A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them
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Abstract
The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism.
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- Authors
- Forés-Martos, J., Forte, A., García-Martínez, J., & Pérez-Ortín, J. E.
- Affiliations
- Universitat de València (ES)
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
- Corresponding author
- Pérez-Ortín, José E.
- Venue
- Cells
- Publisher
- MDPI AG
- Published
- 2021-02-05
- Volume
- 10
- Issue
- 2
- Pages
- 334
- ISSN
- 2073-4409 (ISSN-L)
- PMC
- PMC7914595
- OpenAlex
- W3128917776
- Cited by
- 8
- References
- 89
- Citations by year
- 2026: 1 · 2024: 2 · 2023: 3 · 2022: 2
- FWCI
- 0.55
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cells (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
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- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, other-oa)
- Funders
- Ministerio de Ciencia, Innovación y Universidades (BFU2016-77728-C3-3-P)
- Generalitat Valenciana (AICO/2019/088)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Keywords
- gene expression regulation, mRNA levels, protein abundance, mRNA synthesis rate, protein synthesis rate, protein degradation rate, phylogenetic relationships, Saccharomyces cerevisiae, Schizosaccharomyces pombe, HeLa cells, Escherichia coli, transcription rate, translation (biology), macromolecular complexes
- MeSH terms
- Humans, Saccharomyces cerevisiae, Transcription, Genetic, Gene Expression Regulation, Fungal, RNA Stability
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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