Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.
Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.
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DOI：
10.1261/rna.051144.115
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发表时间：
2015-10
期刊：
影响因子：
--
通讯作者：
Gerbi SA
中科院分区：
文献类型：
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作者：
Doris SM;Smith DR;Beamesderfer JN;Raphael BJ;Nathanson JA;Gerbi SA
核糖体RNA （rRNA）序列的比较分析已经阐明了系统发育关系。然而，这种强大的方法尚未被充分利用来解决核糖体的功能。在这里，我们确定了进化保守序列的延伸，这与高功能重要性的区域相对应。为此，我们开发了一个结构比对数据库FLORA（全长有机rRNA比对），用于从每个系统发育域（真核生物、细菌和古细菌）鉴定23S-28S rRNA中高度保守的核苷酸元件（CNEs）。通用CNEs （Universal CNEs, uCNEs）在这三个结构域中的序列和结构位置都是保守的。那些已知对翻译至关重要的区域验证了我们的方法。重要的是，一些uCNEs位于功能未知的区域，从而识别出可能非常重要的新序列。与uCNEs相比，域特异性CNEs （dsCNEs）仅在一个系统发育结构域中保守。这是首次报道rRNA中具有结构域特异性的保守序列元件；它们在很大程度上是真核生物的现象。真核生物dsCNEs在核糖体结构中的位置提示它们可能在新生多肽通过核糖体通道转运和tRNA从核糖体出口中起作用。我们的发现为核糖体功能研究提供了见解和资源。
Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-length organismal rRNA alignment) to identify highly conserved nucleotide elements (CNEs) in 23S–28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.