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: 1632941
• 负责人: Yuchen Liu
• 金额: $ 25.74万
• 依托单位: Louisiana State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1632941&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.

硫是所有已知生物体的必需元素，存在于氨基酸、核苷酸和辅酶中。 由于其独特的化学性质，它在生命历史早期（可能在3.5 Ga左右或之前）进化的许多基本生化途径中发挥着核心作用。 此时，氧气浓度非常低。 细胞中的许多含硫化合物与O2反应，好氧生物具有高度保守的生物合成途径，与好氧环境相容。 产甲烷古菌是严格厌氧菌的古老谱系，从未开发出在O2存在下生长的能力。 它们的硫代谢也非常独特，这表明它们可能拥有在生物圈中O2丰富之前常见的途径。 与好氧菌不同，大多数产甲烷古菌仅利用硫化物和元素硫作为硫源，而很少利用硫酸盐和其他氧化硫化合物。 最近的生物化学和基因组学研究揭示了其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以及缺乏Fe-S簇和蛋氨酸生物合成的典型酶。 因此，硫是如何结合在产甲烷菌中的仍然是未知的。 了解产甲烷菌中的硫网络将（i）推进我们对产甲烷菌生理学以及它们如何适应其独特生态位的了解;（ii）发现其他厌氧生物中可能常见的新型酶和硫代谢途径;（iii）提供生命中硫化学的更完整的图片以及早期厌氧地球上硫循环的演变;以及（iv）指导产甲烷菌的工程化以生产甲烷（一种碳中性生物燃料）。 这些科学目标将包括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人员。技术说明：硫是所有已知生物体生长所必需的，存在于各种各样具有不同生理功能的分子中。 与其严格的厌氧生活方式一致，大多数产甲烷古菌仅使用硫化物和元素硫作为硫源，很少利用硫酸盐和其他氧化硫化合物。 最近的研究揭示了产甲烷古菌Methanococcus maripaludis中硫同化的新特征。 其中包括：在细菌和真核生物中常见的许多硫代谢基因的同源物是不存在的;半胱氨酸是通过一种新的tRNA依赖性途径生物合成的;半胱氨酸不是Fe-S簇、甲硫氨酸和4-硫尿苷生物合成的中间体; 4-硫尿苷合成酶的硫转移基序与细菌中发现的不同。 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化物是否直接用作硫供体在各种途径或独特的硫载体蛋白参与硫中继。 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）古细菌泛素样途径的硫中继系统，用于tRNA 2-硫尿苷生物合成;（iii）全球硫代谢网络中的酶和载体;以及（iv）可用于这些生化系统的硫化物的细胞内水平。对硫网络的研究将促进我们对产甲烷菌生理学的了解，以及它们如何适应其独特的生态位。 由于硫酸盐在早期缺氧的地球上是有限的，而硫化物和元素硫可能是丰富的，因此同化硫化物和元素硫作为唯一硫源的产甲烷菌为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，我们对硫同化的认识大多是基于好氧菌和兼性厌氧菌。 由于许多已知的硫转移酶从细菌和真核生物中缺失产甲烷菌，阐明硫中继产甲烷菌可能会指导发现新的硫代谢途径，可能是常见的其他厌氧菌，这将有助于更全面地了解硫化学在生活中。 这项工作的广泛影响包括以下方面。 (i)解开产甲烷菌中的硫代谢将有助于它们的代谢和生物工程的甲烷，碳中性生物燃料的生产建模。 (ii)它将为控制甲烷排放的机制提供新的见解，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，这将是非常有价值的系统发现的新途径，在一个古菌模式生物。 (iv)该项目将为下一代科学家，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。 它将鼓励学生查看整个有机体，因为它存在于一个特定的生态环境中。 (v)它将为CoPI的年轻研究员刘博士建立一条独立的道路。

项目成果

A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes

• DOI: 10.1073/pnas.1615732113
• 发表时间: 2016-11-08
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Liu, Yuchen;Vinyard, David J.;Soll, Dieter
• 通讯作者: Soll, Dieter