A deep learning framework for lysine 2-hydroxyisobutyrylation site prediction using evolutionary feature representation

Abstract

Lysine 2-hydroxyisobutyrylation (Khib) has emerged as a crucial Post-Translational Modification (PTM) with significant roles in diverse biological processes ranging from gene expression to metabolic regulation. Despite its importance, computational approaches for accurately predicting Khib sites remain limited. This study introduces BLOS-Khib, a deep-learning framework that utilizes evolutionary information encoded in the BLOSUM62 matrix within a Convolutional Neural Network (CNN) architecture for cross-species Khib site prediction. Through systematic optimization, we found that a 43-amino acid peptide length captures the optimal sequence context for prediction across six taxonomically diverse organisms. Comprehensive comparative analyses demonstrated BLOS-Khib competitive performance compared to existing methods, achieving notable Area Under the ROC Curve (AUC) values on independent test sets: human (0.913), wheat (0.892), T. gondii (0.893), rice (0.887), Candida albicans (0.885), and Botrytis cinerea (0.903). Our framework showed improved performance compared to state-of-the-art approaches, including traditional machine learning classifiers and alternative deep learning architectures. Sequence signature analysis revealed both conserved lysine-rich regions preceding modification sites and species-specific amino acid preferences at positions immediately flanking the target residue. Notably, our cross-species applicability experiments identified high transferability between evolutionarily distant organisms, ensuring the potential convergent evolution of Khib determinants. BLOS-Khib demonstrates competitive performance for PTM prediction, while providing evolutionary insights into the sequence determinants governing this emerging regulatory mechanism across diverse species.