Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
Second Genome, Inc., South San Francisco, CA, USA.
ISME J. 2019 Mar;13(3):789-804. doi: 10.1038/s41396-018-0304-9. Epub 2018 Nov 14.
The vitamin B 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.
已知的维生素 B 族辅因子 cobamides 对于各种微生物代谢至关重要。我们使用 11000 种细菌的比较基因组学分析了 cobamide 产生和利用在细菌中的广泛程度和分布。我们发现，在这个数据集的 86%的细菌中，至少有一种 15 种 cobamide 依赖性酶家族，但只有 37%被预测能从头合成 cobamides。 cobamide 生物合成和利用的分布在门水平上有所不同。虽然 57%的放线菌被预测能生物合成 cobamides，但仅有 0.6%的拟杆菌门有完整的途径，但该门 96%的物种都有 cobamide 依赖性酶。根据特征性低配体生物合成和附着基因的存在，可以预测 58%的 cobamide 产生物种产生的 cobamide 形式。我们的预测还表明，17%的细菌具有部分生物合成途径，但有回收 cobamide 前体的潜力。具有部分 cobamide 生物合成途径的细菌包括那些在新定义的、经过实验验证的缺乏生物合成途径第一步的细菌类别中。这些预测突出了 cobamide 和 cobamide 前体回收的重要性，它们是细菌营养依赖性的例子。
