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We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene,Qua-Quine Starch(QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species.QQSmodulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developingChlamydomonas reinhardtiiandSaccharomyces cerevisiaestrains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression ofQQSinC. reinhardtiimodulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies inS. cerevisiaerevealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, inS. cerevisiaeboth the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.