Blocking protein quality degradation leads to structural stabilization of DHFR indel variants

Gene variants leading to insertions or deletions of amino acid residues (indels) often have detrimental consequences for the folding of the encoded protein. Yet at some positions indels are tolerated or only result in partial unfolding. Typically unfolded proteins are targeted for protein quality control (PQC) degradation via ubiquitin-proteasome system, which in yeast is mediated by specific E3 ubiquitin-protein ligases, including Ubr1 and San1. Here we systematically probed the folding of a library of indel variants in the DHFR protein using sensitive yeast-based protein folding reporter. We show that deletion of Ubr1 and San1 leads to a greater fraction of folded DHFR indel variants, primarily positioned towards the N- and C-termini regions in DHFR. Intriguingly, most of the DHFR indels that are structurally stabilized in the E3 knockout strains, are also stabilized at lowered temperatures and upon binding the DHFR inhibitor methotrexate. This suggests that blocking PQC degradation can restore function to partially unfolded hypomorph variants, thus providing a potential therapeutic avenue for protein misfolding diseases. Overall design: The human DHFR sequence was divided into five tiles. In each tile, we generated indel libraries comprising all possible deletions and insertions of a single glycine residue that was inserted into CPOP folding sensor and cloned into pAG415. The libraries were transformed into the ura5?ura10? strain (WT strain), ura5?ura10?ubr1? strain (Ubr1 strain), and ura5?ura10?san1? strain (San1 strain). Cells were plated on medium without uracil at 30 °C and 35 °C to select for folding of DHFR indel variants. Based on the relative change in frequency, we calculated a CPOP folding score of each DHFR indel variant.