CAREER: Do extraordinarily long enzyme lifetimes drive microbial community assembly in deep subsurface sediments?

职业：极长的酶寿命是否会驱动深层地下沉积物中的微生物群落组装？

• 批准号: 2145434
• 负责人: Andrew Steen
• 金额: $ 120.1万
• 依托单位: University of Tennessee Knoxville
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-01-01 至 2027-12-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2145434&HistoricalAwards=false
• 关键词: CAREER; Do; extraordinarily; long; enzyme

Microbes that live deep in ocean sediments help drive Earth's elemental cycles, influencing key aspects of habitability on the planet, such as the amount of oxygen in the atmosphere. Microbes in the deep subsurface have a remarkable lifestyle. They turn over their biomass on timescales of decades, centuries, or even millennia, while microbes in most other environments do so every few hours or days. The driving hypothesis for this project is the unusually high stability of the deep subsurface microbes' enzymes is key to these microbes' survival. The scientific results of this project will help understand the function of a vast and mysterious ecosystem at the bottom of the ocean and may lead to new discoveries about enzyme structure and function that could have valuable applications in the food or pharmaceutical industries. The project supports the training of undergraduate and graduate students in research and teaching. In addition, K12 students participating in a summer school program called East Tennessee Freedom Schools help generate data and design experiments, giving them early input into the scientific process. The educational program allows a set of young scientists to gain experience with authentic scientific research. The central hypothesis that unusually stable enzymes help subsurface microbes to persist over long timescales is tested via a field program to collect subsurface sediments in the Gulf of Alaska, experimental manipulations of those sediments, laboratory experiments in simplified model systems, and bioinformatic analyses. Metagenomic sequencing of surface and subsurface sediments, followed by construction of metagenome-assembled genomes and computational analysis of enzyme stability, are employed to yield predictions on the stability of enzymes in subsurface sediments and the degree to which enzyme stability affects community assembly. Experimental manipulations of subsurface sediments are then used to test those predictions. The research team is also expressing, purifying, and experimentally determining the structure of a selected set of subsurface enzymes to allow independent testing of the bioinformatic predictions and simplified laboratory experiments. Together, these experiments will reveal the role of enzyme stability in driving microbial community assembly in subsurface sediments.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

生活在海洋沉积物深处的微生物有助于推动地球的元素循环，影响地球上可居住性的关键方面，例如大气中的氧气量。深层地下的微生物有着非凡的生活方式。它们以几十年、几个世纪甚至几千年的时间尺度转换生物量，而大多数其他环境中的微生物每隔几小时或几天就转换一次。该项目的驱动假设是，深层地下微生物酶的异常高稳定性是这些微生物生存的关键。该项目的科学成果将有助于了解海底巨大而神秘的生态系统的功能，并可能导致有关酶结构和功能的新发现，这些发现可能在食品或制药行业中具有宝贵的应用价值。该项目支持对本科生和研究生进行研究和教学方面的培训。此外，K12学生参加了一个名为东田纳西自由学校的暑期学校计划，帮助生成数据和设计实验，让他们早期投入到科学过程中。该教育计划允许一组年轻科学家获得真实科学研究的经验。中心的假设，异常稳定的酶帮助地下微生物长期坚持通过一个现场计划，以收集阿拉斯加湾的地下沉积物，这些沉积物的实验操作，在简化的模型系统的实验室实验，和生物信息学分析进行测试。宏基因组测序的表面和地下沉积物，然后由宏基因组组装的基因组和酶的稳定性的计算分析的建设，产生在地下沉积物中的酶的稳定性和酶的稳定性影响社区组装的程度的预测。然后使用地下沉积物的实验操作来测试这些预测。研究小组还表达，纯化和实验确定一组选定的地下酶的结构，以允许独立测试生物信息学预测和简化的实验室实验。总之，这些实验将揭示酶的稳定性在驱动地下沉积物中微生物群落组装的作用。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

项目成果

Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery

• DOI: 10.1109/bibm58861.2023.10385976
• 发表时间: 2023-12
• 期刊: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
• 作者: Ashley Babjac;Owen Queen;Shawn-Patrick Barhorst;Kambiz Kalhor;Andrew D. Steen;Scott J. Emrich

Biogeochemistry of Earth before exoenzymes

外酶出现之前地球的生物地球化学

• DOI: 10.1038/s41561-023-01266-4
• 发表时间: 2023
• 期刊: Nature Geoscience
• 影响因子: 18.3
• 作者: Mahmoudi, Nagissa;Steen, Andrew D.;Halverson, Galen P.;Konhauser, Kurt O.
• 通讯作者: Konhauser, Kurt O.