Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.
Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.
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DOI：
10.1186/1471-2164-9-220
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发表时间：
2008-05-14
期刊：
影响因子：
4.4
通讯作者：
Li QQ
中科院分区：
文献类型：
--
作者：
Hunt AG;Xu R;Addepalli B;Rao S;Forbes KP;Meeks LR;Xing D;Mo M;Zhao H;Bandyopadhyay A;Dampanaboina L;Marion A;Von Lanken C;Li QQ
mRNA 的多腺苷酸化是几乎所有真核基因表达过程中的关键加工步骤之一。它与转录（特别是其终止）以及其他 RNA 加工事件（即加帽和剪接）紧密结合。 Poly(A) 尾可保护 mRNA 免受不受控制的降解，并且是核输出和翻译起始所必需的。近年来，已经证明多聚腺苷酸化过程也参与基因表达的调控。聚腺苷酸化过程需要两个组件，mRNA 上的顺式元件和一组识别顺式元件并产生 Poly(A) 尾的蛋白质因子。在这里，我们报告了拟南芥中 mRNA 多腺苷酸化蛋白质机制的全面的成对蛋白质-蛋白质相互作用图谱和基因表达谱。通过使用人和酵母多腺苷酸化因子进行蛋白质序列同源性搜索，我们鉴定了 28 种可能是拟南芥多腺苷酸化机制组成部分的蛋白质。为了阐明蛋白质网络及其功能，我们首先测试了它们的蛋白质-蛋白质相互作用谱。在使用酵母双杂交系统进行的 320 项成对蛋白质-蛋白质相互作用测定中，56 项（约 17%）显示出正相互作用。其中 15 种相互作用得到了进一步测试，并且全部通过免疫共沉淀和/或体外共纯化得到证实。这些相互作用组织成三个不同的中心，涉及拟南芥多聚腺苷酸化因子。这些中心以 AtCPSF100、AtCLPS 和 AtFIPS 为中心。前两种与哺乳动物中看到的复合体相似，而第三种则是植物所独有的。当比较从公开可用的微阵列数据集中提取的基因表达谱时，一些多腺苷酸化相关基因显示出组织特异性表达，表明潜在的不同多腺苷酸化复合物配置。植物多聚腺苷酸化机制揭示了一个广泛的蛋白质网络，其中所有预测的蛋白质都被发现与该复合物连接。基因表达谱表明，可以形成专门的亚复合物，以在不同的发育阶段和组织类型中进行 mRNA 的靶向加工。这些结果为蛋白质因子的进一步功能表征以及在测试这些基因在植物生长和发育中的遗传贡献时构建模型提供了路线图。
The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing. The poly(A) tail protects the mRNA from unregulated degradation, and it is required for nuclear export and translation initiation. In recent years, it has been demonstrated that the polyadenylation process is also involved in the regulation of gene expression. The polyadenylation process requires two components, the cis-elements on the mRNA and a group of protein factors that recognize the cis-elements and produce the poly(A) tail. Here we report a comprehensive pairwise protein-protein interaction mapping and gene expression profiling of the mRNA polyadenylation protein machinery in Arabidopsis. By protein sequence homology search using human and yeast polyadenylation factors, we identified 28 proteins that may be components of Arabidopsis polyadenylation machinery. To elucidate the protein network and their functions, we first tested their protein-protein interaction profiles. Out of 320 pair-wise protein-protein interaction assays done using the yeast two-hybrid system, 56 (~17%) showed positive interactions. 15 of these interactions were further tested, and all were confirmed by co-immunoprecipitation and/or in vitro co-purification. These interactions organize into three distinct hubs involving the Arabidopsis polyadenylation factors. These hubs are centered around AtCPSF100, AtCLPS, and AtFIPS. The first two are similar to complexes seen in mammals, while the third one stands out as unique to plants. When comparing the gene expression profiles extracted from publicly available microarray datasets, some of the polyadenylation related genes showed tissue-specific expression, suggestive of potential different polyadenylation complex configurations. An extensive protein network was revealed for plant polyadenylation machinery, in which all predicted proteins were found to be connecting to the complex. The gene expression profiles are indicative that specialized sub-complexes may be formed to carry out targeted processing of mRNA in different developmental stages and tissue types. These results offer a roadmap for further functional characterizations of the protein factors, and for building models when testing the genetic contributions of these genes in plant growth and development.
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影响因子：
4.5
作者：
Brodsky, AS;Silver, PA
通讯作者：
Silver, PA
影响因子：
11.4
作者：
de Vries, H;Rüegsegger, U;Keller, W
通讯作者：
Keller, W
DOI：
10.1073/pnas.0606536103
发表时间：
2006-10-10
影响因子：
11.1
作者：
Herr, Alan J.;Molnar, Attila;Baulcombe, David C.
通讯作者：
Baulcombe, David C.
影响因子：
14.9
作者：
Addepalli B;Hunt AG
通讯作者：
Hunt AG
影响因子：
10.5
作者：
NIWA, M;ROSE, SD;BERGET, SM
通讯作者：
BERGET, SM