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Article ; Online: The ends in sight: Mre11-Rad50-Nbs1 complex structures come into focus.

Wojtaszek, Jessica L / Williams, R Scott

2023 Volume 83, Issue 2, Page(s) 160–162

Abstract: In this issue of Molecular Cell, Rotheneder et al. ...

Abstract	In this issue of Molecular Cell, Rotheneder et al.
MeSH term(s)	MRE11 Homologue Protein/genetics ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; DNA Repair ; DNA/genetics ; Acid Anhydride Hydrolases/genetics
Chemical Substances	MRE11 Homologue Protein (EC 3.1.-) ; Cell Cycle Proteins ; DNA Repair Enzymes (EC 6.5.1.-) ; Nuclear Proteins ; DNA (9007-49-2) ; Acid Anhydride Hydrolases (EC 3.6.-)
Language	English
Publishing date	2023-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.12.016
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Article ; Online: Introduction to the multi-author-review: emerging advances in the structural chemistry of DNA strand break repair.

Williams, R Scott

Cellular and molecular life sciences : CMLS

2019 Volume 77, Issue 1, Page(s) 1–2

Abstract: DNA strand breaks present a complex challenge for our cells, and the integrity of the DNA damage response machinery is critical for preventing cancer, premature aging, and neurodegenerative syndromes amongst other ailments. This multi-author review issue ...

Abstract	DNA strand breaks present a complex challenge for our cells, and the integrity of the DNA damage response machinery is critical for preventing cancer, premature aging, and neurodegenerative syndromes amongst other ailments. This multi-author review issue presents emerging topics relevant to understanding the fundamental structural mechanisms of DNA strand break sensing, signaling, and repair.
MeSH term(s)	Animals ; DNA/genetics ; DNA Breaks ; DNA Repair ; Genomic Instability ; Humans ; Neoplasms/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-11-11
Publishing country	Switzerland
Document type	Introductory Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03364-2
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Article: Introduction to the multi-author-review: emerging advances in the structural chemistry of DNA strand break repair

Williams, R. Scott

Cellular and molecular life sciences. 2020 Jan., v. 77, no. 1

2020

Abstract	DNA strand breaks present a complex challenge for our cells, and the integrity of the DNA damage response machinery is critical for preventing cancer, premature aging, and neurodegenerative syndromes amongst other ailments. This multi-author review issue presents emerging topics relevant to understanding the fundamental structural mechanisms of DNA strand break sensing, signaling, and repair.
Keywords	DNA ; DNA damage ; chemistry
Language	English
Dates of publication	2020-01
Size	p. 1-2.
Publishing place	Springer International Publishing
Document type	Article
Note	NAL-AP-2-clean ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03364-2
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Article ; Online: The three-component helicase/primase complex of herpes simplex virus-1.

Bermek, Oya / Williams, R Scott

Open biology

2021 Volume 11, Issue 6, Page(s) 210011

Abstract: Herpes simplex virus type 1 (HSV-1) is one of the nine herpesviruses that infect humans. HSV-1 encodes seven proteins to replicate its genome in the hijacked human cell. Among these are the herpes virus DNA helicase and primase that are essential ... ...

Abstract	Herpes simplex virus type 1 (HSV-1) is one of the nine herpesviruses that infect humans. HSV-1 encodes seven proteins to replicate its genome in the hijacked human cell. Among these are the herpes virus DNA helicase and primase that are essential components of its replication machinery. In the HSV-1 replisome, the helicase-primase complex is composed of three components including UL5 (helicase), UL52 (primase) and UL8 (non-catalytic subunit). UL5 and UL52 subunits are functionally interdependent, and the UL8 component is required for the coordination of UL5 and UL52 activities proceeding in opposite directions with respect to the viral replication fork. Anti-viral compounds currently under development target the functions of UL5 and UL52. Here, we review the structural and functional properties of the UL5/UL8/UL52 complex and highlight the gaps in knowledge to be filled to facilitate molecular characterization of the structure and function of the helicase-primase complex for development of alternative anti-viral treatments.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Primase/chemistry ; DNA Primase/genetics ; DNA Primase/metabolism ; Drug Development ; Herpes Simplex/drug therapy ; Herpes Simplex/virology ; Herpesvirus 1, Human/drug effects ; Herpesvirus 1, Human/enzymology ; Herpesvirus 1, Human/genetics ; Humans ; Models, Molecular ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Structure-Activity Relationship ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Multienzyme Complexes ; Protein Subunits ; DNA Primase (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2021-06-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.210011
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Article ; Online: Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA.

Wojtaszek, Jessica L / Hoff, Kirsten E / Longley, Matthew J / Kaur, Parminder / Andres, Sara N / Wang, Hong / Williams, R Scott / Copeland, William C

Nucleic acids research

2023 Volume 51, Issue 18, Page(s) 9716–9732

Abstract: The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly binds DNA, although the underlying molecular basis and ... ...

