PTMOverlay: A Proteomic Tool to Visualize Post-Translational Modifications Across Evolution

Area of Science:

• Proteomics
• Bioinformatics
• Evolutionary Biology

Background:

• Evolutionary conservation of post-translational modifications (PTMs) offers insights into fundamental cellular processes.
• Mass spectrometry generates vast amounts of data for PTM identification and quantification, posing analytical challenges.

Purpose of the Study:

• To develop a computational tool for analyzing multiple PTMs across various species.
• To address the bottleneck in analyzing large-scale mass spectrometry data for conserved PTMs.

Main Methods:

• Developed PTMOverlay, a novel protein sequence alignment tool.
• Integrated peptide identification data with protein sequences for multiple species.
• Analyzed PTM sites, including acetylation, phosphorylation, and various methylations, across 31 bacterial isolates.

Main Results:

• Identified conserved modification sites within bacterial central carbon metabolism.
• Revealed potential interactions between methylated residues and phosphosites at the enolase homodimer interface.
• Demonstrated PTMOverlay's capability to parse large datasets efficiently.

Conclusions:

• PTMOverlay facilitates informed selection of PTM sites for future functional studies.
• The tool enhances the analysis of evolutionary conserved PTMs.
• Conserved PTMs play crucial roles in essential cellular functions, particularly in bacterial metabolism.