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Fragkoulis G, Hangas A, Fekete Z, Michell C, Moraes C, Willcox S, Griffith JD, Goffart S, Pohjoismäki JO. Linear DNA-driven recombination in mammalian mitochondria. Nucleic Acids Res 2024; 52:3088-3105. [PMID: 38300793 PMCID: PMC11014290 DOI: 10.1093/nar/gkae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic due to its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we took advantage of a cell model with two different types of mitochondrial genomes and impaired its ability to degrade broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot and by long range PacBio® HiFi sequencing approach. Besides utilizing different electrophoretic methods, we also directly observed molecular complexes between different mtDNA haplotypes and recombination intermediates using transmission electron microscopy. We propose that the known copy-choice recombination by mitochondrial replisome could be sufficient for the needs of the small genome, thus removing the requirement for a specialized mitochondrial recombinase. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.
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Affiliation(s)
- Georgios Fragkoulis
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Zsófia Fekete
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Doctoral School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Craig Michell
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami,FL, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
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2
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Zhou Y, Yuan R, Cone AS, Shifflett KW, Arias GF, Peng A, Chambers MG, McNamara RP, Willcox S, Landis JT, Pan Y, Griffith J, Dittmer DP. Large-scale heparin-based bind-and-elute chromatography identifies two biologically distinct populations of extracellular vesicles. J Extracell Vesicles 2023; 12:e12327. [PMID: 37272197 PMCID: PMC10240191 DOI: 10.1002/jev2.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 06/06/2023] Open
Abstract
Purifying extracellular vesicles (EVs) has been challenging because EVs are heterogeneous in cargo yet share similar sizes and densities. Most surface marker-based affinity separation methods are limited to research or diagnostic scales. We report that heparin chromatography can separate purified EVs into two distinct subpopulations as ascertained by MS/MS: a non-heparin-binding (NHB) fraction that contains classical EV markers such as tetraspanins and a heparin-binding (HB) fraction enriched in fibronectins and histones. Both fractions were similarly fusogenic but induced different transcriptional responses in endothelial cells. While EVs that were purified by conventional, non-affinity methods alone induced ERK1/2 phosphorylation and Ki67, the NHB fraction did not. This result suggests heparin chromatography as an additional novel fractionation step that is inherently scalable, does not lead to loss of material, and separates inflammatory and pyrogenic EVs from unreactive EVs, which will improve clinical applications.
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Affiliation(s)
- Yijun Zhou
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runjie Yuan
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allaura S Cone
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle W Shifflett
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gabriel F Arias
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alice Peng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith G Chambers
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ryan P McNamara
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin T Landis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yue Pan
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jack Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Ledford BT, Akerman AW, Sun K, Gillis DC, Weiss JM, Vang J, Willcox S, Clemons TD, Sai H, Qiu R, Karver MR, Griffith JD, Tsihlis ND, Stupp SI, Ikonomidis JS, Kibbe MR. Peptide Amphiphile Supramolecular Nanofibers Designed to Target Abdominal Aortic Aneurysms. ACS Nano 2022; 16:7309-7322. [PMID: 35504018 PMCID: PMC9733406 DOI: 10.1021/acsnano.1c06258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An abdominal aortic aneurysm (AAA) is a localized dilation of the aorta located in the abdomen that poses a severe risk of death when ruptured. The cause of AAA is not fully understood, but degradation of medial elastin due to elastolytic matrix metalloproteinases is a key step leading to aortic dilation. Current therapeutic interventions are limited to surgical repair to prevent catastrophic rupture. Here, we report the development of injectable supramolecular nanofibers using peptide amphiphile molecules designed to localize to AAA by targeting fragmented elastin, matrix metalloproteinase 2 (MMP-2), and membrane type 1 matrix metalloproteinase. We designed four targeting peptide sequences from X-ray crystallographic data and incorporated them into PA molecules via solid phase peptide synthesis. After coassembling targeted and diluent PAs at different molar ratios, we assessed their ability to form nanofibers using transmission electron microscopy and to localize to AAA in male and female Sprague-Dawley rats using light sheet fluorescence microscopy. We found that three formulations of the PA nanofibers were able to localize to AAA tissue, but the MMP-2 targeting PA substantially outperformed the other nanofibers. Additionally, we demonstrated that the MMP-2 targeting PA nanofibers had an optimal dose of 5 mg (∼12 mg/kg). Our results show that there was not a significant difference in targeting between male and female Sprague-Dawley rats. Given the ability of the MMP-2 targeting PA nanofiber to localize to AAA tissue, future studies will investigate potential diagnostic and targeted drug delivery applications for AAA.
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Affiliation(s)
- Benjamin T. Ledford
- Department of Surgery, University of Virginia, Charlottesville, VA 22903, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam W. Akerman
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kui Sun
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David C. Gillis
- Department of Surgery, University of Virginia, Charlottesville, VA 22903, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenna M. Weiss
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Johnny Vang
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tristan D. Clemons
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Hiroaki Sai
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Ruomeng Qiu
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Mark R. Karver
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nick D. Tsihlis
- Department of Surgery, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel I. Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - John S. Ikonomidis
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melina R. Kibbe
- Department of Surgery, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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McNamara RP, Zhou Y, Eason AB, Landis JT, Chambers MG, Willcox S, Peterson TA, Schouest B, Maness NJ, MacLean AG, Costantini LM, Griffith JD, Dittmer DP. Imaging of surface microdomains on individual extracellular vesicles in 3-D. J Extracell Vesicles 2022; 11:e12191. [PMID: 35234354 PMCID: PMC8888793 DOI: 10.1002/jev2.12191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/18/2022] [Accepted: 01/31/2022] [Indexed: 01/19/2023] Open
Abstract
Extracellular vesicles (EVs) are secreted from all cell types and are intimately involved in tissue homeostasis. They are being explored as vaccine and gene therapy platforms, as well as potential biomarkers. As their size is below the diffraction limit of light microscopy, direct visualizations have been daunting and single-particle studies under physiological conditions have been hampered. Here, direct stochastic optical reconstruction microscopy (dSTORM) was employed to visualize EVs in three-dimensions and to localize molecule clusters such as the tetraspanins CD81 and CD9 on the surface of individual EVs. These studies demonstrate the existence of membrane microdomains on EVs. These were confirmed by Cryo-EM. Individual particle visualization provided insights into the heterogeneity, structure, and complexity of EVs not previously appreciated.
