A prion accelerates proliferation at the expense of lifespan
- Department of Chemical & Systems Biology, Stanford University School of Medicine, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, United States
- Department of Pathology, University of Washington, United States
- Department of Developmental Biology, Stanford University School of Medicine, United States
Figures
Figure 1 with 1 supplement
Cells bearing a prion-like epigenetic element live fast and die young.
(A) Big+ cells proliferate faster than naïve cells. Bars represent the mean of four replicates of maximum growth rate in YPD medium (measured by the peak of the derivative of the growth data), error …
Figure 1—figure supplement 1
Probing lifespan of Big+ cells.
(A) Experimental scheme for growth competition experiment associated with Figure 1B. (B) Experimental scheme for chronological and replicative lifespan (RLS) measurements associated with Figure 1C …
Figure 2 with 1 supplement
Modeling a reversible epigenetic live fast and die young strategy.
(A) A live fast–die young epigenetic element is beneficial for survival in environments with regular, extended nutrient-rich periods. (B) A live slow–die old growth state is beneficial for survival …
Figure 2—figure supplement 1
Modeling a reversible epigenetic live fast and die young strategy.
Time-resolved simulations when (A) the period of starvation is 10 times the period of nutrient repletion; (B) the period of nutrient repletion is 10 times the period of starvation; and (C) the two …
Figure 3 with 1 supplement
Big+ cells are large.
(A) Micrographs of naïve and Big+ haploid yeast cells. (B) Cell size distributions for thousands of naïve and Big+ haploid cells (100% of distribution is shown, n = 4678 for naïve, n = 5501 for Big+,…
Figure 3—figure supplement 1
The large cell phenotype of Big+ emerges during the growth of a culture.
(A) The large phenotype of Big+ cells was stronger after 3 days of growth than after 2 days of growth (4 days of growth yielded similar differences in cell size as for 3 days of growth, data not …
Figure 4 with 1 supplement
[BIG+] has prion-like patterns of inheritance.
(A) Micrographs of diploid yeast cells resulting from crosses of naïve and naïve parents, or naïve and [BIG+] parents. (B) The frequency of diploid cells above the large cell threshold. Bars …
Figure 4—figure supplement 1
Tests for prion-like patterns of inheritance and dependence on Pus4 for [BIG+].
(A) In contrast to mutations, which when arising from one parent are inherited in half of the meiotic progeny, prion-based traits can be inherited in all meiotic progeny. (B) Additional biological …
Figure 5 with 1 supplement
Pus4 activity is maintained in [BIG+].
(A) Radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection. Illustration is adapted from Scheme 1 of Lei and Yi, 2017. (B) High-resolution melting curve analysis …
Figure 5—figure supplement 1
tRNA pseudouridylation and quantitative scaling of gene expression in mRNA sequencing.
(A) In the TΨC loop of tRNAAGC (Ala), mutations resulting from reverse transcription of CMC-treated samples were only observed originating from position 55 (Ψ). Sanger sequencing profiles from …
Figure 6 with 1 supplement
[BIG+] has altered protein synthesis.
(A) [BIG+] cells are resistant to translation elongation inhibitor cycloheximide. Bars represent the mean of the maximum growth rate in YPD + cycloheximide (measured by the peak of the derivative of …
Figure 6—figure supplement 1
Altered cell cycle and translation in [BIG+].
(A) Fraction of GFP-Par32 signal localized to the plasma membrane in naïve vs. [BIG+] cells measured using fluorescence microscopy. Shown are box-and-whisker plots with horizontal black lines in the …
Figure 7 with 1 supplement
Pseudouridylation of mRNA in [BIG+] cells.
(A) CMC-RT and ligation-assisted PCR analysis of Ψ modification (CLAP) (Zhang et al., 2019). (B) Native PAGE showing the CLAP result for TEF1/TEF2 mRNA from multiple replicates of naïve (3), [BIG+] …
Figure 7—figure supplement 1
Pseudouridylation of mRNA in [BIG+] cells.
(A) Sanger sequencing profiles from control and CMC-labeled RNA from naïve, [BIG+], and pus4Δ cells. Naïve and [BIG+] samples show characteristic mixed nucleotide assignments at previously annotated …
Figure 8 with 1 supplement
Epigenetic control of [BIG+]-like phenotypes in wild yeasts.
