Ordering events of biochemical evolution
Ordering events of biochemical evolution
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DOI：
10.1016/j.biochi.2006.12.007
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发表时间：
2007-05-01
期刊：
影响因子：
3.9
通讯作者：
Lecointre, G.
中科院分区：
文献类型：
--
作者：
Cunchillos, C.;Lecointre, G.
代谢途径表现出进化过程产生的结构。从生命的最早时期起，经过修改，路径就被继承了下来。有可能像比较解剖学中所做的那样比较通路的结构，即使用标准的系统发育重建来推断祖先通路或其部分(祖先酶的功能)。因此，途径的系统发育树提供了酶功能上升的相对顺序。甚至有可能在时间上安排每一条完整路径的诞生。回顾了进化生物化学的这种特殊的“无DNA”概念方法，收集了它的所有理由。然后，重新讨论了将给定的途径分配给生化发展的时间跨度的方法。以前的方法使用的是一个隐含的新陈代谢发展的“时钟”，这很难证明是合理的。我们开发了一种新的无时钟方法，使用功能生化参数。两种方法的结果没有显著差异；我们的方法只是更精确。这表明，第一种方法中假设的时钟在描述生化进化的发展过程中没有引起任何重要的假象。没有必要假定这一点。因此，大多数氨基酸代谢途径向前发展，证实了以前的氨基酸分解代谢进化模型，但不是氨基酸合成代谢进化模型。普遍的细胞代谢部分的出现顺序是：(1)氨基酸分解代谢，(2)氨基酸合成代谢和尿素循环的关闭，(3)糖酵解和糖的生成，(4)戊糖-磷酸循环的关闭，(5)Krebs循环和脂肪酸代谢的关闭，(6)Calvin循环的关闭。(C)2007年爱思唯尔·马森公司。版权所有。
Metabolic pathways exhibit structures resulting from an evolutionary process. Pathways have been inherited through time with modification, from the earliest periods of life. It is possible to compare the structure of pathways as done in comparative anatomy, i.e. for inferring ancestral pathways or parts of it (ancestral enzymatic functions), using standard phylogenetic reconstruction. Thus a phylogenetic tree of pathways provides a relative ordering of the rise of enzymatic functions. It even becomes possible to order the birth of each complete pathway in time. This particular "DNA-free" conceptual approach to evolutionary biochemistry is reviewed, gathering all the justifications given for it. Then, the method of assigning a given pathway to a time span of biochemical development is revisited. The previous method used an implicit "clock" of metabolic development that is difficult to justify. We develop a new clock-free approach, using functional biochemical arguments. Results of the two methods are not significantly different; our method is just more precise. This suggests that the clock assumed in the first method does not provoke any important artefact in describing the development of biochemical evolution. It is just unnecessary to postulate it. As a result, most of the amino acid metabolic pathways develop forwards, confirming former models of amino acid catabolism evolution, but not those for amino acid anabolism. The order of appearance of sectors of universal cellular metabolism is: (1) amino acid catabolism, (2) amino acid anabolism and closure of the urea cycle, (3) glycolysis and glycogenesis, (4) closure of the pentose-phosphate cycle, (5) closure of the Krebs cycle and fatty acids metabolism, (6) closure of the Calvin cycle. (C) 2007 Elsevier Masson SAS. All rights reserved.