Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

eLife, Год журнала: 2021, Номер 10

Опубликована: Дек. 7, 2021

Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As list of substrates continues to expand, there need for technologies prepare mono- and poly-ADP-ribosylated proteins biochemical interrogation. Here, we investigate unique peptide ADPr activities PARP1 in absence presence HPF1. We then exploit these develop method that facilitates installation ADP-ribose polymers onto peptides with precise control over chain length site. Importantly, enzymatically are fully compatible protein ligation technologies. This chemoenzymatic synthesis strategy was employed assemble series full-length, ADP-ribosylated histones show at histone H2B serine 6 or H3 10 converts nucleosomes into robust chromatin remodeler ALC1. found ALC1 preferentially remodels ‘activated’ within heterogeneous mononucleosome populations asymmetrically dinucleosome substrates, nucleosome sufficient stimulate activity nuclear extracts. Our study identifies function describes new, highly modular approach explore impact site-specific poly-ADPr have on function.

Язык: Английский

---

Arginine ADP-Ribosylation: Chemical Synthesis of Post-Translationally Modified Ubiquitin Proteins

Journal of the American Chemical Society, Год журнала: 2022, Номер 144(45), С. 20582 - 20589

Опубликована: Ноя. 1, 2022

We describe the development and optimization of a methodology to prepare peptides proteins modified on arginine residue with an adenosine-di-phosphate-ribosyl (ADPr) group. Our method comprises reacting ornithine containing polypeptide on-resin α-linked anomeric isothiourea N-riboside, ensuing installment phosphomonoester at 5'-hydroxyl ribosyl moiety followed by conversion into adenosine diphosphate. use this obtain four regioisomers ADP-ribosylated ubiquitin (UbADPr), each ADP-ribosyl different position within (Ub) protein (Arg42, Arg54, Arg72, Arg74) as first reported examples fully synthetic arginine-linked ADPr-modified proteins. show chemically prepared Arg-linked UbADPr be accepted processed Legionella enzymes compare entire suite in variety biochemical experiments, allowing us profile activity selectivity pneumophila ligase hydrolase enzymes.

Язык: Английский

---

Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 2, 2024

Abstract The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited PARP1/PARP2 and their co-factor HPF1. has emerged as a cancer drug target, but how it recruited to ADP-ribosylated nucleosomes affect positioning near breaks unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest break. To dissect consequences of such asymmetry, generate with defined one side only. cryo-electron microscopy structure bound an asymmetric nucleosome indicates preferential engagement side. Using single-molecule FRET, demonstrate this recruitment gives rise directed sliding away from linker site. Our data suggest mechanism which slides break render more accessible repair factors.

Язык: Английский

---

Histone ADP-ribosylation promotes resistance to PARP inhibitors by facilitating PARP1 release from DNA lesions

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(25)

Опубликована: Июнь 12, 2024

Poly(ADP-ribose) polymerase 1 (PARP1) has emerged as a central target for cancer therapies due to the ability of PARP inhibitors specifically kill tumors deficient DNA repair by homologous recombination. Upon damage, PARP1 quickly binds breaks and triggers ADP-ribosylation signaling. is important recruitment various factors sites well timely dissociation from breaks. Indeed, becomes trapped at in presence inhibitors, mechanism underlying cytotoxitiy these inhibitors. Therefore, any cellular process influencing trapping thought impact inhibitor efficiency, potentially leading acquired resistance patients treated with drugs. There are numerous targets after including itself histones. While recent findings reported that automodification promotes its release lesions, potential other ADP-ribosylated proteins on this remains unknown. Here, we demonstrate histone also crucial dissipation thus contributing Considering crosstalk between marks, our open interesting perspectives development more efficient inhibitor-driven therapies.

Язык: Английский

---

dELTA-MS: A Mass Spectrometry-Based Proteomics Approach for Identifying ADP-Ribosylation Sites and Forms

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

ADP-ribosylation, characterized by the addition of adenosine diphosphate ribose, can occur in both monomeric (MARylation) and polymeric (PARylation) forms. Little is known about specific contributions MARylation PARylation to cellular processes due a lack tools for jointly investigating these individual We present novel mass spectrometry (MS)-based proteomics approach that preserves information native ADP-ribosylation form associated with modification site within single experiment. Our workflow enables simplified, binary identification forms, avoiding some challenges typically presented PARylated peptides during MS analysis. method uses coronaviral enzyme NS2 reverse our previous labeling approach, ELTA, which enzymatically labels terminal ADP-ribose. deconjugates ELTA-labeled free or peptide-conjugated ADP-ribose monomers polymers (thereby termed dELTA), leaving behind signature phosphate. dELTA-MS involves ELTA labeling, dELTA deconjugation, further processing using Deinococcus radiodurans poly(ADP-ribose) glycohydrolase (DrPARG), resulting two distinct shifts sites. demonstrate feasibility this analyses proof-of-principle peptide standards. thus creates possibilities reveal fundamental biology explore its dysregulation, terms sites disease progression.

