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Yin J, Wu S, Yang Y, Wang D, Ma Y, Zhao Y, Sheth S, Huang H, Song B, Chen Z. In Addition to Damaging the Plasma Membrane, Phenolic Monoterpenoid Carvacrol Can Bind to the Minor Groove of DNA of Phytopathogenic Fungi to Potentially Control Tea Leaf Spot Caused by Lasiodiplodia theobromae. PHYTOPATHOLOGY 2024; 114:700-716. [PMID: 37856707 DOI: 10.1094/phyto-07-23-0263-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Carvacrol expresses a wide range of biological activities, but the studies of its mechanisms focused on bacteria, mainly involving the destruction of the plasma membrane. In this study, carvacrol exhibited strong activities against several phytopathogenic fungi and demonstrated a novel antifungal mechanism against Lasiodiplodia theobromae. RNA sequencing indicated that many genes of L. theobromae hyphae were predominately induced by carvacrol, particularly those involved in replication and transcription. Hyperchromic, hypsochromic, and bathochromic effects in the UV-visible absorption spectrum were observed following titration of calf thymus DNA (ctDNA) and carvacrol, which indicated the formation of a DNA-carvacrol complex. Circular dichroism (CD) spectroscopy indicated that the response of DNA to carvacrol was similar to that of 4',6-diamidino-2-phenylindole (DAPI) but different from that of ethidium bromide (EB), implying the ionic bonds between carvacrol and ctDNA. Fluorescence spectrum (FS) analysis indicated that carvacrol quenched the fluorescence of double-stranded DNA (dsDNA) more than single-stranded DNA, indicating that carvacrol mainly bound to dsDNA. A displacement assay showed that carvacrol reduced the fluorescence intensity of the DNA-DAPI complex through competition with DAPI, but this did not occur for DNA-EB. The FS assay revealed that carvacrol bound to the AAA sequence on the minor groove of ds-oligonucleotides. The hydroxyl of carvacrol was verified to bind to ctDNA through a comparative test in which structural analogs of carvacrol, including thymol and 4-ethyl-1,2-dimethyl, were analyzed. The current study indicated carvacrol can destruct plasma membranes and bind to the minor groove of DNA, inhibiting fungal proliferation by disturbing the stability of dsDNA.
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Affiliation(s)
- Jiayu Yin
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Shuang Wu
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yongli Yang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yue Ma
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China
| | - Yongtian Zhao
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, Guizhou, China
| | - Sujitraj Sheth
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
| | - Honglin Huang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhuo Chen
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
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Muylaert I, Tang KW, Elias P. Replication and recombination of herpes simplex virus DNA. J Biol Chem 2011; 286:15619-24. [PMID: 21362621 DOI: 10.1074/jbc.r111.233981] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Replication of herpes simplex virus takes place in the cell nucleus and is carried out by a replisome composed of six viral proteins: the UL30-UL42 DNA polymerase, the UL5-UL8-UL52 helicase-primase, and the UL29 single-stranded DNA-binding protein ICP8. The replisome is loaded on origins of replication by the UL9 initiator origin-binding protein. Virus replication is intimately coupled to recombination and repair, often performed by cellular proteins. Here, we review new significant developments: the three-dimensional structures for the DNA polymerase, the polymerase accessory factor, and the single-stranded DNA-binding protein; the reconstitution of a functional replisome in vitro; the elucidation of the mechanism for activation of origins of DNA replication; the identification of cellular proteins actively involved in or responding to viral DNA replication; and the elucidation of requirements for formation of replication foci in the nucleus and effects on protein localization.
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Affiliation(s)
- Isabella Muylaert
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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4
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Olsson M, Tang KW, Persson C, Wilhelmsson LM, Billeter M, Elias P. Stepwise evolution of the herpes simplex virus origin binding protein and origin of replication. J Biol Chem 2009; 284:16246-16255. [PMID: 19351883 DOI: 10.1074/jbc.m807551200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The herpes simplex virus replicon consists of cis-acting sequences, oriS and oriL, and the origin binding protein (OBP) encoded by the UL9 gene. Here we identify essential structural features in the initiator protein OBP and the replicator sequence oriS, and we relate the appearance of these motifs to the evolutionary history of the alphaherpesvirus replicon. Our results reveal two conserved sequence elements in herpes simplex virus type 1, OBP; the RVKNL motif, common to and specific for all alphaherpesviruses, is required for DNA binding, and the WP XXXGAXXFXX L motif, found in a subset of alphaherpesviruses, is required for specific binding to the single strand DNA-binding protein ICP8. A 121-amino acid minimal DNA binding domain containing conserved residues is not soluble and does not bind DNA. Additional sequences present 220 amino acids upstream from the RVKNL motif are needed for solubility and function. We also examine the binding sites for OBP in origins of DNA replication and how they are arranged. NMR and DNA melting experiments demonstrate that origin sequences derived from many, but not all, alphaherpesviruses can adopt stable boxI/boxIII hairpin conformations. Our results reveal a stepwise evolutionary history of the herpes simplex virus replicon and suggest that replicon divergence contributed to the formation of major branches of the herpesvirus family.
