Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages
Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages
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DOI：
10.1371/journal.pgen.1000402
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发表时间：
2009-03-01
期刊：
影响因子：
4.5
通讯作者：
Takagi, Toshihisa
中科院分区：
文献类型：
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作者：
Iwasaki, Wataru;Takagi, Toshihisa
生物通路的进化史是人们普遍感兴趣的，特别是在这个后基因组时代，因为它可能为理解基因组上编码的复杂系统是如何组织的提供线索。为了解释路径如何从头进化，已经提出了一些值得注意的模型。然而，在基因组水平和生命树深处直接重建途径进化史，在估计祖先物种的基因含量方面受到了人为影响。最近，我们开发了一种算法，可以在没有这些人为影响的情况下有效地重建基因内容进化，并将其应用于这个问题。以160种原核生物的代谢途径为基础，仔细重建的历史证实，途径已经超出了对单个基因的随机获取。途径获得发生得很快，可能消除了在途径进化过程中持有基因的困难。这种快速的进化是由于大规模的水平基因转移作为基因群，其中一些可能是操纵子转移，这将传递现有的途径，但不能产生新的途径。为此，我们分析了这些途径最初是如何出现的，并发现最初获得途径的时间比预期的更多地发生在不同的系统发育分支上。作为解释这一观察结果的一个可能的模型，我们提出了在原核生物群落中双向水平基因转移可能促进新的途径进化。这样的模型将补充现有的途径进化模型。
The evolutionary history of biological pathways is of general interest, especially in this post-genomic era, because it may provide clues for understanding how complex systems encoded on genomes have been organized. To explain how pathways can evolve de novo, some noteworthy models have been proposed. However, direct reconstruction of pathway evolutionary history both on a genomic scale and at the depth of the tree of life has suffered from artificial effects in estimating the gene content of ancestral species. Recently, we developed an algorithm that effectively reconstructs gene-content evolution without these artificial effects, and we applied it to this problem. The carefully reconstructed history, which was based on the metabolic pathways of 160 prokaryotic species, confirmed that pathways have grown beyond the random acquisition of individual genes. Pathway acquisition took place quickly, probably eliminating the difficulty in holding genes during the course of the pathway evolution. This rapid evolution was due to massive horizontal gene transfers as gene groups, some of which were possibly operon transfers, which would convey existing pathways but not be able to generate novel pathways. To this end, we analyzed how these pathways originally appeared and found that the original acquisition of pathways occurred more contemporaneously than expected across different phylogenetic clades. As a possible model to explain this observation, we propose that novel pathway evolution may be facilitated by bidirectional horizontal gene transfers in prokaryotic communities. Such a model would complement existing pathway evolution models.