Biological Sciences Division
Published August 20, 2018 | Version v1
Journal article Open

Fitness effects of altering gene expression noise in Saccharomyces cerevisiae

Creators

  • 1. University of Michigan
  • 2. University of Chicago

Description

Gene expression noise is an evolvable property of biological systems that describes differences in expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the TDH3 gene in Saccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.

Data availability

Flow data (FCS files) used to quantify fluorescence levels produced by the 43 TDH3 promoter alleles are available in the FlowRepository (flowrepository.org) under experiment ID FR-FCM-ZY8Y. Raw bright field and fluorescence images, as well as bright field images where cell division events were annotated, are available on Zenodo (https://zenodo.org) with DOI 10.5281/zenodo.1327545. All other data are provided as source data and/or supplementary files with the manuscript.

The following data sets were generated:

Fabien Duveau (2018) Time-lapse images of yeast cells with different levels of TDH3 median expression and expression noise Publicly available at Zenodo (https://zenodo.org/). https://dx.doi.org/10.5281/zenodo.1327545

Fabien Duveau Patricia J Wittkopp (2016) Activity of 48 TDH3 promoter variants in YPD Publicly available at FlowRepository (accession no. FR-FCM-ZY8Y). http://flowrepository.org/id/FR-FCM-ZY8Y

Fabien Duveau Patricia J Wittkopp (2016) Effects of 20 TDH3 promoter alleles at HO and native TDH3 loci Publicly available at FlowRepository (accession no. FR-FCM-ZYJX). http://flowrepository.org/id/FR-FCM-ZYJX

Fabien Duveau Patricia J Wittkopp (2016) Fitness of 48 TDH3 promoter alleles in YPD Publicly available at FlowRepository (accession no. FR-FCM-ZYJN). http://flowrepository.org/id/FR-FCM-ZYJN

Files

elife-37272-v2.pdf

Files (3.1 MB)

Name Size Download all
Article
md5:d221ac95680afa32ab1defd5caca6723
1.5 MB Preview Download
md5:e26181fc0c6b00dfae4d4fc859dc0a71
1.6 MB Preview Download

Additional details

Identifiers

DOI
10.7554/eLife.37272
Other
oai:uchicago.tind.io:9902

Funding

European Molecular Biology Organization
EMBO ALTF 1114-2012
National Institutes of Health
1F32GM115198
National Institutes of Health
T32 HG000040
National Institutes of Health
R01GM108826
National Science Foundation
MCB-1021398
National Institutes of Health
R35GM118073

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Ecology and Evolution