Abstract
The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae—its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the ‘non-WGD’ Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the ‘post-WGD’ genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae.
Highlights
The yeast Saccharomyces cerevisiae, as well as other sensu stricto Saccharomyces species and a few of their close relatives, has a characteristic physiology that is obviously different from that of other eukaryotic cells and even most yeast species
We investigated the possible site in the upstream regions of the K. lactis genes, which are orthologous to the S. cerevisiae oxygen-responding genes mediated by Rox1p according to the data previously reported [3,4,36,51]
The pre-whole-genome duplication (WGD) genome of K. lactis might lack a specific gene system responding to oxygen-limiting environment In S. cerevisiae, the transcriptional repressor Rox1p and its target genes such as ANB1 and COX5B form a network devoted to respond to low oxygen environments
Summary
The yeast Saccharomyces cerevisiae, as well as other sensu stricto Saccharomyces species and a few of their close relatives, has a characteristic physiology that is obviously different from that of other eukaryotic cells and even most yeast species. One of the specialized features of S. cerevisiae is its regulatory network responding to oxygen availability, which allows this species to live on an exclusively fermentative mode even in fully aerated conditions, and to grow vigorously in the complete absence of oxygen. Such a particular life style must rely on rapid and efficient gene responses to oxygen availability. An increase in the number of some genes resulted in an enhanced glycolytic flux, which is necessary for the fermentation-oriented metabolism of S. cerevisiae [12] This change was regarded as an outcome of the WGD event followed by a selection in glucose-rich environments [13]
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