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

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 27 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, includingSaccharomyces cerevisiaeRNA-mediated transposition and pseudohyphal growth,Candida albicansfilamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement,Tetrahymena thermophilaxylan catabolism and meiosis,Dictyostelium discoideumdevelopment and sexual cycles,Plasmodium falciparuminfection, and the nervous systems ofDrosophila melanogaster, Mus musculusandHomo sapiens. We also show that Q-rich-motif proteins are expanded massively in ten ciliates with reassigned TAA^Qand TAG^Qcodons. Notably, the usage frequency of CAG^Qis much lower in ciliates with reassigned TAA^Qand TAG^Qcodons than in organisms with expanded and unstable Q runs (e.g.,D. melanogasterandH. sapiens), 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.