Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia Foundation, Turin, Italy.
Department of Environment, Land and Infrastructure Engineering, Politecnico di Torino, Turin, Italy.
Microbiol Spectr. 2022 Aug 31;10(4):e0101922. doi: 10.1128/spectrum.01019-22. Epub 2022 Jun 23.
Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus (, , , , , , , sp. AWRP) to systematically identify their intriguingly diversified hydrogenases' repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits' characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases. Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases' functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases' level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.
了解氢代谢的组织和功能特性对于构建支持氢燃料低碳经济的框架至关重要。氢代谢依赖于氢化酶的作用机制。在这项研究中，我们研究了几株工业相关的产乙酸菌属（、、、、、、、、、、）的基因组，以系统地鉴定它们引人入胜的多样化氢化酶库。一个完全基于计算的注释管道揭示了[NiFe]-和[FeFe]-氢化酶功能内容中的常见和菌株特异性特征。通过序列同源性与经过精心整理的非冗余氢化酶数据库相结合，并分析[FeFe]-和[NiFe]-氢化酶作用模式的特征序列模式，对氢化酶进行了鉴定和分类，将其分为功能不同的类别。对催化亚基附近基因的检查表明，它们的基因组排列与以前为预测的氢化酶类开发的基因组织模板之间存在广泛的一致性。对鉴定出的氢化酶的亚基特征分析，使我们能够深入了解电子分叉[FeFe]-氢化酶中电子传递体的氧化还原辅因子结合决定因素。最后，通过对[NiFe]-和[FeFe]-氢化酶生物合成所需成熟蛋白的精确分析，验证了推断出的氢化酶的可靠性。
掌握氢代谢可以支持可持续的碳中和经济。在许多代谢氢的微生物中，产乙酸菌属是吸引人的，其中一些已经被用作工业主力。我们在基因水平上提供了前所未有的数量的梭菌产乙酸菌属的氢化酶含量的详细信息，我们的研究代表了一个有价值的知识库，可以加深我们对氢化酶功能特异性和/或冗余性的理解，并开发出大量的生物技术过程。我们还认为，我们的研究可以作为未来菌株工程方法的基础，这些方法可以作用于氢化酶水平或其成熟蛋白水平。另一方面，与鉴定出的氢化酶有关的丰富功能元素值得进一步进行生化和结构研究，最终将这些酶用作有价值的催化剂。
