Conservation and evolution of cis-regulatory systems in ascomycete fungi.
Conservation and evolution of cis-regulatory systems in ascomycete fungi.
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DOI：
10.1371/journal.pbio.0020398
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发表时间：
2004-12
期刊：
影响因子：
9.8
通讯作者：
Eisen MB
中科院分区：
文献类型：
--
作者：
Gasch AP;Moses AM;Chiang DY;Fraser HB;Berardini M;Eisen MB
对基因表达调控进化的机制知之甚少。为了研究这一点，我们系统地探讨了真菌中的调控网络的保护，通过检查的顺式调控元件，控制共调节基因的表达。我们首先确定了组的共调节酿酒酵母基因丰富的基因与已知的上游或下游顺式调控序列。由于这些基因组中的许多在相关物种中也是共调节的，我们对共调节的S.酿酒酵母基因在其他13个子囊菌物种。我们发现，许多种特异性基因组富含与S.酿酒酵母，表明这些调控系统已在多个子囊菌物种保守。除了这些明确的情况下，监管保守，我们发现顺式元件进化的例子，建议多种模式的监管多样化，包括改变转录因子结合特异性，纳入新的基因靶向到现有的监管系统，和cooption的监管系统，以控制一组不同的基因。我们通过测量S.酿酒酵母转录因子Rpn4p及其来自白色念珠菌和粗糙脉孢菌的直系同源物。我们的研究结果表明，这些蛋白质的DNA结合特异性与Rpn4p靶基因上游发现的序列共同进化，并表明Rpn4p在N.粗鲁。对子囊菌中基因调控元件的系统研究揭示了显著的保守性，沿着着一些调控系统进化方式的例子
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 from S. 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. A systematic examination of the gene regulatory elements in ascomycete fungi reveals striking conservation along with some examples of the ways in which regulatory systems can evolve
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