Lu Yi, Freeland Stephen J
Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 25250, USA.
J Theor Biol. 2008 Jan 21;250(2):349-61. doi: 10.1016/j.jtbi.2007.10.007. Epub 2007 Oct 12.
To date, explanations for the origin and emergence of the alphabet of amino acids encoded by the standard genetic code have been largely qualitative and speculative. Here, with the help of computational chemistry, we present the first quantitative exploration of nature's "choices" set against various models for plausible alternatives. Specifically, we consider the chemical space defined by three fundamental biophysical properties (size, charge, and hydrophobicity) to ask whether the amino acids that entered the genetic code exhibit a higher diversity than random samples of similar size drawn from several different definitions of amino acid possibility space. We found that in terms of the properties studied, the full, standard set of 20 biologically encoded amino acids is indeed significantly more diverse than an equivalently sized group drawn at random from the set of plausible, prebiotic alternatives (using the Murchison meteorite as a model for pre-biotic plausibility). However, when the set of possible amino acids is enlarged to include those that are produced by standard biosynthetic pathways (reflecting the widespread idea that many members of the standard alphabet were recruited in this way), then the genetically encoded amino acids can no longer be distinguished as more diverse than a random sample. Finally, if we turn to consider the overlap between biologically encoded amino acids and those that are prebiotically plausible, then we find that the biologically encoded subset are no more diverse as a group than would be expected from a random sample, unless the definition of "random sample" is adjusted to reflect possible prebiotic abundance (again, using the contents of the Murchison meteorite as our estimator). This final result is contingent on the accuracy of our computational estimates for amino acid properties, and prebiotic abundances, and an exploration of the likely effect of errors in our estimation reveals that our results should be treated with caution. We thus present this work as a first step in quantifying and thus testing various origin-of-life hypotheses regarding the origin and evolution of life's amino acid alphabet, and advocate the progress that would add valuable information in the future.
迄今为止，对于由标准遗传密码编码的氨基酸字母表的起源和出现的解释，大多是定性的和推测性的。在此，借助计算化学，我们首次对针对各种合理替代模型的自然“选择”进行了定量探索。具体而言，我们考虑由三种基本生物物理性质（大小、电荷和疏水性）定义的化学空间，以探讨进入遗传密码的氨基酸是否比从氨基酸可能性空间的几种不同定义中抽取的相同大小的随机样本具有更高的多样性。我们发现，就所研究的性质而言，完整的20种生物编码氨基酸的标准集合确实比从合理的前体生物替代物集合中随机抽取的同等大小的组具有显著更高的多样性（以默奇森陨石作为前体生物合理性的模型）。然而，当可能的氨基酸集合扩大到包括那些由标准生物合成途径产生的氨基酸时（这反映了一种普遍观点，即标准字母表中的许多成员是以这种方式被招募的），那么遗传编码的氨基酸就不再能被区分出比随机样本具有更高的多样性。最后，如果我们转而考虑生物编码氨基酸与那些前体生物合理的氨基酸之间的重叠，那么我们发现，作为一个组，生物编码的子集并不比随机样本所预期的更具多样性，除非“随机样本”的定义被调整以反映可能的前体生物丰度（同样，以默奇森陨石的成分作为我们的估计器）。这一最终结果取决于我们对氨基酸性质和前体生物丰度的计算估计的准确性，对我们估计中误差可能产生的影响的探索表明，我们的结果应谨慎对待。因此，我们将这项工作作为量化并进而检验关于生命氨基酸字母表起源和进化的各种生命起源假说的第一步，并倡导未来将添加有价值信息的进展。
