MCP：蛋白质磷酸化和基因表达联系生物谷
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8月12日, 国际知名学术期刊Molecular and Cellular Proteomics在线发表了中国科学院上海生命科学研究院生物化学与细胞生物学研究所/系统生物学重点实验室曾嵘研究组的工作：运用阴阳多维液相色谱-质谱系统和稳定同位素标记的方法，同步定量细胞蛋白质组及磷酸化蛋白质组，从而系统地揭示了蛋白质磷酸化和基因表达间的关系。
磷酸化是蛋白质最重要的翻译后修饰之一,磷酸化肽段和非磷酸化肽段的不同特性，使得磷酸化肽段和非磷酸化肽段的同步鉴定及定量成为蛋白质组学研究中的难点。生化与细胞所博士生伍一博等人在曾嵘研究员指导下，运用该实验室发明的阴阳多维液相色谱-质谱系统(Yin-Yang-MDLC-MS/MS)及在线pH梯度洗脱对细胞内蛋白质酶解肽段进行分级分离，实现了一次实验中对磷酸化肽段和非磷酸化肽段的同步鉴定。进一步结合稳定同位素标记 (SILAC)的方法，可以同步定量细胞内蛋白质表达及其磷酸化水平。对于单个蛋白质而言，这一方法有助于区分两种不同的磷酸化水平改变方式，即直接受激酶调控，或者通过蛋白质表达量的变化而变化。从系统水平上看，这一方法可以揭示转录因子磷酸化对其下游靶基因的调控关系。该工作以脂肪细胞为研究对象，鉴定到了一些在分化早期磷酸化水平或表达量发生显著变化的蛋白质，进一步的生物信息学分析揭示了一些转录因子磷酸化水平与下游靶基因表达水平的关系。这一工作为系统水平上诠释脂肪细胞分化早期分子事件提供了研究策略和实验依据，发展的技术方法也可以广泛应用于信号转导分子机制研究。
该项工作是与吴家睿研究组和李亦学研究员领导的生物信息中心合作完成的，并得到了科技部，基金委和中科院经费支持。（生物谷Bioon.com）
生物谷推荐原始出处：
Molecular & Cellular Proteomics 8:1839-1849, 2009.
SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications*
Hong Li,,?,||, Xiaobin Xing,,?,||, Guohui Ding, Qingrun Li,?, Chuan Wang, Lu Xie,**, Rong Zeng,** and Yixue Li,,**
1 From the Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China,
2 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China, and
Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
With the rapid expansion of protein post-translational modification (PTM) research based on large-scale proteomic work, there is an increasing demand for a suitable repository to yze PTM data. Here we present a curated, web-accessible PTM data base, SysPTM. SysPTM provides a systematic and sophisticated platform for proteomic PTM research equipped not only with a knowledge base of manually curated multi-type modification data but also with four fully developed, in-depth data mining tools. Currently, SysPTM contains data detailing 117,349 experimentally determined PTM sites on 33,421 proteins involving nearly 50 PTM types, curated from public resources including five data bases and four web servers and more than one hundred peer-reviewed mass spectrometry papers. Protein annotations including Pfam domains, KEGG pathways, GO functional classification, and ortholog groups are integrated into the data base. Four online tools have been developed and incorporated, including PTMBlast, to compare a user's PTM dataset with PTM data in SysPTM; PTMPathway, to map PTM proteins to KEGG pathways; PTMPhylog, to discover potentially conserved PTM sites; and PTMCluster, to find clusters of multi-site modifications. The workflow of SysPTM was demonstrated by yzing an in-house phosphorylation dataset identified by MS/MS. It is shown that in SysPTM, the role of single-type and multi-type modifications can be systematically investigated in a full biological context. SysPTM could be an important contribution to modificomics research.
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