Novel predicted RNA-binding domains associated with the translation machinery
Novel predicted RNA-binding domains associated with the translation machinery
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DOI：
10.1007/pl00006472
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发表时间：
1999-03-01
影响因子：
3.9
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Aravind, L;Koonin, EV
两个以前未检测到的结构域被确定在各种RNA结合蛋白，特别是RNA修饰酶，使用序列分析方法。在核糖体蛋白S4中检测到由60-65个氨基酸残基组成的小结构域、两个假尿苷合成酶家族、一个新的预测RNA甲基化酶家族、含有假尿苷合成酶和脱氨酶结构域的酵母蛋白、细菌酪氨酰-tRNA合成酶以及许多可能参与翻译调节的未表征的小蛋白。在古细菌和真核生物的假尿苷酶、古细菌的古腺苷酶、古细菌和细菌的rRNA甲基化酶中发现了另一个新的结构域，命名为普阿结构域。此外，在一个真核蛋白家族中检测到普阿结构域，该蛋白家族还含有与翻译起始因子eIF 1/SUI 1同源的结构域;这些蛋白质可能包含一种新型的翻译因子。出乎意料的是，普阿结构域也在细菌和酵母谷氨酸激酶中检测到;这与这些酶在调节其他基因表达中的已证实作用是一致的。我们认为S4结构域和普阿结构域结合具有复杂折叠结构的RNA分子，从而增加了与DNA和RNA修饰酶相关的核酸结合结构域的数量。包含S4、普阿和SUI 1结构域的翻译机制组件的进化必须包括几个横向基因转移和基因丢失以及谱系特异性结构域融合的事件。
Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes, using methods for sequence profile analysis. A small domain consisting of 60-65 amino acid residues was detected in the ribosomal protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. Another novel domain, designated PUA domain, after PseudoUridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. We propose that the S4 domain and the PUA domain bind RNA molecules with complex folded structures, adding to the growing collection of nucleic acid-binding domains associated with DNA and RNA modification enzymes. The evolution of the translation machinery components containing the S4, PUA, and SUI1 domains must have included several events of lateral gene transfer and gene loss as well as lineage-specific domain fusions.