Co-option of a seed-like proteome by oil-rich tubers

Co-option is an important aspect of evolution that can occur on several levels. Genes, whose function was molded by selection in the evolutionary past, are readily observed to serve a new function when acting in a different context in an extant system. Whole organs can be co-opted for new roles as well. For example, roots that evolved from shoot-like axes. Finally a framework of genes and its coded proteins can be co-opted to serve a similar molecular function but in a completely different organ, drastically changing its properties. Here, we describe such an example, where a set of proteins important for desiccation tolerance and oil accumulation in seeds of most angiosperms was co-opted in the tubers of yellow nutsedge (Cyperus esculentus). These tubers are not only desiccation tolerant but also store a large amount of lipids--especially TAG, similar to seeds. We generated nanoLC-MS/MS-based proteomes in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to a previously published proteome of Arabidopsis seeds and seedlings indicate that indeed a seed-like proteome was co-opted. This was further supported by an analysis of the proteome of a lipid-droplet enriched fraction of yellow nutsedge, which also displayed seed-like characteristics.