Maize cytolines unmask key nuclear genes that are under the control of retrograde signaling pathways in plants

Abstract

The genomes of the two plant organelles encode for a relatively small number of proteins. Thus, nuclear genes encode the vast majority of their proteome. Organelle-to-nucleus communication takes place through retrograde signaling (RS) pathways. Signals relayed throughRS pathways have an impact onnucleargene expressionbut their target-genes remain elusive inanormal stateof the cell (considering that onlymutants and stress have been used so far). Here, we usemaize cytolines as an alternative. The nucleus of a donor linewas transferred into twoother cytoplasmic environments through at least nine back-crosses, in a time-span of >10 years. The transcriptomes of the resulting cytolines were sequenced and compared. There are 96 differentially regulated nuclear genes in two cytoplasm-donor lines when compared with their nucleus-donor. They are expressed throughout plant development, in various tissues and organs. One-third of the 96 proteins have a human homolog, stressing their potential role in mitochondrial RS. We also identified syntenic orthologous genes in four other grasses and homologous genes inArabidopsis thaliana. These findings contribute to the paradigmwe use to describe the RS in plants. The 96 nuclear genes identified here are not differentially regulated as a result of mutation, or any kind of stress. They are rather key players of the organelle-to-nucleus communication in a normal state of the cell.