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Gross J, Wirth N, Tessmer I. Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair. J Vis Exp 2017:55501. [PMID: 28570512 PMCID: PMC5608143 DOI: 10.3791/55501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
AFM imaging is a powerful technique for the study of protein-DNA interactions. This single molecule method allows the simultaneous resolution of different molecules and molecular assemblies in a heterogeneous sample. In the particular context of DNA interacting protein systems, different protein complex forms and their corresponding binding positions on target sites containing DNA fragments can thus be distinguished. Here, an application of AFM to the study of DNA lesion recognition in the prokaryotic and eukaryotic nucleotide excision DNA repair (NER) systems is presented. The procedures of DNA and protein sample preparations are described and experimental as well as analytical details of the experiments are provided. The data allow important conclusions on the strategies by which target site verification may be achieved by the NER proteins. Interestingly, they indicate different approaches of lesion recognition and identification for the eukaryotic NER system, depending on the type of lesion. Furthermore, distinct structural properties of the two different helicases involved in prokaryotic and eukaryotic NER result in and explain the different strategies observed for these two systems. Importantly, these experimental and analytical approaches can be applied not only to the study of DNA repair but also very similarly to other DNA interacting protein systems such as those involved in replication or transcription processes.
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Affiliation(s)
- Jonas Gross
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg
| | - Nicolas Wirth
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg;
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2
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Moon S, Shin J, Lee D, Seong RH, Lee W. 1H, 15N, and 13C resonance assignments and secondary structure of the SWIRM domain of human BAF155, a chromatin remodeling complex component. Mol Cells 2013; 36:333-9. [PMID: 23996527 PMCID: PMC3887986 DOI: 10.1007/s10059-013-0119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022] Open
Abstract
Mammalian SWI/SNF complexes are evolutionary conserved, ATP-dependent chromatin remodeling units. BAF155 in the SWI/SNF complex contains several highly conserved domains, including SANT, SWIRM, and leucine zipper domains. The biological roles of the SWIRM domain remain unclear; however, both structural and biochemical analyses of this domain have suggested that it could mediate protein-protein or protein-DNA interactions during the chromatin remodeling process. The human BAF155 SWIRM domain was cloned into the Escherichia coli expression vector pMAL-c2X and purified using affinity chromatography for structural analysis. We report the backbone (1)H, (15)N, and (13)C resonance assignments and secondary structure of this domain using nuclear magnetic resonance (NMR) spectroscopy and the TALOS+ program. The secondary structure consists of five α-helices that form a typical histone fold for DNA interactions. Our data suggest that the BAF155 SWIRM domain interacts with nucleosome DNA (Kd = 0.47 μM).
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Affiliation(s)
- Sunjin Moon
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | - Joon Shin
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | - Dongju Lee
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | | | - Weontae Lee
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
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3
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Doherty MT, Kang YS, Lee C, Stumph WE. Architectural arrangement of the small nuclear RNA (snRNA)-activating protein complex 190 subunit (SNAP190) on U1 snRNA gene promoter DNA. J Biol Chem 2012; 287:39369-79. [PMID: 23038247 PMCID: PMC3501025 DOI: 10.1074/jbc.m112.407775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/01/2012] [Indexed: 11/06/2022] Open
Abstract
Myb repeats ∼52 amino acid residues in length were first characterized in the oncogenic Myb transcription factor, which contains three tandem Myb repeats in its DNA-binding domain. Proteins of this family normally contain either one, two, or three tandem Myb repeats that are involved in protein-DNA interactions. The small nuclear RNA (snRNA)-activating protein complex (SNAPc) is a heterotrimeric transcription factor that is required for expression of small nuclear RNA genes. This complex binds to an essential promoter element, the proximal sequence element, centered ∼50 base pairs upstream of the transcription start site of snRNA genes. SNAP190, the largest subunit of SNAPc, uncharacteristically contains 4.5 tandem Myb repeats. Little is known about the arrangement of the Myb repeats in the SNAPc-DNA complex, and it has not been clear whether all 4.5 Myb repeats contact the DNA. By using a site-specific protein-DNA photo-cross-linking assay, we have now mapped specific nucleotides where each of the Myb repeats of Drosophila melanogaster SNAP190 interacts with a U1 snRNA gene proximal sequence element. The results reveal the topological arrangement of the 4.5 SNAP190 Myb repeats relative to the DNA and to each other when SNAP190 is bound to a U1 promoter as a subunit of SNAPc.