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Affiliation(s)
- Monica Olsson
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg
| | - Ka-Wei Tang
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg
| | - Cecilia Persson
- The Swedish NMR Centre at University of Gothenburg, Box 465, S-405 30 Gothenburg
| | - L Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg
| | - Martin Billeter
- Biophysics Group, Department of Chemistry, University of Gothenburg, Box 462, S-405 30 Gothenburg, Sweden
| | - Per Elias
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg.
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5
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Manolaridis I, Mumtsidu E, Konarev P, Makhov AM, Fullerton SW, Sinz A, Kalkhof S, McGeehan JE, Cary PD, Griffith JD, Svergun D, Kneale GG, Tucker PA. Structural and biophysical characterization of the proteins interacting with the herpes simplex virus 1 origin of replication. J Biol Chem 2009; 284:16343-16353. [PMID: 19329432 DOI: 10.1074/jbc.m806134200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C terminus of the herpes simplex virus type 1 origin-binding protein, UL9ct, interacts directly with the viral single-stranded DNA-binding protein ICP8. We show that a 60-amino acid C-terminal deletion mutant of ICP8 (ICP8DeltaC) also binds very strongly to UL9ct. Using small angle x-ray scattering, the low resolution solution structures of UL9ct alone, in complex with ICP8DeltaC, and in complex with a 15-mer double-stranded DNA containing Box I of the origin of replication are described. Size exclusion chromatography, analytical ultracentrifugation, and electrophoretic mobility shift assays, backed up by isothermal titration calorimetry measurements, are used to show that the stoichiometry of the UL9ct-dsDNA15-mer complex is 2:1 at micromolar protein concentrations. The reaction occurs in two steps with initial binding of UL9ct to DNA (Kd approximately 6 nM) followed by a second binding event (Kd approximately 0.8 nM). It is also shown that the stoichiometry of the ternary UL9ct-ICP8DeltaC-dsDNA15-mer complex is 2:1:1, at the concentrations used in the different assays. Electron microscopy indicates that the complex assembled on the extended origin, oriS, rather than Box I alone, is much larger. The results are consistent with a simple model whereby a conformational switch of the UL9 DNA-binding domain upon binding to Box I allows the recruitment of a UL9-ICP8 complex by interaction between the UL9 DNA-binding domains.
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Affiliation(s)
- Ioannis Manolaridis
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany; Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Eleni Mumtsidu
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany
| | - Peter Konarev
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Alexander M Makhov
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295
| | - Stephen W Fullerton
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany
| | - Stefan Kalkhof
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany
| | - John E McGeehan
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Peter D Cary
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295
| | - Dmitri Svergun
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Geoff G Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Paul A Tucker
- From European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany.
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6
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Wei Y, Qu MH, Wang XS, Chen L, Wang DL, Liu Y, Hua Q, He RQ. Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation. PLoS One 2008; 3:e2600. [PMID: 18596978 PMCID: PMC2432501 DOI: 10.1371/journal.pone.0002600] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 06/03/2008] [Indexed: 11/22/2022] Open
Abstract
Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H2O2/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.
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Affiliation(s)
- Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Hua Qu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing-Sheng Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lan Chen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dong-Liang Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qian Hua
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Rong-Qiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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7
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Abstract
Autographa californica nuclear polyhedrosis virus, or AcMNPV, is the type member of the baculoviruses, a family of double-stranded DNA viruses with large circular genomes. The successive and concomitant expression of an assortment of early, late and very late genes is instrumental for successful baculovirus infection, and requires a switch from early dependence on a host cell-derived polymerase II to a novel virus-encoded RNA polymerase that is required for transcription later on in infection. A series of repetitive and highly conserved sequences known as homologous regions, or hrs, function both as origins of DNA replication as well as transcriptional enhancers of late gene expression. An array of AcMNPV genes produced early on in infection, known as late expression factors, or LEFs, are essential for both replication and late gene expression. In this review, an overview of baculovirus LEFs and their roles in viral replication and late gene expression is presented. The role of LEFs in determining baculovirus host range is described. Finally, we compare baculovirus replication and transcription machinery with other viral systems.
