A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif.
A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif.
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DOI：
10.1186/1471-2164-7-55
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发表时间：
2006-03-16
期刊：
影响因子：
4.4
通讯作者：
Graber, Joel H.
中科院分区：
文献类型：
--
作者：
Salisbury, Jesse;Hutchison, Keith W.;Graber, Joel H.
切割刺激因子（CstF）是真核生物mRNA 3 '-加工所必需的蛋白质复合物。CstF通过其64-kDa亚基CstF-64与3 '-加工下游元件（DSE）相互作用;然而，这种相互作用的确切性质仍不清楚。我们使用EST到基因组比对来识别和提取来自十种后生动物物种的大量推定的mRNA 3 '加工位点，包括智人、家犬、褐家鼠、小家鼠、原鸡、斑马鱼、红足东方鲀、黑腹果蝇、冈比亚按蚊和秀丽隐杆线虫。为了进一步描述mRNA-蛋白质相互作用的细节，我们获得了来自相同物种的CstF-64蛋白质序列并进行了多重比对。我们的特点是序列的内容和特定的定位，推定的DSE的范围内的生物体研究。我们的分析将下游元件（DSE）表征为两个不同的部分-近端富含UG的元件和远端富含U的元件。我们发现，虽然富含铀的元素在很大程度上是保守的，在所有的生物体研究，富含UG的元素是不是。CstF-64 RNA识别基序的多重比对显示，虽然它在后生动物中高度保守，但我们可以鉴定与观察到的序列内容和DSE定位变化相关的氨基酸变化。我们的分析证实了早期关于富含铀和铀的DSE的报告。蛋白质序列和mRNA结合序列的相关变化为前体mRNA和3 '加工机制之间的相互作用提供了新的见解。
The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mRNA from ten metazoan species, including Homo sapiens, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Takifugu rubripes, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans. In order to further delineate the details of the mRNA-protein interaction, we obtained and multiply aligned CstF-64 protein sequences from the same species. We characterized the sequence content and specific positioning of putative DSEs across the range of organisms studied. Our analysis characterized the downstream element (DSE) as two distinct parts – a proximal UG-rich element and a distal U-rich element. We find that while the U-rich element is largely conserved in all of the organisms studied, the UG-rich element is not. Multiple alignment of the CstF-64 RNA recognition motif revealed that, while it is highly conserved throughout metazoans, we can identify amino acid changes that correlate with observed variation in the sequence content and positioning of the DSEs. Our analysis confirms the early reports of separate U- and UG-rich DSEs. The correlated variations in protein sequence and mRNA binding sequences provide novel insights into the interactions between the precursor mRNA and the 3'-processing machinery.
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