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Yakubovskaya E, Zaliznyak T, Martínez JM, Taylor GT. Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, Emiliania huxleyi. Front Microbiol 2021; 12:686287. [PMID: 34795644 PMCID: PMC8593419 DOI: 10.3389/fmicb.2021.686287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/26/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Emiliania huxleyi is a cosmopolitan member of the marine phytoplankton. This species’ capacities for carbon sequestration and sulfur mobilization make it a key player in oceanic biogeochemical cycles that influence climate on a planetary scale. Seasonal E. huxleyi blooms are abruptly terminated by viral epidemics caused by a clade of large DNA viruses collectively known as coccolithoviruses (EhVs). EhVs thereby mediate a significant part of material and energy fluxes associated with E. huxleyi population dynamics. In this study, we use spontaneous Raman microspectroscopy to perform label-free and non-invasive measurements of the macromolecular composition of individual virions and E. huxleyi host cells. Our novel autofluorescence suppression protocol enabled spectroscopic visualization of evolving macromolecular redistributions in individual E. huxleyi cells at different stages of EhV infection. Material transfer from E. huxleyi hosts to single EhV-163 virions was confirmed by combining stable isotope probing (SIP) experiments with Raman microspectroscopy. Inheritance of the host cells’ 13C-enriched isotopic signature was quantified based on red shifts of Raman peaks characteristic of phenylalanine’s phenyl ring. Two-dimensional Raman mapping of EhV-infected E. huxleyi cells revealed that the compact region producing an intense Raman DNA signal (i.e., the nucleus) in healthy E. huxleyi cells becomes diffuse during the first hours of infection. Raman DNA emissions integrated throughout individual cells decreased during the infection cycle. Our observations are consistent with EhV-163 degrading the host’s nuclear DNA, scavenging released nucleotides for its own genome replication, and shedding newly-produced virions prior to host lysis via budding.
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Affiliation(s)
- Elena Yakubovskaya
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Tatiana Zaliznyak
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | | | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
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2
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Butler TJ, Estep KN, Sommers JA, Maul RW, Moore AZ, Bandinelli S, Cucca F, Tuke MA, Wood AR, Bharti SK, Bogenhagen DF, Yakubovskaya E, Garcia-Diaz M, Guilliam TA, Byrd AK, Raney KD, Doherty AJ, Ferrucci L, Schlessinger D, Ding J, Brosh RM. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Hum Mol Genet 2021; 29:1292-1309. [PMID: 32191790 DOI: 10.1093/hmg/ddaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/27/2020] [Accepted: 03/18/2020] [Indexed: 01/08/2023] Open
Abstract
As the powerhouses of the eukaryotic cell, mitochondria must maintain their genomes which encode proteins essential for energy production. Mitochondria are characterized by guanine-rich DNA sequences that spontaneously form unusual three-dimensional structures known as G-quadruplexes (G4). G4 structures can be problematic for the essential processes of DNA replication and transcription because they deter normal progression of the enzymatic-driven processes. In this study, we addressed the hypothesis that mitochondrial G4 is a source of mutagenesis leading to base-pair substitutions. Our computational analysis of 2757 individual genomes from two Italian population cohorts (SardiNIA and InCHIANTI) revealed a statistically significant enrichment of mitochondrial mutations within sequences corresponding to stable G4 DNA structures. Guided by the computational analysis results, we designed biochemical reconstitution experiments and demonstrated that DNA synthesis by two known mitochondrial DNA polymerases (Pol γ, PrimPol) in vitro was strongly blocked by representative stable G4 mitochondrial DNA structures, which could be overcome in a specific manner by the ATP-dependent G4-resolving helicase Pif1. However, error-prone DNA synthesis by PrimPol using the G4 template sequence persisted even in the presence of Pif1. Altogether, our results suggest that genetic variation is enriched in G-quadruplex regions that impede mitochondrial DNA replication.
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Affiliation(s)
- Thomas J Butler
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Katrina N Estep
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Ann Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato 09042, Italy
| | - Marcus A Tuke
- Genetics of Complex Traits, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Daniel F Bogenhagen
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Jun Ding
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
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3
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Yakubovskaya E, Zaliznyak T, Martínez Martínez J, Taylor GT. Tear Down the Fluorescent Curtain: A New Fluorescence Suppression Method for Raman Microspectroscopic Analyses. Sci Rep 2019; 9:15785. [PMID: 31673106 PMCID: PMC6823364 DOI: 10.1038/s41598-019-52321-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 06/25/2019] [Accepted: 10/16/2019] [Indexed: 01/30/2023] Open
Abstract
The near exponential proliferation of published Raman microspectroscopic applications over the last decade bears witness to the strengths and versatility of this technology. However, laser-induced fluorescence often severely impedes its application to biological samples. Here we report a new approach for near complete elimination of laser-induced background fluorescence in highly pigmented biological specimens (e.g., microalgae) enabling interrogation by Raman microspectroscopy. Our simple chemiphotobleaching method combines mild hydrogen peroxide oxidation with broad spectrum visible light irradiation of the entire specimen. This treatment permits observing intracellular distributions of macromolecular pools, isotopic tracers, and even viral propagation within cells previously not amenable to Raman microspectroscopic examination. Our approach demonstrates the potential for confocal Raman microspectroscopy becoming an indispensable tool to obtain spatially-resolved data on the chemical composition of highly fluorescent biological samples from individual cells to environmental samples.
