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

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, transcriptomics

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.