Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation

Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels. Overall design: RNA-Seq and Ribo-Seq analyses of wild-type (W303a) and cth1?cth2? knockout strains cultured in Fe-sufficient conditions (0H), and after a short- (3H) or long-term (6H) exposure to Fe deficiency, achieved by the addition of the Fe2+-specific chelator bathophenanthroline disulfonate (BPS).