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Affiliation(s)
- Ryan P. McNamara
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Yijun Zhou
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Anthony B. Eason
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Justin T. Landis
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Meredith G. Chambers
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Tiffany A. Peterson
- Tulane National Primate Research CentreTulane UniversityCovingtonLouisianaUSA
| | - Blake Schouest
- Tulane National Primate Research CentreTulane UniversityCovingtonLouisianaUSA
| | - Nicholas J. Maness
- Tulane National Primate Research CentreTulane UniversityCovingtonLouisianaUSA
| | - Andrew G. MacLean
- Tulane National Primate Research CentreTulane UniversityCovingtonLouisianaUSA
| | - Lindsey M. Costantini
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth CarolinaUSA
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Dirk Peter Dittmer
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA,Lineberger Comprehensive Cancer CentreThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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5
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Mercel AI, Marulanda K, Gillis DC, Sun K, Clemons TD, Willcox S, Griffith J, Peters EB, Karver MR, Tsihlis ND, Maile R, Stupp SI, Kibbe MR. Development of novel nanofibers targeted to smoke-injured lungs. Biomaterials 2021; 274:120862. [PMID: 33975274 DOI: 10.1016/j.biomaterials.2021.120862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/02/2021] [Accepted: 04/26/2021] [Indexed: 11/26/2022]
Abstract
Smoke inhalation injury is associated with significant mortality and current therapies remain supportive. The purpose of our study was to identify proteins upregulated in the lung after smoke inhalation injury and develop peptide amphiphile nanofibers that target these proteins. We hypothesize that nanofibers targeted to angiotensin-converting enzyme or receptor for advanced glycation end products will localize to smoke-injured lungs. METHODS Five targeting sequences were incorporated into peptide amphiphile monomers methodically to optimize nanofiber formation. Nanofiber formation was assessed by conventional transmission electron microscopy. Rats received 8 min of wood smoke. Levels of angiotensin-converting enzyme and receptor for advanced glycation end products were evaluated by immunofluorescence. Rats received the targeted nanofiber 23 h after injury via tail vein injection. Nanofiber localization was determined by fluorescence quantification. RESULTS Peptide amphiphile purity (>95%) and nanofiber formation were confirmed. Target proteins were increased in smoke inhalation versus sham (p < 0.001). After smoke inhalation and injection of targeted nanofibers, we found a 10-fold increase in angiotensin-converting enzyme-targeted nanofiber localization to lung (p < 0.001) versus sham with minimal localization of non-targeted nanofiber (p < 0.001). CONCLUSIONS We synthesized, characterized, and evaluated systemically delivered targeted nanofibers that localized to the site of smoke inhalation injury in vivo. Angiotensin-converting enzyme-targeted nanofibers serve as the foundation for developing a novel nanotherapeutic that treats smoke inhalation lung injury.
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Affiliation(s)
- Alexandra I Mercel
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kathleen Marulanda
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David C Gillis
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kui Sun
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tristan D Clemons
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Smaranda Willcox
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jack Griffith
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Erica B Peters
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Mark R Karver
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Nick D Tsihlis
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Rob Maile
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA; Curriculum of Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Samuel I Stupp
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA; Department of Materials Science & Engineering, Northwestern University, Evanston, IL, 60208, USA; Department of Medicine, Northwestern University, Chicago, IL, 60611, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melina R Kibbe
- Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA; Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Yang R, Lee E, Willcox S, Kim J, Sullivan C, Zhao J, Griffith J, Wang R. 109 Characterization of Polyomavirus encoded-circular RNAs in Merkel Cell Carcinoma. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Amunugama R, Willcox S, Wu RA, Abdullah UB, El-Sagheer AH, Brown T, McHugh PJ, Griffith JD, Walter JC. Replication Fork Reversal during DNA Interstrand Crosslink Repair Requires CMG Unloading. Cell Rep 2019; 23:3419-3428. [PMID: 29924986 PMCID: PMC6086610 DOI: 10.1016/j.celrep.2018.05.061] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 01/08/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are extremely cytotoxic, but the mechanism of their repair remains incompletely understood. Using Xenopus egg extracts, we previously showed that repair of a cisplatin ICL is triggered when two replication forks converge on the lesion. After CDC45/MCM2-7/GINS (CMG) ubiquitylation and unloading by the p97 segregase, FANCI-FANCD2 promotes DNA incisions by XPF-ERCC1, leading to ICL unhooking. Here, we report that, during this cell-free ICL repair reaction, one of the two converged forks undergoes reversal. Fork reversal fails when CMG unloading is inhibited, but it does not require FANCI-FANCD2. After one fork has undergone reversal, the opposing fork that still abuts the ICL undergoes incisions. Our data show that replication fork reversal at an ICL requires replisome disassembly. We present a revised model of ICL repair that involves a reversed fork intermediate.
