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

Abstract

Intrinsically disordered regions (IDRs) are protein sequences lacking fixed or ordered three-dimensional structures. Many IDRs are endowed with important molecular functions such as physical interactions, posttranslational modifications or solubility enhancement. We reveal that several biologically important IDRs can act as N-terminal fusion carriers to promote target protein folding or protein quality control, thereby enhancing protein expression. This nanny function has a reasonably strong correlation with high S/T/Q/N amino acid content in IDRs and it is tunable (e.g., via phosphorylation) to regulate protein homeostasis. We propose a hypothesis that “N-terminal intrinsic disorder facilitates abundance” (NIDFA) to explain how some yeast proteins use their N-terminal IDRs (N-IDRs) to generate high levels of protein product. These N-IDRs are versatile toolkits for functional divergence in signaling and evolution.SignificanceDisorder within an otherwise well-structured protein is mostly found in intrinsically disordered regions (IDRs). IDRs can provide many advantages to proteins, including: (1) mediating protein-protein or protein-peptide interactions by adopting different conformations; (2) facilitating protein regulation via diverse posttranslational modifications; and (3) regulating the half-lives of proteins that have been targeted for proteasomal degradation. Here, we report that several biologically important IDRs in S. cerevisiae can act as N-terminal fusion carriers to promote target protein folding or protein quality control, thereby enhancing protein expression. We demonstrate by genetic and bioinformatic analyses that this nanny function is well correlated with high content of serine, threonine, glutamine and asparagine in IDRs and is tunable (e.g., via phosphorylation) to regulate protein homeostasis.

Budding yeast Rad51: a paradigm for how phosphorylation and intrinsic structural disorder regulate homologous recombination and protein homeostasis

“…Intriguingly, all the above-mentioned N-IDRs in the non-DDR proteins also possess at least one S/T-Q motif that may be susceptible to phosphorylation by Mec1 ATR and Tel1 ATM . For instance, phosphorylation of Sup35-S 17 Q in response to DNA lesions has been assessed in immunoblots (Chuang et al 2020). Therefore, we have proposed the "N-terminal intrinsic disorder facilitates abundance" (NIDFA) hypothesis that N-IDRs with high S/T/Q/N contents facilitate protein folding and some could be subject to proteostasis controlled by Mec1 ATR and Tel1 ATM due to the sporadic emergence of S/T-Q motifs (Chuang et al 2020).…”

“…For instance, phosphorylation of Sup35-S 17 Q in response to DNA lesions has been assessed in immunoblots (Chuang et al 2020). Therefore, we have proposed the "N-terminal intrinsic disorder facilitates abundance" (NIDFA) hypothesis that N-IDRs with high S/T/Q/N contents facilitate protein folding and some could be subject to proteostasis controlled by Mec1 ATR and Tel1 ATM due to the sporadic emergence of S/T-Q motifs (Chuang et al 2020). Our NIDFA hypothesis could account for the functions of proteins that harbor an N-IDR but lack binding partners or that fold prior to protein-protein interaction, distinguishing it from two interesting hypothetical models that have been proposed previously.…”

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

“…For instance, phosphorylation can stabilize the tertiary structural organization of the IDR while enhancing and stabilizing its binding to the protein's ligand (Gsponer et al, 2008;Nishi et al, 2011). Bioinformatic analysis has suggested that this function is tunable by PTMs and correlated with a high content of serine, threonine, glutamine and asparagine (Chuang et al, 2020).…”