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Affiliation(s)
| | - Yoon Soon Kang
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - Cheryn Lee
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - William E. Stumph
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
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4
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Holz-Schietinger C, Matje DM, Harrison MF, Reich NO. Oligomerization of DNMT3A controls the mechanism of de novo DNA methylation. J Biol Chem 2011; 286:41479-41488. [PMID: 21979949 PMCID: PMC3308859 DOI: 10.1074/jbc.m111.284687] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/26/2011] [Indexed: 01/01/2023] Open
Abstract
DNMT3A is one of two human de novo DNA methyltransferases essential for regulating gene expression through cellular development and differentiation. Here we describe the consequences of single amino acid mutations, including those implicated in the development of acute myeloid leukemia (AML) and myelodysplastic syndromes, at the DNMT3A·DNMT3A homotetramer and DNMT3A·DNMT3L heterotetramer interfaces. A model for the DNMT3A homotetramer was developed via computational interface scanning and tested using light scattering and electrophoretic mobility shift assays. Distinct oligomeric states were functionally characterized using fluorescence anisotropy and steady-state kinetics. Replacement of residues that result in DNMT3A dimers, including those identified in AML patients, show minor changes in methylation activity but lose the capacity for processive catalysis on multisite DNA substrates, unlike the highly processive wild-type enzyme. Our results are consistent with the bimodal distribution of DNA methylation in vivo and the loss of clustered methylation in AML patients. Tetramerization with the known interacting partner DNMT3L rescues processive catalysis, demonstrating that protein binding at the DNMT3A tetramer interface can modulate methylation patterning. Our results provide a structural mechanism for the regulation of DNMT3A activity and epigenetic imprinting.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, California 93106-9510
| | - Douglas M Matje
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Madeleine Flexer Harrison
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, California 93106-9510; Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510.
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5
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Hickey JM, Lovell S, Battaile KP, Hu L, Middaugh CR, Hefty PS. The atypical response regulator protein ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily. J Biol Chem 2011; 286:32606-16. [PMID: 21775428 PMCID: PMC3173177 DOI: 10.1074/jbc.m111.220574] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [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: 01/11/2011] [Revised: 07/06/2011] [Indexed: 02/03/2023] Open
Abstract
Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two α-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.
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Affiliation(s)
| | - Scott Lovell
- the Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Kevin P. Battaile
- the Hauptman-Woodward Medical Research Institute, IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lei Hu
- Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045
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Bose K, Meinke G, Bohm A, Baleja JD. Design and characterization of an enhanced repressor of human papillomavirus E2 protein. FASEB J 2011; 25:2354-61. [PMID: 21482558 PMCID: PMC3114532 DOI: 10.1096/fj.10-176461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 12/10/2011] [Accepted: 03/17/2011] [Indexed: 01/11/2023]
Abstract
Papillomaviruses are causative agents of cervical and anogenital cancers. The viral E2 protein mediates viral DNA replication and transactivation of viral oncogenes and thus represents a specific target for therapeutic intervention. Short forms of E2, E2R, contain only the C-terminal dimerization domain, and repress the normal function of E2 due to formation of an inactive heterodimer. Using structure-guided design, we replaced conserved residues at the dimer interface to design a heterodimer with increased stability. One E2R mutant in which histidine was replaced by a glutamate residue showed preferential heterodimer formation in vitro, as well as an increase in plasticity at the interface, as a result of histidine-glutamate pair formation, as observed spectroscopically and in the crystal structure, determined to 2.2-Å resolution. In addition, the enhanced E2R showed greater repression of transcription from E2-responsive reporter plasmids in mammalian cell culture. Recent advances in protein delivery into the cell raise the possibility of using exogenously added proteins as therapeutic agents. More generally, this approach may be used to target the subunit interfaces of any multisubunit protein having a similar mechanism of action.
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Affiliation(s)
- Kakoli Bose
- Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts, USA; and
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Gretchen Meinke
- Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts, USA; and
| | - Andrew Bohm
- Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts, USA; and
| | - James D. Baleja
- Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts, USA; and
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7
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Dolan KT, Duguid EM, He C. Crystal structures of SlyA protein, a master virulence regulator of Salmonella, in free and DNA-bound states. J Biol Chem 2011; 286:22178-85. [PMID: 21550983 PMCID: PMC3121362 DOI: 10.1074/jbc.m111.245258] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [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: 03/29/2011] [Revised: 04/19/2011] [Indexed: 11/06/2022] Open
Abstract
SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.
