Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
ISME J. 2019 Aug;13(8):2005-2017. doi: 10.1038/s41396-019-0414-z. Epub 2019 Apr 5.
Lanthanides (Ln), 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 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-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-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-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.
镧系元素（Ln），又称稀土元素，最近被发现作为酶的辅助因子，与之前认为它们在生物学上惰性的假设相反。到目前为止，已经有几种细菌醇脱氢酶被表征，它们依赖于镧系元素来发挥活性和表达，属于甲醇脱氢酶分支 XoxF 和乙醇脱氢酶分支 ExaF/PedH。在这里，我们编制了一份潜在编码镧系元素依赖酶的基因清单，这些酶与之前表征的 XoxF 和 ExaF/PedH 酶密切相关。我们证明它们在一些数量最多和环境最重要的类群中广泛分布，例如在系统发育上不同的根瘤菌物种和代谢多样的海洋细菌，这表明对镧系元素介导的生物化学的依赖在微生物世界中比之前认为的要广泛得多。通过蛋白质表达和分析，我们在这里将生物化学表征的镧系元素依赖酶的现有集合增加了一倍以上，展示了一系列的催化特性、底物和辅助因子特异性。其中许多酶显示出对甲醇氧化的倾向。这一观察结果，结合对特定物种的甲基营养途径的基于基因组的重建表明，这种代谢能力在细菌物种中更为普遍，因此进一步表明了甲基化化合物作为全球碳循环的一部分的重要性。