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Affiliation(s)
- Ravindra Amunugama
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - R Alex Wu
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ummi B Abdullah
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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8
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Tomaska L, Nosek J, Kar A, Willcox S, Griffith JD. A New View of the T-Loop Junction: Implications for Self-Primed Telomere Extension, Expansion of Disease-Related Nucleotide Repeat Blocks, and Telomere Evolution. Front Genet 2019; 10:792. [PMID: 31475042 PMCID: PMC6702307 DOI: 10.3389/fgene.2019.00792] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022] Open
Abstract
Telomere loops (t-loops) are formed at the ends of chromosomes in species ranging from humans to worms, plants, and with genetic manipulation, some yeast. Recent in vitro studies demonstrated that transcription of telomeric DNA leads to highly efficient t-loop formation. It was also shown that both DNA termini are inserted into the preceding DNA to generate a highly stable t-loop junction. Furthermore, some telomeric RNA remains present at the junction, potentially acting as a plug to further protect and stabilize the t-loop. Modeling the loop junction reveals two mechanisms by which the canonical chromosomal replication factors could extend the telomere in the absence of telomerase. One mechanism would utilize the annealed 3’ terminus as a de novo replication origin. In vitro evidence for the ability of the t-loop to prime telomere extension using the T7 replication factors is presented. A second mechanism would involve resolution of the Holliday junction present in the t-loop bubble by factors such as GEN1 to generate a rolling circle template at the extreme terminus of the telomere. This could lead to large expansions of the telomeric tract. Here, we propose that telomeres evolved as terminal elements containing long arrays of short nucleotide repeats due to the ability of such arrays to fold back into loops and self-prime their replicative extension. In this view, telomerase may have evolved later to provide a more precise mechanism of telomere maintenance. Both pathways have direct relevance to the alternative lengthening of telomeres (ALT) pathway. This view also provides a possible mechanism for the very large repeat expansions observed in nucleotide repeat diseases such as Fragile X syndrome, myotonic dystrophy, familial amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). The evolution of telomeres is discussed in the framework of these models.
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Affiliation(s)
- Lubomir Tomaska
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Tomáška Ĺ, Nosek J, Sepšiová R, Červenák F, Juríková K, Procházková K, Neboháčová M, Willcox S, Griffith JD. Commentary: Single-stranded telomere-binding protein employs a dual rheostat for binding affinity and specificity that drives function. Front Genet 2019; 9:742. [PMID: 30697232 PMCID: PMC6341069 DOI: 10.3389/fgene.2018.00742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/22/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ĺubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Červenák
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarína Juríková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
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10
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Erdel F, Kratz K, Willcox S, Griffith JD, Greene EC, de Lange T. Telomere Recognition and Assembly Mechanism of Mammalian Shelterin. Cell Rep 2017; 18:41-53. [PMID: 28052260 DOI: 10.1016/j.celrep.2016.12.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/13/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022] Open
Abstract
Shelterin is a six-subunit protein complex that plays crucial roles in telomere length regulation, protection, and maintenance. Although several shelterin subunits have been studied in vitro, the biochemical properties of the fully assembled shelterin complex are not well defined. Here, we characterize shelterin using ensemble biochemical methods, electron microscopy, and single-molecule imaging to determine how shelterin recognizes and assembles onto telomeric repeats. We show that shelterin complexes can exist in solution and primarily locate telomeric DNA through a three-dimensional diffusive search. Shelterin can diffuse along non-telomeric DNA but is impeded by nucleosomes, arguing against extensive one-dimensional diffusion as a viable assembly mechanism. Our work supports a model in which individual shelterin complexes rapidly bind to telomeric repeats as independent functional units, which do not alter the DNA-binding mode of neighboring complexes but, rather, occupy telomeric DNA in a "beads on a string" configuration.
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Affiliation(s)
- Fabian Erdel
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Katja Kratz
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA.
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Kar A, Willcox S, Griffith JD. Transcription of telomeric DNA leads to high levels of homologous recombination and t-loops. Nucleic Acids Res 2016; 44:9369-9380. [PMID: 27608724 PMCID: PMC5100571 DOI: 10.1093/nar/gkw779] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022] Open
Abstract
The formation of DNA loops at chromosome ends (t-loops) and the transcription of telomeres producing G-rich RNA (TERRA) represent two central features of telomeres. To explore a possible link between them we employed artificial human telomeres containing long arrays of TTAGGG repeats flanked by the T7 or T3 promoters. Transcription of these DNAs generates a high frequency of t-loops within individual molecules and homologous recombination events between different DNAs at their telomeric sequences. T-loop formation does not require a single strand overhang, arguing that both terminal strands insert into the preceding duplex. The loops are very stable and some RNase H resistant TERRA remains at the t-loop, likely adding to their stability. Transcription of DNAs containing TTAGTG or TGAGTG repeats showed greatly reduced loop formation. While in the cell multiple pathways may lead to t-loop formation, the pathway revealed here does not depend on the shelterins but rather on the unique character of telomeric DNA when it is opened for transcription. Hence, telomeric sequences may have evolved to facilitate their ability to loop back on themselves.
