To improve the nitrogen use efficiency (NUE) of crops to increase yields, one approach is to develop crops with improved NUE. Qua Quine Starch (QQS), a species-specific orphan gene present only in Arabidopsis thaliana, has a novel, unexpected functionality. Approximately 0.5- 8% of genes in a given species are uniquely present in that species, having no homologs in other species. They represent a significant fraction of eukaryotic and prokaryotic genomes, and are thought to be a determinant of the character of a species. However, little is known about the functional significance of these so-called species-specific or orphan genes. QQS can affect the extremely important trait of protein content when expressed in other species, in soybean, maize and rice. Understanding QQS functions has multiple impacts, revealing how plants partition precious carbon and nitrogen resources. Here, we report QQS interactor nuclear factor Y subunit C4 (NF-YC4), affects carbon and nitrogen allocation to protein in soybean and maize. QQS and its related network may be used as a tool to increase the protein content in crops, and to study the 2 nitrogen allocation network. RNA-Sequencing analyses of the QQS mutant materials have identified candidate genes involved in regulation of nitrogen allocation.