ADPriboDB: The Database of ADP-ribosylated Proteins

Vivelo, Christina A.; Wat, Ricky; Agrawal, Charul; Tee, Hui Yi; Leung, Anthony Kwan

doi:10.1101/063768

Cited by 13 publications

(15 citation statements)

References 54 publications

(66 reference statements)

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“…PARP-1 contains three zinc-binding (Zn) domains in its Nterminus, a breast cancer one protein C-terminal (BRCT) domain, and a tryptophan-, glycine-, arginine-rich (WGR) domain at its centre, as well as a C-terminal catalytic domain ( Table of the number of spectral counts from proteins with identified diGly-modified peptides, following pulldown by HALO-NEDP1 CA or the HALO-NEDP1 DAGC reduced binder control. Blue markers indicate known components of the NEDD8 pathway, and red markers indicate proteins that have been identified as substrates of PARP-1 in the database of ADP-ribosylated proteins, ADPriboDB (Vivelo et al, 2017). C Scatter plot of proteins identified by mass spectrometry analysis identifies NEDD8 and components of the NEDD8 conjugation pathway as being the most abundant proteins in HEK 293 NEDP1 KO lysates following NEDP1-CA pulldown.…”

Section: Resultsmentioning

confidence: 99%

“…NEDD8 is the protein most highly modified by NEDD8. D Venn diagram of the proteins enriched by at least sixfold following HALO-NEDP1 CA pulldown compared with proteins identified as PARP-1 substrates in the database of ADP-ribosylated proteins, ADPriboDB (Vivelo et al, 2017). iBAQ analysis of proteins identified in (A) is plotted as the log 2 value of the enrichment ratio (mass spectrometry intensity of the HALO-NEDP1 CA pulldown over HALO-NEDP1 DAGC pulldown) versus the log 10 value of the iBAQ intensity from the HALO-NEDP1 CA pulldown.…”

Section: Resultsmentioning

confidence: 99%

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Unanchored tri‐NEDD8 inhibits PARP‐1 to protect from oxidative stress‐induced cell death

et al. 2019

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NEDD8 is a ubiquitin‐like protein that activates cullin‐RING E3 ubiquitin ligases (CRLs). Here, we identify a novel role for NEDD8 in regulating the activity of poly(ADP‐ribose) polymerase 1 (PARP‐1) in response to oxidative stress. We show that treatment of cells with H2O2 results in the accumulation of NEDD8 chains, likely by directly inhibiting the deneddylase NEDP1. One chain type, an unanchored NEDD8 trimer, specifically bound to the second zinc finger domain of PARP‐1 and attenuated its activation. In cells in which Nedp1 is deleted, large amounts of tri‐NEDD8 constitutively form, resulting in inhibition of PARP‐1 and protection from PARP‐1‐dependent cell death. Surprisingly, these NEDD8 trimers are additionally acetylated, as shown by mass spectrometry analysis, and their binding to PARP‐1 is reduced by the overexpression of histone de‐acetylases, which rescues PARP‐1 activation. Our data suggest that trimeric, acetylated NEDD8 attenuates PARP‐1 activation after oxidative stress, likely to delay the initiation of PARP‐1‐dependent cell death.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Unanchored tri‐NEDD8 inhibits PARP‐1 to protect from oxidative stress‐induced cell death

et al. 2019

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“…Further development of these approaches can be achieved by methodological improvements as well as by combining one or more of the technologies described above for improved detection and identification of targets in different cellular contexts. Recently, the Leung group (Vivelo et al 2016) created a database (http://ADPriboDB.leunglab.org) that provides a comprehensive list of ADP-ribosylated proteins derived from >400 publications. Currently, the database contains information regarding ADP-ribosylation of 2389 unique protein targets (Vivelo et al 2016).…”

Section: Parp Chemical Biology and Nad + Analog Sensitivitymentioning

confidence: 99%

“…Recently, the Leung group (Vivelo et al 2016) created a database (http://ADPriboDB.leunglab.org) that provides a comprehensive list of ADP-ribosylated proteins derived from >400 publications. Currently, the database contains information regarding ADP-ribosylation of 2389 unique protein targets (Vivelo et al 2016). This archive will be a valuable resource for the field, especially if the information that it contains on ADP-ribosylation can be leveraged with new technologies for the synthesis of site-specific ADP-ribosylated peptides (Moyle and Muir 2010;van der Heden van Noort et al 2010;Kistemaker et al 2013Kistemaker et al , 2016, which can be used for binding assays with ARBDs or as antigens for antibody generation.…”

Section: Parp Chemical Biology and Nad + Analog Sensitivitymentioning

confidence: 99%

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

2017

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The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field.ADP-ribosylation is a reversible post-translational modification (PTM) of proteins resulting in the covalent attachment of a single ADP-ribose unit [i.e., mono(ADP-ribose) (MAR)] or polymers of ADP-ribose units [i.e., poly(ADP-ribose) (PAR)] on a variety of amino acid residues on target proteins (Gibson and Kraus 2012;Daniels et al. 2015a). This modification is mediated by a diverse group of ADPribosyl transferase (ADPRT) enzymes that use ADP-ribose units derived from β-NAD + to catalyze the ADP-ribosylation reaction. These enzymes include bacterial ADPRTs (e.g., cholera toxin and diphtheria toxin) as well as members of three different protein families in yeast and animals: (1) arginine-specific ecto-enzymes (ARTCs), (2) sirtuins, and (3) PAR polymerases (PARPs) . Surprisingly, a recent study showed that the bacterial toxin DarTG can ADP-ribosylate DNA . How this fits into the broader picture of cellular ADP-ribosylation has yet to be determined.In this review, we focus on the mono(ADP-ribosyl)ation (MARylation) and poly(ADP-ribosyl)ation (PARylation) of glutamate, aspartate, and lysine residues by PARP family members. While many reviews have been written on PARPs in the past decade, we highlight the current trends and ideas in the field, in particular those discoveries that have been published in the past 2-3 years.

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“…The proteins involved in ADP ribosylation have been included in the database http://ADPriboDB.leunglab.org, curated by the Leung lab [33].…”

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confidence: 99%

ADP-Ribosylation Reactions in Animals, Plants, and Bacteria

Poltronieri

2017

Challenges

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ADPriboDB: The Database of ADP-ribosylated Proteins

Cited by 13 publications

References 54 publications

Unanchored tri‐NEDD8 inhibits PARP‐1 to protect from oxidative stress‐induced cell death

Unanchored tri‐NEDD8 inhibits PARP‐1 to protect from oxidative stress‐induced cell death

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

ADP-Ribosylation Reactions in Animals, Plants, and Bacteria

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