System wide analyses have underestimated protein abundances and the importance of transcription in mammals.
System wide analyses have underestimated protein abundances and the importance of transcription in mammals.
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作者：
Li JJ;Bickel PJ;Biggin MD
在哺乳动物组织培养细胞中进行的大规模调查表明，以中等丰度表达的蛋白质在每个细胞中存在8000 - 16000个分子，并且基因之间mRNA表达的差异仅能解释蛋白质水平差异的10% - 40%。然而，我们发现这些调查严重低估了蛋白质丰度以及转录的相对重要性。通过对61种管家蛋白进行单独测量来重新调整整个蛋白质组数据，我们发现所检测到的蛋白质中位数在每个细胞中以170000个分子的水平表达，并且我们校正后的蛋白质丰度估计值与mRNA丰度的相关性比未校正的蛋白质数据更高。此外，我们利用对mRNA和蛋白质丰度误差的直接实验测量来估计进一步误差的影响。由此产生的分析表明，对于所检测到的4212个基因，mRNA水平至少能解释蛋白质丰度差异的56%，尽管由于一种主要误差来源无法估计，实际的贡献率应该更高。我们还采用了第二种独立的策略来确定mRNA水平对蛋白质表达的贡献。我们表明，通过核糖体图谱直接测量的翻译速率方差仅为之前所推断的12%，并且测量的和推断的翻译速率相关性很差（R² = 0.13）。基于此，我们的第二种策略表明mRNA水平能解释约81%的蛋白质水平方差。我们还使用我们的两种策略确定了转录、RNA降解、翻译和蛋白质降解对蛋白质丰度方差的贡献率。虽然这两种估计值的大小有所不同，但它们都表明转录所起的作用比早期研究暗示的更为重要，而翻译所起的作用要小得多。最后，上述估计仅适用于那些mRNA和蛋白质表达被检测到的基因。根据一项详细分析，我们估计在一个群体中的给定细胞内约40%的基因不表达mRNA。由于在没有mRNA的情况下不可能进行翻译，我们认为翻译速率的差异对于约40%不表达的基因的表达水平不起作用。
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from, we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by, though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by, and that the measured and inferred translation rates correlate poorly (R2 = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates only apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by, we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
4
作者：
Ambros, Victor
通讯作者：
Ambros, Victor
影响因子：
7
作者：
Gennarino VA;D'Angelo G;Dharmalingam G;Fernandez S;Russolillo G;Sanges R;Mutarelli M;Belcastro V;Ballabio A;Verde P;Sardiello M;Banfi S
通讯作者：
Banfi S
影响因子：
48
作者：
Han, Kyuho;Jaimovich, Ariel;Dey, Gautam;Ruggero, Davide;Meyuhas, Oded;Sonenberg, Nahum;Meyer, Tobias
通讯作者：
Meyer, Tobias
影响因子：
7.5
作者：
Hebenstreit, Daniel;Deonarine, Andrew;Teichmann, Sarah A.
通讯作者：
Teichmann, Sarah A.