
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | | |
Collapse
|
16
|
Brown WC, Romano LJ. Effects of benzo[a]pyrene-DNA adducts on a reconstituted replication system. Biochemistry 1991; 30:1342-50. [PMID: 1846752 DOI: 10.1021/bi00219a026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have used a partially reconstituted replication system consisting of T7 DNA polymerase and T7 gene 4 protein to examine the effect of benzo[a]pyrene (B[a]P) adducts on DNA synthesis and gene 4 protein activities. The gene 4 protein is required for T7 DNA replication because of its ability to act as both a primase and helicase. We show here that total synthesis decreases as the level of adducts per molecule of DNA increases, suggesting that the B[a]P adducts are blocking an aspect of the replication process. Polyacrylamide gels indicate that a shorter DNA product is produced on modified templates and this is confirmed by determining the average chain lengths from the ratio of chain initiations to chain elongation. Gene 4 protein primed synthesis reactions display a greater sensitivity to the presence of B[a]P adducts than do oligonucleotide-primed reactions. By challenging synthesis on oligonucleotide-primed B[a]P-modified DNA with unmodified DNA, we present evidence that the T7 DNA polymerase freely dissociates after encountering an adduct. Prior studies [Brown, W. C., & Romano, L. J. (1989) J. Biol. Chem. 264, 6748-6754] have shown that the gene 4 protein alone does not dissociate from the template during translocation upon encountering an adduct. However, when gene 4 protein primed DNA synthesis is challenged, we observe an increase in synthesis but to lesser extent than observed on oligonucleotide-primed synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- W C Brown
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | | |
Collapse
|
17
|
Abstract
The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.
Collapse
Affiliation(s)
- R R Meyer
- Department of Biological Sciences, University of Cincinnati, Ohio 45221
| | | |
Collapse
|
18
|
Serwer P, Watson RH, Son M. Role of gene 6 exonuclease in the replication and packaging of bacteriophage T7 DNA. J Mol Biol 1990; 215:287-99. [PMID: 2170664 DOI: 10.1016/s0022-2836(05)80347-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When bacteriophage T7 gene 6 exonuclease is genetically removed from T7-infected cells, degradation of intracellular T7 DNA is observed. By use of rate zonal centrifugation, followed by either pulsed-field agarose gel electrophoresis or restriction endonuclease analysis, in the present study, the following observations were made. (1) Most degradation of intracellular DNA requires the presence of T7 gene 3 endonuclease and is independent of DNA packaging; rapidly sedimenting, branched DNA accumulates when both the gene 3 and gene 6 products are absent. (2) A comparatively small amount of degradation requires packaging and occurs at both the joint between genomes in a concatemer and near the left end of intracellular DNA; DNA packaging is only partially blocked and end-to-end joining of genomes is not blocked in the absence of gene 6 exonuclease. (3) Fragments produced in the absence of gene 6 exonuclease are linear and do not further degrade; precursors of the fragments are non-linear. (4) Some, but not most, of the cleavages that produce these fragments occur selectively near two known origins of DNA replication. On the basis of these observations, the conclusion is drawn that most degradation that occurs in the absence of T7 gene 6 exonuclease is caused by cleavage at branches. The following hypothesis is presented: most, possibly all, of the extra branching induced by removal of gene 6 exonuclease is caused by strand displacement DNA synthesis at the site of RNA primers of DNA synthesis; the RNA primers, produced by multiple initiations of DNA replication, are removed by the RNase H activity of gene 6 exonuclease during a wild-type T7 infection. Observation of joining of genomes in the absence of gene 6 exonuclease and additional observations indicate that single-stranded terminal repeats required for concatamerization are produced by DNA replication. The observed selective shortening of the left end indicates that gene 6 exonuclease is required for formation of most, possibly all, mature left ends.
