ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins

doi:10.1101/2020.09.24.298851

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[Preprint]. 2020 Sep 25:2020.09.24.298851.

doi: 10.1101/2020.09.24.298851.

ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins

Affiliations

¹ Department of Biomedical Engineering, The G.W.C. Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
² Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
³ Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
⁴ Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
⁵ Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
⁶ Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

PMID: 32995784
PMCID: PMC7523110
DOI: 10.1101/2020.09.24.298851

ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins

Vinay Ayyappan et al. bioRxiv. 2020.

[Preprint]. 2020 Sep 25:2020.09.24.298851.

doi: 10.1101/2020.09.24.298851.

Authors

Affiliations

¹ Department of Biomedical Engineering, The G.W.C. Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
² Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
³ Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
⁴ Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
⁵ Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
⁶ Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

PMID: 32995784
PMCID: PMC7523110
DOI: 10.1101/2020.09.24.298851

Update in

ADPriboDB 2.0: an updated database of ADP-ribosylated proteins.
Ayyappan V, Wat R, Barber C, Vivelo CA, Gauch K, Visanpattanasin P, Cook G, Sazeides C, Leung AKL. Ayyappan V, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D261-D265. doi: 10.1093/nar/gkaa941. Nucleic Acids Res. 2021. PMID: 33137182 Free PMC article.

Abstract

ADP-ribosylation is a protein modification responsible for biological processes such as DNA repair, RNA regulation, cell cycle, and biomolecular condensate formation. Dysregulation of ADP-ribosylation is implicated in cancer, neurodegeneration, and viral infection. We developed ADPriboDB (adpribodb.leunglab.org) to facilitate studies in uncovering insights into the mechanisms and biological significance of ADP-ribosylation. ADPriboDB 2.0 serves as a one-stop repository comprising 48,346 entries and 9,097 ADP-ribosylated proteins, of which 6,708 were newly identified since the original database release. In this updated version, we provide information regarding the sites of ADP-ribosylation in 32,946 entries. The wealth of information allows us to interrogate existing databases or newly available data. For example, we found that ADP-ribosylated substrates are significantly associated with the recently identified human protein interaction networks associated with SARS-CoV-2, which encodes a conserved protein domain called macrodomain that binds and removes ADP-ribosylation. In addition, we create a new interactive tool to visualize the local context of ADP-ribosylation, such as structural and functional features as well as other post-translational modifications (e.g., phosphorylation, methylation and ubiquitination). This information provides opportunities to explore the biology of ADP-ribosylation and generate new hypotheses for experimental testing.

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Conflict of interest statement

Conflict of Interest

None.

Figures

**Figure 1.. Analyses of ADPriboDB v2.0.**
(A) Trends in ADP-ribosylation research shows a progressive increase in the number of publications about ADP-ribosylation biology, substrates and sites. (B) Left: Venn diagram shows the overlap between proteins identified in proteomics-based studies (≥10 proteins) and those identified in other publications. Right: Histogram describes the number of proteins identified by these proteomics studies. (C) Distribution of the number of publications identifying a given ADP-ribosylated substrate. (D) Proteins identified in at least two publications were subjected to gene ontology analysis via EnrichR. Bubble chart shows the enrichment of selected pathways analyzed with REVIGO (26); the full enrichment analysis is available in Supplementary Data S1. (E) Enrichment analysis was also performed on ADP-ribosylated proteins within the SARS-CoV-2 interactome. Bubble chart shows the enrichment of selected pathways analyzed with REVIGO; the full enrichment analysis is available in Supplementary Data S2. (F) Distribution of ADP-ribosylated residues.

**Figure 2.. New Graphical Interface.**
Representative images shown for (A) AXIN1 (all sites have one reference) (B) PARP1, and (C) NPM1.

See this image and copyright information in PMC

References

1. Gupte R., Liu Z. and Kraus W.L. (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev., 31, 101–126. - PMC - PubMed
1. Palazzo L., Mikoč A. and Ahel I. (2017) ADP-ribosylation: new facets of an ancient modification. FEBS J., 284, 2932–2946. - PMC - PubMed
1. Houtkooper R.H., Pirinen E. and Auwerx J. (2012) Sirtuins as regulators of metabolism and healthspan. Nat. Rev. Mol. Cell Biol., 13, 225–238. - PMC - PubMed
1. Hottiger M.O., Hassa P.O., Lüscher B., Schüler H. and Koch-Nolte F. (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem. Sci., 35, 208–219. - PubMed
1. Di Girolamo M., Dani N., Stilla A. and Corda D. (2005) Physiological relevance of the endogenous mono(ADP-ribosyl)ation of cellular proteins. FEBS J., 272, 4565–4575. - PubMed

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[1] Gupte R., Liu Z. and Kraus W.L. (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev., 31, 101–126. - PMC - PubMed

[2] Gupte R., Liu Z. and Kraus W.L. (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev., 31, 101–126. - PMC - PubMed

[3] Palazzo L., Mikoč A. and Ahel I. (2017) ADP-ribosylation: new facets of an ancient modification. FEBS J., 284, 2932–2946. - PMC - PubMed

[4] Palazzo L., Mikoč A. and Ahel I. (2017) ADP-ribosylation: new facets of an ancient modification. FEBS J., 284, 2932–2946. - PMC - PubMed

[5] Houtkooper R.H., Pirinen E. and Auwerx J. (2012) Sirtuins as regulators of metabolism and healthspan. Nat. Rev. Mol. Cell Biol., 13, 225–238. - PMC - PubMed

[6] Houtkooper R.H., Pirinen E. and Auwerx J. (2012) Sirtuins as regulators of metabolism and healthspan. Nat. Rev. Mol. Cell Biol., 13, 225–238. - PMC - PubMed

[7] Hottiger M.O., Hassa P.O., Lüscher B., Schüler H. and Koch-Nolte F. (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem. Sci., 35, 208–219. - PubMed

[8] Hottiger M.O., Hassa P.O., Lüscher B., Schüler H. and Koch-Nolte F. (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem. Sci., 35, 208–219. - PubMed

[9] Di Girolamo M., Dani N., Stilla A. and Corda D. (2005) Physiological relevance of the endogenous mono(ADP-ribosyl)ation of cellular proteins. FEBS J., 272, 4565–4575. - PubMed

[10] Di Girolamo M., Dani N., Stilla A. and Corda D. (2005) Physiological relevance of the endogenous mono(ADP-ribosyl)ation of cellular proteins. FEBS J., 272, 4565–4575. - PubMed

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This is a preprint.

ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins

Affiliations

ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

Figures

Similar articles

References

Publication types

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous