Efimov V M, Efimov K V, Kovaleva V Yu
Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.
Institute of Animal Systematics and Ecology, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091 Russia.
Mol Biol (Mosk). 2025 Mar-Apr;59(2):299-308.
It is generally accepted that the existing set of proteinogenic amino acids encoded by the standard genetic code was formed step by step in the course of evolution. Most studies name Ala, Asp, Glu, Gly, Ile, Leu, Pro, Ser, Thr, and Val as early amino acids, presumably of extraterrestrial origin. However, other studies have chosen a consensus list of early amino acids in which Ile is replaced by Arg. We compared the differences between early and late amino acids for the lists with Ile and with Arg based on their physicochemical properties (AAindex database). The point-biserial correlation coefficient rpb, Student's t-test, and its reliability, the p-value, were calculated between the binary lists with Ile and Arg and each AA index. Since in total 2x553 p-values were obtained, the problem of multiple comparisons was solved using the Bonferroni correction and the Benjamini-Hochberg method. Next, we used the 2B-PLS method, which is applied to two different sets of variables related to the same objects, to find information common to both sets. The first set was the binary lists of Trifonov (Arg) and Wong (Ile), and the second set was 553 AA indexes. The maximum correlation with both the list with Ile and with Arg (1.0 and 0.8, respectively) was demonstrated by the binary AA index CHAM830108, which characterizes the ability of an amino acid to be a charge donor: late amino acids are capable of being donors, while early ones are not. Apparently, this is due to the differences in the conditions under which the standard set of amino acids evolved: prebiotic and biotic. The results of the 2B-PLS analysis also show that in the list of ten evolutionarily early amino acids, Ile appears preferable to Arg. The allocation of the last six amino acids (Cys, His, Met, Phe, Trp, and Tyr) obtained on the basis of the reduction of the HOMO-LUMO gap in a separate, third stage of the evolution of the set of standard amino acids is confirmed. A compact arrangement on the 2B-PLS plane of the physicochemical properties of three groups of amino acids, in which adenine, thymine, and cytosine are located in the second position of the codons, respectively, as well as the maximum dispersion of amino acids with guanine in the second position of the codons, is revealed.
人们普遍认为，由标准遗传密码编码的现有一组蛋白质原氨基酸是在进化过程中逐步形成的。大多数研究将丙氨酸（Ala）、天冬氨酸（Asp）、谷氨酸（Glu）、甘氨酸（Gly）、异亮氨酸（Ile）、亮氨酸（Leu）、脯氨酸（Pro）、丝氨酸（Ser）、苏氨酸（Thr）和缬氨酸（Val）列为早期氨基酸，推测它们起源于地球之外。然而，其他研究选择了一份早期氨基酸的共识列表，其中异亮氨酸被精氨酸（Arg）取代。我们基于早期氨基酸列表（含异亮氨酸）和（含精氨酸）的晚期氨基酸的物理化学性质（AAindex数据库）比较了它们之间的差异。计算了含异亮氨酸和精氨酸的二元列表与每个氨基酸指数之间的点二列相关系数rpb、学生t检验及其可靠性p值。由于总共获得了2×553个p值，因此使用Bonferroni校正和Benjamini-Hochberg方法解决了多重比较问题。接下来，我们使用2B-PLS方法，该方法应用于与同一对象相关的两组不同变量，以找到两组共有的信息。第一组是Trifonov（精氨酸）和Wong（异亮氨酸）的二元列表，第二组是553个氨基酸指数。二元氨基酸指数CHAM830108与含异亮氨酸的列表和含精氨酸的列表的相关性最高（分别为1.0和0.8），该指数表征氨基酸作为电荷供体的能力：晚期氨基酸能够作为供体，而早期氨基酸则不能。显然，这是由于标准氨基酸组进化所处的条件不同：益生元条件和生物条件。2B-PLS分析结果还表明，在十个进化早期氨基酸的列表中，异亮氨酸似乎比精氨酸更合适。基于标准氨基酸组进化的一个单独的第三阶段中最高占据分子轨道（HOMO）-最低未占分子轨道（LUMO）能隙的减小而获得的最后六个氨基酸（半胱氨酸（Cys）、组氨酸（His）、甲硫氨酸（Met）、苯丙氨酸（Phe）、色氨酸（Trp）和酪氨酸（Tyr））的分类得到了证实。揭示了三组氨基酸物理化学性质在2B-PLS平面上的紧凑排列，其中腺嘌呤、胸腺嘧啶和胞嘧啶分别位于密码子的第二位，以及密码子第二位含鸟嘌呤的氨基酸的最大分散情况。
