Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis.
Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis.
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银杏叶绿体蛋白编码基因丰富的RNA编辑位点及进化模式分析
DOI：
10.1186/s12870-016-0944-8
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发表时间：
2016-12-01
影响因子：
5.3
通讯作者：
Yu J
中科院分区：
文献类型：
--
作者：
He P;Huang S;Xiao G;Zhang Y;Yu J
RNA编辑是一个转录后修饰过程，可改变RNA序列，使其偏离基因组DNA序列。 RNA编辑主要发生在叶绿体和线粒体基因组中，而编辑位点的数量在陆生植物中有所不同。 RNA编辑系统的发展以及如何发展仍然是一个谜。银杏是最古老的种子植物之一，具有重要的进化位置。确定古代植物中RNA编辑的模式和分布提供了对RNA编辑的进化趋势的见解，并帮助我们进一步了解了它们的生物学意义。
在本文中，我们研究了G. biloba的叶绿体基因组中的82个蛋白质编码基因，并确定了255个编辑位点，这是裸子植物中报告的RNA编辑事件的最多数量。所有编辑位点均为C-TO-U转换，主要发生在第二个密码子位置，偏向于U_A环境，并导致疏水性氨基酸的增加。 RNA编辑可以改变82种蛋白质的二级结构，并在硅中确定的五种蛋白质中创建或消除跨膜区域。最后，使用非同义基因义替代率选择模式估算了不同基因组中RNA编辑的进化趋势。
G. biloba叶绿体基因组具有迄今为止在种子植物中报告的RNA编辑事件数量最多。大多数RNA编辑位点可以恢复氨基酸的保护，增加疏水性，甚至影响蛋白质结构。类似的纯化选择构成了必需基因的编辑位点的主要进化力，例如PSA，某些PSB和PET组，并且在非必需基因的编辑位点发生了阳性选择，例如大多数NDH和几个PSB基因。
本文的在线版本（doi：10.1186/s12870-016-0944-8）包含补充材料，可供授权用户使用。
BackgroundRNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance.ResultsIn this paper, we investigated 82 protein-coding genes in the chloroplast genome of G. biloba and identified 255 editing sites, which is the highest number of RNA editing events reported in a gymnosperm. All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. RNA editing could change the secondary structures of 82 proteins, and create or eliminate a transmembrane region in five proteins as determined in silico. Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode.ConclusionsThe G. biloba chloroplast genome possesses the highest number of RNA editing events reported so far in a seed plant. Most of the RNA editing sites can restore amino acid conservation, increase hydrophobicity, and even influence protein structures. Similar purifying selections constitute the dominant evolutionary force at the editing sites of essential genes, such as the psa, some psb and pet groups, and a positive selection occurred in the editing sites of nonessential genes, such as most ndh and a few psb genes.
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