Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution.
Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution.
复制标题
DOI：
10.1186/s12862-018-1215-0
复制
发表时间：
2018-06-19
影响因子：
3.4
通讯作者：
Wolf A
中科院分区：
文献类型：
--
作者：
Bräuer KE;Brockers K;Moneer J;Feuchtinger A;Wollscheid-Lengeling E;Lengeling A;Wolf A
特定的mRNAs的翻译可以在不同的细胞、组织或病理条件下受到高度调控。核糖体的异质性可能源于核糖体蛋白的可变表达或翻译后修饰。核糖体加氧酶RIOX1(No66)和RIOX2(MINA53)通过组氨酸羟化修饰核糖体蛋白。在原核生物中也存在类似的机制。因此，核糖体羟化可能是一种保守的调节机制，与疾病和发育有关。然而，关于Riox1和Riox2基因及其编码蛋白在真核生物中的进化历史知之甚少。在这项研究中，我们分析了49种后生动物的Riox1和Riox2同源基因，并构建了这两个基因的系统发育树。我们的基因组和系统发育分析表明，节肢动物、环节动物、线虫和软体动物都缺乏Riox2基因，尽管在早期的线虫门中，Riox1和Riox2基因都存在并表达。Riox1在包括人类在内的几个物种中是一个无内含子的单外显子基因。与Riox2相反，Riox1在整个动物界普遍存在，这表明Riox1是从Riox2进化而来的更古老的基因。这两种蛋白质都保持了独特的蛋白质结构，JmjC结构域、二聚化结构域和翼状螺旋结构域中的活性位点保持不变。此外，Riox1蛋白还具有一个独特的N-末端延伸域。在Hela细胞和普通九头蛇中的免疫荧光分析发现，在人类RIOX1的扩展N-末端结构域中有核仁定位信号，而九头蛇Riox2的亚核定位发生了变化。保守的活性位点残基和统一的蛋白质结构域结构表明，在整个进化过程中，Riox同源基因具有一致的酶活性。然而，基因组结构的差异，如单一外显子基因和亚核定位的变化，如九头蛇所描述的，指向可能与分类群或物种特定需求相关的适应机制。Riox1/Riox2基因结构在整个进化过程中的多样性表明，蛋白质异构体的表达和/或蛋白质的亚细胞定位的功能需求可能是通过适应生活方式而进化的。本文的在线版本(10.1186/s12862-0181215-0)包含向授权用户提供的补充材料。
Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa. In this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2. Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle. The online version of this article (10.1186/s12862-018-1215-0) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
5.6
作者：
Mantri, Monica;Krojer, Tobias;Schofield, Christopher J.
通讯作者：
Schofield, Christopher J.
影响因子：
64.8
作者：
CRICK, F
通讯作者：
CRICK, F
影响因子：
4
作者：
Leclere, Lucas;Copley, Richard R.;Houliston, Evelyn
通讯作者：
Houliston, Evelyn
影响因子：
7
作者：
Carelli FN;Hayakawa T;Go Y;Imai H;Warnefors M;Kaessmann H
通讯作者：
Kaessmann H
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM