QQSorphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

Abstract

The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua-Quine Starch; At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in Arabidopsis and soybean. Here the universality of QQS function in modulating carbon and nitrogen allocation is exemplified by a series of transgenic experiments. We show that ectopic expression of QQS increases soybean protein independent of the genetic background and original protein content of the cultivar. Furthermore, transgenic QQS expression increases the protein content of maize, a C4 species (a species that uses 4-carbon photosynthesis), and rice, a proteinpoor agronomic crop, both highly divergent from Arabidopsis. We determine that QQS protein binds to the transcriptional regulator AtNF-YC4 (Arabidopsis nuclear factor Y, subunit C4). Overexpression of AtNF-YC4 in Arabidopsis mimics the QQS-overexpression phenotype, increasing protein and decreasing starch levels. NF-YC, a component of the NF-Y complex, is conserved across eukaryotes. The NF-YC4 homologs of soybean, rice, and maize also bind to QQS, which provides an explanation of how QQS can act in species where it does not occur endogenously. These findings are, to our knowledge, the first insight into the mechanism of action of QQS in modulating carbon and nitrogen allocation across species. They have major implications for the emergence and function of orphan genes, and identify a nontransgenic strategy for modulating protein levels in crop species, a trait of great agronomic significance.QQS | NF-YC4 | carbon allocation | nitrogen allocation | orphan C arbon and nitrogen allocation to plant proteins, carbohydrates, and lipids is not controlled by a single gene but by many (1). Most of the enzymes promoting accumulation of these products have been identified; however, much less is understood about the mechanisms that regulate this complex metabolic network (2-8).Arabidopsis thaliana QQS (Qua-Quine Starch; At3g30720) lacks sequence similarity to any other protein-coding genes, and is considered an orphan gene that has arisen de novo from noncoding sequence since the divergence of A. thaliana from other species (9, 10). Although orphans typically comprise 2-8% of the genome of eukaryotic and prokaryotic species, their origin and biological function have not been well-explored (11)(12)(13)(14). Proteins encoded by some orphan genes provide a defensive capability by binding to a receptor of a predator organism (11). In contrast, QQS action is endogenous (3): Overexpression of QQS in Arabidopsis increases total protein content and decreases total starch content in leaf, whereas down-regulation of QQS has the converse effect. The increased starch content in QQS RNAi (RNA interference) mutants is due to increased starch accumu...

The Arabidopsis thaliana Nuclear Factor Y Transcription Factors

“…For example, NF-YA2, A3, and A5 participate in nitrogen nutrition (Zhao et al, 2011; Leyva-González et al, 2012); NF-YA2, NF-YA10, and NF-YB2 function in the control of primary root growth (Ballif et al, 2011; Sorin et al, 2014); NF-YB1 affects shoot apical meristem growth (Wenkel et al, 2006); NF-YC4 is involved in starch and protein metabolism (Li et al, 2015); and NF-YA5/B9/C9 associates with chlorophyll biosynthesis (Warpeha et al, 2007). …”

Discovery and Characterization of the 3-Hydroxyacyl-ACP Dehydratase Component of the Plant Mitochondrial Fatty Acid Synthase System

“…RNA-seq was performed as described previously (Li et al, 2015). Specifically, total RNA (three biological replicates) was extracted from 0.5 g of fresh aerial organs of plants (grown in a completely randomized design) at 16 DAI using TRIzol (Invitrogen) and was further purified using the RNeasy Plant Mini Kit (Qiagen) following DNase I (Invitrogen) treatment to remove any DNA contamination.…”

QQS orphan gene and its interactor NF‐YC4 reduce susceptibility to pathogens and pests

“…It has no homology with proteins of genes of other species, including those of A. lyrata and A. halerieii (Li et al ., , ). QQS regulates carbon and nitrogen partitioning to starch and protein in Arabidopsis, and also in the leaves and seeds of transgenic QQS ‐expressing soybean, corn and rice (Li and Wurtele, ; Li et al ., , ). Transgenic plants with perturbed QQS expression have altered starch and protein accumulation but normal development and morphology.…”

“…Transgenic plants with perturbed QQS expression have altered starch and protein accumulation but normal development and morphology. Overexpression of QQS increases protein content and decreases starch content, while down‐regulation of QQS decreases protein and increases starch (Li and Wurtele, , ,b; Li et al ., , ).…”