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Affiliation(s)
- Kyle T. Dolan
- From the Departments of Biochemistry and Molecular Biology and
- Chemistry and
- the Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
| | - Erica M. Duguid
- From the Departments of Biochemistry and Molecular Biology and
| | - Chuan He
- Chemistry and
- the Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
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8
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Hansen JC, Wexler BB, Rogers DJ, Hite KC, Panchenko T, Ajith S, Black BE. DNA binding restricts the intrinsic conformational flexibility of methyl CpG binding protein 2 (MeCP2). J Biol Chem 2011; 286:18938-48. [PMID: 21467044 PMCID: PMC3099709 DOI: 10.1074/jbc.m111.234609] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [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: 02/24/2011] [Revised: 03/29/2011] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry-based hydrogen/deuterium exchange (H/DX) has been used to define the polypeptide backbone dynamics of full-length methyl CpG binding protein 2 (MeCP2) when free in solution and when bound to unmethylated and methylated DNA. Essentially the entire MeCP2 polypeptide chain underwent H/DX at rates faster than could be measured (i.e. complete exchange in ≤10 s), with the exception of the methyl DNA binding domain (MBD). Even the H/DX of the MBD was rapid compared with that of a typical globular protein. Thus, there is no single tertiary structure of MeCP2. Rather, the full-length protein rapidly samples many different conformations when free in solution. When MeCP2 binds to unmethylated DNA, H/DX is slowed several orders of magnitude throughout the MBD. Binding of MeCP2 to methylated DNA led to additional minor H/DX protection, and only locally within the N-terminal portion of the MBD. H/DX also was used to examine the structural dynamics of the isolated MBD carrying three frequent mutations associated with Rett syndrome. The effects of the mutations ranged from very little (R106W) to a substantial increase in conformational sampling (F155S). Our H/DX results have yielded fine resolution mapping of the structure of full-length MeCP2 in the absence and presence of DNA, provided a biochemical basis for understanding MeCP2 function in normal cells, and predicted potential approaches for the treatment of a subset of RTT cases caused by point mutations that destabilize the MBD.
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Affiliation(s)
- Jeffrey C. Hansen
- From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | | | | | - Kristopher C. Hite
- From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Tanya Panchenko
- the Department of Biochemistry and Biophysics
- Graduate Group in Cell and Molecular Biology, and
| | - Sandya Ajith
- the Department of Biochemistry and Biophysics
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059
| | - Ben E. Black
- the Department of Biochemistry and Biophysics
- Graduate Group in Cell and Molecular Biology, and
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059
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9
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Figiel M, Chon H, Cerritelli SM, Cybulska M, Crouch RJ, Nowotny M. The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects. J Biol Chem 2011; 286:10540-50. [PMID: 21177858 PMCID: PMC3060507 DOI: 10.1074/jbc.m110.181974] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/05/2010] [Indexed: 11/09/2022] Open
Abstract
RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 Å crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5')RNA-DNA(3')/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5')RNA-DNA(3') junction and very poorly cleave RNA/DNA hybrids in the presence of Mg(2+) ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition.
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Affiliation(s)
- Małgorzata Figiel
- From the Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland and
| | - Hyongi Chon
- the Program in Genomics of Differentiation, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Susana M. Cerritelli
- the Program in Genomics of Differentiation, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Magdalena Cybulska
- From the Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland and
| | - Robert J. Crouch
- the Program in Genomics of Differentiation, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Marcin Nowotny
- From the Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland and
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10
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Langelier MF, Planck JL, Roy S, Pascal JM. Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity. J Biol Chem 2011; 286:10690-701. [PMID: 21233213 PMCID: PMC3060520 DOI: 10.1074/jbc.m110.202507] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [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: 11/10/2010] [Revised: 12/30/2010] [Indexed: 01/07/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.
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Affiliation(s)
- Marie-France Langelier
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Jamie L. Planck
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Swati Roy
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - John M. Pascal
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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11
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Britt RL, Chitteni-Pattu S, Page AN, Cox MM. RecA K72R filament formation defects reveal an oligomeric RecA species involved in filament extension. J Biol Chem 2011; 286:7830-7840. [PMID: 21193798 PMCID: PMC3048670 DOI: 10.1074/jbc.m110.194407] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [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: 10/14/2010] [Revised: 12/21/2010] [Indexed: 11/06/2022] Open
Abstract
Using an ensemble approach, we demonstrate that an oligomeric RecA species is required for the extension phase of RecA filament formation. The RecA K72R mutant protein can bind but not hydrolyze ATP or dATP. When mixed with other RecA variants, RecA K72R causes a drop in the rate of ATP hydrolysis and has been used to study disassembly of hydrolysis-proficient RecA protein filaments. RecA K72R filaments do not form in the presence of ATP but do so when dATP is provided. We demonstrate that in the presence of ATP, RecA K72R is defective for extension of RecA filaments on DNA. This defect is partially rescued when the mutant protein is mixed with sufficient levels of wild type RecA protein. Functional extension complexes form most readily when wild type RecA is in excess of RecA K72R. Thus, RecA K72R inhibits hydrolysis-proficient RecA proteins by interacting with them in solution and preventing the extension phase of filament assembly.
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Affiliation(s)
- Rachel L Britt
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Asher N Page
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.
