Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
Interdisciplinary Computing and Complex Bio-Systems research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
BMC Evol Biol. 2014 Dec 30;14:265. doi: 10.1186/s12862-014-0265-1.
The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics.
We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition.
Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.
准种模型是指具有错误自我复制能力的信息载体。准种是由主序列突变产生的生物聚合物序列变体的稳态群体。准种误差阈值是指低于该阈值，种群结构就会崩溃的最小复制精度。该模型的理论和实验通常涉及生物聚合物，例如 RNA 分子或病毒基因组，而其前生物背景通常与 RNA 世界情景相关联。在这里，我们研究了这样一种可能性，即与编码序列信息的生物聚合物内在不同的编码组成信息的实体可能表现出准种动力学。
我们采用了一种基于化学的模型，即分级自催化复制域 (GARD)，该模型模拟了组成分子组装内的网络动态。在 GARD 中，一个 compotype 代表了一组类似的组装，它们在组成空间中构成了一个准静态状态。发现 compotype 的质心类似于序列准种的主序列。使用单循环 GARD 动力学，我们测量了从一个质心欧几里得距离到另一个距离的准种转移矩阵 (Q) 的概率。同样，也获得了准种的增长率向量 (A)。这使得可以计算出质心距离的稳态分布，这是从准种方程推导出来的。平行地，通过 GARD 方程动力学获得了一个稳态分布。令人欣慰的是，这两种方法得到的分布之间观察到了显著的相关性。这种相关性仅见于距离 compotype 质心的距离，而不是随机选择的组成。当比较准种向稳态的时间相关动力学时，也发现了类似的对应关系。此外，通过修改 GARD 动力学中基本组装连接率来改变误差率，发现会显示出类似于标准准种模型的误差灾难。进一步增加组成突变会导致类似于主成分的组成完全消失。
我们的结果表明，由 GARD 形式主义模拟的组成组装表现出准种动力学的重要属性。这将准种模型的适用性扩展到基于序列的实体之外，并可能增强 GARD 作为前生物进化模型的有效性。