Язык: Английский

---

PARticular MARks: Histone ADP-ribosylation and the DNA Damage Response

DNA repair, Год журнала: 2024, Номер 140, С. 103711 - 103711

Опубликована: Июнь 22, 2024

Язык: Английский

---

The function and regulation of ADP-ribosylation in the DNA damage response

Biochemical Society Transactions, Год журнала: 2023, Номер 51(3), С. 995 - 1008

Опубликована: Май 12, 2023

ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it synthesised by PARP 1–3, strand break sensors. Recent advances have identified serine residues as the most common targets for during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes catalytic domain. Through ADP-ribosylation, recruit variety of factors to site and control their activities. However, timely removal also key genome stability mostly performed two hydrolases: PARG ARH3. Here, we describe writers, readers erasers contribution mounting We discuss use inhibitors cancer therapy ways tackle PARPi treatment resistance.

Язык: Английский

---

Dispensability of HPF1 for cellular removal of DNA single-strand breaks

Nucleic Acids Research, Год журнала: 2024, Номер 52(18), С. 10986 - 10998

Опубликована: Авг. 20, 2024

In response to DNA damage, the histone PARylation factor 1 (HPF1) regulates PARP1/2 activity, facilitating serine ADP-ribosylation of chromatin-associated factors. While are known for their role in single-strand break repair (SSBR), significance HPF1 this process remains unclear. Here, we investigated impact deficiency on cellular survival and SSBR following exposure various genotoxins. We found that loss did not generally increase sensitivity agents typically induce breaks (SSBs) repaired by PARP1. kinetics HPF1-deficient cells were largely unaffected, though its absence partially influenced accumulation SSB intermediates after specific genotoxins certain cell lines, likely due altered chromatin. Despite reduced mono-ADP-ribosylation, maintained robust poly-ADP-ribosylation at sites, possibly reflecting PARP1 auto-poly-ADP-ribosylation non-serine residues. Notably, poly-ADP-ribose chains sufficient recruit XRCC1, which may explain relatively normal capacity cells. These findings suggest dispensable PARP1-dependent genotoxic stress, highlighting complexity mechanisms maintain genomic stability chromatin remodeling.

Язык: Английский

---

Acidic patch histone mutations and their effects on nucleosome remodeling

Biochemical Society Transactions, Год журнала: 2022, Номер 50(2), С. 907 - 919

Опубликована: Март 31, 2022

Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed ‘the acidic patch' that acts as regulatory hub for function numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, INO80, distinct modes interaction with one or both patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses various human cancers uncovered high-frequency mutations in coding genes, some map patch. How cancer-related patch affect is mainly unknown. Recent advances vitro reconstitution enabled access physiologically relevant nucleosomes, asymmetric nucleosomes possess wild-type mutant copies. Biochemical investigation these substrates revealed unexpected outcomes far-reaching implications alteration structure. This review summarizes recent findings how different families interpret patches functions discusses models remodeler-mediated changes landscapes consequence mutations.

Язык: Английский

---

Macrodomain Mac1 of SARS-CoV-2 Nonstructural Protein 3 Hydrolyzes Diverse ADP-ribosylated Substrates

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Фев. 7, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a global pandemic that resulted in more than 6-million deaths worldwide. The virus encodes several non-structural proteins (Nsps) contain elements capable of disrupting cellular processes. Among these Nsp proteins, Nsp3 contains macrodomains, e.g., Mac1, Mac2, Mac3, with potential effects on host cells. Mac1 has been shown to increase SARS-CoV-2 virulence and disrupt ADP-ribosylation pathways mammalian results from the transfer ADP-ribose moiety NAD + various acceptors, DNA, RNA, contributing cell's biological mechanism action bacterial toxins, Pseudomonas diphtheria toxin protein biosynthetic signaling pathways. On other hand, some viral macrodomains cleavage ADP-ribose-acceptor bond, generating free ADP-ribose. By this reaction, macrodomain-containing interfere homeostasis Here, we examined hydrolytic activities 2, 3 substrates containing cleaved α-NAD , but not β-NAD consistent stereospecificity at C-1" bond. In contrast ARH1 ARH3, did require Mg 2+ optimal activity. also hydrolyzed O -acetyl-ADP-ribose ADP-ribose-1"-phosphat, Mac2 Mac3. However, cleave α-ADP-ribose-(arginine) ADP-ribose-(serine)-histone H3 peptide, suggesting hydrolyzes attached O- N-linked functional groups, specificity catalytic site moiety. We conclude may exert anti-viral activity by reversing host-mediated ADP-ribosylation. New insights shed light therapeutic targets.SARS-CoV-2, COVID-19, within (Nsp3). was previously hydrolyze ADP-ribose-phosphate. Inactivation reduced proliferation. Here report multiple activities, i.e., hydrolyzed. -acetyl-ADP-ribose. ADP-ribose-serine histone peptide (aa1-21), ADP-ribose-arginine, exhibiting substrate selectivity. These data suggest have multi-function as consumer replication disruptor Understanding Mac1's mechanisms important provide possible targets COVID-19.

Язык: Английский

---