Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs.

Abstract

Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including <i>Saccharomyces cerevisiae</i> RNA-mediated transposition and pseudohyphal growth, <i>Candida albicans</i> filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, <i>Tetrahymena thermophila</i> xylan catabolism and meiosis, <i>Dictyostelium discoideum</i> development and sexual cycles, <i>Plasmodium falciparum</i> infection, and the nervous systems of <i>Drosophila melanogaster, Mus musculus</i> and <i>Homo sapiens</i>. We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAA^Q and TAG^Q codons. Notably, the usage frequency of CAG^Q is much lower in ciliates with reassigned TAA^Q and TAG^Q codons than in organisms with expanded and unstable Q runs (e.g. <i>D. melanogaster</i> and <i>H. sapiens</i>), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.