ArticleProceedings of the National Academy of Sciences of the United States of America2010
Gene duplication and the evolution of ribosomal protein gene regulation in yeast.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 74 citations in OpenAlex.
- RiboScreenBiomedicines · 2026Review
- Interplay Between Ribosomal Gene Deficiency and Calorie Restriction in Shaping Yeast Biosynthetic Capacity.Cells · 2025Article
- Discovery of additional ancient genome duplications in yeasts.bioRxiv : the preprint server for biology · 2025Article
- Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.Nature communications · 2025Article
- Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.bioRxiv : the preprint server for biology · 2025Article
- Ribosome Structural Changes Dynamically Affect Ribosome Function.International journal of molecular sciences · 2024Review
- Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis.Molecular and cellular biology · 2023Article
- Duplicated ribosomal protein paralogs promote alternative translation and drug resistance.Nature communications · 2022Article
- Article
- Retention of duplicated genes in evolution.Trends in genetics : TIG · 2022Review
- Yeast Crf1p: An activator in need is an activator indeed.Computational and structural biotechnology journal · 2022Review
- Regulation of ribosomal protein genes: An ordered anarchy.Wiley interdisciplinary reviews. RNA · 2021Review
- Article
- Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress.Nucleic acids research · 2020Article
- Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human PathogenFrontiers in microbiology · 2018Article
- Evolutionary biology through the lens of budding yeast comparative genomics.Nature reviews. Genetics · 2017Review
- Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation.PLoS genetics · 2017Article
- Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.Cell systems · 2017Article
- A prior-based integrative framework for functional transcriptional regulatory network inference.Nucleic acids research · 2017Article
- Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in Saccharomyces cerevisiae, but the cis and trans factors associated with them are surprisingly diverged across Ascomycota fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them. Here, we address this question in the context of the evolution of the regulation of RP gene expression by using a comparative genomics approach together with cross-species functional assays. We show that an activator (Ifh1) and a repressor (Crf1) that control RP gene regulation in normal and stress conditions in S. cerevisiae are derived from the duplication and subsequent specialization of a single ancestral protein. We provide evidence that this regulatory innovation coincides with the duplication of RP genes in a whole-genome duplication (WGD) event and may have been important for tighter control of higher levels of RP transcripts. We find that subsequent loss of the derived repressor led to the loss of a stress-dependent repression of RPs in the fungal pathogen Candida glabrata. Our comparative computational and experimental approach shows how gene duplication can constrain and drive regulatory evolution and provides a general strategy for reconstructing the evolutionary trajectory of gene regulation across species.
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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.