细菌和古细菌这两个生命领域的存在本身就意味着 LUCA 和这些领域的祖先是原生生物。

IF 2 4区 生物学 Q2 BIOLOGY Biosystems Pub Date : 2024-11-21 DOI:10.1016/j.biosystems.2024.105375
Massimo Di Giulio
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引用次数: 0

摘要

生命树最深分支的长度倾向于支持这样的假设,即把古细菌序列和细菌序列分开的分支(即域间分支)的距离比域内分支(即把古细菌序列和细菌序列分开的分支)的距离要长。为什么域间距离要大于域内距离?随着生命领域的出现,氨基酸的替换速度减慢,这似乎意味着进化的过渡。在两个生命领域形成过程中出现的进化速度减慢,应该是原生生物向细胞进化转变的结果。事实上,原生生物的进化阶段具有进化速度加快和进化模式加快的特点,这也许可以解释域间距离相当大的原因,因为在这一分支上积累了许多氨基酸替代物,这表明原生生物的进化阶段也具有氨基酸替代率高的特点。此外,域内距离小于域间距离的事实也证实了在主要植物系出现时实现细胞化的假说。事实上,细胞阶段与原生阶段不同,它明确地确定了基因型与表型之间的关系,从而降低了进化速度。因此,根据所提出的论据,可以得出 LUCA 是原生生物的结论。对 LUCA 基因组复杂性的重建确定了一个非常复杂的 LUCA。我深信,在这些重建中,可能隐藏着推理形式上的缺陷。这些分析都是从同源蛋白质序列开始的,这些序列将确定细菌和古细菌序列之间的多重排列。这些多重蛋白质比对包含很少或极少数保存完好的氨基酸区域。尽管如此,我们还是假定 LUCA 中已经存在该特定蛋白质的功能及其结构。这一假设可能是错误的。事实上,这只是一种可能性,一种假设,不应该被用来推断 LUCA 的复杂性。事实上,我们并不知道 LUCA 中的蛋白质是什么形态,而这正是我们想知道的。也就是说,我们不知道该基因处于哪个进化阶段。虽然有人假定--仅仅是基于在多重排列中蛋白质的某些区域保存完好--基因是现代类型的,但这很可能是错误的。总之,支持原生 LUCA 的观点和论据似乎比支持细胞 LUCA 的观点和论据更有价值。
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The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes
The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.e. those that separate the sequences of archaea and those of bacteria within them. Why should interdomain distance be larger than intradomain distances? The fact that the rate of amino acid substitutions was slowed as the domains of life appeared would seem to imply an evolutionary transition. The slowdown in the speed of evolution that occurred during the formation of the two domains of life would be the consequence of the progenote- > cell evolutionary transition. Indeed, the evolutionary stage of the progenote being characterized by an accelerated tempo and mode of evolution might explain the considerable interdomain distance because the accumulation of many amino acid substitutions on this branch would indicate the progenote stage that is also characterized by a high rate of amino acid substitutions. Furthermore, the fact that intradomain distances are smaller than interdomain distances would corroborate the hypothesis of the achievement of cellularity at the appearance of the main phyletic lineages. Indeed, the cell stage, unlike the progenotic one, definitively establishes the relationship between the genotype and phenotype, lowering the rate of evolution. Therefore, the arguments presented lead to the conclusion that LUCA was a progenote.
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来源期刊
Biosystems
Biosystems 生物-生物学
CiteScore
3.70
自引率
18.80%
发文量
129
审稿时长
34 days
期刊介绍: BioSystems encourages experimental, computational, and theoretical articles that link biology, evolutionary thinking, and the information processing sciences. The link areas form a circle that encompasses the fundamental nature of biological information processing, computational modeling of complex biological systems, evolutionary models of computation, the application of biological principles to the design of novel computing systems, and the use of biomolecular materials to synthesize artificial systems that capture essential principles of natural biological information processing.
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