CAREER: De novo emergence of novel regulatory mechanisms that determine carbon and nitrogen resource allocations in plants

生物系统的整体分子组成是由复杂的代谢网络决定的，这些代谢网络主要调节碳(C)和氮(N)的分配，以组装大分子，如蛋白质、油和碳水化合物。这种代谢分配对决定植物种子的营养品质具有重要意义，从根本上影响种子作为繁殖体的能力，对粮食、饲料和生物基原料的农业生产也具有重要意义。拟南芥QQS （Qua-Quine Starch, At3g30720）基因有可能成为蛋白质和碳水化合物组装中碳氮分配的通用新调控因子。QQS是一类“孤儿”基因的原型，在任何其他物种中都没有序列同源性，是“黑暗基因组”的典范。QQS在作物中表达时，增加蛋白质含量，降低淀粉含量。QQS与调节真核生物转录的三聚体核因子Y （NF-Y）的C4亚基相互作用。该项目的更广泛影响包括研究的内在性质，它可以为我们系统地指导新陈代谢以生产食物和饲料以及生物可再生资源的能力提供重大突破。此外，该项目将为密西西比州的博士后研究人员、研究生、本科生和高中/初中/小学学生和植物生物技术教育提供优秀的项目，提供跨学科培训，以增加学生早期接触生物学，并增加早期职业研究人员的数量，他们可能会刺激STEM研究的创新。总体研究目标是确定和扩展新的调控网络，使QQS控制植物中蛋白质和碳水化合物的组成。最重要的假设是，最近才进化出现的蛋白质编码孤儿基因（如QQS）可以通过作用于现有的代谢网络来调节赋予选择优势的反应，从而在进化中被选择和维持。本研究旨在阐明QQS破坏的调控网络，从而影响决定蛋白质和碳水化合物含量的代谢网络。这项研究将为理解孤儿基因如何整合到已建立的遗传和生化网络中，并促进新性状的快速获得提供一个范例。具体来说，QQS蛋白与NF-YC4调节复合体相互作用，影响淀粉和蛋白质储备之间的C和N分配。这一特性可以跨物种屏障进行转基因转移，并具有调节植物储备以造福人类消费的潜力。此外，QQS基因提供了独特的机会，从根本上了解遗传和代谢网络之间的交集，这些网络调节着农业中最重要的性状之一：种子成分决定因素。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The bulk molecular composition of biological systems is determined by complex metabolic networks that mediate the allocation of primarily carbon (C) and nitrogen (N) to the assembly of macromolecules such as proteins, oils, and carbohydrates. This metabolic allocation is of major importance in determining the nutritional quality of plant seeds, which fundamentally affects the ability of the seed to act as the propagule and is also of major importance to agricultural production of food, feed and bio-based feedstocks. The Arabidopsis QQS (Qua-Quine Starch, At3g30720) gene has the potential of being a universal novel regulator of C and N allocation to the assembly of proteins and carbohydrates. QQS is archetypal of a class of “orphan” genes that shares no sequence homology in any other species and is exemplary of the “dark-genome”. When QQS is expressed in crops, it increases protein and decreases starch content. QQS physically interacts with the C4 subunit of the trimeric Nuclear Factor Y (NF-Y) that regulates eukaryotic transcription. The broader impacts of the project include the intrinsic nature of the research, which could provide a major breakthrough in our ability to systematically direct metabolism towards the production of food and feed, and biorenewable resources. In addition, the project will provide excellent projects for postdoctoral researchers, graduate, undergraduate and high/middle/elementary school students and education of plant biotechnology in Mississippi, accessible inter-disciplinary training to increase student exposure to biology early, and to increase the number of early career researchers who may spur innovation in STEM research. The overall research goal is to identify and expand the novel regulatory network that enables QQS to control protein and carbohydrate composition in plants. The overarching hypothesis is that protein-coding orphan genes, which have evolutionarily only recently emerged (e.g., QQS), can be selected and maintained in evolution by acting on existing metabolic networks to mediate responses that confer selective advantages. This research proposes to elucidate the regulatory network that QQS disrupts, which impacts the metabolic network determining protein and carbohydrate content. This research will provide a paradigm for understanding how an orphan gene can be integrated into established genetic and biochemical networks and spur the rapid acquisition of novel traits. Specifically, the QQS protein interacts with NF-YC4 regulatory complex, affecting the C and N partitioning between starch and protein reserves. This attribute is transgenically transferable across species barriers and has the potential to regulate plant reserves to the benefit of human consumption. Moreover, the QQS gene offers unique opportunities to fundamentally understand the intersection between genetic and metabolic networks regulating one of the most important traits in agriculture: seed composition determinants.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.