Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast
Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast
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DOI：
10.1093/molbev/msn138
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发表时间：
2008-09-01
影响因子：
10.7
通讯作者：
Li, Wen-Hsiung
中科院分区：
文献类型：
--
作者：
Chang, Ya-Wen;Liu, Fu-Guo Robert;Li, Wen-Hsiung
酿酒酵母在含葡萄糖的培养基中迅速增殖。随着葡萄糖逐渐耗尽，酵母细胞进入从发酵代谢到非发酵代谢的转变，称为二次突变，这与基因表达的主要变化有关。为了了解物种内二次突变和非发酵代谢相关基因的表达演变，本研究使用了实验室菌株（BY）、野生菌株（RM）和临床分离株（YJM）。我们的数据表明，RM株进入二倍体移位类似1小时前比BY株更早，更高的诱导参与二倍体移位的许多关键转录因子（TF）。我们的序列数据显示，在大多数这些TF的编码区和启动子区的BY和RM之间的序列变异。关键的TF Cat 8 p是一种锌指簇蛋白，在非发酵生长条件下，许多基因的表达都需要TF Cat 8 p，其去阻遏是由Mig 1 p的失活介导的。我们对CAT 8表达的动力学研究表明，CAT 8诱导与BY和RM中葡萄糖消耗的时间相对应，并且CAT 8在RM中被诱导高达50至90倍，而在BY中仅为20至30倍。为了解释在二次突变过程中，顺式和反式变异在致突变途径中表达差异的相对重要性，我们研究了MIG 1、CAT 8及其下游靶基因在共培养物和BY-RM、BY-YJM和RM-YJM的杂交二倍体以及具有交换启动子的菌株中的表达水平。我们的数据表明，BY和RM之间在CAT 8的上游调节因子MIG 1的表达上的差异主要受顺式元件的变化的影响，尽管也受反式作用因子的变化的影响，而CAT 8及其下游靶基因的差异主要受反式作用因子的变化的影响。
The yeast Saccharomyces cerevisiae proliferates rapidly in glucose-containing media. As glucose is getting depleted, yeast cells enter the transition from fermentative to nonfermentative metabolism, known as the diauxic shift, which is associated with major changes in gene expression. To understand the expression evolution of genes involved in the diauxic shift and in nonfermentative metabolism within species, a laboratory strain (BY), a wild strain (RM), and a clinical isolate (YJM) were used in this study. Our data showed that the RM strain enters into the diauxic shift similar to 1 h earlier than the BY strain with an earlier, higher induction of many key transcription factors (TFs) involved in the diauxic shift. Our sequence data revealed sequence variations between BY and RM in both coding and promoter regions of the majority of these TFs. The key TF Cat8p, a zinc-finger cluster protein, is required for the expression of many genes in gluconeogenesis under nonfermentative growth, and its derepression is mediated by deactivation of Mig1p. Our kinetic study of CAT8 expression revealed that CAT8 induction corresponded to the timing of glucose depletion in both BY and RM and CAT8 was induced up to 50- to 90-folds in RM, whereas only 20- to 30-folds in BY. In order to decipher the relative importance of cis - and trans-variations in expression divergence in the gluconeogenic pathway during the diauxic shift, we studied the expression levels of MIG1 , CAT8 , and their downstream target genes in the cocultures and in the hybrid diploids of BY-RM, BY-YJM, and RM-YJM and in strains with swapped promoters. Our data showed that the differences between BY and RM in the expression of MIG1 , the upstream regulator of CAT8 , were affected mainly by changes in cis -elements, though also by changes in trans -acting factors, whereas those of CAT8 and its downstream target genes were predominantly affected by changes in trans -acting factors.