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Affiliation(s)
- Elena Yakubovskaya
- School Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tatiana Zaliznyak
- School Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Gordon T Taylor
- School Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA.
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Khan I, Crouch JD, Bharti SK, Sommers JA, Carney SM, Yakubovskaya E, Garcia-Diaz M, Trakselis MA, Brosh RM. Biochemical Characterization of the Human Mitochondrial Replicative Twinkle Helicase: SUBSTRATE SPECIFICITY, DNA BRANCH MIGRATION, AND ABILITY TO OVERCOME BLOCKADES TO DNA UNWINDING. J Biol Chem 2016; 291:14324-14339. [PMID: 27226550 DOI: 10.1074/jbc.m115.712026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 12/22/2015] [Indexed: 01/08/2023] Open
Abstract
Mutations in the c10orf2 gene encoding the human mitochondrial DNA replicative helicase Twinkle are linked to several rare genetic diseases characterized by mitochondrial defects. In this study, we have examined the catalytic activity of Twinkle helicase on model replication fork and DNA repair structures. Although Twinkle behaves as a traditional 5' to 3' helicase on conventional forked duplex substrates, the enzyme efficiently dissociates D-loop DNA substrates irrespective of whether it possesses a 5' or 3' single-stranded tailed invading strand. In contrast, we report for the first time that Twinkle branch-migrates an open-ended mobile three-stranded DNA structure with a strong 5' to 3' directionality preference. To determine how well Twinkle handles potential roadblocks to mtDNA replication, we tested the ability of the helicase to unwind substrates with site-specific oxidative DNA lesions or bound by the mitochondrial transcription factor A. Twinkle helicase is inhibited by DNA damage in a unique manner that is dependent on the type of oxidative lesion and the strand in which it resides. Novel single molecule FRET binding and unwinding assays show an interaction of the excluded strand with Twinkle as well as events corresponding to stepwise unwinding and annealing. TFAM inhibits Twinkle unwinding, suggesting other replisome proteins may be required for efficient removal. These studies shed new insight on the catalytic functions of Twinkle on the key DNA structures it would encounter during replication or possibly repair of the mitochondrial genome and how well it tolerates potential roadblocks to DNA unwinding.
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Affiliation(s)
- Irfan Khan
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Jack D Crouch
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Sean M Carney
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
| | - Michael A Trakselis
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260,; Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224,.
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Yakubovskaya E, Guja KE, Eng ET, Choi WS, Mejia E, Beglov D, Lukin M, Kozakov D, Garcia-Diaz M. Organization of the human mitochondrial transcription initiation complex. Nucleic Acids Res 2014; 42:4100-12. [PMID: 24413562 PMCID: PMC3973321 DOI: 10.1093/nar/gkt1360] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 11/26/2022] Open
Abstract
Initiation of transcription in human mitochondria involves two factors, TFAM and TFB2M, in addition to the mitochondrial RNA polymerase, POLRMT. We have investigated the organization of the human mitochondrial transcription initiation complex on the light-strand promoter (LSP) through solution X-ray scattering, electron microscopy (EM) and biochemical studies. Our EM results demonstrate a compact organization of the initiation complex, suggesting that protein–protein interactions might help mediate initiation. We demonstrate that, in the absence of DNA, only POLRMT and TFAM form a stable interaction, albeit one with low affinity. This is consistent with the expected transient nature of the interactions necessary for initiation and implies that the promoter DNA acts as a scaffold that enables formation of the full initiation complex. Docking of known crystal structures into our EM maps results in a model for transcriptional initiation that strongly correlates with new and existing biochemical observations. Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, Cryo-Electron Microscopy Facility, New York Structural Biology Center, New York, NY 10027 and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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6
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Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M. A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site. PLoS One 2013; 8:e76700. [PMID: 24116139 PMCID: PMC3792054 DOI: 10.1371/journal.pone.0076700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 06/04/2013] [Accepted: 08/23/2013] [Indexed: 11/26/2022] Open
Abstract
Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A), that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the PolD714A mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced kpol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.