(A) Transient inhibition of Hsp70 in diploid wild yeast strains from different niches around the globe leads to a permanent reduction in cell size. Violin plots show all data from thousands of cells …
Figure 8—figure supplement 1
Transient Pus4 overexpression does not permanently increase the size of uncured BC187 cells.
Violin plots show all data from thousands of cells from three biological replicates of each strain. The solid white line bisecting each distribution indicates mean; dotted lines indicate upper and …
Author response image 1
Author response image 2
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | See Supplementary file 4 | |||
| Antibody | Anti-FLAG M2 mouse monoclonal antibody | Sigma | RRID:AB_262044 | (1:1000) |
| Antibody | Goat anti-mouse IgG peroxidase | Sigma | RRID:AB_257993 | (1:10,000) |
| Antibody | Mouse anti-PGK1 monoclonal antibody | Invitrogen | RRID:AB_2532235 | (1:1000) |
| Recombinant DNA reagent | See Supplementary file 4 | |||
| Sequence-based reagent | See Supplementary file 4 | |||
| Commercial assay or kit | Dual-Luciferase Reporter Assay | Promega | Catalog# E1910 | |
| Commercial assay or kit | ERCC ExFold RNA Spike-In Mixes | Invitrogen | Catalog# 4456739 | |
| Chemical compound, drug | Cycloheximide | Sigma | Catalog# C1988 | CAS# 66-81-9 |
| Chemical compound, drug | Radicicol | Research Products International | Catalog#R20020-0.001 | CAS# 12772-57-5 |
| Chemical compound, drug | Rapamycin | LC Laboratories | Catalog# R-5000 | CAS# 53123-88-9 |
| Chemical compound, drug | Canavanine | Sigma | Catalog# C9758 | CAS# 2219-31-0 |
| Chemical compound, drug | 5-Fluoroorotic acid monohydrate (5-FOA) | GoldBio | Catalog# F-230–2.5 | CAS# 220141-70-8 |
| Chemical compound, drug | Guanidine hydrochloride | Sigma | Catalog# G3272 | CAS# 50-01-1 |
| Chemical compound, drug | [35S]-methionine | Perkin Elmer | Catalog# NEG709A500UC | |
| Chemical compound, drug | N-Cyclohexyl-N′-(2-morpholinoethyl)carbodiimide methyl-p-toluenesulfonate (CMC) | Sigma | Catalog# C106402 | CAS# 2491-17-0 |
| Software, algorithm | ImageJ software | ImageJ (http://imagej.nih.gov/ij/) | RRID:SCR_003070 | |
| Software, algorithm | GraphPad Prism software | GraphPad Prism (https://graphpad.com) | RRID:SCR_002798 | |
| Software, algorithm | Model | https://github.com/cjakobson/liveFastDieYoung |
Additional files
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Supplementary file 1
See .docx file for parameter values used for the competitive fitness models shown in Figure 2 and Figure 2—figure supplement 1.
- https://cdn.elifesciences.org/articles/60917/elife-60917-supp1-v1.docx
-
Supplementary file 2
RNA-sequencing results.
See .xlsx file for transcripts per kilobase million for each gene in four replicates of naïve and four replicates of [BIG+]. Genes that showed significant differences are listed in a separate tab.
- https://cdn.elifesciences.org/articles/60917/elife-60917-supp2-v1.xlsx
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Supplementary file 3
Proteins whose expression is changed in [BIG+] cells.
- https://cdn.elifesciences.org/articles/60917/elife-60917-supp3-v1.xlsx
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Supplementary file 4
Yeast strains, plasmids, and oligonucleotides used in this study.
See .xlsx file.
- https://cdn.elifesciences.org/articles/60917/elife-60917-supp4-v1.xlsx
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Supplementary file 5
Yeast genes with predicted Pus4 target sites based on scanning the yeast genome using a position weight matrix.
See .csv file.
- https://cdn.elifesciences.org/articles/60917/elife-60917-supp5-v1.csv
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Transparent reporting form
- https://cdn.elifesciences.org/articles/60917/elife-60917-transrepform1-v1.docx
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Reporting standard 1
Statistical reporting.
- https://cdn.elifesciences.org/articles/60917/elife-60917-repstand1-v1.xlsx
