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

NSF 生物学博士后奖学金：探索马齿苋中 CAM 和 C4 光合作用的细胞类型调节动力学

• 批准号: 2208915
• 负责人: Ian Gilman
• 金额: $ 21.6万
• 依托单位: Gilman, Ian S
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2208915&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; Exploring

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.

该行动为2022财年的生物学生物学研究金奖学金提供了一项NSF植物基因组研究奖学金。该奖学金支持该研究员的主机实验室研究和培训计划，该研究员还提出了扩大生物学参与计划的计划。该奖学金的研究和培训计划的标题是伊恩·吉尔曼（Ian S.奖学金的主持机构是密歇根州立大学，赞助科学家是罗伯特·范伯伦（Robert Vanburen）博士。C4光合作用和crassuracean酸代谢（CAM）是提高光合作用效率的植物适应。世界上许多最重要的农作物都使用C4光合作用，包括玉米，甘蔗和小米，这使它们可以在低营养和高光环境中迅速生长。 CAM大大提高了植物用水的效率，因此通常在水砂环境中（例如北美沙漠的仙人掌）中发现。曾经认为植物可以使用C4光合作用或CAM，但这并不是因为它们会竞争使用相同必要的酶和代谢物。但是，被发现与C4光合作用和凸轮相结合的curolanes（Portulaca）（portulaca）（portulaca），这使它们在低营养和低水栖息地（如人行道裂缝）中得以极快地生长。了解如何将C4光合作用和CAM组合在一起，将提供新的方法，以通过C4光合作用来提高农作物的干旱耐受性，并阐明如何调节基因的多种角色基因。该项目的更广泛影响将增强与校园内外的当地社区的参与，以突出植物学与计算机科学之间的联系，展示共同的杂草如何彻底改变一致性，并讨论基因工程的好处。培训对象包括获得园艺，系统生物学，分子和计算方法开发以及数据积分方面的专业知识。C4光合作用（C4）和Crassuracean酸代谢代谢（CAM）是碳浓缩机制（CCMS），这些机制（CCMS）已随着对过去3000万年的植物反应而发展，这些机制已进化为植​​物对植物的反应。这两个CCM都选择了相同的古代代谢模块，以提高光合作用所需的二氧化碳浓度，但以相反的方式部署了这些模块。 C4浓度通过两组CO2泵在空间上二氧化碳，而CAM可以通过临时协调的碳存储和重新释放来实现二氧化碳浓度。 These adaptations conference C4 species with the highest rates of plant photosynthesis, characterized by maize and sugarcane, and 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具有C4+CAM的多个独立起源，为如何整合多个CCM提供了独特的见解，以提高高产C4作物的干旱耐受性。该项目将利用系统和计算生物学来确定控制CAM和C4在细胞类型水平上CAM和C4的临时和空间协调的遗传因素。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力学，并使用测序使用测序（AtacSeq）使用测定对转座酶可访问的染色质的测定法识别与CCM相关的顺式调节元件。基于机器学习的方法将使用这些数据来构建区分CIS元素和控制C4和CAM的调节动态的基因调节网络。最后，将比较物种之间的监管网络，以识别portulaca中CCMS演变的共享和独特元素。该项目生成的数据将通过NCBI的简短阅读存档（SRA）和Datadryad（https://datadryad.org）提供给公众，分析的分步演练将托管在Github（https：//github.com）。酸性代谢，Atacseq，转录组学奖反映了NSF的法定任务，并通过使用基金会的知识分子优点和更广泛的影响评估标准评估，被认为是宝贵的支持。