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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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2
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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3
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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4
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Rossi MJ, Lai WKM, Pugh BF. Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Res 2018; 28:497-508. [PMID: 29563167 PMCID: PMC5880240 DOI: 10.1101/gr.229518.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/05/2018] [Indexed: 01/01/2023]
Abstract
General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence. It is assumed that sequence recognition via direct base readout suffices for specificity and that spurious nonfunctional sites are rendered inaccessible by chromatin. We tested these assumptions through genome-wide mapping of GRFs in vivo and in purified biochemical systems at near–base pair (bp) resolution using several ChIP-exo–based assays. We find that computationally predicted DNA shape features (e.g., minor groove width, helix twist, base roll, and propeller twist) that are not defined by a unique consensus sequence are embedded in the nonunique portions of GRF motifs and contribute critically to sequence-specific binding. This dual source specificity occurs at GRF sites in promoter regions where chromatin organization starts. Outside of promoter regions, strong consensus sites lack the shape component and consequently lack an intrinsic ability to bind cognate GRFs, without regard to influences from chromatin. However, sites having a weak consensus and low intrinsic affinity do exist in these regions but are rendered inaccessible in a chromatin environment. Thus, GRF site-specificity is achieved through integration of favorable DNA sequence and shape readouts in promoter regions and by chromatin-based exclusion from fortuitous weak sites within gene bodies. This study further revealed a severe G/C nucleotide cross-linking selectivity inherent in all formaldehyde-based ChIP assays, which includes ChIP-seq. However, for most tested proteins, G/C selectivity did not appreciably affect binding site detection, although it does place limits on the quantitativeness of occupancy levels.
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Affiliation(s)
- Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Koc KN, Singh SP, Stodola JL, Burgers PM, Galletto R. Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ. Nucleic Acids Res 2016; 44:3811-9. [PMID: 27001517 PMCID: PMC4856994 DOI: 10.1093/nar/gkw181] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
Using an in vitro reconstituted system in this work we provide direct evidence that the yeast repressor/activator protein 1 (Rap1), tightly bound to its consensus site, forms a strong non-polar barrier for the strand displacement activity of DNA polymerase δ. We propose that relief of inhibition may be mediated by the activity of an accessory helicase. To this end, we show that Pif1, a 5'-3' helicase, not only stimulates the strand displacement activity of Pol δ but it also allows efficient replication through the block, by removing bound Rap1 in front of the polymerase. This stimulatory activity of Pif1 is not limited to the displacement of a single Rap1 molecule; Pif1 also allows Pol δ to carry out DNA synthesis across an array of bound Rap1 molecules that mimics a telomeric DNA-protein assembly. This activity of Pif1 represents a novel function of this helicase during DNA replication.
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Affiliation(s)
- Katrina N Koc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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6
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Feldmann EA, Galletto R. The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes. Biochemistry 2014; 53:7471-83. [PMID: 25382181 PMCID: PMC4263426 DOI: 10.1021/bi501049b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Saccharomyces cerevisiae repressor-activator protein
1 (Rap1) is an essential protein involved in multiple steps of DNA
regulation, as an activator in transcription, as a repressor at silencer
elements, and as a major component of the shelterin-like complex at
telomeres. All the known functions of Rap1 require the known high-affinity
and specific interaction of the DNA-binding domain with its recognition
sequences. In this work, we focus on the interaction of the DNA-binding
domain of Rap1 (Rap1DBD) with double-stranded DNA substrates.
Unexpectedly, we found that while Rap1DBD forms a high-affinity
1:1 complex with its DNA recognition site, it can also form lower-affinity
complexes with higher stoichiometries on DNA. These lower-affinity
interactions are independent of the presence of the recognition sequence,
and we propose they originate from the ability of Rap1DBD to bind to DNA in two different binding modes. In one high-affinity
binding mode, Rap1DBD likely binds in the conformation
observed in the available crystal structures. In the other alternative
lower-affinity binding mode, we propose that a single Myb-like domain
of the Rap1DBD makes interactions with DNA, allowing for
more than one protein molecule to bind to the DNA substrates. Our
findings suggest that the Rap1DBD does not simply target
the protein to its recognition sequence but rather it might be a possible
point of regulation.
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Affiliation(s)
- Erik A Feldmann
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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Bonazza K, Rottensteiner H, Seyfried BK, Schrenk G, Allmaier G, Turecek PL, Friedbacher G. Visualization of a protein-protein interaction at a single-molecule level by atomic force microscopy. Anal Bioanal Chem 2013; 406:1411-21. [PMID: 24363113 DOI: 10.1007/s00216-013-7563-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 01/24/2023]
Abstract
Atomic force microscopy is unmatched in terms of high-resolution imaging under ambient conditions. Over the years, substantial progress has been made using this technique to improve our understanding of biological systems on the nanometer scale, such as visualization of single biomolecules. For monitoring also the interaction between biomolecules, in situ high-speed imaging is making enormous progress. Here, we describe an alternative ex situ imaging method where identical molecules are recorded before and after reaction with a binding partner. Relocation of the identical molecules on the mica surface was thereby achieved by using a nanoscale scratch as marker. The method was successfully applied to study the complex formation between von Willebrand factor (VWF) and factor VIII (FVIII), two essential haemostatic components of human blood. FVIII binding was discernible by an appearance of globular domains appended to the N-terminal large globular domains of VWF. The specificity of the approach could be demonstrated by incubating VWF with FVIII in the presence of a high salt buffer which inhibits the interaction between these two proteins. The results obtained indicate that proteins can maintain their reactivity for subsequent interactions with other molecules when gently immobilized on a solid substrate and subjected to intermittent drying steps. The technique described opens up a new analytical perspective for studying protein-protein interactions as it circumvents some of the obstacles encountered by in situ imaging and other ex situ techniques.
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Affiliation(s)
- Klaus Bonazza
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-IAC, 1060, Wien, Austria
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