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Affiliation(s)
- Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
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12
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Sepsiova R, Necasova I, Willcox S, Prochazkova K, Gorilak P, Nosek J, Hofr C, Griffith JD, Tomaska L. Evolution of Telomeres in Schizosaccharomyces pombe and Its Possible Relationship to the Diversification of Telomere Binding Proteins. PLoS One 2016; 11:e0154225. [PMID: 27101289 PMCID: PMC4839565 DOI: 10.1371/journal.pone.0154225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/11/2016] [Indexed: 11/30/2022] Open
Abstract
Telomeres of nuclear chromosomes are usually composed of an array of tandemly repeated sequences that are recognized by specific Myb domain containing DNA-binding proteins (telomere-binding proteins, TBPs). Whereas in many eukaryotes the length and sequence of the telomeric repeat is relatively conserved, telomeric sequences in various yeasts are highly variable. Schizosaccharomyces pombe provides an excellent model for investigation of co-evolution of telomeres and TBPs. First, telomeric repeats of S. pombe differ from the canonical mammalian type TTAGGG sequence. Second, S. pombe telomeres exhibit a high degree of intratelomeric heterogeneity. Third, S. pombe contains all types of known TBPs (Rap1p [a version unable to bind DNA], Tay1p/Teb1p, and Taz1p) that are employed by various yeast species to protect their telomeres. With the aim of reconstructing evolutionary paths leading to a separation of roles between Teb1p and Taz1p, we performed a comparative analysis of the DNA-binding properties of both proteins using combined qualitative and quantitative biochemical approaches. Visualization of DNA-protein complexes by electron microscopy revealed qualitative differences of binding of Teb1p and Taz1p to mammalian type and fission yeast telomeres. Fluorescence anisotropy analysis quantified the binding affinity of Teb1p and Taz1p to three different DNA substrates. Additionally, we carried out electrophoretic mobility shift assays using mammalian type telomeres and native substrates (telomeric repeats, histone-box sequences) as well as their mutated versions. We observed relative DNA sequence binding flexibility of Taz1p and higher binding stringency of Teb1p when both proteins were compared directly to each other. These properties may have driven replacement of Teb1p by Taz1p as the TBP in fission yeast.
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Affiliation(s)
- Regina Sepsiova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Ivona Necasova
- Chromatin Molecular Complexes, Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Katarina Prochazkova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Peter Gorilak
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Ctirad Hofr
- Chromatin Molecular Complexes, Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Lubomir Tomaska
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
- * E-mail:
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13
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Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell Rep 2015; 11:1749-59. [PMID: 26051933 DOI: 10.1016/j.celrep.2015.05.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/11/2015] [Indexed: 12/15/2022] Open
Abstract
MicroDNAs are <400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5'-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair.
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Affiliation(s)
- Laura W Dillon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Shunichi Takeda
- CREST Research Project, Japan Science and Technology Corporation, Radiation Genetics, Faculty of Medicine, Kyoto University, Konoe Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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14
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Lewis SC, Joers P, Willcox S, Griffith JD, Jacobs HT, Hyman BC. A rolling circle replication mechanism produces multimeric lariats of mitochondrial DNA in Caenorhabditis elegans. PLoS Genet 2015; 11:e1004985. [PMID: 25693201 PMCID: PMC4334201 DOI: 10.1371/journal.pgen.1004985] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.
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Affiliation(s)
- Samantha C. Lewis
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Priit Joers
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Estonian Biocentre, Tartu, Estonia
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Howard T. Jacobs
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Bradley C. Hyman
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
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15
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Bermek O, Willcox S, Griffith JD. DNA replication catalyzed by herpes simplex virus type 1 proteins reveals trombone loops at the fork. J Biol Chem 2014; 290:2539-45. [PMID: 25471368 DOI: 10.1074/jbc.m114.623009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Using purified replication factors encoded by herpes simplex virus type 1 and a 70-base minicircle template, we obtained robust DNA synthesis with leading strand products of >20,000 nucleotides and lagging strand fragments from 600 to 9,000 nucleotides as seen by alkaline gel electrophoresis. ICP8 was crucial for the synthesis on both strands. Visualization of the deproteinized products using electron microscopy revealed long, linear dsDNAs, and in 87%, one end, presumably the end with the 70-base circle, was single-stranded. The remaining 13% had multiple single-stranded segments separated by dsDNA segments 500 to 1,000 nucleotides in length located at one end. These features are diagnostic of the trombone mechanism of replication. Indeed, when the products were examined with the replication proteins bound, a dsDNA loop was frequently associated with the replication complex located at one end of the replicated DNA. Furthermore, the frequency of loops correlated with the fraction of DNA undergoing Okazaki fragment synthesis.
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Affiliation(s)
- Oya Bermek
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
| | - Smaranda Willcox
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
| | - Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
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16
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Chen SH, Plank JL, Willcox S, Griffith JD, Hsieh TS. Top3α is required during the convergent migration step of double Holliday junction dissolution. PLoS One 2014; 9:e83582. [PMID: 24392087 PMCID: PMC3879244 DOI: 10.1371/journal.pone.0083582] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 11/19/2022] Open
Abstract
Although Blm and Top3α are known to form a minimal dissolvasome that can uniquely undo a double Holliday junction structure, the details of the mechanism remain unknown. It was originally suggested that Blm acts first to create a hemicatenane structure from branch migration of the junctions, followed by Top3α performing strand passage to decatenate the interlocking single strands. Recent evidence suggests that Top3α may also be important for assisting in the migration of the junctions. Using a mismatch-dHJ substrate (MM-DHJS) and eukaryotic Top1 (in place of Top3α), we show that the presence of a topoisomerase is required for Blm to substantially migrate a topologically constrained Holliday junction. When investigated by electron microscopy, these migrated structures did not resemble a hemicatenane. However, when Blm is together with Top3α, the dissolution reaction is processive with no pausing at a partially migrated structure. Potential mechanisms are discussed.
