Samanta Manoj P, Lai Stella M, Daniels Charles J, Gopalan Venkat
Systemix Institute, Redmond, WA 98053, USA.
Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
Biomolecules. 2016 Apr 20;6(2):22. doi: 10.3390/biom6020022.
RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5'-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.
核糖核酸酶P（RNase P）是一种基于核酶的核糖核蛋白（RNP）复合物，可催化tRNA 5'端成熟，在生命的所有领域中普遍存在，但其蛋白质成分（RNase P蛋白，RPP）的进化尚未得到很好的理解。古菌RPP可能为该复合物如何从古老的核酶演变为具有多种古菌和真核生物（同源）RPP的RNP提供线索，这些RPP与单一的细菌RPP无关。在这里，我们分析了来自600多个可用基因组的古菌RPP的序列和结构。所有五种RPP都存在于八个古菌门中，这表明这些RPP在古菌进化历史早期就已出现。古菌RPP的推定祖先基因组位点包括编码核糖体、外切体和蛋白酶体复合物的几个成员的基因，这可能表明RNase P与其他核心细胞机制的共同进化/协调调节。尽管RPP很古老，但与其他通用蛋白质相比，它们通常缺乏序列保守性。通过在每个RPP的高分辨率结构（单独或作为功能性二元复合物）的背景下分析每个位置的残基相对频率，我们提出了用于突变分析的残基，这可能有助于揭示RPP中的结构-功能关系。
