细胞区分是蛋白质进化速度的预测器,但不是预期的方式:反对扩展复杂性假设的证据
Juan Rivas-Santisteban1,2, Pablo Yubero1, Laurence D Hurst2
1Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
Genome biology and evolution
|June 28, 2025
概括
蛋白质进化速率因细胞位置而异. 虽然细胞质蛋白缓慢进化,而膜蛋白快速进化而不会占丰富度,但控制丰富度显示膜蛋白的进化速度最慢. 这凸显了共同变量控制在进化研究中的重要性.
科学领域:
- 进化生物学是进化的生物学.
- 分子进化是分子进化的过程.
- 基因组学就是基因组学.
背景情况:
- 蛋白质进化速率 (dN/dS,或 ω) 差异很大.
- 以前的研究将细胞内蛋白质的较慢进化与细胞位置联系起来,支持扩展复杂性假设.
- 基因表达水平是 ω 的强有力的预测因素,许多影响 ω 的因素都通过其与表达的共变性来解释.
研究的目的:
- 调查观察到的细胞区对蛋白质演化速率的影响是否由共变量解释,特别是蛋白质丰度.
- 重新评估细胞区和蛋白质进化速率之间的关系,使用大肠杆菌和大肠杆菌 (Saccharomyces cerevisiae) 的数据.
- 确定共变控制对解释细胞区间对进化速率影响的影响.
主要方法:
- 在E. coli和S. cerevisiae*中使用信息性物种三元组对特定分支的ω值进行分析.
- 在控制蛋白质丰度之前和之后,在不同细胞区 (细胞质与膜) 中比较蛋白质进化速率.
- 应用多种替代方法来控制丰度,以确保结果的可靠性.
主要成果:
- 在这两种物种中,当蛋白质丰富度不受控制时,细胞质蛋白质的进化速度比预期的要慢,膜蛋白质的进化速度要快.
- 在对蛋白质丰富度进行控制后,膜蛋白表现出最慢的进化速率,扭转了最初的观察.
- 细胞区块的影响仍然显著,并且与蛋白质基本性相比,即使控制了丰富度.
结论:
- 细胞区对蛋白质进化速率的观察到的影响是真实的,但它们的方向取决于蛋白质丰度是否受到控制.
- 这些发现质疑了细胞质蛋白的较慢进化,此前被引用作为扩展复杂性假设的支持,这些发现被质疑.
- 共同变量控制,特别是蛋白质丰富性,对于准确解释蛋白质进化速率的变化和理解分子进化至关重要.
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