Schreiber Gabriele, Rueda Facundo, Renner Florian, Polat Asya Fatima, Lorenz Philipp, Klipp Edda
Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.
Cells. 2025 Mar 11;14(6):412. doi: 10.3390/cells14060412.
Cell cycle progression of the yeast is largely driven by the expression of cyclins, which in turn bind the cyclin-dependent kinase CDK1 providing specificity. Due to the duplication of the yeast genome during evolution, most of the cyclins are present as a pair of paralogues, which are considered to have similar functions and periods of expression. Here, we use single molecule inexpensive fluorescence in situ hybridization (smiFISH) to measure the expression of five pairs of paralogous genes relevant for cell cycle progression (/, /, /, / and /) in a large number of unsynchronized single cells representing all cell cycle phases. We systematically compare their expression patterns and strengths. In addition, we also analyze the effect of the knockout of one part of each pair on the expression of the other gene. In order to classify cells into specific cell cycle phases, we developed a convolutional neural network (CNN). We find that the expression levels of some cell-cycle related paralogues differ in their correlation, with and showing strong correlation and and showing weakest correlation. The temporal profiles of some pairs also differ. Upon deletion of their paralogue, and seem to compensate for the expression of the other gene, while this was not observed for /. Interestingly, and also seem to share work between mother and bud in the G2 phase, where is primarily expressed in the bud and in the mother. Taken together, our results suggest that paralogues related to yeast cell cycle progression should not be considered as the same but differ both in their expression strength and timing as well in their precise role in cell cycle regulation.
酵母的细胞周期进程在很大程度上由细胞周期蛋白的表达驱动，细胞周期蛋白反过来结合细胞周期蛋白依赖性激酶CDK1以提供特异性。由于酵母基因组在进化过程中发生了复制，大多数细胞周期蛋白以一对旁系同源物的形式存在，它们被认为具有相似的功能和表达时期。在这里，我们使用单分子低成本荧光原位杂交（smiFISH）来测量在代表所有细胞周期阶段的大量未同步化的单细胞中，与细胞周期进程相关的五对旁系同源基因（/、/、/、/和/）的表达。我们系统地比较了它们的表达模式和强度。此外，我们还分析了每对中的一个部分基因敲除对另一个基因表达的影响。为了将细胞分类到特定的细胞周期阶段，我们开发了一个卷积神经网络（CNN）。我们发现，一些与细胞周期相关的旁系同源物的表达水平在相关性上存在差异，其中和显示出强相关性，而和显示出最弱的相关性。一些基因对的时间分布也有所不同。在其旁系同源物缺失后，和似乎能补偿另一个基因的表达，而对于/则未观察到这种情况。有趣的是，和在G2期似乎也在母细胞和芽之间分担工作，其中主要在芽中表达，而在母细胞中表达。综上所述，我们的结果表明，与酵母细胞周期进程相关的旁系同源物不应被视为相同，它们在表达强度和时间以及在细胞周期调控中的精确作用方面都存在差异。
