van den Brink Joost, Daran-Lapujade Pascale, Pronk Jack T, de Winde Johannes H
Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
BMC Genomics. 2008 Feb 27;9:100. doi: 10.1186/1471-2164-9-100.
The capacity of respiring cultures of Saccharomyces cerevisiae to immediately switch to fast alcoholic fermentation upon a transfer to anaerobic sugar-excess conditions is a key characteristic of Saccharomyces cerevisiae in many of its industrial applications. This transition was studied by exposing aerobic glucose-limited chemostat cultures grown at a low specific growth rate to two simultaneous perturbations: oxygen depletion and relief of glucose limitation.
The shift towards fully fermentative conditions caused a massive transcriptional reprogramming, where one third of all genes within the genome were transcribed differentially. The changes in transcript levels were mostly driven by relief from glucose-limitation. After an initial strong response to the addition of glucose, the expression profile of most transcriptionally regulated genes displayed a clear switch at 30 minutes. In this respect, a striking difference was observed between the transcript profiles of genes encoding ribosomal proteins and those encoding ribosomal biogenesis components. Not all regulated genes responded with this binary profile. A group of 87 genes showed a delayed and steady increase in expression that specifically responded to anaerobiosis.
Our study demonstrated that, despite the complexity of this multiple-input perturbation, the transcriptional responses could be categorized and biologically interpreted. By comparing this study with public datasets representing dynamic and steady conditions, 14 up-regulated and 11 down-regulated genes were determined to be anaerobic specific. Therefore, these can be seen as true "signature" transcripts for anaerobicity under dynamic as well as under steady state conditions.
酿酒酵母在转移到厌氧糖过量条件下能够立即切换到快速酒精发酵,这是酿酒酵母在许多工业应用中的一个关键特性。通过将以低比生长速率生长的好氧葡萄糖限制恒化器培养物暴露于两种同时发生的扰动来研究这种转变:氧气耗尽和葡萄糖限制的解除。
向完全发酵条件的转变导致了大规模的转录重编程,基因组中三分之一的基因转录发生差异。转录水平的变化主要由葡萄糖限制的解除驱动。在对添加葡萄糖的初始强烈反应之后,大多数转录调控基因的表达谱在30分钟时显示出明显的转变。在这方面,观察到编码核糖体蛋白的基因和编码核糖体生物合成成分的基因的转录谱之间存在显著差异。并非所有受调控的基因都以这种二元模式做出反应。一组87个基因显示出表达的延迟和稳定增加,这是对厌氧的特异性反应。
我们的研究表明,尽管这种多输入扰动很复杂,但转录反应可以进行分类并从生物学角度进行解释。通过将本研究与代表动态和稳定条件的公共数据集进行比较,确定了14个上调基因和11个下调基因是厌氧特异性的。因此,这些可以被视为动态和稳态条件下厌氧性的真正“特征”转录本。