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12
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García MT, Blázquez MA, Ferrándiz MJ, Sanz MJ, Silva-Martín N, Hermoso JA, de la Campa AG. New alkaloid antibiotics that target the DNA topoisomerase I of Streptococcus pneumoniae. J Biol Chem 2011; 286:6402-13. [PMID: 21169356 PMCID: PMC3057782 DOI: 10.1074/jbc.m110.148148] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 12/15/2010] [Indexed: 11/06/2022] Open
Abstract
Streptococcus pneumoniae has two type II DNA-topoisomerases (DNA-gyrase and DNA topoisomerase IV) and a single type I enzyme (DNA-topoisomerase I, TopA), as demonstrated here. Although fluoroquinolones target type II enzymes, antibiotics efficiently targeting TopA have not yet been reported. Eighteen alkaloids (seven aporphine and 11 phenanthrenes) were semisynthesized from boldine and used to test inhibition both of TopA activity and of cell growth. Two phenanthrenes (seconeolitsine and N-methyl-seconeolitsine) effectively inhibited both TopA activity and cell growth at equivalent concentrations (∼17 μM). Evidence for in vivo TopA targeting by seconeolitsine was provided by the protection of growth inhibition in a S. pneumoniae culture in which the enzyme was overproduced. Additionally, hypernegative supercoiling was observed in an internal plasmid after drug treatment. Furthermore, a model of pneumococcal TopA was made based on the crystal structure of Escherichia coli TopA. Docking calculations indicated strong interactions of the alkaloids with the nucleotide-binding site in the closed protein conformation, which correlated with their inhibitory effect. Finally, although seconeolitsine and N-methyl-seconeolitsine inhibited TopA and bacterial growth, they did not affect human cell viability. Therefore, these new alkaloids can be envisaged as new therapeutic candidates for the treatment of S. pneumoniae infections resistant to other antibiotics.
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Affiliation(s)
- María Teresa García
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Amparo Blázquez
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - María José Ferrándiz
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Jesús Sanz
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - Noella Silva-Martín
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A. Hermoso
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Adela G. de la Campa
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
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13
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Kingston IJ, Yung JSY, Singleton MR. Biophysical characterization of the centromere-specific nucleosome from budding yeast. J Biol Chem 2011; 286:4021-6. [PMID: 21115484 PMCID: PMC3030402 DOI: 10.1074/jbc.m110.189340] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/09/2010] [Indexed: 01/22/2023] Open
Abstract
The centromeric DNA of all eukaryotes is assembled upon a specialized nucleosome containing a histone H3 variant known as CenH3. Despite the importance and conserved nature of this protein, the characteristics of the centromeric nucleosome are still poorly understood. In particular, the stoichiometry and DNA-binding properties of the CenH3 nucleosome have been the subject of some debate. We have characterized the budding yeast centromeric nucleosome by biochemical and biophysical methods and show that it forms a stable octamer containing two copies of the Cse4 protein and wraps DNA in a left-handed supercoil, similar to the canonical H3 nucleosome. The DNA-binding properties of the recombinant nucleosome are identical to those observed in vivo demonstrating that the octameric structure is physiologically relevant.
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Affiliation(s)
- Isabel J. Kingston
- From the Macromolecular Structure and Function Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY and
| | - Jasmine S. Y. Yung
- the Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin R. Singleton
- From the Macromolecular Structure and Function Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY and
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14
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Abstract
Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.
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Affiliation(s)
| | | | | | - Gregory L. Verdine
- From the Departments of Stem Cell and Regenerative Biology
- Chemistry and Chemical Biology, and
- Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138 and
- the Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115
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15
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Siponen MI, Wisniewska M, Lehtiö L, Johansson I, Svensson L, Raszewski G, Nilsson L, Sigvardsson M, Berglund H. Structural determination of functional domains in early B-cell factor (EBF) family of transcription factors reveals similarities to Rel DNA-binding proteins and a novel dimerization motif. J Biol Chem 2010; 285:25875-9. [PMID: 20592035 PMCID: PMC2923972 DOI: 10.1074/jbc.c110.150482] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 06/16/2010] [Indexed: 11/17/2022] Open
Abstract
The early B-cell factor (EBF) transcription factors are central regulators of development in several organs and tissues. This protein family shows low sequence similarity to other protein families, which is why structural information for the functional domains of these proteins is crucial to understand their biochemical features. We have used a modular approach to determine the crystal structures of the structured domains in the EBF family. The DNA binding domain reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors but contains a unique zinc binding structure, termed zinc knuckle. Further the EBF proteins contain an IPT/TIG domain and an atypical helix-loop-helix domain with a novel type of dimerization motif. The data presented here provide insights into unique structural features of the EBF proteins and open possibilities for detailed molecular investigations of this important transcription factor family.
