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Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

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VPTMdb: a viral posttranslational modification database.

Yujia Xiang¹, Quan Zou², Lilin Zhao³

¹State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences.

Briefings in Bioinformatics

|October 23, 2020

Summary

This summary is machine-generated.

This study introduces VPTMdb, the first comprehensive database of viral posttranslational modifications (PTMs) and their roles in virus-human interactions. It aids in understanding viral infections and identifying drug targets.

Keywords:

bioinformatics database posttranslational modifications virus

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Last Updated: Dec 4, 2025

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

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Published on: March 5, 2022

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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Published on: May 22, 2018

Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins

Published on: January 8, 2018

Area of Science:

Virology
Molecular Biology
Bioinformatics

Background:

Posttranslational modifications (PTMs) are crucial for viral life cycles and virus-human interactions.
Limited comprehensive datasets exist for viral PTMs, hindering research into their roles and potential as drug targets.

Purpose of the Study:

To develop the first comprehensive database (VPTMdb) for viral PTMs in human viruses and infected host cells.
To systematically collect and analyze viral PTM data to understand their mechanisms in viral infections.

Main Methods:

Compiled 1240 unique viral PTM sites (8 types) from 43 viruses, including experimentally verified sites and SwissProt data.
Integrated 13,650 PTMs from infected host cells across six human viruses from proteomics experiments.
Analyzed viral PTM sequence motifs, disordered regions, and domain-domain interactions.

Main Results:

Identified consensus motifs between viral PTMs and human proteins, particularly in phosphorylation.
Found distinct preferences for ordered or disordered regions for glycosylation sites based on virus type (e.g., dsDNA viruses in disordered regions).
Domain-domain interaction analysis suggested roles for viral PTMs in infection mechanisms.

Conclusions:

VPTMdb provides a valuable resource for studying virus-human interactions and identifying therapeutic targets.
The findings highlight conserved PTM motifs and virus-specific structural preferences.
A novel classifier, VPTMpre, was developed for predicting viral protein phosphorylation sites.