3-Methylhopanoids in modern bacteria: molecular fossils of stress survival?

地球的历史以剧烈的气候变化为标志，这些变化对生命的进化产生了重大影响。地球科学家特别感兴趣的是古代微生物如何对这种戏剧性的事件做出反应。由于微生物不会留下易于识别的化石，因此需要替代策略来研究古代微生物群落。一种方法是研究某些可以保存在古代岩石中的生物分子（脂质）。这些脂质起着分子化石或生物标志物的作用，可以告诉我们古代微生物群落和它们曾经生活的环境条件。其中一组生物标志物是3-甲基藿烷，这是一种环状分子，通常被认为是甲烷氧化细菌的指示剂。然而，这些假设可能并不可靠，需要进一步研究。该提案将利用分子和生物化学工具来研究3-甲基藿烷的生产如何在现代细菌中受到遗传和环境控制。这项研究将提供有价值的信息，以更好地解释岩石记录中的3-甲基藿烷模式，并最终导致更好地了解古代微生物群落如何应对过去的大气变化，以及类似的微生物群落如何应对未来的气候事件。调查人员将涉及通过斯坦福大学地球科学与工程暑期本科研究（SURGE）计划招募的暑期学生。该提案将通过斯坦福大学的普通地球科学实习计划，为低收入暑期高中实习生提供资金，让他们在研究人员的实验室进行研究。这些活动将为代表性不足的学生提供亲身体验地球生物学研究的机会，并鼓励他们追求地球科学的职业生涯。甲基藿烷是五环细菌脂质，其成岩产物甲基藿烷在沉积岩中很容易检测到。基于现代细菌中甲基霍帕烷的产生，岩石记录中的甲基霍帕烷特征有可能作为生物标志物，将细菌分类群及其代谢与地球上的特定时间或事件联系起来。的历史。特别是，已经提出3-甲基藿烷是好氧甲烷氧化菌的可靠替代物和重要的甲烷地球化学循环的指示物。然而，最近的研究表明，现存的3-甲基藿烷类生产者的多样性超出了好氧甲烷氧化菌。这些研究结果还表明，为了正确解释岩石记录中甲基藿烷生物特征的发生，需要了解甲基藿烷在现代细菌中的功能和调节。为此，研究人员和合作者已经开始研究3-甲基hopanoid在好氧甲烷氧化菌Methylococcus capsulatus的生理学。在这种生物体中，C-3甲基化所需的基因（hpnR）已被鉴定并随后被删除。甲基化酶突变体，只产生未甲基化的hopanoids的生理研究，揭示了一个潜在的作用3-methylhopanoids在稳定期生存。在这个项目中，研究人员的目标是直接确定3-methylhopanoids在稳定期生存中的作用，希望为正确解释岩石记录中的3-methylhopane签名提供所需的基础。提出了以下三条调查路线：1。生理学研究将继续与M。capsulatus 3-甲基藿烷类突变体，以确定3-甲基藿烷类是否参与氧限制条件下的稳定期存活，2.将分离表现出与野生型菌株相似的稳定期存活水平的Δ hpnR抑制突变体。利用高通量全基因组测序，研究者将鉴定恢复甲基化酶突变体活力的基因间突变，以及3.为了确定3-甲基hopanoid功能是否在其他细菌类群中是保守的，3-甲基hopanoid生理学的生理和遗传分析将在嗜碱、耐盐的好氧甲烷营养菌嗜碱甲基杆菌和放线菌加纳链霉菌中进行。

Earth's history is marked by dramatic climate changes that have had a significant impact on the evolution of life. Of particular interest to earth scientists is how ancient microbes have responded to such dramatic events. Because microbial organisms do not leave readily recognizable fossils, alternate strategies are needed to investigate ancient microbial communities. One approach is to study certain biological molecules (lipids) that can be preserved in ancient rocks. These lipids function as molecular fossils, or biomarkers, that can inform us about ancient microbial communities and environmental conditions under which they used to live. One such group of biomarkers is the 3-methylhopanes, cyclic molecules that are often assumed to be indicators for methane-oxidizing bacteria. However, these assumptions may not be robust and further studies are needed. This proposal will utilize molecular and biochemical tools to study how 3-methylhopane production is genetically and environmentally controlled in modern bacteria. This research will provide valuable information to better interpret 3-methylhopane patterns in the rock record and will ultimately lead to a better understanding of how ancient microbial communities responded to atmospheric change in the past and how similar microbial communities may respond to future climate events. The investigator will involve summer students recruited through the Summer Undergraduate Research in Geosciences and Engineering (SURGE) program at Stanford University. This proposal will provide funding for low-income summer high school interns to perform research in the researcher's laboratory through the General Earth Sciences Internship program at Stanford. These activities will provide underrepresented students with the opportunity to experience geobiology research first hand and encourage them to pursue a career in the Earth Sciences.Methylhopanoids are pentacyclic bacterial lipids whose diagenetic products, methylhopanes, are readily detected in sedimentary rocks. Based on the production of methylhopanoids in modern bacteria, methylhopane signatures in the rock record have the potential to function as biomarkers that can link bacterial taxa and their metabolisms to a specific time or event in Earth?s history. In particular, it has been proposed that 3-methylhopanes are reliable proxies for aerobic methanotrophs and indicators for significant methane biogeochemical cycling. However, recent studies have demonstrated that the diversity of extant 3-methylhopanoid producers extends beyond aerobic methanotrophs. These findings have also revealed that an understanding of the function and regulation of methylhopanoids in modern bacteria is needed in order to properly interpret the occurrence of methylhopane biosignatures in the rock record. To this end, the investigator and collaborators have begun investigating 3-methylhopanoid physiology in the aerobic methanotroph Methylococcus capsulatus. In this organism, a gene (hpnR) required for C-3 methylation has been identified and subsequently deleted. Physiological studies of the methylase mutant, which only produces unmethylated hopanoids, have revealed a potential role for 3-methylhopanoids in stationary phase survival. In this project, the investigator aims to directly pinpoint the role of 3-methylhopanoids in stationary phase survival in hopes of providing the foundation needed to properly interpret 3-methylhopane signatures in the rock record. The following three lines of investigation are proposed: 1. Physiological studies will be pursued with the M. capsulatus 3-methylhopanoid mutant to determine whether 3-methylhopanoids are involved in stationary phase survival under oxygen limited conditions, 2. ÄhpnR suppressor mutants that exhibit stationary phase survival levels similar to the wild type strain will be isolated. Utilizing high-throughput whole genome sequencing the investigator will identify intergenic mutations that restore viability of the methylase mutant, and 3. To determine if 3-methylhopanoid function is conserved in other bacterial taxa, physiological and genetic analyses of 3-methylhopanoid physiology will be undertaken in the alkaliphilic, halotolerant aerobic methanotroph Methylobacterium alcaliphilum and the actinomycete Streptomyces ghanaensis.