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Affiliation(s)
- Marina I. Siponen
- From the Structural Genomics Consortium and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magdalena Wisniewska
- From the Structural Genomics Consortium and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Lari Lehtiö
- the Department of Biosciences, Pharmaceutical Sciences, Åbo Akademi University, FI-20520 Turku, Finland
| | - Ida Johansson
- From the Structural Genomics Consortium and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Linda Svensson
- From the Structural Genomics Consortium and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Grzegorz Raszewski
- the Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden, and
| | - Lennart Nilsson
- the Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden, and
| | - Mikael Sigvardsson
- the Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty for Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Helena Berglund
- From the Structural Genomics Consortium and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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16
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Zhou T, Zhang Y, Macchiarulo A, Yang Z, Cellanetti M, Coto E, Xu P, Pellicciari R, Wang L. Novel polymorphisms of nuclear receptor SHP associated with functional and structural changes. J Biol Chem 2010; 285:24871-81. [PMID: 20516075 PMCID: PMC2915723 DOI: 10.1074/jbc.m110.133280] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [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: 04/13/2010] [Revised: 05/12/2010] [Indexed: 11/06/2022] Open
Abstract
We identified three heterozygous nonsynonymous single nucleotide polymorphisms in the small heterodimer partner (SHP, NROB2) gene in normal subjects and CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy)-like patients, including two novel missense mutations (p.R38H, p.K170N) and one of the previously reported polymorphism (p.G171A). Four novel heterozygous mutations were also identified in the intron ((Intron)1265T-->A), 3'-untranslated region ((3'-UTR)101C-->G, (3'-UTR)186T-->C), and promoter ((Pro)-423C-->T) of the SHP gene. The exonic R38H and K170N mutants exhibited impaired nuclear translocation. K170N made SHP more susceptible to ubiquitination mediated degradation and blocked SHP acetylation, which displayed lost repressive activity on its interacting partners ERRgamma and HNF4alpha but not LRH-1. In contrast, G171A increased SHP mRNA and protein expression and maintained normal function. In general, the interaction of SHP mutants with LRH-1 and EID1 was enhanced. K170N also markedly impaired the recruitment of SHP, HNF4alpha, HDAC1, and HDAC3 to the apoCIII promoter. Molecular dynamics simulations of SHP showed that G171A stabilized the nuclear receptor boxes, whereas K170N promoted the conformational destabilization of all the structural elements of the receptor. This study suggests that genetic variations in SHP are common among human subjects and the Lys-170 residue plays a key role in controlling SHP ubiquitination and acetylation associated with SHP protein stability and repressive function.
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Affiliation(s)
- Taofeng Zhou
- From the Departments of Medicine and Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132
- The First Affiliated Hospital, Sun Yat-sen University of Medical Sciences, Guangzhou 510080, China
| | - Yuxia Zhang
- From the Departments of Medicine and Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Antonio Macchiarulo
- the Dipartimento Chimica e Tecnologia del Farmaco, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy, and
| | - Zhihong Yang
- From the Departments of Medicine and Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Marco Cellanetti
- the Dipartimento Chimica e Tecnologia del Farmaco, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy, and
| | - Eliecer Coto
- the Genetica Molecular, Hospital Central Asturias, 33006 Oviedo, Spain
| | - Pingyi Xu
- The First Affiliated Hospital, Sun Yat-sen University of Medical Sciences, Guangzhou 510080, China
| | - Roberto Pellicciari
- the Dipartimento Chimica e Tecnologia del Farmaco, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy, and
| | - Li Wang
- From the Departments of Medicine and Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132
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17
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Rothe R, Liguori L, Villegas-Mendez A, Marques B, Grunwald D, Drouet E, Lenormand JL. Characterization of the cell-penetrating properties of the Epstein-Barr virus ZEBRA trans-activator. J Biol Chem 2010; 285:20224-33. [PMID: 20385549 PMCID: PMC2888435 DOI: 10.1074/jbc.m110.101550] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 04/08/2010] [Indexed: 11/06/2022] Open
Abstract
The Epstein-Barr virus basic leucine zipper transcriptional activator ZEBRA was shown recently to cross the outer membrane of live cells and to accumulate in the nucleus of lymphocytes. We investigated the potential application of the Epstein-Barr virus trans-activator ZEBRA as a transporter protein to facilitate transduction of cargo proteins. Analysis of different truncated forms of ZEBRA revealed that the minimal domain (MD) required for internalization spans residues 170-220. MD efficiently transported reporter proteins such as enhanced green fluorescent protein (EGFP) and beta-galactosidase in several normal and tumor cell lines. Functionality of internalized cargo proteins was confirmed by beta-galactosidase activity in transduced cells, and no MD-associated cell toxicity was detected. Translocation of MD through the cell membrane required binding to cell surface-associated heparan sulfate proteoglycans as shown by strong inhibition of protein uptake in the presence of heparin. We found that internalization was blocked at 4 degrees C, whereas no ATP was required as shown by an only 25% decreased uptake efficiency in energy-depleted cells. Common endocytotic inhibitors such as nystatin, chlorpromazine, and wortmannin had no significant impact on MD-EGFP uptake. Only methyl-beta-cyclodextrin inhibited MD-EGFP uptake by 40%, implicating the lipid raft-mediated endocytotic pathway. These data suggest that MD-reporter protein transduction occurs mostly via direct translocation through the lipid bilayer and not by endocytosis. This mechanism of MD-mediated internalization is suitable for the efficient delivery of biologically active proteins and renders ZEBRA-MD a promising candidate for therapeutic protein delivery applications.
