The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

Abstract

Aneuploidy, an imbalance in chromosome copy numbers, causes genetic disorders, and drives cancer progression, drug tolerance, and antimicrobial resistance. While aneuploidy can confer stress resistance, it is not well understood how cells overcome the fitness burden caused by aberrant chromosomal copy numbers. Studies using both systematically generated and natural aneuploid yeasts triggered an intense debate about the role of dosage compensation, concluding that aneuploidy is transmitted to the transcriptome and proteome without significant buffering at the chromosome-wide level, and is, at least in lab strains, associated with significant fitness costs. Conversely, systematic sequencing and phenotyping of large collections of natural isolates revealed that aneuploidy is frequent and has few - if any - fitness costs in nature. To address these discrepant findings at the proteomic level, we developed a platform that yields highly precise proteomic measurements across large numbers of genetically diverse samples, and applied it to natural isolates collected as part of the 1011 genomes project. For 613 of the isolates, we were able to match the proteomes to their corresponding transcriptomes and genomes, subsequently quantifying the effect of aneuploidy on gene expression by comparing 95 aneuploid with 518 euploid strains. We find, as in previous studies, that aneuploid gene dosage is not buffered chromosome-wide at the transcriptome level. Importantly, in the proteome, we detect an attenuation of aneuploidy by about 25% below the aneuploid gene dosage in natural yeast isolates. Furthermore, this chromosome-wide dosage compensation is associated with the ubiquitin-proteasome system (UPS), which is expressed at higher levels and has increased activity across natural aneuploid strains. Thus, through systematic exploration of the species-wide diversity of the yeast proteome, we shed light on a long-standing debate about the biology of aneuploids, revealing that aneuploidy tolerance is mediated through chromosome-wide dosage compensation at the proteome level.

The Proteomic Landscape of Genome-Wide Genetic Perturbations

“…The samples were measured on two identical LC-MS setups, consisting of microflow-rate liquid chromatography (nanoAcquity, Waters) and TripleTOF 6600 instruments (SCIEX). The peptides were separated with a 19-min non-linear gradient (~30 min total runtime; Table S2) using microflow (5 µl/min) and an adapted acquisition scheme using variable window SWATH (Muenzner et al, 2022). The raw data was processed by DIA-NN, which we provide as a free software to facilitate large scale proteomic DIA experiments using short gradient chromatography (Demichev et al, 2020).…”

“…To facilitate the generation of thousands of (yeast) proteome profiles, we have recently generated a high-throughput proteomics pipeline that uses a semi-automated sample-preparation workflow, microflow-SWATH-MS, and DIA-NN analysis (Demichev et al, 2020; Gillet et al, 2012; Muenzner et al, 2022). Herein, we further streamlined the procedures for reaching the scale of the yeast KO collection without compromising data quality (Figure 1B and 1C).…”

“…Aneuploidies are a common confounder to both growth and the proteome, as they cause broad expression changes by affecting all proteins encoded on an aneuploid chromosome (Torres et al, 2007). In lab strains, aneuploidies are transmitted to transcriptome and proteome with a minimum amount of gene-dosage buffering, and as a consequence are identifiable by proteomics similarly well as with genomics or transcriptomics, respectively (Muenzner et al, 2022; Pavelka et al, 2010; Torres et al, 2007). We sorted our protein-expression profiles according to the chromosomal localisation of the encoding genes, and analysed their expression patterns (Muenzner et al, 2022).…”

“…Recently, we and others have demonstrated that through the application of robust chromatographic regimes, new sample preparation strategies that reduce batch effects, and new acquisition schemes and software (Bache et al, 2018; Bekker-Jensen et al, 2020; Bian et al, 2020; Bruderer et al, 2019; Demichev et al, 2020; Geyer et al, 2016; Messner et al, 2021; Muenzner et al, 2022), proteomics can be scaled to thousands of samples, without compromising measurement precision. Herein, we apply high-throughput proteomics in order to understand the proteomic landscape of genome-wide genetic perturbations by measuring precise quantitative proteomes for all non-essential gene deletions in Saccharomyces cerevisiae .…”

OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale

“…7,12–17 Furthermore, through advances in sample preparation and novel data acquisition strategies, MS-based technologies have also reached a level of robustness and throughput for large-scale, high-throughput investigations that involve the measurement of thousands of samples. 18–22…”