Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability
Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability
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DOI：
10.1186/1471-2164-5-45
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发表时间：
2004-07-16
期刊：
影响因子：
4.4
通讯作者：
Aravind, L
中科院分区：
文献类型：
--
作者：
Anantharaman, V;Aravind, L
背景：真核生物的出现的特征是几个古老的RNA结合域的扩展和多样化以及新的RNA结合域的明显从头创新。这些RNA结合结构域的识别可能会阐明RNA代谢的真核生物特异性系统的出现。分泌：使用敏感序列曲线搜索，基于同源性的折叠识别和序列结构叠加，我们确定SCD6P蛋白质家族中的SM域。除了拥有一些独特的保守特征之外，这个与SM相关的域家族具有连接RNA所需的常规SM域的某些特征。我们还表明，这些蛋白质包含第二个先前未表征的C末端结构域，称为FDF结构域（在该域中的保守序列基序之后）。 FDF结构域也可以在真菌DCP3P样和类似FLJ22128样蛋白的动物中发现，并在其中融合到YJEF-N域家族的C末端域。除FDF域外，FLJ22128样蛋白还在其极端N末端还包含SM域的另一个不同版本。我们表明，YJEF-N域代表了Rossmann Fold的新颖版本，该版本获得了一组催化残基和结构特征，这些残基和结构特征将它们与常规脱氢酶区分开来。结论：几行上下文信息表明SCD6P家族和DCP3P - 蛋白质是真核RNA代谢系统的保守成分。我们建议这里报道的新域，即SM结构域和FDF结构域的不同版本可能介导细胞质核糖核蛋白复合物中的特定RNA - 蛋白质和蛋白质蛋白相互作用。更具体地说，预计包含SCD6P家族的SM样结构域的蛋白质复合物可以调节编码与细胞周期进程和囊泡组装有关的mRNA编码蛋白的稳定性。 DCP3P和FLJ22128蛋白可能定位于细胞质加工体，并可能催化decapping虫途径中的特定处理步骤。 SM结构域的爆炸性多样化似乎在几种独特的真核核糖核蛋白复合物的出现中起着作用，包括涉及decapping和mRNA稳定性的核蛋白蛋白。
Background: The emergence of eukaryotes was characterized by the expansion and diversification of several ancient RNA-binding domains and the apparent de novo innovation of new RNA-binding domains. The identification of these RNA-binding domains may throw light on the emergence of eukaryote-specific systems of RNA metabolism.Results: Using sensitive sequence profile searches, homology-based fold recognition and sequence-structure superpositions, we identified novel, divergent versions of the Sm domain in the Scd6p family of proteins. This family of Sm-related domains shares certain features of conventional Sm domains, which are required for binding RNA, in addition to possessing some unique conserved features. We also show that these proteins contain a second previously uncharacterized C-terminal domain, termed the FDF domain (after a conserved sequence motif in this domain). The FDF domain is also found in the fungal Dcp3p-like and the animal FLJ22128-like proteins, where it fused to a C-terminal domain of the YjeF-N domain family. In addition to the FDF domains, the FLJ22128-like proteins contain yet another divergent version of the Sm domain at their extreme N-terminus. We show that the YjeF-N domains represent a novel version of the Rossmann fold that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases.Conclusions: Several lines of contextual information suggest that the Scd6p family and the Dcp3p-like proteins are conserved components of the eukaryotic RNA metabolism system. We propose that the novel domains reported here, namely the divergent versions of the Sm domain and the FDF domain may mediate specific RNA-protein and protein-protein interactions in cytoplasmic ribonucleoprotein complexes. More specifically, the protein complexes containing Sm-like domains of the Scd6p family are predicted to regulate the stability of mRNA encoding proteins involved in cell cycle progression and vesicular assembly. The Dcp3p and FLJ22128 proteins may localize to the cytoplasmic processing bodies and possibly catalyze a specific processing step in the decapping pathway. The explosive diversification of Sm domains appears to have played a role in the emergence of several uniquely eukaryotic ribonucleoprotein complexes, including those involved in decapping and mRNA stability.