Collaborative Research: Unraveling Sulfur Networks in Methanogenic Archaea

合作研究：解开产甲烷古菌中的硫网络

• 批准号: 1410079
• 负责人: Yuchen Liu
• 金额: $ 39.2万
• 依托单位: Yale University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1410079&HistoricalAwards=false
• 关键词: Collaborative; Research; Unraveling; Sulfur; Networks

Sulfur is an essential element for all known organisms and is present in amino acids, nucleotides and coenzymes. Because of its distinctive chemistry, it plays central roles in many essential biochemical pathways that likely evolved early in life's history, possibly around or before 3.5 Ga. At this time, the O2 concentrations were very low. Many sulfur-containing compounds in cells react with O2, and aerobic organisms possess highly conserved pathways for their biosynthesis that are compatible with an aerobic environment. The methanogenic archaea are an ancient lineage of strict anaerobes that never developed the ability to grow in the presence of O2. Their sulfur metabolism is also very distinctive, suggesting that they may possess pathways common before O2 became abundant in the biosphere. Unlike aerobes, most methanogenic archaea only use sulfide and elemental sulfur as the sulfur sources, and sulfate and other oxidized sulfur compounds are seldom utilized. Recent biochemical and genomics studies have revealed unusual features of their sulfur assimilation, including a unique tRNA-dependent cysteine biosynthesis pathway and the absence of canonical enzymes for Fe-S cluster and methionine biosynthesis. Thus, how sulfur is incorporated in methanogens remains unknown. Understanding the sulfur networks in methanogens will (i) advance our knowledge of the physiology of methanogens and how they are adapted to their unique ecological niche; (ii) discover novel enzymes and pathways of sulfur metabolism that may be common in other anaerobes; (iii) provide a more complete picture of sulfur chemistry in life and the evolution of the sulfur cycle on the early, anaerobic Earth; and (iv) guide engineering of methanogens for production of methane, a carbon neutral biofuel. Integrated into these scientific goals will be interdisciplinary training of the next generation of scientists, including high school, undergraduate and graduate students, and a young investigator.Technical description: Sulfur is essential for the growth of all known organisms and is present in a wide variety of molecules with different physiological functions. Consistent with their strictly anaerobic lifestyle, most methanogenic archaea only use sulfide and elemental sulfur as sulfur sources, and sulfate and other oxidized sulfur compounds are seldom utilized. Recent studies have revealed novel features of sulfur assimilation in the methanogenic archaeon Methanococcus maripaludis. These include: homologs of many sulfur metabolic genes common in bacteria and eukaryotes are absent; cysteine is biosynthesized by a novel tRNA-dependent pathway; cysteine is not an intermediate for Fe-S cluster, methionine and 4-thiouridine biosynthesis; and the sulfur transfer motif of the 4-thiouridine synthetase is distinct from that found in bacteria. These discoveries greatly broadened our view of physiological sulfur chemistry. However, many aspects of the sulfur transfer processes in methanococci remain to be elucidated. An important question is whether sulfide is directly used as the sulfur donor in various pathways or unique sulfur carrier proteins are involved in sulfur relay. This research specifically seeks to understand (i) the physiological sulfur transfer mechanism of tRNA-dependent cysteine biosynthesis; (ii) the sulfur relay system of the archaeal ubiquitin-like pathway for tRNA 2-thiouridine biosynthesis; (iii) the enzymes and carriers in a global sulfur metabolic network; and (iv) the intracellular levels of sulfide available for these biochemical systems. Research on sulfur networks will advance our knowledge of the physiology of methanogens and how they are adapted to their unique ecological niche. Since sulfate was limited on the early, anoxic Earth while sulfide and elemental sulfur were presumably abundant, methanogens that assimilate sulfide and elemental sulfur as sole sulfur sources provide a living window into the primitive sulfur metabolism and shed light on the evolutionary processes of early Earth. Furthermore, most of our knowledge on sulfur assimilation is based upon aerobes and facultative anaerobes. As many of the known sulfur transfer enzymes from bacteria and eukaryotes are missing in methanogens, the elucidation of sulfur relay in methanogens may guide discovery of novel sulfur metabolic pathways that may be common in other anaerobes; this will contribute to a more complete understanding of sulfur chemistry in life. The broader impacts of this work include the following. (i) Unraveling S metabolism in methanogens will assist modeling of their metabolism and bioengineering the production of methane, a carbon neutral biofuel. (ii) It will provide new insights into mechanisms to control emissions of methane, a potent greenhouse gas that contributes to global warming. (iii) This study will develop a new genome-wide screening method, which will be of great value for systematic discoveries of novel pathways in an archaeal model organism. (iv) This project will provide interdisciplinary training to the next generation of scientists, including high school, undergraduate and graduate students, in microbial physiology, biochemistry and genetics. It will encourage students to view the entirety of the organism as it exists within a specific ecological context. (v) It will establish a path to independence for the CoPI Dr. Liu, a young investigator.

