Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae

Methods Enzymol. 2023:686:321-344. doi: 10.1016/bs.mie.2023.02.017. Epub 2023 Apr 4.

Abstract

N-terminal protein sequences and their proteolytic processing and modifications influence the stability and turnover of proteins by creating potential degrons for cellular proteolytic pathways. Understanding the impact of genetic perturbations of components affecting the processing of protein N-termini and thereby their stability, requires methods compatible with proteome-wide studies of many N-termini simultaneously. Tandem fluorescent timers (tFT) allow the in vivo measurement of protein turnover completely independent of protein abundance and can be deployed for proteome-wide studies. Here we present a protocol for Multiplexed Protein Stability (MPS) profiling of tFT-libraries encoding large numbers of different protein N-termini fused to tFT in the yeast Saccharomyces cerevisiae. This protocol includes fluorescence cell sorting based profiling of these libraries using a pooling approach. Analysis of the sorted pools is done by using multiplexed deep sequencing, in order to generate a stability index for each N-terminally peptide fused to the tFT reporter, and to evaluate half-life changes across all species represented in the library.

Keywords: FACS; N-degron; N-terminal reporter; NGS; Stability profiling; Tandem fluorescent protein timer; Yeast library.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Protein Stability
  • Proteolysis
  • Proteome / metabolism
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Saccharomyces cerevisiae* / genetics
  • Saccharomyces cerevisiae* / metabolism

Substances

  • Proteome
  • Saccharomyces cerevisiae Proteins