The effects of holoparasitism on plant organellar translation and tRNA metabolism

The mitochondria and chloroplasts found in eukaryotes are derived from bacteria and retain their own genomes and their own molecular machinery for protein translation. This translation machinery is more conserved and bacterial-like in plants than in other eukaryotes. To test the hypothesis that the intense demands for protein production associated with photosynthesis are responsible for the natural selection that conserves plant mitochondrial and chloroplast translation machinery, this project will investigate the evolution of holoparasitic plants. These organisms have entirely lost the ability to photosynthesize and instead acquire energy by tapping into the vasculature of a host plant or consuming soil fungi. Many genes have been lost from the organellar genomes of these plants, and this research will help understand how bacterial-like enzymes can be functionally replaced by their eukaryotic counterparts even after billions of years of evolutionary divergence. In addition, it will provide insights into how the very last remaining genes in mitochondrial and chloroplast genomes can be lost and thereby complete the final steps of integrating these organelles into the eukaryotic cell. The project will also provide training for researchers at undergraduate, graduate, and postdoctoral levels in bioinformatics, molecular genetics, biochemistry, and evolutionary biology. It will also be coupled with international collaborations, outreach workshops, and a program for first-year undergraduates to broaden access to career opportunities in computational biology. Initial observations indicate that numerous components of the mitochondrial and chloroplast translation machinery in holoparasites have been lost and functionally replaced with corresponding machinery from the cytosol that is typically responsible for translating proteins encoded by nuclear genes. The perturbations to organellar translation machinery resulting from loss of photosynthesis appear to be associated with extensive rewiring of interactions between tRNAs and aminoacyl-tRNA synthetases (aaRSs). These changes will be assessed through a combination of comparative genomics, subcellular localization analysis (fluorescence microscopy), specialized tRNA sequencing methods, and in vitro aminoacylation assays. These analyses will determine the extent to which changes in subcellular targeting and aaRS substrate specificity facilitate the process of gene loss and functional replacement. They will also determine how the well-characterized parallel roles of chloroplast tRNA-Glu in both translation and tetrapyrrole biosynthesis can both be functionally replaced, leading to the loss of this gene and eventually to the loss of the entire chloroplast genome. 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.