Universal and taxon-specific trends in protein sequences as a function of age.
Universal and taxon-specific trends in protein sequences as a function of age.
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DOI：
10.7554/elife.57347
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发表时间：
2021-01-08
期刊：
影响因子：
7.7
通讯作者：
Masel J
中科院分区：
文献类型：
--
作者：
James JE;Willis SM;Nelson PG;Weibel C;Kosinski LJ;Masel J
现存的蛋白质编码序列跨越了巨大的年龄范围，从最近才出现的到最后一个普遍共同祖先出现的。因为进化作用于年轻层序的时间较少，所以随着年龄的增长而缓慢进化的任何属性都可能存在“系统地层学”趋势。在以前的分类限制研究中发现疏水性和疏水性聚类的长期减少。在这里，我们对435个完全测序的物种进行了综合的系统地层学，使用敏感的HMM方法检测蛋白质结构域同源性。我们发现疏水聚类的减少在整个谱系中是普遍的。然而，只有年轻的动物领域有较高的结构紊乱的倾向。在古代结构域中，氨基酸组成的趋势反映了进入遗传密码的顺序，这表明古代序列的当代后代的组成反映了这些序列首次出现时生命最早阶段的氨基酸可用性。
Extant protein-coding sequences span a huge range of ages, from those that emerged only recently to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be ‘phylostratigraphy’ trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.