Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA.
Earth Observation Center (EOC), German Aerospace Center (DLR), Oberpfaffenhofen-Wessling, Germany.
J Mol Evol. 2022 Aug;90(3-4):307-323. doi: 10.1007/s00239-022-10061-5. Epub 2022 Jun 6.
Recent findings, in vitro and in silico, are strengthening the idea of a simpler, earlier stage of genetically encoded proteins which used amino acids produced by prebiotic chemistry. These findings motivate a re-examination of prior work which has identified unusual properties of the set of twenty amino acids found within the full genetic code, while leaving it unclear whether similar patterns also characterize the subset of prebiotically plausible amino acids. We have suggested previously that this ambiguity may result from the low number of amino acids recognized by the definition of prebiotic plausibility used for the analysis. Here, we test this hypothesis using significantly updated data for organic material detected within meteorites, which contain several coded and non-coded amino acids absent from prior studies. In addition to confirming the well-established idea that "late" arriving amino acids expanded the chemistry space encoded by genetic material, we find that a prebiotically plausible subset of coded amino acids generally emulates the patterns found in the full set of 20, namely an exceptionally broad and even distribution of volumes and an exceptionally even distribution of hydrophobicities (quantified as logP) over a narrow range. However, the strength of this pattern varies depending on both the size and composition the library used to create a background (null model) for a random alphabet, and the precise definition of exactly which amino acids were present in a simpler, earlier code. Findings support the idea that a small sample size of amino acids caused previous ambiguous results, and further improvements in meteorite analysis, and/or prebiotic simulations will further clarify the nature and extent of unusual properties. We discuss the case of sulfur-containing amino acids as a specific and clear example and conclude by reviewing the potential impact of better understanding the chemical "logic" of a smaller forerunner to the standard amino acid alphabet.
最近的研究结果，无论是体外的还是计算机模拟的，都增强了这样一种观点，即遗传编码蛋白存在一个更简单、更早的阶段，该阶段使用的是前生物化学产生的氨基酸。这些发现促使人们重新审视之前的工作，这些工作已经确定了在完整遗传密码中发现的 20 种氨基酸集合的不寻常特性，而不清楚类似的模式是否也具有前生物 plausibility 氨基酸的子集。我们之前曾提出，这种模糊性可能是由于用于分析的前生物 plausibility 定义所识别的氨基酸数量较少所致。在这里，我们使用陨石中检测到的有机物质的更新数据来测试这一假设，这些陨石中包含了一些前研究中没有的编码和非编码氨基酸。除了证实“晚期”到达的氨基酸扩展了遗传物质编码的化学空间这一既定观点外，我们还发现，前生物 plausibility 编码氨基酸子集通常模拟了在完整的 20 种氨基酸集中发现的模式，即体积非常广泛且均匀分布，疏水性（用 logP 量化）也非常均匀，分布范围狭窄。然而，这种模式的强度取决于用于为随机字母创建背景（null 模型）的库的大小和组成，以及在更简单、更早的代码中存在的确切氨基酸的确切定义。研究结果支持这样一种观点，即氨基酸的样本量较小导致了之前结果的模糊性，进一步改进陨石分析和/或前生物模拟将进一步阐明不寻常特性的性质和程度。我们讨论了含硫氨基酸的情况，作为一个具体而明确的例子，并通过回顾更好地理解标准氨基酸字母表的前身的化学“逻辑”的潜在影响来结束讨论。