Collapse
Affiliation(s)
- P Serwer
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760
| | | | | |
Collapse
|
19
|
Abstract
Bacteriophage T7 DNA replication is initiated at a site 15% of the distance from the genetic left end of the chromosome. This primary origin contains two tandem T7 RNA polymerase promoters (phi 1.1A and phi 1.1B) followed by an A + T-rich region. When the primary origin region is deleted replication initiates at secondary origins. We have analyzed the ability of plasmids containing cloned fragments of T7 to replicate after infection of Escherichia coli with bacteriophage T7. All cloned T7 fragments that support plasmid replication contain a T7 promoter but a T7 promoter alone is not sufficient for replication. Replication of plasmids containing the primary origin is dependent on T7 DNA polymerase and gene 4 protein (helicase/primase) and a portion of the A + T-rich region. The other T7 fragments that support plasmid replication after T7 infection are promoter regions phi OR, phi 13 and phi 6.5 (secondary origins). When both the primary and secondary origins are present simultaneously on compatible plasmids, replication of each is temporally regulated. Such regulation may play a role during T7 DNA replication.
Collapse
Affiliation(s)
- S D Rabkin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | | |
Collapse
|
20
|
Myers TW, Romano LJ. Mechanism of stimulation of T7 DNA polymerase by Escherichia coli single-stranded DNA binding protein (SSB). J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37490-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
21
|
Nakai H, Richardson CC. The effect of the T7 and Escherichia coli DNA-binding proteins at the replication fork of bacteriophage T7. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81592-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
22
|
Sugimoto K, Miyasaka T, Fujiyama A, Kohara Y, Okazaki T. Change in priming sites for discontinuous DNA synthesis between the monomeric and concatemeric stages of phage T7 replication. MOLECULAR & GENERAL GENETICS : MGG 1988; 211:400-6. [PMID: 2452962 DOI: 10.1007/bf00425692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have analyzed the transition sites between primer RNA and DNA in a 589 bp segment of the bacteriophage T7 genome. In the monomeric replication stage, RNA-DNA transition sites are predominantly on the light (L) strand (with 5'----3' polarity on the genetic map) but rarely on the heavy (H) strand, indicating that replication proceeds semidiscontinuously with the H and L strands corresponding to the leading and lagging strands, respectively. The direction of replication is that expected from the position of the primary origin and also indicates that secondary origins are seldom if ever used. In the concatemeric stage of replication, RNA-DNA transition sites are instead distributed on both strands of the segment with equally high frequency, showing that initiation occurs within the concatemeric molecule per se and by a different mechanism.
Collapse
Affiliation(s)
- K Sugimoto
- Department of Molecular Biology, School of Science, Nagoya University, Japan
| | | | | | | | | |
Collapse
|
23
|
Huber HE, Tabor S, Richardson CC. Escherichia coli thioredoxin stabilizes complexes of bacteriophage T7 DNA polymerase and primed templates. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47719-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
24
|
Abstract
A minimal mechanism is proposed which describes the transcriptional and translational processes for four phage proteins (RNA polymerase, DNase, primase and DNA polymerase) involved in T3/T7 DNA replication. Phage DNA replication is also included. It is shown how lag times may be incorporated into a kinetic mechanism. The distinct three-stage transport of phage DNA into the bacterial host (E. coli) is considered. DNA transport is assumed to be rate-determining for the transcription of class I and II proteins. Transcriptional and translational lag times have been calculated on the basis of available gene mapping of T7 phages. The kinetic behavior of T7 and T3 phage infection is practically identical. The hydrolysis of bacterial DNA by phage DNase (endonculease and exonuclease) as well as the subsequent phosphorylation to the deoxymononucleoside triphosphates are assumed to be rate-determining in phage DNA replication. Good agreement with experiment is obtained in our computer simulations.
Collapse
|
25
|
Ikeda R, Richardson C. Enzymatic properties of a proteolytically nicked RNA polymerase of bacteriophage T7. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61425-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
26
|
Huber HE, Russel M, Model P, Richardson CC. Interaction of mutant thioredoxins of Escherichia coli with the gene 5 protein of phage T7. The redox capacity of thioredoxin is not required for stimulation of DNA polymerase activity. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66820-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
27
|
Interactions of the DNA polymerase and gene 4 protein of bacteriophage T7. Protein-protein and protein-DNA interactions involved in RNA-primed DNA synthesis. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66855-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
28
|
Dissection of RNA-primed DNA synthesis catalyzed by gene 4 protein and DNA polymerase of bacteriophage T7. Coupling of RNA primer and DNA synthesis. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66856-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
29
|
Marians KJ, Minden JS, Parada C. Replication of superhelical DNAs in vitro. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1986; 33:111-40. [PMID: 3541040 DOI: 10.1016/s0079-6603(08)60021-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
30
|
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
|