Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs
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DOI：
10.1073/pnas.0900604106
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发表时间：
2009-06-23
影响因子：
11.1
通讯作者：
Yanagawa, Hiroshi
中科院分区：
文献类型：
--
作者：
Kosugi, Shunichi;Hasebe, Masako;Yanagawa, Hiroshi
蛋白质的细胞周期依赖性核质转运主要受CDK激酶活性调节;然而，目前很难预测由此调节的蛋白质，这主要是因为所涉及的基序的预测效率较低。在这里，我们报告了成功的预测CDK 1调节的核质穿梭蛋白使用预测系统的核定位信号（NLS）。通过在芽殖酵母中进行系统的氨基酸置换分析，我们创建了不同类别的输入α依赖性NLS的基于活性的谱，其代表NLS类别内每个位置处不同氨基酸的功能贡献。然后，我们开发了一种用于预测经典输入-α/β途径特异性NLS的计算机程序（cNLS Mapper，可在http//nls-mapper.iab.keio.ac.jp/上获得），其通过使用这些谱和基于加和性的基序评分算法来计算NLS活性。这种计算方法在灵敏度和特异性方面都比目前的方法实现了显着更高的预测准确性。通过使用cNLS Mapper搜索与共有CDK 1磷酸化位点重叠的NLS，鉴定了所有先前报道的和5种先前未表征的酵母蛋白（Yen 1，Psy 4，Pds 1，Msa 1和Dna 2），这些蛋白显示CDK 1和细胞周期调节的核转运。CDK 1激活或抑制其核输入活性，这取决于NLS内CDK 1磷酸化位点的位置。这一策略的应用，其他功能的线性模体应该是有用的蛋白质-蛋白质网络的系统研究。
The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-alpha-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-alpha/beta pathway-specific NLSs ( cNLS Mapper, available at http//nls-mapper.iab.keio.ac.jp/) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1- and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1- phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein-protein networks.