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，其特点是具有独特的生物学特征，例如具有细菌和真核特性的新陈代谢，但也具有独特的途径和酶。其中，(超级)嗜热菌特别有趣，因为这些古生菌适应极端的环境条件(温度、pH等)。这使得他们的酶系成为发现生物技术应用的新酶(相应地通常被称为极端酶)的一个有趣的来源。然而，目前缺乏合适的方法来鉴定和系统研究(超)嗜热古菌的酶以及对其独特代谢途径的分子洞察，这一点受到阻碍。在这项提议中，我们想要建立和应用新的方法来克服目前的瓶颈。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图谱(ABPP)，作为研究(超)嗜热古菌中这些酶和途径的一种新方法；2)应用ABPP和其他方法，如转录组学、(Meta)基因组学和生物化学方法，在三个具有异常碳水化合物降解特性的模式菌株中表征这些酶和途径；3)通过原位浓缩策略分离新的(超)嗜热菌株，并用我们的ABPP以及更成熟的多态组学和生化方法对它们进行表征；4)定义ABPP用于环境群落培养的化学图谱的范围。因此，拟议的项目在很大程度上取决于俄罗斯和德国伙伴之间的科学合作，因为双方拥有互补的专门知识和资源。俄罗斯的合作伙伴是分离新型(超)嗜热菌株及其通过(Meta)基因组学和转录组学鉴定的专家，而德国的合作伙伴将与他们的生化以及ABPP和蛋白质组学专业知识相辅相成。我们预计，联合项目不仅将在古生物生物学、生物技术和ABPP方面产生新的见解，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.