4 figures, 2 tables and 6 additional files

Figures

Figure 1 with 1 supplement
Genetic perturbation analyses.

(A) Protein burden changes with copy number. The bar plot shows the relative fitness of yEVenus overexpressing and control genotypes as a function of plasmid copy number, a proxy of gene expression …

https://doi.org/10.7554/eLife.29845.003
Figure 1—figure supplement 1
Additional analyses of the genetic interaction screen.

(A) Scatterplot of the genetic interaction scores and biomass-normalized fluorescence levels using knock-out strains with wild type cell size only. A prior systematic study (Jorgensen et al., 2002) …

https://doi.org/10.7554/eLife.29845.004
Environmental screens under protein burden.

(A) Impact of translation inhibition on protein burden in wild type yeast. The bar plot shows the cost of yEVenus in wild type strain as a function of increasing cycloheximide concentration. …

https://doi.org/10.7554/eLife.29845.006
Figure 3 with 1 supplement
Link between protein burden and proteotoxic stress.

(A) Impact of heat stress on protein burden. The bar plot shows the fitness cost of yEVenus in wild type strain as a function of increasing temperature. Protein burden significantly increased with …

https://doi.org/10.7554/eLife.29845.007
Figure 3—figure supplement 3
Additional investigation of protein burden across different yEVenus plasmids and different chaperone-deficient mutants.

(A) Monitoring yEVenus fluorescence intensity in wild type cells across five different yEVenus plasmids. The figure shows fluorescence histograms of wild type cells with different plasmids. The …

https://doi.org/10.7554/eLife.29845.008
Overview of the proteostasis network.

Malfunction of the protein quality control system impairs the proteome balance by driving cellular proteins into toxic metastable (partially folded or misfolded) conformations from their correctly …

https://doi.org/10.7554/eLife.29845.009

Tables

Table 1
Functional enrichment analysis of genes showing synergistic interactions with yEVenus overexpression.

At an ε = - 0.05 cutoff value (and using a p<0.05 cutoff based on bootstrapping), 184 genes showed negative interactions with yEVenus. This gene set was tested for GO Slim category enrichment. A GO …

https://doi.org/10.7554/eLife.29845.005
Go.idTermNOdds ratioP valueFDR corrected P value
GO:0002181cytoplasmic translation112.271.52E-021.69E-01
GO:0006325chromatin organization151.704.65E-022.93E-01
GO:0006353DNA-templated transcription, termination34.174.60E-022.93E-01
GO:0006354DNA-templated transcription, elongation168.432.73E-092.73E-07
GO:0006360transcription from RNA polymerase I promoter65.861.24E-033.10E-02
GO:0006366transcription from RNA polymerase II promoter292.292.01E-046.71E-03
GO:0006397mRNA processing92.847.77E-031.11E-01
GO:0006414translational elongation53.312.45E-022.34E-01
GO:0006457protein folding103.063.26E-035.43E-02
GO:0007005mitochondrion organization282.594.13E-052.07E-03
GO:0009408response to heat73.171.05E-021.31E-01
GO:0009451RNA modification72.532.91E-022.34E-01
GO:0016570histone modification82.333.05E-022.34E-01
GO:0032543mitochondrial translation122.961.78E-033.55E-02
GO:0048308organelle inheritance53.232.68E-022.34E-01
Key resources table
Reagent type (species)
or resource
DesignationSource or referenceIdentifiersAdditional information
Strain (Saccharomyces cerevisiae)Y7092PMID: 16118434SGA query strain, mat alpha
Othernon-essential gene deletion collection (BY4741, MATa)PMID:12140549YSC1053Open BioSystem (Dharmacon)
Othersynthetic genetic array (SGA) techniquePMID: 16118434
Software, algorithmImageJ softwarePMID: 22930834RRID:SCR_003070
Software, algorithmGene Onthology term enrichment with topGO (version 2.28)PMID: 16606683
Software, algorithmorg.Sc.sgd.db (version 3.3.0) packages in RCore Team, 2017http://www.R-project.org
Software, algorithmMachine learning-based phenotypic analysisPMID: 21807964
Software, algorithmAdvanced Cell ClassifierPMID: 28647475http://www.cellclassifier.org/
Software, algorithmProteome Discoverer (v 1.4)Thermo Fisher Scientific (Germany)
Recombinant DNAreagentpKT0090 plasmidPMID: 15197731Addgene:Plasmid #8714contains yEVenus
Recombinant DNAreagentYEplac181 plasmidPMID: 3073106Addgene:Plasmid #8628high copy plasmid
Recombinant DNAreagentYCplac111 plasmidPMID: 3073106Addgene:Plasmid #53249single copy plasmid
Recombinant DNAreagentpRS315 plasmidPMID: 2659436ATCC 77144low copy plasmid
Recombinant DNAreagentpFA6a-TEV-6xGly-3xFlag-HphMX plasmidTim FormosaAddgene:Plasmid #44083
Recombinant DNAreagentpGAL-VHL-mCherryPMID: 18756251galactose inducible VHL-mCherry
Commercial assayor kitµMACS GFP Isolation KitMiltenyi Biotec (Germany)130-091-125
Commercial assayor kitμMACS DYKDDDDK Isolation KitMiltenyi Biotec (Germany)130-101-591*DYKDDDDK is also known as FLAG tag

Additional files

Supplementary file 1

Results of the Synthetic Genetic Array with yEVenus.

This file contains information of the Synthetic Genetic Array with yEVenus in single gene deletion backgrounds and was used to create the following figures/tables: Figure 1C, D, E and F, Figure 1—figure supplement 1 A–C, and Table 1.

https://doi.org/10.7554/eLife.29845.010
Supplementary file 2

Genetic interaction screen using alternative promoters.

The table contains fitness and genetic interaction data of chaperone-deficient mutants overexpressing yEVenus driven by alternative promoters. This file contains the dataset used to create Figure 3—figure supplement 1C.

https://doi.org/10.7554/eLife.29845.011
Supplementary file 3

Results of the GFP co-immunoprecipitation assay with yEVenus.

This file contains information of the GFP co-IP assay performed on the yEVenus overexpressing strain.

https://doi.org/10.7554/eLife.29845.012
Supplementary file 4

Results of the Sti1p co-immunoprecipitation assay.

This file contains information of the Sti1p co-IP assay performed on wild type and Sti1-3xFLAG strains under high and low protein burden, that is with high and low copy yEVenus plasmid, respectively. This file contains the dataset used to create Figure 3D.

https://doi.org/10.7554/eLife.29845.013
Supplementary file 5

All data used to create figures in the manuscript.

The file contains the datasets used to create specific manuscript figures: it contains the data for Figures 1A, 2A, B, C, D, 3A, B and C, Figure 3—figure supplement 1A,B.

https://doi.org/10.7554/eLife.29845.014
Transparent reporting form
https://doi.org/10.7554/eLife.29845.015

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