ArticleBMC genomics2008
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 56 citations in OpenAlex.
- The fitness trade-off between growth and stress resistance determines the phenotypic landscape.BMC biology · 2024Article
- Article
- Article
- JAZF1: A metabolic actor subunit of the NuA4/TIP60 chromatin modifying complex.Frontiers in cell and developmental biology · 2023Review
- Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors.Microbial biotechnology · 2023Article
- Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program.PLoS computational biology · 2019Article
- Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates.Microbial cell factories · 2016Article
- Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations.Frontiers in bioengineering and biotechnology · 2016Review
- Bacterial transcriptome reorganization in thermal adaptive evolution.BMC genomics · 2015Article
- In Pichia pastoris, growth rate regulates protein synthesis and secretion, mating and stress response.Biotechnology journal · 2014Article
- Growth rate-coordinated transcriptome reorganization in bacteria.BMC genomics · 2013Article
- Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2013Article
- Promoters maintain their relative activity levels under different growth conditions.Molecular systems biology · 2013Article
- Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory.Biotechnology journal · 2013Review
- Pattern and synchrony of gene expression among sympatric marine microbial populations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.PloS one · 2013Article
- Physiological heterogeneities in microbial populations and implications for physical stress tolerance.Microbial cell factories · 2012Article
- Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast.FEMS yeast research · 2012Review
- Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures.FEMS yeast research · 2011Article
- Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae.Molecular systems biology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCharacterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae. The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability.
resultsWe identified 268 growth rate dependent genes, independent of nutrient limitation and oxygen availability. The transcriptional response was used to identify key areas in metabolism around which mRNA expression changes are significantly associated. Among key metabolic pathways, this analysis revealed de novo synthesis of pyrimidine ribonucleotides and ATP producing and consuming reactions at fast cellular growth. By scoring the significance of overlap between growth rate dependent genes and known transcription factor target sets, transcription factors that coordinate balanced growth were also identified. Our analysis shows that Fhl1, Rap1, and Sfp1, regulating protein biosynthesis, have significantly enriched target sets for genes up-regulated with increasing growth rate. Cell cycle regulators, such as Ace2 and Swi6, and stress response regulators, such as Yap1, were also shown to have significantly enriched target sets.
conclusionOur work, which is the first genome-wide gene expression study to investigate specific growth rate and consider the impact of oxygen availability, provides a more conservative estimate of growth rate dependent genes than previously reported. We also provide a global view of how a small set of transcription factors, 13 in total, contribute to control of cellular growth rate. We anticipate that multi-factorial designs will play an increasing role in elucidating cellular regulation.
Indexed as
Identifiers
What OpenQuestion holds
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.