比较基因组学预测钴胺素生物合成的不均匀分布和在细菌中的依赖性。,The ISME Journal

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比较基因组学预测钴胺素生物合成的不均匀分布和在细菌中的依赖性。
The ISME Journal ( IF 10.8 ) Pub Date : 2018-Nov-14 , DOI: 10.1038/s41396-018-0304-9
Amanda N Shelton ₁ , Erica C Seth ₁ , Kenny C Mok ₁ , Andrew W Han _{1,

2} , Samantha N Jackson ₃ , David R Haft ₃ , Michiko E Taga ₁

Affiliation

维生素B ₁₂称为cobamides的辅因子家族对于多种微生物代谢必不可少。我们使用了11,000种细菌的比较基因组学来分析钴胺素在细菌中产生和使用的程度和分布。我们发现该数据集中86％的细菌具有15种依赖cobamide的酶家族中的至少一种，但预计只有37％的细菌从头合成cobamides。甲酰胺生物合成的分布和用途在门的水平上有所不同。尽管预计放线菌中有57％会生物合成钴酰胺，但只有0.6％的拟杆菌属具有完整的途径，但该门类中仍有96％的物种具有依赖钴酰胺的酶。基于特征性低配体生物合成和附着基因的存在，可以预测细菌产生的钴胺素的形式可用于58％的钴胺素生产物种。我们的预测还表明，17％的细菌具有部分生物合成途径，但仍有挽救钴胺素前体的潜力。具有部分钴胺素生物合成途径的细菌包括那些在新定义的，经过实验验证的细菌类别中的细菌，这些细菌缺乏生物合成途径中的第一步。这些预测突出了挽救钴胺素和钴胺素前体作为细菌中营养依赖性的例子的重要性。

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Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics.

The vitamin B₁₂ family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.

更新日期：2019-01-25

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