Phylogenomic Reconstruction of Hsp90 Gene Family Evolution Across Extremodural Archaea Using Targeted HMM Profiling

The Heat shock protein 90 (Hsp90) gene family plays a critical role in cellular proteostasis and stress response across all domains of life. Despite its conserved function, the evolutionary trajectory and specific adaptations of Hsp90 in extremophilic organisms, particularly within the diverse Extremodural Archaea, remain underexplored. This study employed a targeted Hidden Markov Model (HMM) profiling approach to systematically identify and characterize Hsp90 homologs across a comprehensive set of 85 publicly available Extremodural Archaea genomes, encompassing hyperthermophilic, acidophilic, and halophilic representatives. Subsequent phylogenomic analysis, utilizing maximum likelihood methods, revealed distinct clades within the archaeal Hsp90 family, suggesting ancient gene duplication events and lineage-specific diversification. We observed notable variations in domain architecture and sequence features correlating with the extreme environmental niches occupied by these archaea, potentially reflecting adaptive modifications to maintain chaperone function under harsh conditions. This research provides a robust phylogenomic framework for understanding Hsp90 evolution in Extremodural Archaea, highlighting the sophisticated molecular strategies employed by these organisms to ensure protein integrity and cellular survival in extreme environments, and offering insights into the broader evolutionary landscape of chaperones.