Evolutionary turnover of key amino acids explains conservation of function without conservation of sequence in transcriptional activation domains

TL;DR

This study shows how transcription factors can maintain their function over long evolutionary times despite significant changes in their protein sequences.

Contribution

The paper reveals that evolutionary turnover of key amino acids in disordered regions maintains function without sequence conservation.

Findings

The central activation domain of Gcn4 shows strong functional conservation despite sequence divergence.

Evolutionary turnover of acidic and aromatic residues and short linear motifs contributes to functional conservation.

Turnover of entire activation domains in full-length transcription factors supports functional stability over time.

Abstract

In folded protein domains, protein function is frequently more conserved than amino acid sequence because highly diverged sequences can fold into equivalent 3D structures with identical function. During evolution, intrinsically disordered protein regions (IDRs) often experience rapid amino acid sequence divergence, but because they do not fold into stable 3D structures, it remains largely unknown when and how function is conserved. As a model system for studying the evolution of IDRs, we examined transcriptional activation domains, the regions of transcription factors that bind to coactivator complexes. We systematically identified activation domains on 502 homologs of the transcriptional activator Gcn4 spanning 600 MY of fungal evolution in the Ascomycota. We found that the central activation domain shows strong conservation of function without conservation of sequence. This conservation of function without conservation of sequence arises from evolutionary turnover (gain and loss) at two length scales. Within the central activation domain, we see turnover of acidic and aromatic residues, but primarily loss of short linear motifs. In the full-length transcription factor, we see turnover of entire activation domains. Stabilizing selection and evolutionary turnover at multiple length scales are likely a general mechanism for conservation of function without conservation of sequence in IDRs.

When and where genes are turned on determine what an organism looks like and how it responds to its environment. The turning on and off of genes is controlled by proteins known as transcription factors. Transcription factors have two main jobs: to bind the genome and to turn genes on or off. The protein regions of the transcription factors that bind the genome have been conserved for billions of years. However, throughout this time the rest of the transcription factor protein sequence has changed substantially. In this study, we investigate how changes in the sequences of these other regions impact the ability of transcription factors to turn on genes. We find that these transcription factor regions are still able to turn on genes despite large changes in protein sequence. The function of these transcription factors is much more conserved than their protein sequences. The protein sequence of these activating regions can change dramatically while maintaining function. These findings improve our understanding of how these transcription factors turn on genes and how they are evolving.

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