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Affiliation(s)
- Agata Jacewicz
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Trzemecka
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kip E. Guja
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Danuta Plochocka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Anna Bebenek
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (AB); (MGD)
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail: (AB); (MGD)
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7
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Guja KE, Venkataraman K, Yakubovskaya E, Shi H, Mejia E, Hambardjieva E, Karzai AW, Garcia-Diaz M. Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1. Nucleic Acids Res 2013; 41:7947-59. [PMID: 23804760 PMCID: PMC3763538 DOI: 10.1093/nar/gkt547] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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: 12/31/2022] Open
Abstract
Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a role analogous to KsgA/Dim1 proteins. This modification has been linked to mitochondrial dysfunctions leading to maternally inherited deafness, aminoglycoside sensitivity and diabetes. Here, we present the first structural characterization of the mammalian TFB1 factor. We have solved two X-ray crystallographic structures of TFB1M with (2.1 Å) and without (2.0 Å) its cofactor S-adenosyl-L-methionine. These structures reveal that TFB1M shares a conserved methyltransferase core with other KsgA/Dim1 methyltransferases and shed light on the structural basis of S-adenosyl-L-methionine binding and methyltransferase activity. Together with mutagenesis studies, these data suggest a model for substrate binding and provide insight into the mechanism of methyl transfer, clarifying the role of this factor in an essential process for mitochondrial function.
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Affiliation(s)
- Kip E Guja
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA, Medical Scientist Training Program, Stony Brook University Medical Center, Stony Brook, NY 11794, USA and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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8
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Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E, Garcia-Diaz M. 125 Put a stop to it: termination of mitochondrial transcription. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786367] [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: 10/26/2022]
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Yakubovskaya E, Guja KE, Mejia E, Castano S, Hambardjieva E, Choi WS, Garcia-Diaz M. Structure of the essential MTERF4:NSUN4 protein complex reveals how an MTERF protein collaborates to facilitate rRNA modification. Structure 2012; 20:1940-7. [PMID: 23022348 DOI: 10.1016/j.str.2012.08.027] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/15/2022]
Abstract
MTERF4 is the first MTERF family member shown to bind RNA and plays an essential role as a regulator of ribosomal biogenesis in mammalian mitochondria. It forms a complex with the rRNA methyltransferase NSUN4 and recruits it to the large ribosomal subunit. In this article, we characterize the interaction between both proteins, demonstrate that MTERF4 strongly stimulates the specificity of NSUN4 during in vitro methylation experiments, and present the 2.0 Å resolution crystal structure of the MTERF4:NSUN4 protein complex, lacking 48 residues of the MTERF4 C-terminal acidic tail, bound to S-adenosyl-L-methionine, thus revealing the nature of the interaction between both proteins and the structural conservation of the most divergent of the human MTERF family members. Moreover, the structure suggests a model for RNA binding by the MTERF4:NSUN4 complex, providing insight into the mechanism by which an MTERF family member facilitates rRNA methylation.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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10
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Shen B, Zheng L, Zhou M, Guo Z, Lu H, Qian L, Dai H, Qiu J, Yakubovskaya E, Bogenhagen DF, Demple B. Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates and defective in myopathy. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.646.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Li Zheng
- Cancer BiologyCity of HopeDuarteCA
| | | | | | | | | | | | | | - Elena Yakubovskaya
- Pharmacological SciencesState University of New York at Stony BrookStony BrookNY
| | - Daniel F. Bogenhagen
- Pharmacological SciencesState University of New York at Stony BrookStony BrookNY
| | - Bruce Demple
- Genetics and Complex DiseaseHarvard School of Public HealthBostonMA
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11
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Hambardjieva E, Derkunt B, Yakubovskaya E, Mejia E, Diaz MG. Bypass of 8‐oxo‐G by DNA polymerase lambda. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.lb50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Burak Derkunt
- Molecular and Cellular PharmacologyStony Brook UniversityStony BrookNY
| | | | - Edison Mejia
- Molecular and Cellular PharmacologyStony Brook UniversityStony BrookNY
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12
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Garcia‐Diaz M, Yakubovskaya E, Mejia E. A unique DNA binding mode enables human mterf1 to regulate mitochondrial transcription. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.492.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Edison Mejia
- Pharmacological SciencesStony Brook UniversityStony BrookNY
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13
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Zheng L, Zhou M, Guo Z, Lu H, Qian L, Dai H, Qiu J, Yakubovskaya E, Bogenhagen DF, Demple B, Shen B. Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates. Mol Cell 2008; 32:325-36. [PMID: 18995831 DOI: 10.1016/j.molcel.2008.09.024] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 07/30/2008] [Accepted: 09/26/2008] [Indexed: 10/21/2022]
Abstract
DNA2, a helicase/nuclease family member, plays versatile roles in processing DNA intermediates during DNA replication and repair. Yeast Dna2 (yDna2) is essential in RNA primer removal during nuclear DNA replication and is important in repairing UV damage, base damage, and double-strand breaks. Our data demonstrate that, surprisingly, human DNA2 (hDNA2) does not localize to nuclei, as it lacks a nuclear localization signal equivalent to that present in yDna2. Instead, hDNA2 migrates to the mitochondria, interacts with mitochondrial DNA polymerase gamma, and significantly stimulates polymerase activity. We further demonstrate that hDNA2 and flap endonuclease 1 synergistically process intermediate 5' flap structures occurring in DNA replication and long-patch base excision repair (LP-BER) in mitochondria. Depletion of hDNA2 from a mitochondrial extract reduces its efficiency in RNA primer removal and LP-BER. Taken together, our studies illustrate an evolutionarily diversified role of hDNA2 in mitochondrial DNA replication and repair in a mammalian system.