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Affiliation(s)
- Stefanie Hartman Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jody L. Plank
- Department of Microbiology, University of California Davis, Davis, California, United States of America
| | - Smaranda Willcox
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tao-shih Hsieh
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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17
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Abstract
Previously, we published a method for creating a novel DNA substrate, the double Holliday junction substrate. This substrate contains two Holliday junctions that are mobile, topologically constrained and separated by a distance comparable with conversion tract lengths. Although useful for studying late stage homologous recombination in vitro, construction of the substrate requires significant effort. In particular, there are three bottlenecks: (i) production of large quantities of single-stranded DNA; (ii) the loss of a significant portion of the DNA following the recombination step; and (iii) the loss of DNA owing to inefficient gel extraction. To address these limitations, we have made the following changes to the protocol: (i) use of a helper plasmid, rather than exogenous helper phage, to produce single-stranded DNA; (ii) use of the unidirectional ϕC31 integrase system in place of the bidirectional Cre recombinase reaction; and (iii) gel extraction by DNA diffusion. Here, we describe the changes made to the materials and methods and characterize the substrates that can be produced, including migratable single Holliday junctions, hemicatenanes and a quadruple Holliday junction substrate.
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18
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Willcox S, Butt P, Hakaraia-Tino T, Sullivan B, Hudson R. WAI wise: a fun, practical and effective water safety experience for young adults. Inj Prev 2012. [DOI: 10.1136/injuryprev-2012-040590h.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Visacka K, Hofr C, Willcox S, Necasova I, Pavlouskova J, Sepsiova R, Wimmerova M, Simonicova L, Nosek J, Fajkus J, Griffith JD, Tomaska L. Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres. J Biol Chem 2012; 287:32206-15. [PMID: 22815473 DOI: 10.1074/jbc.m112.385591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Double-stranded regions of the telomeres are recognized by proteins containing Myb-like domains conferring specificity toward telomeric repeats. Although biochemical and structural studies revealed basic molecular principles involved in DNA binding, relatively little is known about evolutionary pathways leading to various types of Myb domain-containing proteins in divergent species of eukaryotes. Recently we identified a novel type of telomere-binding protein YlTay1p from the yeast Yarrowia lipolytica containing two Myb domains (Myb1, Myb2) very similar to the Myb domain of mammalian TRF1 and TRF2. In this study we prepared mutant versions of YlTay1p lacking Myb1, Myb2, or both Myb domains and found that YlTay1p carrying either Myb domain exhibits preferential affinity to both Y. lipolytica (GGGTTAGTCA)(n) and human (TTAGGG)(n) telomeric sequences. Quantitative measurements of the protein binding to telomeric DNA revealed that the presence of both Myb domains is required for a high affinity of YlTay1p to either telomeric repeat. Additionally, we performed detailed thermodynamic analysis of the YlTay1p interaction with its cognate telomeric DNA, which is to our knowledge the first energetic description of a full-length telomeric-protein binding to DNA. Interestingly, when compared with human TRF1 and TRF2 proteins, YlTay1p exhibited higher affinity not only for Y. lipolytica telomeres but also for human telomeric sequences. The duplication of the Myb domain region in YlTay1p thus produces a synergistic effect on its affinity toward the cognate telomeric sequence, alleviating the need for homodimerization observed in TRF-like proteins possessing a single Myb domain.
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Affiliation(s)
- Katarina Visacka
- Department of Genetics and Biochemistry, Comenius University, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava, Slovakia
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20
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Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 2012; 336:82-6. [PMID: 22403181 DOI: 10.1126/science.1213307] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5'-untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in the adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a previously unknown DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.
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Affiliation(s)
- Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
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21
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Amunugama R, He Y, Willcox S, Forties RA, Shim KS, Bundschuh R, Luo Y, Griffith J, Fishel R. RAD51 protein ATP cap regulates nucleoprotein filament stability. J Biol Chem 2012; 287:8724-36. [PMID: 22275364 DOI: 10.1074/jbc.m111.239426] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RAD51 mediates homologous recombination by forming an active DNA nucleoprotein filament (NPF). A conserved aspartate that forms a salt bridge with the ATP γ-phosphate is found at the nucleotide-binding interface between RAD51 subunits of the NPF known as the ATP cap. The salt bridge accounts for the nonphysiological cation(s) required to fully activate the RAD51 NPF. In contrast, RecA homologs and most RAD51 paralogs contain a conserved lysine at the analogous structural position. We demonstrate that substitution of human RAD51(Asp-316) with lysine (HsRAD51(D316K)) decreases NPF turnover and facilitates considerably improved recombinase functions. Structural analysis shows that archaebacterial Methanococcus voltae RadA(D302K) (MvRAD51(D302K)) and HsRAD51(D316K) form extended active NPFs without salt. These studies suggest that the HsRAD51(Asp-316) salt bridge may function as a conformational sensor that enhances turnover at the expense of recombinase activity.
