Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.
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DOI：
10.3389/fmicb.2016.00128
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发表时间：
2016
影响因子：
5.2
通讯作者：
Thiele I
中科院分区：
文献类型：
--
作者：
Ravcheev DA;Thiele I
泛醌和菜醌是细胞呼吸所必需的电子的膜脂可溶载体。真核细胞可以合成泛醌，但不能合成菜醌，而原核生物可以合成这两种醌。到目前为止，大多数人肠道微生物组(HGM)的研究都是基于元基因组分析。在这里，我们应用对单个hGM基因组的分析来鉴定泛醌和菜喹酮的生物合成途径。在我们看来，从元基因组学到个体基因组分析的转变是包括HGM在内的细菌群落研究的一个关键里程碑。本研究的主要成果如下。(I)HGM基因组中典型途径的分布与以前的报道以及电子受体的苯醌依赖的还原酶的分布一致。(2)比较基因组学分析确定了以前已知的苯二酚生物合成酶的四种替代形式。(3)鉴定了呋喃他罗辛途径未知部分的基因，并提出了相应的生化反应。我们讨论了在一些微生物中的菜醌和泛醌途径中的剩余缺口，这表明存在更多的替代基因或途径。综上所述，这些发现为进一步了解细菌中苯醌的生物合成和HGM的生理学提供了进一步的见解。
Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.