The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover.
The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover.
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DNA 在 RNA 世界中的出现：基因接管的计算机模拟研究
DOI：
10.1186/s12862-015-0548-1
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发表时间：
2015-12-07
影响因子：
3.4
通讯作者：
Feng Y
中科院分区：
文献类型：
--
作者：
Ma W;Yu C;Zhang W;Wu S;Feng Y
现在人们普遍认为，在生命的早期进化中存在着一个“RNA世界”。这个想法有一个直接的结果，那就是后来应该会有遗传物质——RNA被DNA接管。然而，由于遗传物质携带着遗传信息，即所有生命活动的“源代码”，因此对这种“革命性”转变的合理性提出质疑实际上是合理的。由于我们无法在现实中建立相关的“原始生命系统”模型，因此尚不可能通过实验来探索“遗传接管”的合理性和机制。本文采用蒙特卡罗方法对该问题进行了计算机模拟研究。这表明，在纯RNA系统中，具有中等活性的核苷酸还原酶核酶的出现可能触发RNA- dna遗传接管。这种转变在规模上是不稳定的和有限的（即不能在群体中传播），但如果某些参数被改变而不利于RNA（即有利于DNA），则可以得到加强和全球化。在随后的进化中，一个具有更大基因组的高级系统被建模，该系统使用DNA作为遗传物质，RNA作为功能物质，如果核苷酸还原酶核酶被“关闭”（因此，DNA不能合成），系统将无法维持。此外，如果DNA的稳定性、模板适用性或复制保真度（三者中的任何一个）被降低到RNA的水平，那么先进的系统就无法维持。基因接管应该是合理的。在RNA世界中，这种接管可能是由一些有利于脱氧核苷酸形成的核酶的出现引发的。这种转变最初可能是“微弱的”，但可能会被对RNA不利的环境变化（如温度或pH值上升）所加强，并最终随着基因组的扩大而变得不可逆转。DNA的几个优点（与RNA相比）——抗水解的稳定性更高，作为模板的适用性更强，复制的保真度更高，每一个优点都应该以自己的方式对进化中的遗传接管具有重要意义。这项研究加深了我们对现实世界中信息与物质关系的理解。本文的在线版本（doi:10.1186/s12862-015-0548-1）包含补充材料，可供授权用户使用。
It is now popularly accepted that there was an “RNA world” in early evolution of life. This idea has a direct consequence that later on there should have been a takeover of genetic material – RNA by DNA. However, since genetic material carries genetic information, the “source code” of all living activities, it is actually reasonable to question the plausibility of such a “revolutionary” transition. Due to our inability to model relevant “primitive living systems” in reality, it is as yet impossible to explore the plausibility and mechanisms of the “genetic takeover” by experiments. Here we investigated this issue by computer simulation using a Monte-Carlo method. It shows that an RNA-by-DNA genetic takeover may be triggered by the emergence of a nucleotide reductase ribozyme with a moderate activity in a pure RNA system. The transition is unstable and limited in scale (i.e., cannot spread in the population), but can get strengthened and globalized if certain parameters are changed against RNA (i.e., in favor of DNA). In relation to the subsequent evolution, an advanced system with a larger genome, which uses DNA as genetic material and RNA as functional material, is modeled – the system cannot sustain if the nucleotide reductase ribozyme is “turned off” (thus, DNA cannot be synthesized). Moreover, the advanced system cannot sustain if only DNA’s stability, template suitability or replication fidelity (any of the three) is turned down to the level of RNA’s. Genetic takeover should be plausible. In the RNA world, such a takeover may have been triggered by the emergence of some ribozyme favoring the formation of deoxynucleotides. The transition may initially have been “weak”, but could have been reinforced by environmental changes unfavorable to RNA (such as temperature or pH rise), and would have ultimately become irreversible accompanying the genome’s enlargement. Several virtues of DNA (versus RNA) – higher stability against hydrolysis, greater suitability as template and higher fidelity in replication, should have, each in its own way, all been significant for the genetic takeover in evolution. This study enhances our understandings of the relationship between information and material in the living world. The online version of this article (doi:10.1186/s12862-015-0548-1) contains supplementary material, which is available to authorized users.