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Affiliation(s)
- Li Zheng
- Department of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
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14
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Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. EMBO J 2007; 26:4283-91. [PMID: 17762861 PMCID: PMC2230839 DOI: 10.1038/sj.emboj.7601843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 08/08/2007] [Indexed: 02/07/2023] Open
Abstract
We used electron microscopy to examine the structure of human DNA pol gamma, the heterotrimeric mtDNA replicase implicated in certain mitochondrial diseases and aging models. Separate analysis of negatively stained preparations of the catalytic subunit, pol gammaA, and of the holoenzyme including a dimeric accessory factor, pol gammaB(2), permitted unambiguous identification of the position of the accessory factor within the holoenzyme. The model explains protection of a partial chymotryptic cleavage site after residue L(549) of pol gammaA upon binding of the accessory subunit. This interaction region is near residue 467 of pol gammaA, where a disease-related mutation has been reported to impair binding of the B subunit. One pol gammaB subunit dominates contacts with the catalytic subunit, while the second B subunit is largely exposed to solvent. A model for pol gamma is discussed that considers the effects of known mutations in the accessory subunit and the interaction of the enzyme with DNA.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Mark Lukin
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Zhixin Chen
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - John Berriman
- New York Structural Biology Center, New York, NY, USA
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Ryuji Kobayashi
- Department Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany
| | - Daniel F Bogenhagen
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
- Department of Pharmacological Sciences, State University of New York at Stony Brook, bst8-140, Stony Brook, NY 11794-8651, USA. Tel.: +1 631 444 3068; Fax: +1 631 444 3218; E-mail:
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15
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Gabibov A, Yakubovskaya E, Lukin M, Favorov P, Reshetnyak A, Monastyrsky M. Catalytic transformations of supercoiled DNA as studied by flow linear dichroism technique. FEBS J 2006; 272:6336-43. [PMID: 16336270 DOI: 10.1111/j.1742-4658.2005.05027.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A catalytic turnover of supercoiled DNA (scDNA) transformation mediated by topoisomerases leads to changes in the linking number (Lk) of the polymeric substrate by 1 or 2 per cycle. As a substrate of the topoisomerization reaction it is chemically identical to its product; even a single catalytic event results in the quantum leap in the scDNA topology. Non-intrusive continuous assay to measure the kinetics of the scDNA topoisomerization was performed. The development of such a technique was hindered because of multiple DNA species of intermediate topology present in the reaction mixture. The interrelation of DNA topology, its hydrodynamics, and optical anisotropy enable us to use the flow linear dichroism technique (FLD) for continuous monitoring of the scDNA topoisomerization reaction. This approach permits us to study the kinetics of DNA transformation catalyzed by eukaryotic topoisomerases I and II, as well as mechanistic characteristics of these enzymes and their interactions with anticancer drugs. Moreover, FLD assay can be applied to any enzymatic reaction that involves scDNA as a substrate. It also provides a new way of screening drugs dynamically and is likely to be potent in various biomedical applications.
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Affiliation(s)
- Alexander Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Abstract
Mitochondrial DNA polymerase gamma (pol gamma) is responsible for replication and repair of mtDNA and is mutated in individuals with genetic disorders such as chronic external ophthalmoplegia and Alpers syndrome. pol gamma is also an adventitious target for toxic side effects of several antiviral compounds, and mutation of its proofreading exonuclease leads to accelerated aging in mouse models. We have used a variety of physical and functional approaches to study the interaction of the human pol gamma catalytic subunit with both the wild-type accessory factor, pol gammaB, and a deletion derivative that is unable to dimerize and consequently is impaired in its ability to stimulate processive DNA synthesis. Our studies clearly showed that the functional human holoenzyme contains two subunits of the processivity factor and one catalytic subunit, thereby forming a heterotrimer. The structure of pol gamma seems to be variable, ranging from a single catalytic subunit in yeast to a heterodimer in Drosophila and a heterotrimer in mammals.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences and Center for Structural Biology, State University of New York, Stony Brook, New York 11794-8651, USA
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