Integrative proteomics and bioinformatics pipelines for PTM profiling

Area of Science:

• Plant biology
• Molecular biology
• Biochemistry

Background:

• Post-translational modifications (PTMs) are vital for protein function and plant stress response.
• Over 450 PTM types exist, with 23-33 confirmed in plants, including phosphorylation and acetylation.
• PTMs are dynamic, reversible, and often interact (crosstalk) to regulate cellular processes.

Purpose of the Study:

• To review O-phosphorylation and Lys-N(ε)-acetylation in plants.
• To integrate historical, methodological, and bioinformatic perspectives on these PTMs.
• To identify challenges and future research directions for PTM studies in plants.

Main Methods:

• Review of proteomic and bioinformatics approaches.
• Analysis of mass spectrometry workflows and enrichment strategies.
• Examination of bioinformatics tools, databases, and challenges in non-model plants.

Main Results:

• O-phosphorylation and Lys-N(ε)-acetylation are the most studied and crosstalking PTMs in plants.
• High-resolution mass spectrometry and bioinformatics tools have advanced PTM site identification and prediction.
• Challenges remain, especially in non-model plant species.

Conclusions:

• Future research should integrate multi-omics data and AI for PTM prediction.
• Understanding PTMs can enhance crop stress resilience and breeding applications.
• Continued study of plant PTMs is essential for agricultural advancement.