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Affiliation(s)
- Romy Rothe
- From TheREx-HumProTher, TIMC-IMAG Laboratory, CNRS UMR5525, University Joseph Fourier, UFR de Médecine, 38700 La Tronche
| | - Lavinia Liguori
- the Fondation RTRA “Nanosciences,” University Joseph Fourier, TIMC-GMCAO, 38706 La Tronche
| | - Ana Villegas-Mendez
- From TheREx-HumProTher, TIMC-IMAG Laboratory, CNRS UMR5525, University Joseph Fourier, UFR de Médecine, 38700 La Tronche
| | - Bruno Marques
- From TheREx-HumProTher, TIMC-IMAG Laboratory, CNRS UMR5525, University Joseph Fourier, UFR de Médecine, 38700 La Tronche
| | - Didier Grunwald
- iRTSV-TS, U873 INSERM, Commissariat à l'Energie Atomique Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, and
| | - Emmanuel Drouet
- the Unit of Virus Host Cell Interactions, UMR5233 University Joseph Fourier EMBL-CNRS, 6 rue Jules Horowitz, F-38042 Grenoble Cedex 9, France
| | - Jean-Luc Lenormand
- From TheREx-HumProTher, TIMC-IMAG Laboratory, CNRS UMR5525, University Joseph Fourier, UFR de Médecine, 38700 La Tronche
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18
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Green SM, Coyne HJ, McIntosh LP, Graves BJ. DNA binding by the ETS protein TEL (ETV6) is regulated by autoinhibition and self-association. J Biol Chem 2010; 285:18496-504. [PMID: 20400516 PMCID: PMC2881775 DOI: 10.1074/jbc.m109.096958] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [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: 12/21/2009] [Revised: 04/08/2010] [Indexed: 01/19/2023] Open
Abstract
The ETS protein TEL, a transcriptional repressor, contains a PNT domain that, as an isolated fragment in vitro, self-associates to form a head-to-tail polymer. How such polymerization might affect the DNA-binding properties of full-length TEL is unclear. Here we report that monomeric TEL binds to a consensus ETS site with unusually low affinity (K(d) = 2.8 x 10(-8) M). A deletion analysis demonstrated that the low affinity was caused by a C-terminal inhibitory domain (CID) that attenuates DNA binding by approximately 10-fold. An NMR spectroscopically derived structure of a TEL fragment, deposited in the Protein Data Bank, revealed that the CID consists of two alpha-helices, one of which appears to block the DNA binding surface of the TEL ETS domain. Based on this structure, we substituted two conserved glutamic acids (Glu-431 and Glu-434) with alanines and found that this activated DNA binding and enhanced trypsin sensitivity in the CID. We propose that TEL displays a conformational equilibrium between inhibited and activated states and that electrostatic interactions involving these negatively charged residues play a role in stabilizing the inhibited conformation. Using a TEL dimer as a model polymer, we show that self-association facilitates cooperative binding to DNA. Cooperativity was observed on DNA duplexes containing tandem consensus ETS sites at variable spacing and orientations, suggesting flexibility in the region of TEL linking its self-associating PNT domain and DNA-binding ETS domain. We speculate that TEL compensates for the low affinity, which is caused by autoinhibition, by binding to DNA as a cooperative polymer.