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Affiliation(s)
- Ravindra Amunugama
- Biophysics Graduate Program, Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University, Columbus, Ohio 43210, USA
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22
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Kramara J, Willcox S, Gunisova S, Kinsky S, Nosek J, Griffith JD, Tomaska L. Tay1 protein, a novel telomere binding factor from Yarrowia lipolytica. J Biol Chem 2010; 285:38078-92. [PMID: 20923774 DOI: 10.1074/jbc.m110.127605] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inspection of the complete genome of the yeast Yarrowia lipolytica for the presence of genes encoding homologues of known telomere-binding proteins surprisingly revealed no counterparts of typical yeast Myb domain-containing telomeric factors including Rap1 or Taz1. Instead, we identified a gene, YALIOD10923g, encoding a protein containing two Myb domains, exhibiting a high degree of similarity to the Myb domain of human telomeric proteins TRF1 and TRF2 and homologous to an essential fission yeast protein Mug152 whose expression is elevated during meiosis. The protein, which we named Tay1p (telomere-associated in Yarrowia lipolytica 1), was purified for biochemical studies. Using a model Y. lipolytica telomere, we demonstrate that the protein preferentially binds to Y. lipolytica telomeric tracts. Tay1p binds along the telomeric tract as dimers and larger oligomers, and it is able to remodel the telomeric DNA into both looped structures and synaptic complexes of two model telomere DNAs. The ability of Tay1p to induce dimerization of telomeres in vitro goes in line with its oligomeric nature, where each oligomer can employ several Myb domains to form intermolecular telomere clusters. We also provide experimental evidence that Tay1p may be associated with Y. lipolytica telomeres in vivo. Together with its homologues from Schizosaccharomyces pombe and several basidiomycetous fungi (Sánchez-Alonso, P., and Guzman, P. (2008) Fungal Genet. Biol. 45, S54-S62), Tay1p constitutes a novel family of putative telomeric factors whose analysis may be instrumental in understanding the function and evolution of double-stranded DNA telomeric proteins.
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Affiliation(s)
- Juraj Kramara
- Department of Genetics, Comenius University, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava, Slovakia
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Holmes JB, Pohjoismäki JL, Yang MY, Yasukawa T, Cluett TJ, Reyes A, Goffart S, Willcox S, Rigby RE, Jackson AP, Spelbrink JN, Griffith JD, Crouch RJ, Jacobs HT, Holt IJ. 89 Analysis of extensive RNA/DNA hybrids in the replicating mammalian mitochondrial genome. Mitochondrion 2010. [DOI: 10.1016/j.mito.2009.12.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Pohjoismäki JLO, Goffart S, Tyynismaa H, Willcox S, Ide T, Kang D, Suomalainen A, Karhunen PJ, Griffith JD, Holt IJ, Jacobs HT. Human heart mitochondrial DNA is organized in complex catenated networks containing abundant four-way junctions and replication forks. J Biol Chem 2009; 284:21446-57. [PMID: 19525233 PMCID: PMC2755869 DOI: 10.1074/jbc.m109.016600] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Analysis of human heart mitochondrial DNA (mtDNA) by electron microscopy and agarose gel electrophoresis revealed a complete absence of the θ-type replication intermediates seen abundantly in mtDNA from all other tissues. Instead only Y- and X-junctional forms were detected after restriction digestion. Uncut heart mtDNA was organized in tangled complexes of up to 20 or more genome equivalents, which could be resolved to genomic monomers, dimers, and linear fragments by treatment with the decatenating enzyme topoisomerase IV plus the cruciform-cutting T7 endonuclease I. Human and mouse brain also contained a population of such mtDNA forms, which were absent, however, from mouse, rabbit, or pig heart. Overexpression in transgenic mice of two proteins involved in mtDNA replication, namely human mitochondrial transcription factor A or the mouse Twinkle DNA helicase, generated abundant four-way junctions in mtDNA of heart, brain, and skeletal muscle. The organization of mtDNA of human heart as well as of mouse and human brain in complex junctional networks replicating via a presumed non-θ mechanism is unprecedented in mammals.
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Griffith JD, Willcox S, Powers DW, Nelson R, Baxter BK. Discovery of abundant cellulose microfibers encased in 250 Ma Permian halite: a macromolecular target in the search for life on other planets. Astrobiology 2008; 8:215-228. [PMID: 18366344 DOI: 10.1089/ast.2007.0196] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this study, we utilized transmission electron microscopy to examine the contents of fluid inclusions in halite (NaCl) and solid halite crystals collected 650 m below the surface from the Late Permian Salado Formation in southeastern New Mexico (USA). The halite has been isolated from contaminating groundwater since deposition approximately 250 Ma ago. We show that abundant cellulose microfibers are present in the halite and appear remarkably intact. The cellulose is in the form of 5 nm microfibers as well as composite ropes and mats, and was identified by resistance to 0.5 N NaOH treatment and susceptibility to cellulase enzyme treatment. These cellulose microfibers represent the oldest native biological macromolecules to have been directly isolated, examined biochemically, and visualized (without growth or replication) to date. This discovery points to cellulose as an ideal macromolecular target in the search for life on other planets in our Solar System.
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Affiliation(s)
- Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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Fouché N, Cesare AJ, Willcox S, Ozgür S, Compton SA, Griffith JD. The basic domain of TRF2 directs binding to DNA junctions irrespective of the presence of TTAGGG repeats. J Biol Chem 2006; 281:37486-95. [PMID: 17052985 DOI: 10.1074/jbc.m608778200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The replication of long tracts of telomeric repeats may require specific factors to avoid fork regression (Fouché, N., Ozgür, S., Roy, D., and Griffith, J. (2006) Nucleic Acids Res., in press). Here we show that TRF2 binds to model replication forks and four-way junctions in vitro in a structure-specific but sequence-independent manner. A synthetic peptide encompassing the TRF2 basic domain also binds to DNA four-way junctions, whereas the TRF2 truncation mutant (TRF2(DeltaB)) and a mutant basic domain peptide do not. In the absence of the basic domain, the ability of TRF2 to localize to model telomere ends and facilitate t-loop formation in vitro is diminished. We propose that TRF2 plays a key role during telomere replication in binding chickenfoot intermediates of telomere replication fork regression. Junction-specific binding would also allow TRF2 to stabilize a strand invasion structure that is thought to exist at the strand invasion site of the t-loop.
