Publications by authors named "A Khmelinskii"
Functional genomics with libraries of knockout alleles is limited to non-essential genes and convoluted by the potential accumulation of suppressor mutations in knockout backgrounds, which can lead to erroneous functional annotations. To address these limitations, we constructed genome-wide libraries of conditional alleles based on the auxin-inducible degron (AID) system for inducible degradation of AID-tagged proteins in the budding yeast Saccharomyces cerevisiae. First, we determined that N-terminal tagging is at least twice as likely to inadvertently impair protein function across the proteome.
View Article and Find Full Text PDFArticle Synopsis
- Selective protein degradation involves recognizing specific short sequences called degrons, which are present in proteins from bacteria to mammals.
- This study focuses on C-degrons in budding yeast, identifying over 5000 potential C-degrons using advanced techniques like machine learning and genetic screening.
- The research reveals that a single receptor, Das1, targets about 40% of these C-degrons and plays a crucial role in the degradation of certain protein complex subunits, showcasing the complexity and importance of C-degron pathways in maintaining cellular protein balance.
Article Synopsis
- Chitin synthase Chs3 is a complex protein that must be properly folded to exit the endoplasmic reticulum (ER), with its stability in the ER suggesting limited recognition by quality control systems.
- Proper N-glycosylation of Chs3's luminal domain prevents protein aggregation and protects it from degradation by the Hrd1-dependent ERAD-L pathway.
- Additionally, Chs3 interacts with its chaperone Chs7 to hide degradation signals, allowing misfolded proteins to be sorted to the inner nuclear membrane for degradation by the INMAD system, making Chs3 a key model for studying cellular quality control processes.
Article Synopsis
- The stability and turnover of proteins are influenced by their N-terminal sequences and how these sequences are processed, potentially leading to degradation signals.
- Researchers can gain insights into the effects of genetic changes on protein stability through methods that assess many N-terminal proteins at once, such as using tandem fluorescent timers (tFT).
- The protocol described allows for Multiplexed Protein Stability (MPS) profiling in yeast by sorting and analyzing large libraries of proteins with different N-termini, ultimately generating a stability index for each variant through deep sequencing.
Selective degradation of unnecessary or abnormal proteins by the ubiquitin-proteasome system is an essential part of proteostasis. Ubiquitin ligases recognize substrates of selective protein degradation and modify them with polyubiquitin chains, which mark them for proteasomal degradation. Substrate recognition by ubiquitin ligases often involves degradation signals or degrons, which are typically short linear motifs found in intrinsically disordered regions, e.
View Article and Find Full Text PDF