The DOI matches its Crossref record; 11 of the 11 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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Cites
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815
Self-citationTranscriptional Regulatory Networks in Saccharomyces cerevisiae
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956
E2F integrates cell cycle progression with DNA repair, replication, and G 2 /M checkpoints
Ren, B., Cam, H., Takahashi, Y., Volkert, T., Terragni, J., Young, R. A., & Dynlacht, B. D. (2002) · Genes & Development · doi:10.1101/gad.949802 · Cited by 1,125
Signal Transduction Cascades Regulating Fungal Development and Virulence
Lengeler, K. B., Davidson, R. C., D'souza, C., Harashima, T., Shen, W.-C., Wang, P., Pan, X., Waugh, M., & Heitman, J. (2000) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.64.4.746-785.2000 · Cited by 915
Global transcriptional responses of fission yeast to environmental stress
Chen, D., Toone, W. M., Mata, J., Lyne, R., Burns, G., Kivinen, K., Brazma, A., Jones, N., & Bähler, J. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-08-0499 · Cited by 796 · cited 3×
“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
Self-citationDermitzakis, E. T., & Clark, A. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004169 · Cited by 463
Yoshimoto, H., Saltsman, K., Gasch, A. P., Li, H. X., Ogawa, N., Botstein, D., Brown, P. O., & Cyert, M. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202718200 · Cited by 404
Self-citationDevelopmental gene regulatory network architecture across 500 million years of echinoderm evolution
Hinman, V. F., Nguyen, A. T., Cameron, R. A., & Davidson, E. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235868100 · Cited by 272
Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces cerevisiae
Shakoury-Elizeh, M., Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., & Philpott, C. C. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-09-0642 · Cited by 204
Cited by
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.”
BackgroundThe evolution of combinatorial gene regulation in fungi
Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H., & Johnson, A. D. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060038 · Cited by 228
Comparative genomics of the environmental stress response in ascomycete fungi
Gasch, A. P. (2007) · Yeast · doi:10.1002/yea.1512 · Cited by 210
Self-citationLai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E. (2006) · Eukaryotic Cell · doi:10.1128/ec.00107-06 · Cited by 97
Role of Ndt80p in Sterol Metabolism Regulation and Azole Resistance in Candida albicans
Sellam, A., Tebbji, F., & Nantel, A. (2009) · Eukaryotic Cell · doi:10.1128/ec.00074-09 · Cited by 91
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
- 11
- FWCI
- 5.79
- Type
- journal article
- Language
- en
- Open access
- gold
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