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Macao B, Olsson M, Elias P. Functional properties of the herpes simplex virus type I origin-binding protein are controlled by precise interactions with the activated form of the origin of DNA replication. J Biol Chem 2004; 279:29211-7. [PMID: 15133043 DOI: 10.1074/jbc.m400371200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The herpes simplex virus, type I origin-binding protein, OBP, is a superfamily II DNA helicase encoded by the UL9 gene. OBP binds in a sequence-specific and cooperative way to the viral origin of replication oriS. OBP may unwind partially and introduce a hairpin into the double-stranded origin of replication. The formation of the novel conformation referred to as oriS* also requires the single-stranded DNA-binding protein, ICP8, and ATP hydrolysis. OBP forms a stable complex with oriS*. The hairpin in oriS* provides a site for sequence-specific attachment, and a single-stranded region triggers ATP hydrolysis. Here we use Escherichia coli exonuclease I to map the binding of the C-terminal domain of OBP to the hairpin and the helicase domains to the single-stranded tail. The helicase domains cover a stretch of 23 nucleotides of single-stranded DNA. Using streptavidin-coated magnetic beads, we show that OBP may bind two copies of double-stranded DNA (one biotin-labeled and the other one radioactively labeled) but only one copy of oriS*. It is the length of the single-stranded tail that determines the stoichiometry of OBP.DNA complexes. OBP interacts with the bases of the single-stranded tail, and ATP hydrolysis is triggered by position-specific interactions between OBP and bases in the single-stranded tail of oriS*.
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Affiliation(s)
- Bertil Macao
- Department of Medical Biochemistry, Göteborg University, Box 440, S-405 30 Göteborg, Sweden
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Hefferon KL, Miller LK. Reconstructing the replication complex of AcMNPV. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:6233-40. [PMID: 12473119 DOI: 10.1046/j.1432-1033.2002.03342.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Baculoviruses are well known for their large, circular, double-stranded DNA genomes. The type member, AcMNPV, is the best characterized and undergoes a succession of early, late and very late gene expression during its infection cycle. The viral genes involved in DNA replication have previously been identified and their products are required for the activation of late gene expression. In this study, we FLAG- and HA-tagged the replication late expression factors of AcMNPV, examined their expression and functional activities by CAT assay and Western blot analysis, and determined their subcellular localization in transfected cells by subcellular fractionation and immunofluorescent microscopy. We found that all replication LEFs with the exception of P143 and P35 resided in the nucleus of transfected cells. We further investigated the interactions among various replication LEFs using both yeast two-hybrid and coprecipitation strategies. A summary of the interactive properties of the replication LEFs is presented and a model for a putative AcMNPV replication complex is offered.
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Affiliation(s)
- Kathleen L Hefferon
- Center for Virology, Department of Botany, University of Toronto, Ontario, Canada
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Aslani A, Olsson M, Elias P. ATP-dependent unwinding of a minimal origin of DNA replication by the origin-binding protein and the single-strand DNA-binding protein ICP8 from herpes simplex virus type I. J Biol Chem 2002; 277:41204-12. [PMID: 12183471 DOI: 10.1074/jbc.m208270200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Herpes simplex virus type I origin-binding protein, OBP, is encoded by the UL9 gene. OBP binds the origin of DNA replication, oriS, in a cooperative and sequence-specific manner. OBP is also an ATP-dependent DNA helicase. We have recently shown that single-stranded oriS folds into a unique and evolutionarily conserved conformation, oriS*, which is stably bound by OBP. OriS* contains a stable hairpin formed by complementary base pairing between box I and box III in oriS. Here we show that OBP, in the presence of the single-stranded DNA-binding protein ICP8, can convert an 80-base pair double-stranded minimal oriS fragment to oriS* and form an OBP-oriS* complex. The formation of an OBP-oriS* complex requires hydrolysable ATP. We also demonstrate that OBP in the presence of ICP8 and ATP promotes slow but specific and complete unwinding of duplex minimal oriS. The possibility that the OBP-oriS* complex may serve as an assembly site for the herpes virus replisome is discussed.