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Affiliation(s)
- Sean M. Green
- From the
Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550 and
| | - H. Jerome Coyne
- the
Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lawrence P. McIntosh
- the
Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Barbara J. Graves
- From the
Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550 and
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19
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Mendillo ML, Putnam CD, Mo AO, Jamison JW, Li S, Woods VL, Kolodner RD. Probing DNA- and ATP-mediated conformational changes in the MutS family of mispair recognition proteins using deuterium exchange mass spectrometry. J Biol Chem 2010; 285:13170-82. [PMID: 20181951 PMCID: PMC2857143 DOI: 10.1074/jbc.m110.108894] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [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: 01/28/2010] [Revised: 02/23/2010] [Indexed: 11/06/2022] Open
Abstract
We have performed deuterium exchange mass spectrometry (DXMS) to probe the conformational changes that the bacterial MutS homodimer and the homologous eukaryotic heterodimer Msh2-Msh6 undergo when binding to ATP or DNA. The DXMS data support the view that high affinity binding to mispair-containing DNA and low affinity binding to fully base-paired DNA both involve forming rings by MutS protein family dimers around the DNA; however, mispair binding protects additional regions from deuterium exchange. DXMS also reveals two distinct conformations upon binding one or two ATP molecules and that binding of two ATP molecules propagates conformational changes to other regions of the protein complexes. The regions showing major changes in deuterium exchange upon ATP binding tend to occur in regions distinct from those involved in DNA binding, suggesting that although communication occurs between DNA and nucleotide binding, sliding clamps formed by binding both ATP and mispairs could result from the simultaneous action of two independent conformational changes.
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Affiliation(s)
- Marc L. Mendillo
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
| | - Christopher D. Putnam
- From the Departments of
Medicine and
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
| | | | | | - Sheng Li
- From the Departments of
Medicine and
| | | | - Richard D. Kolodner
- From the Departments of
Medicine and
- Cellular and Molecular Medicine
- Cancer Center, and
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
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20
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Wakamatsu T, Kitamura Y, Kotera Y, Nakagawa N, Kuramitsu S, Masui R. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J Biol Chem 2010; 285:9762-9769. [PMID: 20129927 PMCID: PMC2843225 DOI: 10.1074/jbc.m109.096487] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/29/2010] [Indexed: 11/06/2022] Open
Abstract
RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.
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Affiliation(s)
- Taisuke Wakamatsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871
| | - Yoshiaki Kitamura
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148
| | - Yutaro Kotera
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Noriko Nakagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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21
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Naryshkin N, Druzhinin S, Revyakin A, Kim Y, Mekler V, Ebright RH. Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes. Methods Mol Biol 2009; 543:403-437. [PMID: 19378179 PMCID: PMC2733221 DOI: 10.1007/978-1-60327-015-1_25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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] [Indexed: 05/27/2023]
Abstract
Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking - involving rapid-quench-flow mixing and pulsed-laser irradiation - permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes.
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Affiliation(s)
| | | | | | | | | | - Richard H. Ebright
- To whom correspondence should be addressed [mailing address: HHMI, Waksman Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway NJ 08854; telephone: (732) 445-5179; telefax: (732) 445-5735; ]
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22
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Abstract
Expression of almost every gene is regulated at the transcription level. Therefore, transcriptional factor Transcription factors, consequently, have marked effects on the fate of a cell by establishing the gene expression patterns that determine biological processes. In the auditory and vestibular systems, transcription factors have been found to be responsible for development, cell growth, and apoptosis. It is vital to identify the transcription factor target genes and the mechanisms by which transcription factors control and guide gene expression and regulation pathways. Compared with earlier methods devised to study transcription factor-DNA interactions, the advantage of the chromatin immunoprecipitation (ChIP) assay is that the interaction of a transcription factor with its target genes is captured in the native context of chromatin in living cells. Therefore, ChIP base assays are powerful tools to identify the direct interaction of transcription factors and their target genes in vivo. More importantly, ChIP assays have been used in combination with molecular biology techniques, such as PCR and real time PCR, gene cloning, and DNA microarrays, to determine the interaction of transcription factor-DNA from a few potential individual targets to genome-wide surveys.
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23
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Abstract
Brachyury proteins, a conserved subgroup of the T domain transcription factors, specify gut and posterior mesoderm derivatives throughout the animal kingdom. The T domain confers DNA-binding properties to Brachyury proteins, but little is known how these proteins regulate their target genes. We characterized a direct target gene of the Drosophila Brachyury-homolog Brachyenteron. Brachyenteron activates the homeobox gene orthopedia in a dose-dependent manner via multiple binding sites with the consensus (A/G)(A/T)(A/T)NTN(A/G)CAC(C/T)T. The sites and their A/T-rich flanking regions are conserved between D. melanogaster and Drosophila virilis. Reporter assays and site-directed mutagenesis demonstrate that Brachyenteron binding sites confer in part additive, in part synergistic effects on otp transcription levels. This suggests an interaction of Brachyenteron proteins on the DNA, which we could map to a conserved motif within the T domain. Mouse Brachyury also interacts with Brachyenteron through this motif. We further show that the Xenopus and mouse Brachyury homologs activate orthopedia expression when expressed in Drosophila embryonic cells. We propose that the mechanisms to achieve target gene expression through variable binding sites and through defined protein-protein interactions might be conserved for Brachyury relatives.
