Investigating Evolutionary Dynamics of RHA1 Operons.
Investigating Evolutionary Dynamics of RHA1 Operons.
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研究 RHA1 操纵子的进化动力学
DOI：
10.4137/ebo.s39753
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Zhang S
中科院分区：
文献类型：
--
作者：
Chen Y;Geng D;Ehrhardt K;Zhang S
操纵子是原核生物基因组的一个重要特征。对操纵子组织的全面了解将有助于破译原核生物基因组的转录机制、细胞通路和进化景观。虽然成千上万的原核生物已被测序，这些基因组中的操纵子的进化动力学（分裂和重组）的全基因组调查仍然没有探索。在这里，我们通过比较从不同属中精心挑选的340个原核基因组，系统地分析了霍氏红球菌RHA 1（RHA 1）的操纵子动力学，RHA 1是一种在生物燃料中具有高潜力应用的产油细菌。有趣的是，在340个比较的基因组中，观察到99%的RHA1操纵子表现出分裂和重组的进化事件。一个操纵子，编码所有的酶相关的组氨酸生物合成RHA1（组氨酸操纵子）被发现被分割成更小的基因组（子操纵子）在不同的基因组。这些子操纵子进一步与不同的功能基因重组，成为与不同生化过程相关的新型操纵子。相对而言，参与脂质转运和代谢功能的操纵子在340个比较基因组中相对保守。在通路水平，发现RHA1操纵子是显着保守的参与核糖体合成，氧化磷酸化，脂肪酸合成。这些分析提供了操纵子组织的进化见解和不同原核生物中各种生化途径的动态关联。
Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.