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Affiliation(s)
- Alireza Aslani
- Department of Medical Biochemistry, Göteborg University, Box 440, SE 405 30 Göteborg University, Sweden
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11
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Kwok Y, Zhang W, Schroth GP, Liang CH, Alexi N, Bruice TW. Allosteric interaction of minor groove binding ligands with UL9-DNA complexes. Biochemistry 2001; 40:12628-38. [PMID: 11601987 DOI: 10.1021/bi0109865] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The herpes simplex virus type 1 origin binding protein (UL9) is a sequence-specific DNA binding protein. Several studies have demonstrated that UL9 binds to the 11-base pair sequence 5'-CGTTCGCACTT-3' primarily, or solely, through interaction with the major groove. Minor groove binding ligands, such as distamycin, netropsin, and GLX, an indole-linked dimer of netropsin, can effectively disrupt the UL9-DNA complex only when their DNA binding sites are coincident with the right side of the DNA binding site of the protein and overlap with the protein binding site by two (TT) base pairs. These results suggest that the right side of the UL9-DNA complex has a unique structure that is sensitive to minor groove ligand binding. In addition, a biphasic displacement curve was observed with GLX, which suggests two modes of ligand binding which have different effects on UL9-DNA complexes. Using a fluorescence-based hybridization stabilization assay, we determined that GLX can bind to its binding site as an overlapping dimer (i.e., 2:1 stoichiometry). Footprinting of UL9-DNA complexes with the minor groove directed chemical nuclease 1,10-phenanthroline copper confirms that the DNA conformation at the position of the right-side ligand binding site of GLX is altered and has a widened minor groove. In contrast, it is well established that at 1:1 stoichiometries, AT sequence specific ligands, such as netropsin, distamycin, and GLX, prefer uniform, narrow minor grooves. The opposing conformational requirements of UL9 and lower concentrations of GLX at the ligand binding A-tract overlapping the right side of the protein binding site indicate that allosteric inhibition, rather than direct steric competition, contributes to ligand-induced protein displacement. At higher GLX concentrations, giving 2:1 binding in a widened minor groove, co-binding with UL9 is allowed. A model is presented that is consistent with these observations, and implications for targeted regulation of gene transcription are discussed.
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Affiliation(s)
- Y Kwok
- Genelabs Technologies, Inc., 505 Penobscot Drive, Redwood City, California 94063, USA
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12
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Aslani A, Macao B, Simonsson S, Elias P. Complementary intrastrand base pairing during initiation of Herpes simplex virus type 1 DNA replication. Proc Natl Acad Sci U S A 2001; 98:7194-9. [PMID: 11416203 PMCID: PMC34645 DOI: 10.1073/pnas.121177198] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The herpes simplex virus type 1 origin of DNA replication, oriS, contains three copies of the recognition sequence for the viral initiator protein, origin binding protein (OBP), arranged in two palindromes. The central box I forms a short palindrome with box III and a long palindrome with box II. Single-stranded oriS adopts a conformation, oriS*, that is tightly bound by OBP. Here we demonstrate that OBP binds to a box III-box I hairpin with a 3' single-stranded tail in oriS*. Mutations designed to destabilize the hairpin abolish the binding of OBP to oriS*. The same mutations also inhibit DNA replication. Second site complementary mutations restore binding of OBP to oriS* as well as the ability of mutated oriS to support DNA replication. OriS* is also an efficient activator of the hydrolysis of ATP by OBP. Sequence analyses show that a box III-box I palindrome is an evolutionarily conserved feature of origins of DNA replication from human, equine, bovine, and gallid alpha herpes viruses. We propose that oriS facilitates initiation of DNA synthesis in two steps and that OBP exhibits exquisite specificity for the different conformations oriS adopts at these stages. Our model suggests that distance-dependent cooperative binding of OBP to boxes I and II in duplex DNA is succeeded by specific recognition of a box III-box I hairpin in partially unwound DNA.
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Affiliation(s)
- A Aslani
- Department of Medical Biochemistry, Göteborg University, Box 440, SE-405 30, Göteborg, Sweden
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13
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Krug LT, Inoue N, Pellett PE. Sequence requirements for interaction of human herpesvirus 7 origin binding protein with the origin of lytic replication. J Virol 2001; 75:3925-36. [PMID: 11264381 PMCID: PMC114883 DOI: 10.1128/jvi.75.8.3925-3936.2001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As do human herpesvirus 6 variants A and B (HHV-6A and -6B), HHV-7 encodes a homolog of the alphaherpesvirus origin binding protein (OBP), which binds at sites in the origin of lytic replication (oriLyt) to initiate DNA replication. In this study, we sought to characterize the interaction of the HHV-7 OBP (OBP(H7)) with its cognate sites in the 600-bp HHV-7 oriLyt. We expressed the carboxyl-terminal domain of OBP(H7) and found that amino acids 484 to 787 of OBP(H7) were sufficient for DNA binding activity by electrophoretic mobility shift analysis. OBP(H7) has one high-affinity binding site (OBP-2) located on one flank of an AT-rich spacer element and a low-affinity site (OBP-1) on the other. This is in contrast to the HHV-6B OBP (OBP(H6B)), which binds with similar affinity to its two cognate OBP sites in the HHV-6B oriLyt. The minimal recognition element of the OBP-2 site was mapped to a 14-bp sequence. The OBP(H7) consensus recognition sequence of the 9-bp core, BRTYCWCCT (where B is a T, G, or C; R is a G or A; Y is a T or C; and W is a T or A), overlaps with the OBP(H6B) consensus YGWYCWCCY and establishes YCWCC as the roseolovirus OBP core recognition sequence. Heteroduplex analysis suggests that OBP(H7) interacts along one face of the DNA helix, with the major groove, as do OBP(H6B) and herpes simplex virus type 1 OBP. Together, these results illustrate both conserved and divergent DNA binding properties between OBP(H7) and OBP(H6B).
