The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Open accessAbstract
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by examining the cis-regulatory elements that govern the expression of coregulated genes. We first identified groups of coregulated Saccharomyces cerevisiae genes enriched for genes with known upstream or downstream cis-regulatory sequences. Reasoning that many of these gene groups are coregulated in related species as well, we performed similar analyses on orthologs of coregulated S. cerevisiae genes in 13 other ascomycete species. We find that many species-specific gene groups are enriched for the same flanking regulatory sequences as those found in the orthologous gene groups fromS. cerevisiae, indicating that those regulatory systems have been conserved in multiple ascomycete species. In addition to these clear cases of regulatory conservation, we find examples of cis-element evolution that suggest multiple modes of regulatory diversification, including alterations in transcription factor-binding specificity, incorporation of new gene targets into an existing regulatory system, and cooption of regulatory systems to control a different set of genes. We investigated one example in greater detail by measuring the in vitro activity of the S. cerevisiae transcription factor Rpn4p and its orthologs from Candida albicans and Neurospora crassa. Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa.
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Citations
Cites
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
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Self-citationTranscriptional Regulatory Networks in Saccharomyces cerevisiae
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Signal Transduction Cascades Regulating Fungal Development and Virulence
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Global transcriptional responses of fission yeast to environmental stress
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“For example, the proteasome subunits and the ribosomal proteins are among the most highly conserved proteins, and the genes that encode them are expressed with similar patterns in S. cerevisiae, C. albicans, and Sch. pombe (Gasch et al. 2000; Chen et al. 2003; Enjalbert et al. 2003).”
BackgroundInfluentialGasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.10.2987 · Cited by 542
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Self-citationDevelopmental gene regulatory network architecture across 500 million years of echinoderm evolution
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Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces cerevisiae
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The frailty of adaptive hypotheses for the origins of organismal complexity
Lynch, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702207104 · Cited by 817
A Phenotypic Profile of the Candida albicans Regulatory Network
Homann, O. R., Dea, J., Noble, S. M., & Johnson, A. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000783 · Cited by 444
“Given the significant rewiring of transcriptional networks documented in the fungal lineages [4,5,35,63,64], the high degree of phenotypic conservation we observed between S.”
BackgroundHigh-resolution DNA-binding specificity analysis of yeast transcription factors
Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z., Berger, M. F., Newburger, D. E., Saulrieta, K., Smith, Z., Shah, M. V., Radhakrishnan, M., et al. (2009) · Genome Research · doi:10.1101/gr.090233.108 · Cited by 398
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Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi
Slot, J. C., & Rokas, A. (2011) · Current Biology · doi:10.1016/j.cub.2010.12.020 · Cited by 269
Metadata
- Authors
- Gasch, A. P., Moses, A. M., Chiang, D. Y., Fraser, H. B., Berardini, M., & Eisen, M. B.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2004-11-09
- Volume
- 2
- Issue
- 12
- Pages
- e398
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2037652809
- Cited by
- 227
- References
- 12
- FWCI
- 5.79
- Type
- journal article
- Language
- en
- Open access
- gold
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