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Affiliation(s)
- Thomas Kusch
- Institut für Genetik, Universität zu Köln, 50931 Köln, Germany
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24
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Donald LJ, Hosfield DJ, Cuvelier SL, Ens W, Standing KG, Duckworth HW. Mass spectrometric study of the Escherichia coli repressor proteins, Ic1R and Gc1R, and their complexes with DNA. Protein Sci 2001; 10:1370-80. [PMID: 11420439 PMCID: PMC2374109 DOI: 10.1110/ps.780101] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
In Escherichia coli, the IclR protein regulates both the aceBAK operon and its own synthesis. Database homology searches have identified many IclR-like proteins, now known as the IclR family, which can be identified by a conserved C-terminal region. We have cloned and purified one of these proteins, which we have named GclR (glyoxylate carboligase repressor). Although purification is straightforward, both the IclR and GclR proteins are difficult to manipulate, requiring high salt (up to 0.6 M KCl) for solubility. With the advent of nanospray ionization, we could transfer the proteins into much higher concentrations of volatile buffer than had been practical with ordinary electrospray. In 0.5 M ammonium bicarbonate buffer, both proteins were stable as tetramers, with a small amount of dimer. In a separate experiment, we found that IclR protein selected from a random pool a sequence which matched exactly that of the presumed binding region of the GclR protein, although IclR does not regulate the gcl gene. We designed a 29 bp synthetic DNA to which IclR and GclR bind, and with which we were able to form noncovalent DNA-protein complexes for further mass spectrometry analysis. These complexes were far more stable than the proteins alone, and we have evidence of a stoichiometry which has not been described previously with (protein monomer : dsDNA) = (4 : 1).
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Affiliation(s)
- L J Donald
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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25
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Steitz TA, Richmond TJ, Wise D, Engelman D. The lac repressor protein: molecular shape, subunit structure, and proposed model for operator interaction based on structural studies of microcrystals. Proc Natl Acad Sci U S A 1974; 71:593-7. [PMID: 4595565 PMCID: PMC388057 DOI: 10.1073/pnas.71.3.593] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Electron microscopic and powder x-ray diffraction studies of small crystals of the lac repressor protein provide evidence on its molecular shape and subunit structure which in turn suggests a possible mode of repressor-operator interaction. The crystals are probably orthorhombic space group P222(1) with unit cell dimensions of a = 140, b = 91, c = 117 A. This tetrameric protein appears rather asymmetric, having approximate molecular dimensions of 140 A by 60 A by 45 A. The dumbbell shape of the projected molecular outline observed in the electron micrographs can be explained by assuming that the subunits are related by 222 symmetry and are placed at the corners of a plane rectangle. We propose a model for repressor-operator interaction in which the DNA binds to the repressor with its long axis aligned with that of the repressor and with its 2-fold axis coincident with a twofold axis of the repressor.
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26
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Lin SY, Riggs AD. Photochemical attachment of lac repressor to bromodeoxyuridine-substituted lac operator by ultraviolet radiation. Proc Natl Acad Sci U S A 1974; 71:947-51. [PMID: 4522804 PMCID: PMC388134 DOI: 10.1073/pnas.71.3.947] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The transducing phage lambdah80dlac carries the lac operator, whereas wild-type lambdah80 does not. We find that in high salt (0.18 M KCl), ultraviolet radiation causes the formation of a very stable complex between repressor and 5-bromodeoxyuridine (BrdU)-substituted lambdah80dlac but not to BrdU-lambdah80 DNA. Studies with inducers of the lac operon confirm the specificity of attachment. In low slat (0.01 M KCl), ultraviolet radiation will also attach repressor nonspecifically to BrdU-lambdah80 DNA. The stability of the complex suggests that covalent bonds are formed. We also report that another regulatory protein, the catabolite gene activator protein, can be attached similarly to DNA.
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27
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Abstract
The amino-acid sequence of lac repressor from Escherichia coli has been determined. The sequence contains 347 residues in the subunit single peptide chain. It shows no similarities with the sequences of histones or the known part of beta-galactosidase.
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Lin SY, Riggs AD. Lac operator analogues: bromodeoxyuridine substitution in the lac operator affects the rate of dissociation of the lac repressor. Proc Natl Acad Sci U S A 1972; 69:2574-6. [PMID: 4560692 PMCID: PMC426991 DOI: 10.1073/pnas.69.9.2574] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
As measured by a decreased rate of dissociation, lac repressor binds 10-times tighter to 5-bromodeoxyuridine-substituted lac operator than it does to normal lac operator. This result is obtained both in the absence and in the presence of isopropylthiogalactoside, an inducing ligand. These data are significant with regard to the mechanism of sequence-specific protein-DNA interaction, and also suggest a possible explanation for the effects of bromodeoxyuridine on the expression of differentiated functions in eukaryotic cells.
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