Archetti Marco, Di Giulio Massimo
Department of Zoology, Oxford University, South Parks Road, OX1 3PS Oxford, UK.
J Theor Biol. 2007 Mar 7;245(1):169-74. doi: 10.1016/j.jtbi.2006.09.025. Epub 2006 Sep 24.
We have compared orthologous proteins from an aerobic organism, Cytophaga hutchinsonii, and from an obligate anaerobe, Bacteroides thetaiotaomicron. This comparison allows us to define the oxyphobic ranks of amino acids, i.e. a scale of the relative sensitivity to oxygen of the amino acid residues. The oxyphobic index (OI), which can be simply obtained from the amino acids' oxyphobic ranks, can be associated to any protein and therefore to the genetic code, if the number of synonymous codons attributed to the amino acids in the code is assumed to be the frequency with which the amino acids appeared in ancestral proteins. Sampling of the OI variable from the proteins of obligate anaerobes and aerobes has established that the OI value of the genetic code is not significantly different from the mean OI value of anaerobe proteins, while it is different from that of aerobe proteins. This observation would seem to suggest that the terminal phases of the evolution of genetic code organization took place in an anaerobic environment. This result is discussed in the framework of hypotheses suggested to explain the timing of the evolutionary appearance of the aerobic metabolism.
我们比较了来自需氧生物哈氏噬纤维菌（Cytophaga hutchinsonii）和专性厌氧菌多形拟杆菌（Bacteroides thetaiotaomicron）的直系同源蛋白。这种比较使我们能够确定氨基酸的疏氧等级，即氨基酸残基对氧的相对敏感程度的一种衡量标准。疏氧指数（OI）可以简单地从氨基酸的疏氧等级中获得，如果假设遗传密码中赋予氨基酸的同义密码子数量就是这些氨基酸在祖先蛋白中出现的频率，那么疏氧指数就可以与任何蛋白质相关联，进而与遗传密码相关联。对专性厌氧菌和好氧菌蛋白质的OI变量进行抽样分析后发现，遗传密码的OI值与厌氧菌蛋白质的平均OI值没有显著差异，而与需氧菌蛋白质的OI值不同。这一观察结果似乎表明，遗传密码组织进化的末期阶段是在厌氧环境中发生的。我们在为解释有氧代谢进化出现的时间而提出的假说框架内对这一结果进行了讨论。
