ArticleGenetics2016
Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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Who cites it
19 citing papers in PubMed.
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- 6PPD and 6PPD-Q Induce Mitochondrial Dysfunction inInternational journal of molecular sciences · 2026Article
- Evidence for G6PD variant classification from multiplexed functional assays.Genome biology · 2026Article
- Evidence forbioRxiv : the preprint server for biology · 2025Article
- popDMS infers mutation effects from deep mutational scanning data.Bioinformatics (Oxford, England) · 2024Article
- popDMS infers mutation effects from deep mutational scanning data.bioRxiv : the preprint server for biology · 2024Article
- ACIDES: on-line monitoring of forward genetic screens for protein engineering.Nature communications · 2023Article
- A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- High-throughput approaches to functional characterization of genetic variation in yeast.Current opinion in genetics & development · 2022Review
- Article
- MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.Genome biology · 2019Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
- Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences.Genome research · 2017Article
- Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter.Molecular biology and evolution · 2017Article
- A statistical framework for analyzing deep mutational scanning data.Genome biology · 2017Article
- Differential paralog divergence modulates genome evolution across yeast species.PLoS genetics · 2017Article
- High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations.PLoS genetics · 2016Article
- The power of multiplexed functional analysis of genetic variants.Nature protocols · 2016Article
- Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.Cell · 2016Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
In the yeast Saccharomyces cerevisiae, beneficial mutations selected during sulfate-limited growth are typically amplifications of the SUL1 gene, which encodes the high-affinity sulfate transporter, resulting in fitness increases of >35% . Cis-regulatory mutations have not been observed at this locus; however, it is not clear whether this absence is due to a low mutation rate such that these mutations do not arise, or they arise but have limited fitness effects relative to those of amplification. To address this question directly, we assayed the fitness effects of nearly all possible point mutations in a 493-base segment of the gene's promoter through mutagenesis and selection. While most mutations were either neutral or detrimental during sulfate-limited growth, eight mutations increased fitness >5% and as much as 9.4%. Combinations of these beneficial mutations increased fitness only up to 11%. Thus, in the case of SUL1, promoter mutations could not induce a fitness increase similar to that of gene amplification. Using these data, we identified functionally important regions of the SUL1 promoter and analyzed three sites that correspond to potential binding sites for the transcription factors Met32 and Cbf1 Mutations that create new Met32- or Cbf1-binding sites also increased fitness. Some mutations in the untranslated region of the SUL1 transcript decreased fitness, likely due to the formation of inhibitory upstream open reading frames. Our methodology-saturation mutagenesis, chemostat selection, and DNA sequencing to track variants-should be a broadly applicable approach.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.