Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
Department of Biology II, Ludwig Maximillians University, Munich, Großhaderner Strasse 2, 82152 Planegg-, Martinsried, Germany.
BMC Evol Biol. 2018 Jun 19;18(1):96. doi: 10.1186/s12862-018-1215-0.
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.
在不同的细胞、组织或病理条件下，特定 mRNA 的翻译可以受到高度调控。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，对于 Riox1 和 Riox2 基因及其编码蛋白在真核生物分类群中的进化历史知之甚少。
在这项研究中，我们分析了来自 49 种后生动物物种的 Riox1 和 Riox2 直系同源基因，并为这两个基因构建了系统基因组学树。我们的基因组和系统发育分析表明，节肢动物、环节动物、线虫动物和软体动物缺乏 Riox2 基因，尽管在早期的刺胞动物门中，两个基因 Riox1 和 Riox2 都存在并表达。在包括人类在内的几个物种中，Riox1 是一个无内含子的单外显子基因。与 Riox2 不同，Riox1 在整个动物王国中普遍存在，这表明 Riox1 是进化上更古老的基因，而 Riox2 是从它进化而来的。这两种蛋白质都保持了独特的蛋白质结构，在 JmjC 结构域、二聚化结构域和翼状螺旋结构域内保持了活性位点的保守。此外，Riox1 蛋白还具有独特的 N 端延伸结构域。在 Hela 细胞和 Hydra vulgaris 中的免疫荧光分析鉴定出人 RIOX1 的延伸 N 端结构域内存在核仁定位信号，以及 Hydra Riox2 的核内亚定位改变。
保守的活性位点残基和一致的蛋白质结构域架构表明，在整个进化过程中，Riox 直系同源物具有一致的酶活性。然而，像 Hydra 那样，基因组结构的差异，如单外显子基因和亚核定位的改变，表明可能存在与分类群或物种特异性需求相关的适应机制。Riox1/Riox2 基因结构在进化过程中的多样化表明，在蛋白质同工型的表达或蛋白质的亚细胞定位方面的功能需求可能是通过适应生活方式而进化的。
