Pereira José A
ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto, Portugal; REQUIMTE/CEQUP - Centro de Química da Universidade do Porto, R. D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal.
Biosystems. 2014 Aug;122:38-54. doi: 10.1016/j.biosystems.2014.06.011. Epub 2014 Jun 24.
Theoretical models designed to test the metabolism-first hypothesis for prebiotic evolution have yield strong indications about the hypothesis validity but could sometimes use a more extensive identification between model objects and real objects towards a more meaningful interpretation of results. In an attempt to go in that direction, the string-based model SSE ("steady state evolution") was developed, where abstract molecules (strings) and catalytic interaction rules are based on some of the most important features of carbon compounds in biological chemistry. The system is open with a random inflow and outflow of strings but also with a permanent string food source. Although specific catalysis is a key aspect of the model, used to define reaction rules, the focus is on energetics rather than kinetics. Standard energy change tables were constructed and used with standard formation reactions to track energy flows through the interpretation of equilibrium constant values. Detection of metabolic networks on the reaction system was done with elementary flux mode (EFM) analysis. The combination of these model design and analysis options enabled obtaining metabolic and catalytic networks showing several central features of biological metabolism, some more clearly than in previous models: metabolic networks with stepwise synthesis, energy coupling, catalysts regulation, SN2 coupling, redox coupling, intermediate cycling, coupled inverse pathways (metabolic cycling), autocatalytic cycles and catalytic cascades. The results strongly suggest that the main biological metabolism features, including the genotype-phenotype interpretation, are caused by the principles of catalytic systems and are prior to modern genetic systems principles. It also gives further theoretical support to the thesis that the basic features of biologic metabolism are a consequence of the time evolution of a random catalyst search working on an open system with a permanent food source. The importance of the food source characteristics and evolutionary possibilities are discussed.
旨在检验益生元进化的代谢优先假说的理论模型已经给出了关于该假说有效性的有力指示，但有时可能需要在模型对象与实际对象之间进行更广泛的识别，以便对结果进行更有意义的解释。为了朝这个方向发展，开发了基于字符串的模型SSE（“稳态进化”），其中抽象分子（字符串）和催化相互作用规则基于生物化学中碳化合物的一些最重要特征。该系统是开放的，字符串有随机的流入和流出，还有一个永久性的字符串食物来源。虽然特定催化是模型的一个关键方面，用于定义反应规则，但重点是能量学而非动力学。构建了标准能量变化表，并与标准生成反应一起使用，通过平衡常数值得以跟踪能量流。利用基本通量模式（EFM）分析对反应系统中的代谢网络进行检测。这些模型设计和分析选项的结合使得能够获得显示生物代谢几个核心特征的代谢和催化网络，其中一些特征比以前的模型更清晰：具有逐步合成、能量耦合、催化剂调节、SN2耦合、氧化还原耦合、中间循环、耦合逆途径（代谢循环）、自催化循环和催化级联的代谢网络。结果强烈表明，包括基因型-表型解释在内的主要生物代谢特征是由催化系统的原理引起的，并且先于现代遗传系统原理。它还为生物代谢的基本特征是在具有永久性食物来源的开放系统上进行随机催化剂搜索的时间演化结果这一论点提供了进一步的理论支持。文中讨论了食物来源特征和进化可能性的重要性。
