Shedding light on the microbial dark matter with photons from Synchrotron radiation: structural biology of mesocosms by an explorative pipel

The microbial world is constantly shaping the planet by governing the carbon, nitrogen, and sulfur cycles. While recent developments in ¿omics¿ opened a window of the complexity of this world, it is still problematic to attribute a function to a gene product or predict enzymatic reactions simply from its sequence. Then, how can enzymes be studied from uncultivated microbes? In this proposal, we are using an explorative approach to open a new field: the structural elucidation of catabolic enzymes from microbial mesocosms. We will study two models, an anaerobic bioreactor containing a methane-degrading consortium, and a microbial community from wastewater treatment. As a proof of concept, we recently isolated, crystallized, and structurally characterized the methane-generating enzyme from an archaeon living in this activated sludge. Now, we will go beyond and isolate more enzymes of catabolic pathways from these "microbial dark matter", playing a key role in the carbon cycle.

微生物群落通过驱动碳、氮、硫元素的生物地球化学循环，持续塑造地球生态格局。尽管近年来组学（omics）技术的发展为揭示该类群的复杂性提供了新视角，但仅通过基因序列来注释基因产物功能或预测酶促反应仍存在诸多挑战。那么，如何从未培养微生物中开展酶类研究呢？本研究提案采用探索性研究方法，开辟全新研究方向：解析微生物中型生态系统（microbial mesocosms）中分解代谢酶的结构。本研究将选取两类模型体系：其一为搭载甲烷降解菌群的厌氧生物反应器，其二为污水处理系统中的微生物群落。作为概念验证，我们近期从该活性污泥中的古菌体内分离得到产甲烷酶，并完成结晶与结构表征。在此基础上，我们将进一步拓展研究范围，从这些“微生物暗物质（microbial dark matter）”中分离更多在碳循环中发挥关键作用的分解代谢通路相关酶类。