Analysis of ribosomal protein gene structures: implications for intron evolution.
Analysis of ribosomal protein gene structures: implications for intron evolution.
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DOI：
10.1371/journal.pgen.0020025
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发表时间：
2006-03
期刊：
影响因子：
4.5
通讯作者：
Kenmochi, Naoya
中科院分区：
文献类型：
--
作者：
Yoshihama, Maki;Nakao, Akihiro;Nguyen, Hung D.;Kenmochi, Naoya
真核基因组中存在许多剪接体内含子。尽管有很多研究，但剪接体内含子的进化仍然知之甚少。在本文中，我们试图通过比较细胞质核糖体蛋白(CRPS)和线粒体核糖体蛋白(MRPs)的基因结构，从一个新的角度深入了解内含子的进化，这两种蛋白分别被认为是来自古生物和细菌。我们分析了25对同源的CRP和MRP基因，它们总共有527个内含子位置。我们发现，CRP和MRP基因共有的所有12个内含子位置都是由平行内含子获得的，没有一个可以被认为是“保守的”，即同一祖先的后代。在这些共享位置上的高频率的原剪接位点进一步支持了这一点；原剪接位点被认为是内含子插入的位点。虽然我们不能明确地驳斥剪接体内含子已经存在于最后一个通用共同祖先中的说法，但我们的结果更支持内含子获得较晚的观点。至少，我们的结果表明，在内生共生时，MRP基因是无内含子的。CRP和MRP基因之间的平行内含子增量占总内含子位置的2.3%，这将为未来内含子进化的推断提供可靠的估计。真核生物中的基因通常被称为内含子的额外DNA序列所干预，这些内含子在基因转录成RNA后必须被移除。为什么真核基因中存在内含子？高等真核生物内含子密度增加的原因是什么？有许多关于内含子的未知之处。这项研究试图通过比较两种核糖体蛋白的基因结构来阐明内含子产生的进化过程；一种在细胞质中，另一种在细胞的线粒体中。由于细胞质和线粒体分别起源于古细菌和细菌，细胞质核糖体蛋白(CRPS)和线粒体核糖体蛋白(MRPs)被认为随着古生菌和细菌的分化而同时分化。因此，对CRP和MRP基因的比较分析可能揭示古菌和细菌的最后一个共同祖先是否已经存在内含子(内含子-早期)，或者它们是否出现得较晚(内含子-晚期)。这些结果至少表明，MRP基因的所有内含子都是在真核生物进化过程中获得的，从而为内含子晚期理论提供了更多的支持。
Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be “conserved,” i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution. Genes in eukaryotes are usually intervened by extra bits of DNA sequence, called introns, that have to be removed after the genes are transcribed into RNA. Why do introns exist in eukaryotic genes? What is the reason for the increased intron density in higher eukaryotes? There is much that is not known about introns. This research tries to clarify the evolutionary process by which introns arose by comparing the gene structures of two types of ribosomal proteins; one in cytoplasm and the other in mitochondria of the cell. Since cytoplasm and mitochondria are of archaeal and bacterial origin, respectively, cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) are believed to diverge at the same time with the divergence of archaea and bacteria. Thus, a comparative analysis of CRP and MRP genes may reveal whether introns already existed at the last common ancestor of archaea and bacteria (introns-early) or whether they emerged late (introns-late). The results make it clear, at least, that all of the introns in MRP genes were gained during the course of eukaryotic evolution and therefore lend more support to the introns-late theory.
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影响因子：
4.3
作者：
Nguyen, Hung D.;Yoshihama, Maki;Kenmochi, Naoya
通讯作者：
Kenmochi, Naoya
影响因子：
56.9
作者：
DARNELL, JE
通讯作者：
DARNELL, JE
影响因子：
4.4
作者：
Kenmochi, N;Suzuki, T;Tanaka, T
通讯作者：
Tanaka, T
DOI：
10.1073/pnas.0400975101
发表时间：
2004-06-29
影响因子：
11.1
作者：
Boussau, B;Karlberg, EO;Andersson, SGE
通讯作者：
Andersson, SGE
影响因子：
3.5
作者：
O'Brien, TW
通讯作者：
O'Brien, TW