Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes
Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes
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DOI：
10.1038/s41396-019-0414-z
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发表时间：
2019-08-01
期刊：
影响因子：
11
通讯作者：
Chistoserdova, Ludmila
中科院分区：
文献类型：
--
作者：
Huang, Jing;Yu, Zheng;Chistoserdova, Ludmila
镧系元素(Ln(3+))，又称稀土元素，最近以酶辅助因子的形式出现，与先前的生物惰性假设背道而驰。到目前为止，已鉴定出几种依赖Ln(3+)活性和表达的细菌乙醇脱氢酶，分别属于甲醇脱氢酶分支XoxF和乙醇脱氢酶分支ExaF/PedH。在这里，我们汇编了一个潜在的编码Ln(3+)依赖酶的基因清单，这些基因与先前描述的XoxF和ExaF/PedH酶密切相关。我们证明了它们在一些数量最丰富和对环境最重要的分类群中的广泛分布，例如在系统发育上不同的根瘤菌物种和生活在世界海洋中的代谢多功能细菌，这表明对Ln(3+)介导的生物化学的依赖在微生物世界中比之前假设的要广泛得多。通过蛋白质表达和分析，我们在这里展示了一系列依赖Ln(3+)的生物化学特征的酶的现有收集，展示了一系列催化特性以及底物和辅因子的特异性。这些酶中的许多都显示了甲醇氧化的倾向。这一观察结果，再加上对选定物种的甲基化营养途径的基因组重建，表明这种代谢能力在细菌物种中出现得更广泛，从而进一步表明甲基化化合物作为全球碳循环的一部分的重要性。
Lanthanides (Ln(3+)), known as rare earth elements, have recently emerged as enzyme cofactors, contrary to prior assumption of their biological inertia. Several bacterial alcohol dehydrogenases have been characterized so far that depend on Ln(3+) for activity and expression, belonging to the methanol dehydrogenase clade XoxF and the ethanol dehydrogenase clade ExaF/PedH. Here we compile an inventory of genes potentially encoding Ln(3+)-dependent enzymes, closely related to the previously characterized XoxF and ExaF/PedH enzymes. We demonstrate their wide distribution among some of the most numerically abundant and environmentally important taxa, such as the phylogenetically disparate rhizobial species and metabolically versatile bacteria inhabiting world's oceans, suggesting that reliance on Ln(3+)-mediated biochemistry is much more widespread in the microbial world than previously assumed. Through protein expression and analysis, we here more than double the extant collection of the biochemically characterized Ln(3+)-dependent enzymes, demonstrating a range of catalytic properties and substrate and cofactor specificities. Many of these enzymes reveal propensity for oxidation of methanol. This observation, in combination with genome-based reconstruction of methylotrophy pathways for select species suggests a much wider occurrence of this metabolic capability among bacterial species, and thus further suggests the importance of methylated compounds as parts of the global carbon cycling.