College of Life Sciences, Wuhan University, Wuhan 430072, P,R, China.
Biol Direct. 2013 Aug 23;8:21. doi: 10.1186/1745-6150-8-21.
It is now popularly accepted that an "RNA world" existed in early evolution. During division of RNA-based protocells, random distribution of individual genes (simultaneously as ribozymes) between offspring might have resulted in gene loss, especially when the number of gene types increased. Therefore, the emergence of a chromosome carrying linked genes was critical for the prosperity of the RNA world. However, there were quite a few immediate difficulties for this event to occur. For example, a chromosome would be much longer than individual genes, and thus more likely to degrade and less likely to replicate completely; the copying of the chromosome might start at middle sites and be only partial; and, without a complex transcription mechanism, the synthesis of distinct ribozymes would become problematic.
Inspired by features of viroids, which have been suggested as "living fossils" of the RNA world, we supposed that these difficulties could have been overcome if the chromosome adopted a circular form and small, self-cleaving ribozymes (e.g. the hammer head ribozymes) resided at the sites between genes. Computer simulation using a Monte-Carlo method was conducted to investigate this hypothesis. The simulation shows that an RNA chromosome can spread (increase in quantity and be sustained) in the system if it is a circular one and its linear "transcripts" are readily broken at the sites between genes; the chromosome works as genetic material and ribozymes "coded" by it serve as functional molecules; and both circularity and self-cleavage are important for the spread of the chromosome.
In the RNA world, circularity and self-cleavage may have been adopted as a strategy to overcome the immediate difficulties for the emergence of a chromosome (with linked genes). The strategy suggested here is very simple and likely to have been used in this early stage of evolution. By demonstrating the possibility of the emergence of an RNA chromosome, this study opens on the prospect of a prosperous RNA world, populated by RNA-based protocells with a number of genes, showing complicated functions.
现在人们普遍接受，在早期进化中存在一个“RNA 世界”。在基于 RNA 的原细胞分裂过程中，个体基因（同时作为核酶）在后代之间的随机分配可能导致基因丢失，尤其是当基因类型数量增加时。因此，出现携带连锁基因的染色体对于 RNA 世界的繁荣至关重要。然而，这一事件的发生存在许多直接的困难。例如，染色体比单个基因长得多，因此更容易降解，也不太可能完全复制；染色体的复制可能从中间位点开始，并且是部分的；而且，如果没有复杂的转录机制，不同核酶的合成就会成为问题。
受类病毒的特征启发，类病毒被认为是 RNA 世界的“活化石”，我们假设如果染色体采用圆形形式，并且小的、自我切割的核酶（如锤头核酶）位于基因之间的位置，这些困难就可以克服。使用蒙特卡罗方法进行计算机模拟来研究这一假设。模拟表明，如果 RNA 染色体是圆形的，并且其线性“转录物”很容易在基因之间的位点断裂，那么它可以在系统中传播（数量增加并得以维持）；染色体作为遗传物质，其编码的核酶作为功能分子；圆形和自我切割对于染色体的传播都很重要。
在 RNA 世界中，圆形和自我切割可能被采用为一种策略，以克服出现带有连锁基因的染色体的直接困难。这里提出的策略非常简单，很可能在进化的早期阶段就被使用了。通过证明 RNA 染色体出现的可能性，本研究为一个繁荣的 RNA 世界开辟了前景，这个 RNA 世界由具有多个基因的基于 RNA 的原细胞组成，表现出复杂的功能。
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