ADPriboDB 2.0: an updated database of ADP-ribosylated proteins

Author:

Ayyappan Vinay1,Wat Ricky2,Barber Calvin3,Vivelo Christina A2,Gauch Kathryn4,Visanpattanasin Pat4,Cook Garth4,Sazeides Christos2,Leung Anthony K L256ORCID

Affiliation:

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

Abstract

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 9097 ADP-ribosylated proteins, of which 6708 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.

Funder

American Cancer Society

National Institute of General Medical Sciences

National Cancer Institute

Publisher

Oxford University Press (OUP)

Subject

Genetics

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