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Binding, Competitive
- Cell Line
- Consensus Sequence/genetics
- DNA Replication
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Herpesvirus 7, Human/genetics
- Herpesvirus 7, Human/metabolism
- Heteroduplex Analysis
- Humans
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- RNA, Viral/analysis
- RNA, Viral/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Replication Origin/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Thermodynamics
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- L T Krug
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia, USA
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14
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Abstract
Dimethyl suberimidate is a bifunctional reagent that is used for cross-linking the protein components of oligomeric macromolecules. In this report, dimethyl suberimidate is shown to specifically cross-link oligo(dT) of varying lengths to the DNA-binding subunits of a multimeric helicase-primase encoded by herpes simplex virus type 1. This result indicates that dimethyl suberimidate and other imidoester cross-linking reagents may be useful for characterizing the interaction of oligo(dT) with proteins that bind single-stranded DNA.
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Affiliation(s)
- M S Dodson
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721-0088, USA
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Aslani A, Simonsson S, Elias P. A novel conformation of the herpes simplex virus origin of DNA replication recognized by the origin binding protein. J Biol Chem 2000; 275:5880-7. [PMID: 10681580 DOI: 10.1074/jbc.275.8.5880] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Herpes simplex virus type I origin binding protein (OBP) is a sequence-specific DNA-binding protein and a dimeric DNA helicase encoded by the UL9 gene. It is required for the activation of the viral origin of DNA replication oriS. Here we demonstrate that the linear double-stranded form of oriS can be converted by heat treatment to a stable novel conformation referred to as oriS*. Studies using S1 nuclease suggest that oriS* consists of a central hairpin with an AT-rich sequence in the loop. Single-stranded oligonucleotides corresponding to the upper strand of oriS can adopt the same structure. OBP forms a stable complex with oriS*. We have identified structural features of oriS* recognized by OBP. The central oriS palindrome as well as sequences at the 5' side of the oriS palindrome were required for complex formation. Importantly, we found that mutations that have been shown to reduce oriS-dependent DNA replication also reduce the formation of the OBP-oriS* complex. We suggest that oriS* serves as an intermediate in the initiation of DNA replication providing the initiator protein with structural information for a selective and efficient assembly of the viral replication machinery.
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Affiliation(s)
- A Aslani
- Department of Medical Biochemistry, Göteborg University, Box 440, SE 405 30 Göteborg, Sweden
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Murata LB, Dodson MS. The herpes simplex virus type 1 origin-binding protein. sequence-specific activation of adenosine triphosphatase activity by a double-stranded DNA containing box I. J Biol Chem 1999; 274:37079-86. [PMID: 10601266 DOI: 10.1074/jbc.274.52.37079] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Origin-dependent replication of the herpes simplex virus type 1 genome requires the virally encoded origin-binding protein, UL9. UL9 binds specifically to the herpes simplex virus type 1 replication origin at two high affinity binding sites on the DNA, Boxes I and II. UL9 also has ATP-dependent DNA helicase and DNA-stimulated ATPase activities that are used to unwind the origin DNA. Origin-specific binding is mediated by the C-terminal domain (C-domain) of the enzyme. ATPase and helicase activities are mediated by the N-terminal domain (N-domain). Previous studies have shown that single-stranded DNA is a good coeffector for ATPase activity. We have analyzed several DNAs for their ability to stimulate the ATPase activity of UL9 and of a truncated UL9 protein (UL9/N) consisting only of the N-domain. We report here that duplex Box I DNA specifically and potently stimulates the ATPase activity of UL9 but not of UL9/N. We also find that removal of the C-domain significantly increases the ATPase activity of UL9. We have incorporated these results into a model for initiation in which the C-domain of UL9 serves to regulate the enzymatic activity of the N-domain.
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Affiliation(s)
- L B Murata
- Department of Biochemistry, University of Arizona, Tucson, Arizona 85721-0088, USA
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