Reference : Genomic analysis of the human gut microbiome suggests novel enzymes involved in quino...
Scientific journals : Article
Life sciences : Microbiology
http://hdl.handle.net/10993/23829
Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis
English
Ravcheev, Dmitry mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Thiele, Ines mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
25-Jan-2016
Frontiers in Microbiology
Frontiers Research Foundation
7
128
Yes
1664-302X
Lausanne
Switzerland
[en] Human gut Microbiome ; Comparative genomic ; Quinone biosynthesis ; Non-orthologous displacements ; energy production
[en] 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.
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group)
http://hdl.handle.net/10993/23829
10.3389/fmicb.2016.00128

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QuinonesHGM Suppl Figure S1.pdf400.83 kBView/Open
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QuinonesHGM Suppl Figure S2.pdf398.76 kBView/Open
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QuinonesHGM Suppl Figure S3.pdf401.22 kBView/Open
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QuinonesHGM Suppl Figure S4.pdf394.55 kBView/Open
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QuinonesHGM Suppl Figure S5.pdf443.14 kBView/Open
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QuinonesHGM Suppl Sequences S1.fasta551.41 kBView/Open
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QuinonesHGM Suppl Table S1.xlsx46.82 kBView/Open
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QuinonesHGM Suppl Table S2.xlsx34.24 kBView/Open
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QuinonesHGM Suppl Table S3.pdf187.15 kBView/Open
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QuinonesHGM Suppl Table S4.pdf105.47 kBView/Open

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