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Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth.
Journal of Theoretical Biology ( IF 1.9 ) Pub Date : 2020-08-13 , DOI: 10.1016/j.jtbi.2020.110446
Suvam Roy 1 , Niraja V Bapat 2 , Julien Derr 3 , Sudha Rajamani 2 , Supratim Sengupta 1
Affiliation  

The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.



中文翻译:

益生元地球上富含矿物质的泥浆池中出现核酶和类 tRNA 结构。

RNA 世界假说虽然是关于地球上生命起源的可行假说,但迄今为止未能为通过非生物过程从游离核苷酸合成 RNA 酶提供令人信服的解释。为了解决这个长期存在的问题,我们使用实验确定的聚合反应速率为 RNA 世界的开始开发了一个现实的模型。我们从对仅需要存在短寡聚体或仅需要游离核苷酸的初始状态的最小假设开始,并通过将一天分为干、半湿和湿阶段来考虑环境循环的影响,这些阶段由反应的性质来区分他们支持。最大长度有时超过 100 个核苷酸的长聚合物由于非酶促、非模板聚合物延伸和模板导向引物延伸过程。前者有助于增加 RNA 链的长度,而后者有助于产生链的互补拷贝。链也以结构依赖的方式进行水解,有利于断开连接未配对核苷酸的键。我们确定了核酶和 tRNA 样结构以及双链 RNA 分子出现所需的最有利条件,根据其二级结构对所有 RNA 链进行分类,并确定它们在种群中的丰度。我们的研究结果表明,在合适的环境条件下,非酶促过程足以导致各种具有复杂二级结构和潜在催化功能的核酶样分子的出现。

更新日期:2020-08-20
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