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Affiliation(s)
- Nicole Fouché
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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27
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Grove DE, Willcox S, Griffith JD, Bryant FR. Differential single-stranded DNA binding properties of the paralogous SsbA and SsbB proteins from Streptococcus pneumoniae. J Biol Chem 2005; 280:11067-73. [PMID: 15647253 DOI: 10.1074/jbc.m414057200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The naturally transformable Gram-positive bacterium Streptococcus pneumoniae has two single-stranded DNA-binding (SSB) proteins, designated SsbA and SsbB. The SsbA protein is similar in size to the well characterized SSB protein from Escherichia coli (SsbEc). The SsbB protein, in contrast, is a smaller protein that is specifically induced during natural transformation and has no counterpart in E. coli. In this report, the single-stranded DNA (ssDNA) binding properties of the SsbA and SsbB proteins were examined and compared with those of the SsbEc protein. The ssDNA binding characteristics of the SsbA protein were similar to those of the SsbEc protein in every ssDNA binding assay used in this study. The SsbB protein differed from the SsbA and SsbEc proteins, however, both in its binding to short homopolymeric dT(n) oligomers (as judged by polyacrylamide gel-shift assays) and in its binding to the longer naturally occurring X and M13 ssDNAs (as judged by agarose gel-shift assays and electron microscopic analysis). The results indicate that an individual SsbB protein binds to ssDNA with an affinity that is similar or higher than that of the SsbA and SsbEc proteins. However, the manner in which multiple SsbB proteins assemble onto a ssDNA molecule differs from that observed with the SsbA and SsbEc proteins. These results represent the first analysis of paralogous SSB proteins from any bacterial species and provide a foundation for further investigations into the biological roles of these proteins.
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Affiliation(s)
- Diane E Grove
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Reuven NB, Willcox S, Griffith JD, Weller SK. Catalysis of strand exchange by the HSV-1 UL12 and ICP8 proteins: potent ICP8 recombinase activity is revealed upon resection of dsDNA substrate by nuclease. J Mol Biol 2004; 342:57-71. [PMID: 15313607 PMCID: PMC4412345 DOI: 10.1016/j.jmb.2004.07.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 07/09/2004] [Accepted: 07/12/2004] [Indexed: 11/29/2022]
Abstract
The replication of herpes simplex virus type 1 (HSV-1) is associated with a high degree of homologous recombination, which is likely to be mediated, in part, by HSV-1-encoded proteins. We have previously shown that the HSV-1 encoded ICP8 protein and alkaline nuclease UL12 are capable of catalyzing an in vitro strand-exchange reaction. Here, we show, by electron microscopy, that the products of the strand exchange reaction between linear double-stranded DNA and circular single-stranded DNA consist of the expected joint molecule forms: sigma, alpha, and gapped circles. Other exonucleases, such as lambda Red alpha, which, like UL12, digests 5'-3', as well as Escherichia coli exonuclease III (ExoIII), which digests 3'-5', could substitute for UL12 in the strand exchange reaction by providing a resected DNA end. ICP8 generated the same intermediates and strand exchange products when the double-stranded DNA substrate was preresected by any of the nucleases. Using substrates with large regions of non-homology we found that pairing by ICP8 could be initiated from the middle of a DNA molecule and did not require a homologous end. In this reaction, the resection of a DNA end by the nuclease is required to reveal homologous sequences capable of being paired by ICP8. This study further illustrates the complexity of the multi-functional ICP8 protein.
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Affiliation(s)
- Nina B. Reuven
- Department of Molecular Microbial, and Structural Biology, University of Connecticut Health Center Farmington, CT 06030-3205 USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill NC 27599, USA
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill NC 27599, USA
| | - Sandra K. Weller
- Department of Molecular Microbial, and Structural Biology, University of Connecticut Health Center Farmington, CT 06030-3205 USA
- Corresponding author:
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Tomaska L, Willcox S, Slezakova J, Nosek J, Griffith JD. Taz1 binding to a fission yeast model telomere: formation of telomeric loops and higher order structures. J Biol Chem 2004; 279:50764-72. [PMID: 15383525 DOI: 10.1074/jbc.m409790200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Similar to its human homologues TRF1 and TRF2, fission yeast Taz1 protein is a component of telomeric chromatin regulating proper telomere maintenance. As mammalian TRF1 and TRF2 proteins have been shown to directly bind telomeric DNA to form protein arrays and looped structures, termed t-loops, the ability of Taz1p to act on fission yeast telomeric DNA in similar ways was examined using purified protein and model DNA templates. When incubated with Taz1p, model telomeres containing 3' single-stranded telomeric overhangs formed t-loops at a frequency approaching 13%. Termini with blunt ends and non-telomeric overhangs were deficient in t-loop formation. In addition, we observed arrays of multiple Taz1p molecules bound to the telomeric regions, resembling the pattern of TRF1 binding. The presence of t-loops larger than the telomeric tract, a high frequency of end-bound DNAs and a donut shape of the Taz1p complex suggest that Taz1p binds the 3' overhang then extrudes a loop that grows in size as the donut slides along the duplex DNA. Based on these in vitro results we discuss possible general implications for fission yeast telomere dynamics.
