Exploration of carbohydrate metabolism in hyperthermophilic archaea: novel approaches, enzymes and metabolic pathways

古生菌是生命的第三个领域，具有独特的生物学特征，例如具有细菌和真核生物共同的代谢特性，但也具有独特的途径和酶。其中，（超）嗜热菌特别有趣，因为这些古菌适应极端环境条件（温度，pH等），将它们的酶库转变为发现用于生物技术应用的新酶（因此通常称为极端酶）的有趣来源。然而，由于缺乏合适的方法进行鉴定和系统研究，对（超）嗜热古菌酶的广泛使用以及对其独特代谢途径的分子见解目前受到阻碍。在本建议中，我们希望建立和应用新的方法来克服这些当前的瓶颈。作为展示，我们将重点介绍糖苷酶家族及其相应的碳水化合物降解途径的应用。为此，我们将1)建立基于活性的蛋白质谱（ABPP）作为研究（超）嗜热古菌中这些酶和途径的新方法；2)应用ABPP和其他方法，如转录组学、（元）基因组学和生化方法来表征三种具有不同碳水化合物降解特性的模型菌株中的这些酶和途径；3)通过原位富集策略分离新的（超）嗜热菌株，并使用我们的ABPP以及更成熟的多组学和生化方法对它们进行表征；4)定义ABPP用于环境群落培养化学分析的范围。因此，拟议的项目在很大程度上取决于俄罗斯和德国合作伙伴之间的科学合作，因为双方具有互补的专业知识和资源。俄罗斯合作伙伴是分离新型（超）嗜热菌株的专家，并通过（元）基因组学和转录组学对其进行鉴定，而德国团队将补充他们的生化、ABPP和蛋白质组学专业知识。我们预计，这一合作项目不仅将在古细菌生物学、生物技术和ABPP方面带来新的见解，而且还将为两国之间广泛的知识流动提供基础。

Archaea, the third domain of life, are characterized by unique biological traits such as a metabolism that shares bacterial and eukaryotic properties but also features unique pathways and enzymes. Among them, (hyper)thermophiles are particular interesting because these archaea are adapted to extreme environmental conditions (temperature, pH, etc.) that turn their enzyme repertoire into an intriguing source for the discovery of novel enzymes (accordingly often referred to as extremozymes) for biotechnological applications. A broader use of enzymes from (hyper)thermophilic archaea as well as molecular insights into their unique metabolic pathways is however currently hampered by a lack of suitable methodologies for their identification and systematic study.In this proposal, we want to establish and apply novel methodologies for overcoming these current bottlenecks. As a showcase, we will focus in our application on the glycosidase enzyme family as well as their corresponding carbohydrate degradation pathways. To this end, we will 1) establish activity-based protein profiling (ABPP) as a new approach for studying these enzymes and pathways in (hyper)thermophilic archaea, 2) apply ABPP and other methodologies such as transcriptomics, (meta)genomics and biochemical approaches to characterize these enzymes and pathways in three model strains with unusual properties in carbohydrate degradation, 3) isolate novel (hyper)thermophilic strains by in situ enrichment strategies and characterize them with our ABPP as well as the more established Polyomics and biochemical approaches and 4) define the scope of ABPP for chemical profiling of environmental community cultures. The proposed project thereby critically depends on the scientific collaboration between the Russian and German partners as both sides have complementary expertise and resources. The Russian partners are experts in isolation of novel (hyper)thermophilic strains and their characterization via (meta)genomics and transcriptomics while the German groups will complement with their biochemical as well as ABPP and proteomics expertise. We anticipate that the conjoint project will thus not only lead to novel insights in archaeal biology, biotechnology and ABPP but also provide the basis for extensive knowledge flow between both countries.