硫是所有已知生物的基本元素，存在于氨基酸、核苷酸和辅酶中。由于其独特的化学性质，它在许多重要的生化途径中起着核心作用，这些途径可能在生命历史的早期进化，可能在3.5亿年左右或之前。此时，氧气浓度非常低。细胞中许多含硫化合物与O2反应，好氧生物具有高度保守的与好氧环境相容的生物合成途径。产甲烷古细菌是一种古老的严格厌氧菌，从未发展出在氧气存在下生长的能力。它们的硫代谢也非常独特，这表明在生物圈中氧气变得丰富之前，它们可能拥有共同的途径。与需氧菌不同，大多数产甲烷古菌只利用硫化物和单质硫作为硫源，很少利用硫酸盐和其他氧化硫化合物。最近的生化和基因组学研究揭示了它们硫同化的不寻常特征，包括独特的trna依赖的半胱氨酸生物合成途径和缺乏Fe-S簇和蛋氨酸生物合成的典型酶。因此，硫是如何与产甲烷菌结合的仍然是未知的。了解产甲烷菌中的硫网络将(i)提高我们对产甲烷菌生理以及它们如何适应其独特生态位的认识；（ii）发现可能在其他厌氧菌中常见的新的硫代谢酶和途径；（iii）对生命中的硫化学和早期厌氧地球上硫循环的演化提供更完整的描述；(4)指导产甲烷菌的工程设计，用于生产甲烷，一种碳中性生物燃料。与这些科学目标相结合的是对下一代科学家的跨学科培训，包括高中生、本科生和研究生，以及一名年轻的研究者。技术描述：硫是所有已知生物生长所必需的，存在于各种具有不同生理功能的分子中。与它们严格的厌氧生活方式一致，大多数产甲烷古菌只使用硫化物和单质硫作为硫源，而硫酸盐和其他氧化硫化合物很少被利用。最近的研究揭示了产甲烷古菌马里帕卢氏甲烷球菌硫同化的新特征。这些包括：细菌和真核生物中常见的许多硫代谢基因的同源物缺失；半胱氨酸是通过一种新的trna依赖途径生物合成的；半胱氨酸不是Fe-S簇、蛋氨酸和4-硫脲生物合成的中间体；4-硫脲合成酶的硫转移基序与细菌中的硫转移基序不同。这些发现大大拓宽了我们对生理硫化学的认识。然而，甲烷球菌中硫转移过程的许多方面仍有待阐明。一个重要的问题是硫是否在各种途径中被直接用作硫供体，或者是否有独特的硫载体蛋白参与硫接力。本研究旨在了解(i) trna依赖性半胱氨酸生物合成的生理硫转移机制；（ii）古菌泛素样tRNA - 2-硫脲生物合成途径的硫接力系统；（iii）全球硫代谢网络中的酶和载体；（iv）这些生化系统可用的细胞内硫化物水平。对硫网络的研究将促进我们对产甲烷菌的生理学以及它们如何适应其独特的生态位的认识。由于硫酸盐在早期缺氧的地球上是有限的，而硫化物和单质硫可能是丰富的，吸收硫化物和单质硫作为唯一硫源的产甲烷菌为研究原始硫代谢提供了一个活生生的窗口，并揭示了早期地球的进化过程。此外，我们对硫同化的大部分知识是基于好氧菌和兼性厌氧菌。由于许多已知的来自细菌和真核生物的硫转移酶在产甲烷菌中缺失，对产甲烷菌中硫接力的阐明可能指导发现其他厌氧菌中常见的新型硫代谢途径；这将有助于更全面地了解生命中的硫化学。这项工作的更广泛影响包括以下方面。(i)揭示产甲烷菌的S代谢将有助于对其代谢进行建模，并对甲烷（一种碳中性生物燃料）的生产进行生物工程。它将为控制甲烷排放机制提供新的见解，甲烷是一种导致全球变暖的强效温室气体。（iii）本研究将开发一种新的全基因组筛选方法，对系统地发现古细菌模式生物的新途径具有重要价值。这个项目将向下一代科学家，包括高中生、本科生和研究生，提供微生物生理学、生物化学和遗传学方面的跨学科培训。它将鼓励学生观察有机体的整体，因为它存在于特定的生态环境中。（五）为青年研究员刘博士建立一条独立的道路。