Abstract	The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly binds DNA, although the underlying molecular basis and functional significance are unknown. Here, data from Atomic Force Microscopy (AFM) and X-ray structures of PolG2-DNA complexes define dimeric and hexameric PolG2 DNA binding modes. Targeted disruption of PolG2 DNA-binding interfaces impairs processive DNA synthesis without diminishing Pol γ subunit affinities. In addition, a structure-specific DNA-binding role for PolG2 oligomers is supported by X-ray structures and AFM showing that oligomeric PolG2 localizes to DNA crossings and targets forked DNA structures resembling the mitochondrial D-loop. Overall, data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG2 disruption in mitochondrial disease.
MeSH term(s)	Humans ; DNA Polymerase gamma/genetics ; DNA Polymerase gamma/metabolism ; DNA Replication/genetics ; DNA, Mitochondrial/genetics ; DNA, Mitochondrial/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondrial Diseases/genetics ; Mitochondrial Diseases/metabolism
Chemical Substances	DNA Polymerase gamma (EC 2.7.7.7) ; DNA, Mitochondrial ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; POLG2 protein, human (EC 2.7.7.7)
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad679
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Article ; Online: CtIP/Ctp1/Sae2, molecular form fit for function.

Andres, Sara N / Williams, R Scott

DNA repair

2017 Volume 56, Page(s) 109–117

Abstract: Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of ... ...

Abstract	Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of the Mre11/Rad50/Nbs1 (MRN) DSB repair processing and signaling complex, CtIP/Ctp1/Sae2/Com1 is integral to the channeling of DNA double strand breaks through DSB repair by homologous recombination (HR). Nearly two decades since its discovery, emerging new data are defining the molecular underpinnings for CtIP DSB repair regulatory activities. CtIP homologs are largely intrinsically unstructured proteins comprised of expanded regions of low complexity sequence, rather than defined folded domains typical of DNA damage metabolizing enzymes and nucleases. A compact structurally conserved N-terminus forms a functionally critical tetrameric helical dimer of dimers (THDD) region that bridges CtIP oligomers, and is flexibly appended to a conserved C-terminal Sae2-homology DNA binding and DSB repair pathway choice regulatory hub which influences nucleolytic activities of the MRN core nuclease complex. The emerging evidence from structural, biophysical, and biological studies converges on CtIP having functional roles in DSB repair that include: 1) dynamic DNA strand coordination through direct DNA binding and DNA bridging activities, 2) MRN nuclease complex cofactor functions that direct MRN endonucleolytic cleavage of protein-blocked DSB ends and 3) acting as a protein binding hub targeted by the cell cycle regulatory apparatus, which influences CtIP expression and activity via layers of post-translational modifications, protein-protein interactions and DNA binding.
MeSH term(s)	Arabidopsis Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Cycle Proteins/metabolism ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA-Binding Proteins/metabolism ; Endonucleases/metabolism ; Eukaryota/enzymology ; Eukaryota/genetics ; Humans ; Nuclear Proteins/metabolism ; Recombinational DNA Repair ; Saccharomyces cerevisiae Proteins/metabolism ; Schizosaccharomyces pombe Proteins/metabolism
Chemical Substances	Arabidopsis Proteins ; AtGR1 protein, Arabidopsis ; Carrier Proteins ; Cell Cycle Proteins ; Ctp1 protein, S pombe ; DNA-Binding Proteins ; Nuclear Proteins ; SAE2 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Schizosaccharomyces pombe Proteins ; DNA (9007-49-2) ; Endonucleases (EC 3.1.-) ; RBBP8 protein, human (EC 3.1.-)
Language	English
Publishing date	2017-06-09
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2017.06.013
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Article: Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity.

Terrón-Bautista, José / Martínez-Sánchez, María Del Mar / López-Hernández, Laura / Vadusevan, Ananda Ayyappan / García-Domínguez, Mario / Williams, R Scott / Aguilera, Andrés / Millán-Zambrano, Gonzalo / Cortés-Ledesma, Felipe

bioRxiv : the preprint server for biology

2024

Abstract: Human type-II topoisomerases, TOP2A and TOP2B, remove transcription associated DNA supercoiling, thereby affecting gene-expression programs, and have recently been associated with 3D genome architecture. Here, we study the regulatory roles of TOP2 ... ...

Abstract	Human type-II topoisomerases, TOP2A and TOP2B, remove transcription associated DNA supercoiling, thereby affecting gene-expression programs, and have recently been associated with 3D genome architecture. Here, we study the regulatory roles of TOP2 paralogs in response to estrogen, which triggers an acute transcriptional induction that involves rewiring of genome organization. We find that, whereas TOP2A facilitates transcription, as expected for a topoisomerase, TOP2B limits the estrogen response. Consistent with this, TOP2B activity is locally downregulated upon estrogen treatment to favor the establishment and stabilization of regulatory chromatin contacts, likely through an accumulation of DNA supercoiling. We show that estrogen-mediated inhibition of TOP2B requires estrogen receptor α (ERα), a non-catalytic function of TOP2A, and the action of the atypical SUMO-ligase ZATT. This mechanism of topological transcriptional-control, which may be shared by additional gene-expression circuits, highlights the relevance of DNA topoisomerases as central actors of genome dynamics.
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.22.576640
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Article ; Online: Molecular mechanisms of topoisomerase 2 DNA-protein crosslink resolution.

