Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli
Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli
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DOI：
10.1073/pnas.2014567117
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发表时间：
2020-11-17
影响因子：
11.1
通讯作者：
Inouye, Keiko
中科院分区：
文献类型：
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作者：
Inouye, Masayori;Takino, Risa;Inouye, Keiko
在20种氨基酸中，亮氨酸（Leu）、精氨酸（Arg）和丝氨酸（Ser）这三种氨基酸由六种不同的密码子编码。相比之下，所有其他17个氨基酸由4、3、2或1个密码子编码。特别地，Ser被分成两个不同的Ser密码子盒，其区别在于至少两个碱基取代，而Leu和Arg的密码子可通过单碱基取代相互交换。我们认为这两种不同的Ser密码子是在进化过程中独立出现的。在这个假说中，在生命起源的时候，只有七种原始氨基酸：缬氨酸（由GUX [X = U，C，A或G]编码），丙氨酸（由GCX编码），天冬氨酸（由GAY [Y = U或C]编码），谷氨酸（由GAZ [Z = A或G]编码），甘氨酸（由GGX编码），Ser（由AGY编码）和Arg（由CGX和AGZ编码）。所有这些都是由GGX通过单碱基取代甘氨酸衍生而来的。在进化后期，另一类Ser密码子UCX衍生自丙氨酸密码子GCX，与另一种原始Ser密码子AGY明显不同。通过对大肠杆菌基因组的分析，我们发现这两种Ser密码子的使用存在广泛的差异，因为有些基因在其基因中仅使用AGY作为Ser。相比之下，其他人只使用UCX，这表明它们的起源存在明显差异，与我们的假设一致。
Among the 20 amino acids, three of them-leucine (Leu), arginine (Arg), and serine (Ser)-are encoded by six different codons. In comparison, all of the other 17 amino acids are encoded by either 4, 3, 2, or 1 codon. Peculiarly, Ser is separated into two disparate Ser codon boxes, differing by at least two-base substitutions, in contrast to Leu and Arg, of which codons are mutually exchange-able by a single-base substitution. We propose that these two different Ser codons independently emerged during evolution. In this hypothesis, at the time of the origin of life there were only seven primordial amino acids: Valine (coded by GUX [X = U, C, A or G]), alanine (coded by GCX), aspartic acid (coded by GAY [Y = U or C]), glutamic acid (coded by GAZ [Z = A or G]), glycine (coded by GGX), Ser (coded by AGY), and Arg (coded by CGX and AGZ). All of these were derived from GGX for glycine by single base substitutions. Later in evolution, another class of Ser codons, UCX, were derived from alanine codons, GCX, distinctly different from the other primordial Ser codon, AGY. From the analysis of the Escherichia coli genome, we find extensive disparities in the usage of these two Ser codons, as some genes use only AGY for Ser in their genes. In contrast, others use only UCX, pointing to distinct differences in their origins, consistent with our hypothesis.