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.
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.
