Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.
Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.
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DOI：
10.1186/1741-7007-5-32
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发表时间：
2007-07-30
期刊：
影响因子：
5.4
通讯作者：
Jorgensen RA
中科院分区：
文献类型：
--
作者：
Hayden CA;Jorgensen RA
上游开放阅读框（uORF）可以介导响应于饥饿、多胺浓度和蔗糖浓度的最大或主要ORF（mORF）的翻译控制。具有保守肽序列的一种植物uORF已显示以氨基酸序列依赖性方式发挥这种控制，但通常不清楚什么类型的基因受到调节，或者在给定基因组中这种机制的程度如何。通过比较拟南芥和水稻的全长cDNA序列，我们确定了26个不同的保守肽uORF的同源性组，其中只有三个已被报道过。配对Ka/Ks分析表明，纯化选择作用于几乎所有保守肽uORF及其相关mORF。预测的mORF蛋白质的功能可以推断为16个同源组，并且这些蛋白质中的许多似乎具有调节功能，包括6个转录因子，5个信号转导因子，3个发育信号分子，翻译起始因子eIF 5的同源物和RING指蛋白。与整个基因组计算的频率相比，转录因子在该数据集中明显过高（p = 1.2 × 10-7）。由具有保守uORF的全基因组重复产生的重复基因对（ohnologs）比其他基因的ohnologs更有可能保留在拟南芥（Arabidopsis thaliana）中（39%对14%的祖先基因，p = 5 × 10-3）。在动物中发现了两个uORF组，表明这些推定的调控元件的古老起源。uORF氨基酸序列的保守性、与同源mORF在长进化时间内的关联性、全基因组复制后的优先保留性以及与编码转录因子的mORF的优先关联性表明，本研究中鉴定的保守肽uORF是调控基因的翻译控制器的强有力的候选者。
Upstream open reading frames (uORFs) can mediate translational control over the largest, or major ORF (mORF) in response to starvation, polyamine concentrations, and sucrose concentrations. One plant uORF with conserved peptide sequences has been shown to exert this control in an amino acid sequence-dependent manner but generally it is not clear what kinds of genes are regulated, or how extensively this mechanism is invoked in a given genome. By comparing full-length cDNA sequences from Arabidopsis and rice we identified 26 distinct homology groups of conserved peptide uORFs, only three of which have been reported previously. Pairwise Ka/Ks analysis showed that purifying selection had acted on nearly all conserved peptide uORFs and their associated mORFs. Functions of predicted mORF proteins could be inferred for 16 homology groups and many of these proteins appear to have a regulatory function, including 6 transcription factors, 5 signal transduction factors, 3 developmental signal molecules, a homolog of translation initiation factor eIF5, and a RING finger protein. Transcription factors are clearly overrepresented in this data set when compared to the frequency calculated for the entire genome (p = 1.2 × 10-7). Duplicate gene pairs arising from a whole genome duplication (ohnologs) with a conserved uORF are much more likely to have been retained in Arabidopsis (Arabidopsis thaliana) than are ohnologs of other genes (39% vs 14% of ancestral genes, p = 5 × 10-3). Two uORF groups were found in animals, indicating an ancient origin of these putative regulatory elements. Conservation of uORF amino acid sequence, association with homologous mORFs over long evolutionary time periods, preferential retention after whole genome duplications, and preferential association with mORFs coding for transcription factors suggest that the conserved peptide uORFs identified in this study are strong candidates for translational controllers of regulatory genes.
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