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是如何对这种戏剧性事件做出反应的。因为微生物不会留下容易辨认的化石，所以需要替代的策略来研究古老的微生物群落。一种方法是研究可以保存在古代岩石中的某些生物分子(脂)。这些脂质的功能是分子化石或生物标记物，可以告诉我们古代微生物群落和它们过去生活的环境条件。其中一组这样的生物标记物是3-甲基藿烷，环状分子通常被认为是甲烷氧化菌的指示物。然而，这些假设可能并不可靠，还需要进一步研究。这项提议将利用分子和生化工具来研究现代细菌如何从遗传和环境上控制3-甲基何宾的生产。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，并最终有助于更好地了解古代微生物群落如何响应过去的大气变化，以及类似的微生物群落可能如何响应未来的气候事件。调查人员将包括通过斯坦福大学地球科学与工程暑期本科生研究(Surge)项目招聘的暑期学生。这项提案将通过斯坦福大学的普通地球科学实习计划，为低收入夏季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。这些活动将为未被充分代表的学生提供亲身体验地球生物学研究的机会，并鼓励他们在地球科学领域追求职业生涯。甲基藿烷是一种五环细菌脂类，其成岩产物甲基藿烷很容易在沉积岩中检测到。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发挥作用，将细菌分类群及其代谢与地球-S历史上的特定时间或事件联系起来。特别是，有人提出，3-甲基藿烷是好氧甲烷氧化菌的可靠替代品，也是重要的甲烷生物地球化学循环的指示剂。然而，最近的研究表明，现存的3-甲基并吡喃产生菌的多样性超出了好氧甲烷氧化菌的范围。这些发现还表明，为了正确解释岩石记录中甲基霍帕烷生物签名的出现，需要了解甲基霍帕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好氧甲烷纳豆菌甲氧基球菌壳中的3-甲基霍帕宁生理学。在这种生物中，C-3甲基化所需的基因(HpnR)已被鉴定并随后被删除。对该甲基酶突变体的生理学研究揭示了3-甲基荷浦碱在静止期存活中的潜在作用，它只产生未甲基化的荷帕诺。在这个项目中，研究人员的目标是直接确定3-甲基霍帕烷在静止相存活中的作用，希望为正确解释岩石记录中的3-甲基霍普烷特征提供所需的基础。建议进行以下三个方面的研究：1.对3-甲基霍帕尼醇突变体进行生理学研究，以确定3-甲基霍帕尼醇是否参与了氧限制条件下的稳定期生存；2.将分离出与野生型菌株相似的稳定期存活水平的hpnR抑制突变体。利用高通量全基因组测序，研究人员将识别恢复甲基酶突变体生存能力的基因间突变，以及3。为了确定3-甲基Hopanid功能是否在其他细菌分类群中保守，将在嗜碱、耐盐的好氧甲烷营养菌Methylobacterium alcalPhilum和放线菌Streptomyces ganaensis中进行3-甲基Hopanid生理活性的生理和遗传分析。

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.