How essential trans-active factors that control gene expression evolved while maintaining their ability to interact with their natural effectors and cis-active elements on DNA is a fundamental question that requires multidisciplinary approaches. Focusing on a ligand-activated transcription factor (TF), namely androgen receptor (AR), we addressed how exonic eukaryotic linear motifs (ELMs), homorepeats (HReps), and amino acids subject to post-translational modifications (PTMs) evolved in 536 species from cartilaginous fish to Homo sapiens. By combining in silico (SWISS-Model and Alphafold3), computational (molecular dynamics), and biochemical and molecular approaches, we identify functionally active ELMs present in the H. sapiens AR and trace them back to Chondrichthyes, including one in the ligand-binding domain (LBD) required for androgen binding. Moreover, we provide evidence that an ELM dynamically regulated via PTM through a cryptic phosphorylation site is an old suppressive signal from fish to human. Furthermore, we identify a similar phospho-site in the LBD of the other steroid receptors and their ancestors. These findings shed light on the timing and enduring establishment of specific ELMs and their PTMs within the steroid hormone receptor (SHR) family, while highlighting early AR-specific ELMs conserved from fish to humans, as well as ELMs that emerged later in mammals.
The evolution of eukaryotic linear motifs governing the function of androgen receptor from fish to Homo sapiens
Falconieri A.;Boarolo G.;Boschelle C.;Marchioretti C.;Zuccaro E.;Tosatto L.;Dalla Valle L.;Grapputo A.;Pennuto M.
2025
Abstract
How essential trans-active factors that control gene expression evolved while maintaining their ability to interact with their natural effectors and cis-active elements on DNA is a fundamental question that requires multidisciplinary approaches. Focusing on a ligand-activated transcription factor (TF), namely androgen receptor (AR), we addressed how exonic eukaryotic linear motifs (ELMs), homorepeats (HReps), and amino acids subject to post-translational modifications (PTMs) evolved in 536 species from cartilaginous fish to Homo sapiens. By combining in silico (SWISS-Model and Alphafold3), computational (molecular dynamics), and biochemical and molecular approaches, we identify functionally active ELMs present in the H. sapiens AR and trace them back to Chondrichthyes, including one in the ligand-binding domain (LBD) required for androgen binding. Moreover, we provide evidence that an ELM dynamically regulated via PTM through a cryptic phosphorylation site is an old suppressive signal from fish to human. Furthermore, we identify a similar phospho-site in the LBD of the other steroid receptors and their ancestors. These findings shed light on the timing and enduring establishment of specific ELMs and their PTMs within the steroid hormone receptor (SHR) family, while highlighting early AR-specific ELMs conserved from fish to humans, as well as ELMs that emerged later in mammals.
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