Structural insights into DNA repair by RNase T

DNA repair is generally accomplished by a coordinated effort via several types of DNA enzymes, including endonucleases, exonucleases, helicases, polymerases and ligases. Among all these DNA enzymes, the molecular functions of exonucleases, which bind at the 3′ or 5′ end of DNA and cleave one nucleotide at a time, are least understood in how they select DNA substrates for binding and trimming. Here we show that the DEDDh family exonuclease RNase T is critical for Escherichia coli resistance to various DNA damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Our crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DEDDh-family exonucleases in DNA 3′-end processing.

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Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways

PLoS Biology ◽

10.1371/journal.pbio.1001803 ◽

2014 ◽

Vol 12 (3) ◽

pp. e1001803 ◽

Cited By ~ 18

Author(s):

Yu-Yuan Hsiao ◽

Woei-Horng Fang ◽

Chia-Chia Lee ◽

Yi-Ping Chen ◽

Hanna S. Yuan

Keyword(s):

Dna Repair ◽

Repair Pathways ◽

Structural Insights

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DNA Repair Pathways in Cancer Therapy and Resistance

Frontiers in Pharmacology ◽

10.3389/fphar.2020.629266 ◽

2021 ◽

Vol 11 ◽

Author(s):

Lan-ya Li ◽

Yi-di Guan ◽

Xi-sha Chen ◽

Jin-ming Yang ◽

Yan Cheng

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Mammalian Cells ◽

Chemotherapeutic Agents ◽

Cancer Therapies ◽

Exogenous Dna ◽

Dna Damaging Agents ◽

Anti Cancer ◽

Mitochondria Dna ◽

Repair Pathways

DNA repair pathways are triggered to maintain genetic stability and integrity when mammalian cells are exposed to endogenous or exogenous DNA-damaging agents. The deregulation of DNA repair pathways is associated with the initiation and progression of cancer. As the primary anti-cancer therapies, ionizing radiation and chemotherapeutic agents induce cell death by directly or indirectly causing DNA damage, dysregulation of the DNA damage response may contribute to hypersensitivity or resistance of cancer cells to genotoxic agents and targeting DNA repair pathway can increase the tumor sensitivity to cancer therapies. Therefore, targeting DNA repair pathways may be a potential therapeutic approach for cancer treatment. A better understanding of the biology and the regulatory mechanisms of DNA repair pathways has the potential to facilitate the development of inhibitors of nuclear and mitochondria DNA repair pathways for enhancing anticancer effect of DNA damage-based therapy.

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Ruthenium(II) Complexes Bearing Thioether-Appended α- Iminopyridine Ligands: Arene Precursors Permit Access to K2-N,N and K3-N,N,S Complexes

10.26434/chemrxiv.9693506.v1 ◽

2019 ◽

Author(s):

Victoria A. Ternes ◽

Hannah A. Morgan ◽

Austin P. Lanquist ◽

Michael P. Murray ◽

Bradley Wile

Keyword(s):

Crystal Structure ◽

Solid State ◽

Strong Field ◽

Active Role ◽

Binding Mode ◽

Phenethyl Alcohol ◽

Ru Complexes

Herein we report the preparation of a series of Ru(II) complexes featuring alpha-iminopyridine ligands bearing thioether functionality (NNSR, where R = Me, CH2Ph, Ph). Metallation using (p cymene)RuCl dimer permits access to (k2-N,N)Ru complexes in which the thioether moiety remains uncoordinated. In the presence of a strong field ligand such as acetonitrile or triphenylphosphine, the p-cymene moiety is displaced, and the ligand adopts a k3-N,N,S binding mode. These complexes are characterized using a combination of solution and solid state methods, including the crystal structure of [(NNSMe)Ru(NCMe)2Cl]Cl. The k2-N,N Ru(II) complexes are shown to serve as efficient precatalysts for the oxidation of sec-phenethyl alcohol at 5 mol% loadings, using a variety of external oxidants and solvents. The complex bearing an S-Ph donor was found to be the most active of those surveyed, suggesting that the thioether donor plays an active role in catalyst speciation for this transformation.

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Effects of aphidicolin and/or 2‘,3‘-dideoxythymidine on DNA repair induced in HeLa cells by four types of DNA-damaging agents.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)85098-6 ◽

1985 ◽

Vol 260 (19) ◽

pp. 10412-10417

Author(s):

K Yamada ◽

F Hanaoka ◽

M Yamada

Keyword(s):

Dna Repair ◽

Hela Cells ◽

Dna Damaging Agents

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Histone methylation can either promote or reduce cellular radiosensitivity by regulating DNA repair pathways

Mutation Research/Reviews in Mutation Research ◽

10.1016/j.mrrev.2020.108362 ◽

2021 ◽

Vol 787 ◽

pp. 108362

Author(s):

Yuchuan Zhou ◽

Chunlin Shao

Keyword(s):

Dna Repair ◽

Histone Methylation ◽

Cellular Radiosensitivity ◽

Repair Pathways

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Targeting DNA Repair and Chromatin Crosstalk in Cancer Therapy

Cancers ◽

10.3390/cancers13030381 ◽

2021 ◽

Vol 13 (3) ◽

pp. 381

Author(s):

Danielle P. Johnson ◽

Mahesh B. Chandrasekharan ◽

Marie Dutreix ◽

Srividya Bhaskara

Keyword(s):

Dna Repair ◽

Cancer Therapy ◽

Therapeutic Intervention ◽

Synthetic Lethality ◽

Checkpoint Proteins ◽

Cellular Processes ◽

Repair Pathways ◽

Made In

Aberrant DNA repair pathways that underlie developmental diseases and cancers are potential targets for therapeutic intervention. Targeting DNA repair signal effectors, modulators and checkpoint proteins, and utilizing the synthetic lethality phenomena has led to seminal discoveries. Efforts to efficiently translate the basic findings to the clinic are currently underway. Chromatin modulation is an integral part of DNA repair cascades and an emerging field of investigation. Here, we discuss some of the key advancements made in DNA repair-based therapeutics and what is known regarding crosstalk between chromatin and repair pathways during various cellular processes, with an emphasis on cancer.

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HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones

Nature Communications ◽

10.1038/s41467-021-21302-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Fa-Hui Sun ◽

Peng Zhao ◽

Nan Zhang ◽

Lu-Lu Kong ◽

Catherine C. L. Wong ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Active Site ◽

Negative Charge ◽

Structural Data ◽

Dna Breaks ◽

Adp Ribosylation ◽

Local Conformation ◽

Key Residues ◽

Structural Insights

AbstractUpon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.

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Crystal structures of Ca2+–calmodulin bound to NaV C-terminal regions suggest role for EF-hand domain in binding and inactivation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818618116 ◽

2019 ◽

Vol 116 (22) ◽

pp. 10763-10772 ◽

Cited By ~ 10

Author(s):

Bernd R. Gardill ◽

Ricardo E. Rivera-Acevedo ◽

Ching-Chieh Tung ◽

Filip Van Petegem

Keyword(s):

Crystal Structure ◽

Binding Sites ◽

Binding Mode ◽

Conformational Switch ◽

Channel Inactivation ◽

Dependent Inactivation ◽

Ef Hand ◽

Inherited Arrhythmia ◽

A Site

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

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