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Affiliation(s)
- Lubomir Tomaska
- Department of Genetics, Comenius University, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava, Slovakia
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Abstract
Telomeres vary greatly in size among plants and, in most higher plants, consist of a long array of 5'-TTTAGGG-3'/3'-AAATCCC-5' (TTTAGGG) repeats. Recently, telomeric DNA in human, mouse, oxytricha, and trypanosome chromosomes have been found arranged into loops (t-loops), proposed to sequester the telomere from unwanted repair events and prevent activation of DNA damage checkpoints. We have asked whether t-loops exist in the higher order plant Pisum sativum (garden pea). DNA was isolated from the shoots and root tips of germinating seeds. Analysis of the telomeric restriction fragments showed that DNA hybridizing to a (TTTAGGG)n probe migrated as a smear centering around 25 kb, and direct sequencing verified the repeat to be (TTTAGGG)n. Total DNA in isolated nuclei was photo-cross-linked, and the telomeric restriction fragments were purified by gel filtration. Electron microscopic (EM) analysis revealed DNA molecules arranged as t-loops with a size distribution consistent with that seen by gel electrophoresis. Some molecules had loops as large as 75 kb. These results show that the arrangement of telomeric DNA into loops occurs in higher plants.
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Affiliation(s)
- Anthony J Cesare
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
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He ZG, Rezende LF, Willcox S, Griffith JD, Richardson CC. The carboxyl-terminal domain of bacteriophage T7 single-stranded DNA-binding protein modulates DNA binding and interaction with T7 DNA polymerase. J Biol Chem 2003; 278:29538-45. [PMID: 12766155 DOI: 10.1074/jbc.m304318200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene 2.5 of bacteriophage T7 is an essential gene that encodes a single-stranded DNA-binding protein (gp2.5). Previous studies have demonstrated that the acidic carboxyl terminus of the protein is essential and that it mediates multiple protein-protein interactions. A screen for lethal mutations in gene 2.5 uncovered a variety of essential amino acids, among which was a single amino acid substitution, F232L, at the carboxyl-terminal residue. gp2.5-F232L exhibits a 3-fold increase in binding affinity for single-stranded DNA and a slightly lower affinity for T7 DNA polymerase when compared with wild type gp2.5. gp2.5-F232L stimulates the activity of T7 DNA polymerase and, in contrast to wild-type gp2.5, promotes strand displacement DNA synthesis by T7 DNA polymerase. A carboxyl-terminal truncation of gene 2.5 protein, gp2.5-Delta 26C, binds single-stranded DNA 40-fold more tightly than the wild-type protein and cannot physically interact with T7 DNA polymerase. gp2.5-Delta 26C is inhibitory for DNA synthesis catalyzed by T7 DNA polymerase on single-stranded DNA, and it does not stimulate strand displacement DNA synthesis at high concentration. The biochemical and genetic data support a model in which the carboxyl-terminal tail modulates DNA binding and mediates essential interactions with T7 DNA polymerase.
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Affiliation(s)
- Zheng-Guo He
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
The annealing of complementary strands of DNA is a vital step during the process of DNA replication, recombination, and repair. In bacteriophage T7-infected cells, the product of viral gene 2.5, a single-stranded DNA-binding protein, performs this function. We have identified a single amino acid residue in gene 2.5 protein, arginine 82, that is critical for its DNA annealing activity. Expression of gene 2.5 harboring this mutation does not complement the growth of a T7 bacteriophage lacking gene 2.5. Purified gene 2.5 protein-R82C binds single-stranded DNA with a greater affinity than the wild-type protein but does not mediate annealing of complementary strands of DNA. A carboxyl-terminal-deleted protein, gene 2.5 protein-Delta26C, binds even more tightly to single-stranded DNA than does gene 2.5 protein-R82C, but it anneals homologous strands of DNA as well as does the wild-type protein. The altered protein forms dimers and interacts with T7 DNA polymerase comparable with the wild-type protein. Gene 2.5 protein-R82C condenses single-stranded M13 DNA in a manner similar to wild-type protein when viewed by electron microscopy.
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Affiliation(s)
- Lisa F Rezende
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
Health insurance policy in Australia has been distinguished by considerable instability over the past five years. This paper reviews the rationale and emerging evidence on three major policy initiatives--a move to allow selective contracting, the introduction of a 30 percent government subsidy for private health insurance, and the abolition of pure community rating. Policy making on private health insurance has been characterized by insufficient attention to research that might provide a stronger evidence basis for policy reforms.
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Affiliation(s)
- S Willcox
- Institute for Health Care Research and Policy, Georgetown University, USA
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Willcox S. Evaluating scientific resources on the Web. Natl Netw 1996; 20:26, 28, 32. [PMID: 10158181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Willcox S. Response from the inner city. Midwives Chron 1988; 101:18-9. [PMID: 3347174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Abstract
A national survey of 23,359 Australian schoolchildren who were predominantly in the age range of 12-17 years was undertaken in 1984 to determine their levels of use of tobacco and alcohol. The prevalence of current smoking behaviour (that is, at least one cigarette in the past week) rose with age to 34% among girls and 29% among boys at 15 years of age. The prevalence of current drinking behaviour (that is, at least one drink in the past week) rose with age to 49% among girls and 56% among boys at 17 years of age. Very few pupils reported daily drinking but from 15 years of age between 12% and 14% of the sampled students reported smoking every day. Boys who currently smoked and drank reported higher consumptions of tobacco and alcohol than did girls who currently smoked and drank. Most smoking and drinking took place at weekends. Normal responses for intention to smoke in the future, and for drinkers and smokers "self-referent labels" are also reported, and it is suggested that health education programmes for schoolchildren usefully could be focused on these psychological factors.
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