Riccio, Amanda A / Schellenberg, Matthew J / Williams, R Scott

Cellular and molecular life sciences : CMLS

2019 Volume 77, Issue 1, Page(s) 81–91

Abstract: The compaction of DNA and the continuous action of DNA transactions, including transcription and DNA replication, create complex DNA topologies that require Type IIA Topoisomerases, which resolve DNA topological strain and control genome dynamics. The ... ...

Abstract	The compaction of DNA and the continuous action of DNA transactions, including transcription and DNA replication, create complex DNA topologies that require Type IIA Topoisomerases, which resolve DNA topological strain and control genome dynamics. The human TOP2 enzymes catalyze their reactions via formation of a reversible covalent enzyme DNA-protein crosslink, the TOP2 cleavage complex (TOP2cc). Spurious interactions of TOP2 with DNA damage, environmental toxicants and chemotherapeutic "poisons" perturbs the TOP2 reaction cycle, leading to an accumulation of DNA-protein crosslinks, and ultimately, genomic instability and cell death. Emerging evidence shows that TOP2-DNA protein crosslink (DPC) repair entails multiple strand break repair activities, such as removal of the poisoned TOP2 protein and rejoining of the DNA ends through homologous recombination (HR) or non-homologous end joining (NHEJ). Herein, we discuss the molecular mechanisms of TOP2-DPC resolution, with specific emphasis on the recently uncovered ZATT
MeSH term(s)	Aminoacyltransferases/chemistry ; Aminoacyltransferases/metabolism ; Animals ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Breaks ; DNA Repair ; DNA Topoisomerases, Type II/chemistry ; DNA Topoisomerases, Type II/metabolism ; Humans ; Poly-ADP-Ribose Binding Proteins/chemistry ; Poly-ADP-Ribose Binding Proteins/metabolism ; Protein Conformation ; Sumoylation ; Transcription Factors/chemistry ; Transcription Factors/metabolism
Chemical Substances	Poly-ADP-Ribose Binding Proteins ; Transcription Factors ; DNA (9007-49-2) ; Aminoacyltransferases (EC 2.3.2.-) ; ZNF451 protein, human (EC 2.3.2.-) ; DNA Topoisomerases, Type II (EC 5.99.1.3) ; TOP2A protein, human (EC 5.99.1.3)
Language	English
Publishing date	2019-11-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03367-z
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Article ; Online: Correction: Ctp1 protein-DNA filaments promote DNA bridging and DNA double-strand break repair.

Andres, Sara N / Li, Zimeng M / Erie, Dorothy A / Williams, R Scott

The Journal of biological chemistry

2020 Volume 295, Issue 3, Page(s) 896

Language	English
Publishing date	2020-01-15
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.AAC119.012364
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Article: Molecular mechanisms of topoisomerase 2 DNA–protein crosslink resolution

Riccio, Amanda A / Schellenberg, Matthew J / Williams, R. Scott

Cellular and molecular life sciences. 2020 Jan., v. 77, no. 1

2020

Abstract	The compaction of DNA and the continuous action of DNA transactions, including transcription and DNA replication, create complex DNA topologies that require Type IIA Topoisomerases, which resolve DNA topological strain and control genome dynamics. The human TOP2 enzymes catalyze their reactions via formation of a reversible covalent enzyme DNA–protein crosslink, the TOP2 cleavage complex (TOP2cc). Spurious interactions of TOP2 with DNA damage, environmental toxicants and chemotherapeutic “poisons” perturbs the TOP2 reaction cycle, leading to an accumulation of DNA–protein crosslinks, and ultimately, genomic instability and cell death. Emerging evidence shows that TOP2-DNA protein crosslink (DPC) repair entails multiple strand break repair activities, such as removal of the poisoned TOP2 protein and rejoining of the DNA ends through homologous recombination (HR) or non-homologous end joining (NHEJ). Herein, we discuss the molecular mechanisms of TOP2-DPC resolution, with specific emphasis on the recently uncovered ZATTZⁿᶠ⁴⁵¹-licensed TDP2-catalyzed TOP2-DPC reversal mechanism.
Keywords	DNA ; DNA damage ; DNA replication ; cell death ; crosslinking ; drug therapy ; enzymes ; genetic instability ; genome ; homologous recombination ; humans ; topology ; toxic substances
Language	English
Dates of publication	2020-01
Size	p. 81-91.
Publishing place	Springer International Publishing
Document type	Article
Note	NAL-AP-2-clean ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03367-z
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