CAREER: Evolutionary dynamics of polycistronic gene expression in Archaeplastida: implications for stress adaptation and evolution

About This Grant

In prokaryotes, the expression of clusters of genes, typically functionally related, often is controlled by a single regulatory sequence leading to a single transcript molecule that encodes multiple proteins. In contrast, in eukaryotes, each nuclear gene has its own regulatory sequence, and each gene leads to a separate transcript encoding a single protein. A few organisms in the animal kingdom show exceptions to this paradigm, and transcripts encoding multiple proteins have recently been found in green algae, which are related to land plants. This suggests that the expression of clusters of genes resulting in transcripts encoding multiple proteins might be more common in the plant kingdom than previously thought. This project uses DNA and RNA sequencing, bioinformatics approaches, and a combination of in vitro and in vitro experiments to explore the presence and functional significance of transcripts encoding multiple proteins among species in the plant kingdom. Plants are the primary producers on our planet, and a better understanding of the mechanisms they employ for gene expression, may enable new approaches for plant breeding. The research program will be integrated with educational and outreach activities designed to engage learners of all ages and increase exposure to STEM disciplines. The education-by-research component of this project will help inspire and train the next generation of scientists. Recent studies have provided evidence of polycistronic gene expression in diverse green alga, highlighting the evolutionary conservation of polycistronic mRNAs among Chlorophytes. Polycistronic mRNAs in land plants have often been regarded as the result of accidental read-through, and little research has studied the prevalence of polycistronic gene expression across Archaeplastida. This CAREER project aims to determine how widespread polycistronic expression is in Archaeplastida and investigate its functional and evolutionary significance. Research activities will (1) generate a map of the polycistron landscape of key Archaeplastida species using long-read sequencing platforms for whole genome sequencing and poly(A)-tailed RNA sequencing, along with database mining and bioinformatic approaches; (2) study the evolutionary dynamics of polycistronic transcripts through ribosome deep sequencing to assess active translation; and (3) investigate the mechanisms of polycistron translation using in vivo and in vitro assays. These experiments will test the hypothesis that polycistrons are evolutionarily conserved at the structural and functional levels within Archaeplastida. The project integrates an education and outreach program, which includes Science Discussion Seminars and training in all aspects of research. It also includes science demonstrations, hands-on activities, and the development of educational materials for K-12 students and the public. A central product of these efforts will be a public database documenting polycistronic sequences across Archaeplastida species. The outcomes of this research are expected to significantly advance our understanding of the evolutionary dynamics of gene organization and expression in Archaeplastida and shed light on the broader implications of polycistronic gene regulation. 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.