Research Projects

To adapt to daily fluctuations in light and temperature, organisms have evolved circadian clocks that temporally coordinate metabolism. By anticipating environmental changes, these clocks regulate metabolic activity in a time-of-day-dependent manner. While most studies have focused on mRNA and protein abundance as proxies for pathway activity, we propose that post-translational regulation plays a critical and underexplored role in shaping temporal rhythms in metabolic outputs. An emerging layer of posttranslational regulation involves the RNA-binding “moonlighting” function of metabolic enzymes, a phenomenon conserved across diverse species. RNA binding has been shown to modulate the catalytic activity of these enzymes, thereby directly influencing their associated metabolic pathways. RNA-interactome capture (RIC) studies from our lab and others have identified a wide array of RNA-binding metabolic enzymes involved in central pathways such as glycolysis, the TCA cycle, the pentose phosphate pathway, the photosynthetic apparatus, fatty acid metabolism, and reactive oxygen species (ROS) metabolism, pathways that are conserved from cyanobacteria to plants and humans. Building on this, our lab has employed a time-resolved RIC approach, revealing that many of these enzymes exhibit circadian variation in RNA-binding activity. Notably, many evolutionarily conserved metabolic enzymes display time-of-day-dependent RNA-binding activity. This temporal dynamicity provides a unique and tractable test bed to investigate how circadian regulation of RNA–enzyme interactions mechanistically contributes to daily metabolic rhythms. In this proposal, we aim to uncover the mechanistic basis of circadian RNA–enzyme interactions and investigate their role in circadian riboregulation, a regulatory mode wherein RNAs modulate the enzymatic activity of their cognate proteins, thereby driving daily metabolic rhythms. Building on our previous work, which showed that the circadian dynamics of RNA-binding are independent of the total protein abundance, we hypothesize that non-transcriptional mechanisms, such as post-translational modifications (PTMs), may underlie the temporal regulation of RNA-binding activity. Given that RNA-binding has been shown to modulate enzymatic function, such dynamics may result in differential regulation of metabolism across the day-night cycle. To investigate these mechanisms, we will use the genetically tractable and biochemically accessible phytoplankton Chlamydomonas reinhardtii (eukaryote) and Synechococcus elongatus (prokaryote) as model systems. Their complementary features make them ideal for studying circadian regulation, photosynthesis, and environmental responses. Both organisms possess highly conserved metabolic pathways analogous to those in multicellular plants and animals, enabling the dissection of fundamental principles of metabolic regulation. Our multidisciplinary approach will combine molecular genetics, biochemistry, and high-throughput RNA and protein sequencing, along with genetic engineering, biophysical assays, and imaging. Specifically, we aim to (i) characterize the molecular determinants underlying the temporal specificity of RNA-binding, (ii) identify RNA targets of key metabolic enzymes across circadian time, and (iii) assess the functional impact of these interactions on cellular metabolism. This work will deepen our understanding of RNA-mediated regulation of metabolism, offering novel insights into the non-genomic pathways of circadian control. The outcomes have broad implications, from harnessing small RNAs as regulators in drug discovery, to informing the metabolic engineering of algae for biofuel production. Ultimately, this study will advance the fundamental biology of circadian riboregulation and its role in orchestrating daily metabolic rhythms across life forms.