Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast.
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast.
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DOI：
10.1186/1752-0509-6-128
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发表时间：
2012-09-27
影响因子：
--
通讯作者：
Masel J
中科院分区：
文献类型：
--
作者：
Brettner LM;Masel J
枢纽蛋白是一种与许多功能伙伴相互作用的蛋白。枢纽蛋白的注释，或者更一般地说，每个基因的蛋白质-蛋白质相互作用的“程度”，需要高质量的全基因组数据。使用酵母双杂交方法获得的数据包含许多在活细胞中很少遇到彼此的蛋白质之间的假阳性相互作用，并且这样的数据已经不受欢迎。我们发现，在表面上低质量的酵母双杂交数据中，以网络度衡量的蛋白质“粘性”是比功能性蛋白质-蛋白质相互作用数量更具预测性的基因组指标，正如通过据称更高质量的高通量亲和捕获质谱数据评估的那样。在酵母中，一种蛋白质的高粘性，而不是其大量的功能相互作用，预示着基因表达的低随机噪声，基因在不同环境下表达的低可塑性，以及形成同质寡聚物的高概率。我们的结果对于校正其他已知预测因素（包括蛋白质丰度、TATA盒子的存在以及基因是否必需）的多元回归分析是稳健的。一旦控制了高黏性的同聚物，我们发现同聚物比其他蛋白质具有更嘈杂和更可塑性的基因表达，这与同聚物在调节鲁棒性中的作用一致。我们的工作验证了使用酵母双杂交相互作用的数量作为蛋白质粘性的度量。粘性蛋白在基因表达中表现出较低的随机噪声，在不同环境下表达的可塑性较低。
A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction “degree” of each gene, requires quality genome-wide data. Data obtained using yeast two-hybrid methods contain many false positive interactions between proteins that rarely encounter each other in living cells, and such data have fallen out of favor. We find that protein “stickiness”, measured as network degree in ostensibly low quality yeast two-hybrid data, is a more predictive genomic metric than the number of functional protein-protein interactions, as assessed by supposedly higher quality high throughput affinity capture mass spectrometry data. In the yeast Saccharomyces cerevisiae, a protein’s high stickiness, but not its high number of functional interactions, predicts low stochastic noise in gene expression, low plasticity of gene expression across different environments, and high probability of forming a homo-oligomer. Our results are robust to a multiple regression analysis correcting for other known predictors including protein abundance, presence of a TATA box and whether a gene is essential. Once the higher stickiness of homo-oligomers is controlled for, we find that homo-oligomers have noisier and more plastic gene expression than other proteins, consistent with a role for homo-oligomerization in mediating robustness. Our work validates use of the number of yeast two-hybrid interactions as a metric for protein stickiness. Sticky proteins exhibit low stochastic noise in gene expression, and low plasticity in expression across different environments.
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