Enhancer-driven random gene overexpression (ERGO): a method to study gene function in Chlamydomonas

Abstract

Gene overexpression can be used to study gene function and is more suitable to characterize essential and redundant genes than gene knockout. A forward genetic approach based on random gene overexpression, also known as activation tagging, was previously used to study gene function in angiosperms. However, such an approach has never been applied to algae. Here, we present enhancer-driven random gene overexpression (ERGO), a forward genetic screen that we utilized to study genes involved in carotenoid metabolism in the green alga Chlamydomonas reinhardtii. We generated a library of over 33,000 insertional mutants in a yellow-in-the-dark background strain, which is incapable of producing chlorophyll in the dark. Each mutant contained a randomly inserted enhancer, Ehist cons, capable of activating gene expression in the C. reinhardtii nuclear genome. After visually screening the mutant colonies for a color change from yellow to orange, we isolated a mutant with increased carotenoid content and remarkable resistance to high-light stress. RNA-seq data analysis revealed substantial upregulation of a gene, that we name CMRP1, encoding a putative F-box protein. CRISPR-mediated knockout of this gene resulted in decreased carotenoid concentrations, confirming that CMRP1 is involved in the regulation of carotenoid metabolism. Our study shows that a gene overexpression screen can be successfully adapted to C. reinhardtii and potentially other plants and algae, thereby expanding the palette of genetic tools to study gene function.