NSF Postdoctoral Fellowship in Biology: Exploring Cell-type Regulatory Dynamics of CAM and C4 Photosynthesis in Portulaca

本行动资助2022财年美国国家科学基金会植物基因组生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Ian S. Gilman博士的研究和培训计划的标题是“探索马齿苋中CAM和C4光合作用的细胞型调节动力学”。该奖学金的主办机构是密歇根州立大学，赞助科学家是罗伯特·范布伦博士。C4光合作用和天冬酸代谢（CAM）是植物提高光合作用效率的适应性。世界上许多最重要的作物都使用C4光合作用，包括玉米、甘蔗和小米，这使它们能够在低营养和高光环境下快速生长。CAM大大提高了植物对水的利用效率，因此在缺水环境中的植物中普遍存在，例如北美沙漠中的仙人掌。人们曾经认为，植物可以利用C4光合作用或CAM光合作用，但不能同时利用两者，因为它们会竞争使用相同的必要酶和代谢物。然而，马齿苋（马齿苋）——全球常见的杂草——被发现结合了C4光合作用和CAM，这使得它们能够在低营养和低水的栖息地（如人行道裂缝）生长得非常快。了解C4光合作用和CAM如何结合将为提高C4光合作用作物的耐旱性提供新的途径，并揭示基因如何发挥多种作用的基本问题。这个项目的广泛影响将加强与当地社区的接触，无论是在校内还是校外，突出植物学和计算机科学之间的联系，展示常见杂草如何彻底改变农业，并讨论基因工程的好处。培训目标包括获得园艺学、系统生物学、分子和计算方法开发以及数据集成方面的专业知识。C4光合作用（C4）和天冬酸代谢（CAM）是碳浓缩机制（CCMs），是植物在过去3000万年中对低二氧化碳世界的反应而进化出来的。两种CCMs都采用了相同的一套古老的代谢模块来提高光合作用所需的二氧化碳浓度，但它们以不同的方式部署这些模块。C4通过双电池CO2泵在空间上浓缩CO2，而CAM通过时间协调的碳储存和再释放来完成CO2的浓缩。这些适应性使C4植物具有最高的光合速率，以玉米和甘蔗为特征，而CAM植物具有极高的水分利用效率，以仙人掌、芦荟和龙舌兰为代表。虽然C4和CAM在数百个谱系中独立进化，并共享许多生化成分，但已知只有两个陆地植物谱系同时使用C4和CAM (C4+CAM)：马蹄苋和Trianthema， C4植物在应对非生物胁迫时同时表现出CAM。Portulaca拥有多个独立的C4+CAM来源，为如何整合多个ccm以提高高产C4作物的耐旱性提供了独特的见解。该项目将利用系统和计算生物学来确定在细胞类型水平上控制马齿苋中CAM和C4时空协调的遗传因素。该项目的第一个目标是使用单细胞RNAseq捕获单个细胞的表达动态，并使用转座酶可及染色质测序（ATACseq）鉴定ccm相关的顺式调控元件。基于机器学习的方法将使用这些数据来构建基因调控网络，以区分C4和CAM的顺式元件和调控动态。最后，将比较不同物种之间的调控网络，以确定葡萄牙ccm进化背后的共同和独特因素。该项目生成的数据将通过NCBI的短读档案（SRA）和DataDryad （https://datadryad.org）向公众提供，并将在GitHub (https://github.com).Keywords)上托管逐步分析的步骤。基因调控网络、单细胞测序、C4光合作用、天冬氨酸代谢、ATACseq、转录组学。该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行了评估，认为值得支持。

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Ian S. Gilman is “Exploring Cell-type Regulatory Dynamics of CAM and C4 Photosynthesis in Portulaca”. The host institution for the fellowship is Michigan State University and the sponsoring scientist is Dr. Robert VanBuren.C4 photosynthesis and Crassulacean Acid Metabolism (CAM) are plant adaptations that increase the efficiency of photosynthesis. Many of the world’s most important crops use C4 photosynthesis, including maize, sugarcane, and millet, which allows them to quickly grow in low nutrient and high light environments. CAM greatly increases the efficiency of plants’ water use and is therefore commonly found in plants in water-scarce environments, such as the cacti of North American deserts. It was once thought that plants could use either C4 photosynthesis or CAM, but not both because they would compete for use of the same necessary enzymes and metabolites. However, the Purslanes (Portulaca)—common weeds across the globe—were discovered to combine C4 photosynthesis and CAM, which allows them to grow extremely fast in low nutrient and low water habitats like sidewalk cracks. Understanding how C4 photosynthesis and CAM can be combined will provide new ways to improve the drought tolerance of crops with C4 photosynthesis and shed light on fundamental questions of how genes are regulated for multiple roles. Broader impacts from this project will enhance engagement with the local community, both on and off campus, to highlight connections between botany and computer science, demonstrate how common weeds could revolutionize agriculture, and discuss the benefits of genetic engineering. Training objectives include obtaining expertise in horticulture, systems biology, molecular and computational methods development, and data integration.C4 photosynthesis (C4) and Crassulacean Acid Metabolism (CAM) are carbon concentrating mechanisms (CCMs) that have evolved as plant responses to the low CO2 world of the past 30 million years. Both CCMs have co-opted the same set of ancient metabolic modules to boost the concentration of CO2 needed for photosynthesis, but have deployed these modules in contrasting ways. C4 concentrates CO2 spatially through a two-cell CO2 pump, while CAM accomplishes CO2 concentration with temporally coordinated carbon storage and re-release. These adaptations confer C4 species with the highest rates of plant photosynthesis, characterized by maize and sugarcane, and CAM plants with extremely high water use efficiencies, emblematic of cacti, aloes, and agaves. Although C4 and CAM have evolved independently in hundreds of lineages and share many biochemical components, only two land plant lineages are known to use both C4 and CAM (C4+CAM): Portulaca and Trianthema, C4 plants that facultatively exhibit CAM in response to abiotic stress. Portulaca, with multiple independent origins of C4+CAM, offers unique insights into how multiple CCMs can be integrated to increase the drought tolerance of highly productive C4 crops. This project will leverage systems and computational biology to identify the genetic elements controlling the temporal and spatial coordination of CAM and C4 in Portulaca at the cell-type level. The first goal of the project is to capture expression dynamics of individual cells using single cell RNAseq and identify CCM-related cis-regulatory elements using assay for transposase-accessible chromatin using sequencing (ATACseq). Machine learning based methods will use these data to construct gene regulatory networks that distinguish cis-elements and regulatory dynamics governing C4 and CAM. Finally, regulatory networks will be compared between species to identify shared and unique elements underlying the evolution of CCMs in Portulaca. Data generated for this project will be made available to the public though NCBI's Short Read Archive (SRA) and DataDryad (https://datadryad.org), and step-by-step walkthroughs of analyses will be hosted on GitHub (https://github.com).Keywords: gene regulatory networks, single-cell sequencing, C4 photosynthesis, Crassulacean Acid Metabolism, ATACseq, transcriptomicsThis 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.