Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?
Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?
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DOI：
10.1186/1745-6150-3-43
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发表时间：
2008-10-21
期刊：
影响因子：
5.5
通讯作者：
Qiu YL
中科院分区：
文献类型：
--
作者：
Jobson RW;Qiu YL
在陆生植物的细胞器基因组中经常观察到C↔U型的RNA编辑。尽管人们做了各种各样的尝试来解释为什么这样一个看似低效的遗传机制会进化，但在我们看来，没有一个令人满意的解释。在这项研究中，我们研究了角蒿（Anthoceros formosae）和蕨类植物Adiantum capillus-veneris的叶绿体基因组编辑模式，以及被子植物拟南芥（Arabidopsis thaliana）、Beta vulgaris和Oryza sativa的线粒体基因组编辑模式，以了解RNA编辑是如何起源的问题。我们发现，1)大多数编辑位点分布在第2和第1密码子位置；2)编辑影响的密码子导致疏水性较大，分子大小变化的频率远高于影响较小的密码子；3)编辑均匀地增加了蛋白质的疏水性；4)编辑更频繁地发生在具有丰富t基因的序列中。与编码可溶性蛋白的基因相比，编码具有许多疏水氨基酸的膜结合蛋白的基因更丰富，并且5)编辑最常发生在被发现具有强选择性约束的基因中。这些分析表明，编辑主要影响功能重要和进化保守的密码子位置、密码子和编码膜结合蛋白的基因。特别是，植物细胞器基因组中RNA编辑的丰度可能与这两个基因组中编码膜结合蛋白的基因比例过高有关，这些蛋白富含疏水氨基酸并有选择性地受到限制。这些数据支持了一个假设，即在超过4亿年的时间里，由蛋白质功能限制施加的自然选择促成了某些编辑位点的选择性固定和植物细胞器中编辑活性的维持。编码RNA编辑活性的基因的保留可能是由这些植物的两个细胞器基因组中形成核苷酸组成平衡的力量驱动的。然而，大部分RNA编辑位点的谱系特异性发生的原因仍有待确定。本文由迈克尔·格雷（劳伦斯·赫斯特提名）、克尔斯滕·克劳斯（马丁·勒彻提名）和杰弗瑞·莫厄尔（大卫·阿德尔提名）审阅。
The C↔U substitution types of RNA editing have been observed frequently in organellar genomes of land plants. Although various attempts have been made to explain why such a seemingly inefficient genetic mechanism would have evolved, no satisfactory explanation exists in our view. In this study, we examined editing patterns in chloroplast genomes of the hornwort Anthoceros formosae and the fern Adiantum capillus-veneris and in mitochondrial genomes of the angiosperms Arabidopsis thaliana, Beta vulgaris and Oryza sativa, to gain an understanding of the question of how RNA editing originated. We found that 1) most editing sites were distributed at the 2nd and 1st codon positions, 2) editing affected codons that resulted in larger hydrophobicity and molecular size changes much more frequently than those with little change involved, 3) editing uniformly increased protein hydrophobicity, 4) editing occurred more frequently in ancestrally T-rich sequences, which were more abundant in genes encoding membrane-bound proteins with many hydrophobic amino acids than in genes encoding soluble proteins, and 5) editing occurred most often in genes found to be under strong selective constraint. These analyses show that editing mostly affects functionally important and evolutionarily conserved codon positions, codons and genes encoding membrane-bound proteins. In particular, abundance of RNA editing in plant organellar genomes may be associated with disproportionately large percentages of genes in these two genomes that encode membrane-bound proteins, which are rich in hydrophobic amino acids and selectively constrained. These data support a hypothesis that natural selection imposed by protein functional constraints has contributed to selective fixation of certain editing sites and maintenance of the editing activity in plant organelles over a period of more than four hundred millions years. The retention of genes encoding RNA editing activity may be driven by forces that shape nucleotide composition equilibrium in two organellar genomes of these plants. Nevertheless, the causes of lineage-specific occurrence of a large portion of RNA editing sites remain to be determined. This article was reviewed by Michael Gray (nominated by Laurence Hurst), Kirsten Krause (nominated by Martin Lercher), and Jeffery Mower (nominated by David Ardell).
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