Integrative Analysis of Post-Translational Modifications Identifies a PTM-Enriched Regulatory Core in Human Metabolic Enzymes

TL;DR

This study maps how post-translational modifications regulate human metabolic enzymes, revealing a core group of enzymes with dense regulatory modifications.

Contribution

The paper introduces a systems-level framework for analyzing multiple PTMs across metabolic enzymes, identifying a regulatory core with high PTM density.

Findings

PTMs are unevenly distributed, with phosphorylation, acetylation, ubiquitination, and methylation being the most common.

A PTM-enriched regulatory group includes rate-limiting enzymes with frequent hotspot regions and crosstalk.

The regulatory core forms a discrete subnetwork in central metabolic pathways.

Abstract

Background: Metabolic enzymes catalyze biochemical pathways that sustain cellular metabolism. Their activity, stability, and molecular interactions are extensively regulated by post-translational modifications (PTMs). However, an integrated systems-level understanding of how diverse PTMs are organized across the human metabolic network remains poorly defined. Methods: We integrated experimentally reported PTM annotations from PhosphoSitePlus, dbPTM, and the quantitative PTM database (qPTM), and identified 29 distinct PTM types present across the 771 human metabolic enzymes. PTM features were quantitatively characterized at multiple levels, including sequence- and composition-based metrics (modification density and PTM potentiality rate), recurrence- and co-occurrence-based features (predominant sites, hotspot regions and PTM crosstalk), and functional-context annotations (protein-region localization and mutation overlap). These integrated features were subsequently used for unsupervised clustering to evaluate higher-order organizational patterns. Results: The analysis revealed that PTMs are unevenly distributed across metabolic enzymes, with phosphorylation, acetylation, ubiquitination, and methylation representing the most prevalent and recurrent regulatory modifications. Clustering segregated enzymes into two regulatory groups: (i) a PTM-enriched regulatory group characterized by high PTM density, frequent hotspot and crosstalk regions, and enrichment of rate-limiting enzymes, and (ii) a broad metabolic group with comparatively sparse PTM regulation. This non-uniform organization reflects the preferential accumulation of multiple regulatory PTMs on enzymes occupying key control points in central metabolic pathways, thereby forming a discrete regulatory subnetwork within metabolism. Conclusions: This study presents a systems-level, multi-PTM atlas of human metabolic enzymes and provides a quantitative framework for prioritizing PTM-regulated enzymes and pathways relevant to signaling–metabolism integration and disease-associated metabolic regulation.

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