RUI: Regulation Of Pyrimidine Metabolism In Plants

嘧啶核苷酸是生物合成DNA和RNA的前体，这些分子包含植物和所有其他生物体生长发育所必需的遗传信息。udp糖也是合成某些类型脂质的活化中间体，也是植物中主要的碳水化合物储存产物（蔗糖）和细胞壁多糖（纤维素、半纤维素、果胶），占地球生物量和食物和纤维生产的大部分。生物化学研究有助于确定主要的酶和途径，包括嘧啶代谢，但植物仍然是唯一的主要生物群体，其控制嘧啶代谢的基本机制尚未阐明。功能基因组学方法将用于研究模式植物拟南芥的嘧啶代谢。利用生物信息学工具从集成基因组学数据库中“挖掘”信息，确定了146个基因编码嘧啶代谢（核苷酸的从头合成、核苷酸间转换、预形成的核碱基/核苷转化为核苷酸、分解代谢途径）和相关途径（udp -葡萄糖和精氨酸合成）的每个主要领域的功能特征或假定酶。本研究的目标是1)在基因表达水平上使用DNA微阵列来表征途径活动的协调，并鉴定潜在的调控基因2)在体外（定义突变体的互补，生化研究）或植物中(T-DNA敲除，rnai介导的基因沉默，3)研究每个基因的表达对植物组织中嘧啶有效性变化的响应(N-（phosphonacetyl)- l -aspartate （PALA）抑制de novo合成、外源嘧啶等）。与The Institute for Genomic Research的合作将确保生成高质量的阵列数据。而全长cdna /ESTs和拟南芥T-DNA敲除突变体的可用性将有助于拟议的研究。更广泛的影响：这些研究将显著推进我们对植物中嘧啶代谢调控的理解，并将为这些活动与植物代谢其他领域的协调提供重要的见解。该项目将为本科生提供生物信息学和植物功能基因组学方面的培训机会。来自阵列实验的基因表达数据也将用于未来古彻学院生物信息学课程的学生研究驱动项目，扩大该研究的教育影响。学生将在科学会议上展示他们的研究，并将共同发表论文。如果过去的趋势继续下去，他们中的大多数人将在排名靠前的研究生或专业学校攻读学士学位后的培训。

Pyrimidine nucleotides are precursors in the biosynthesis of DNA and RNA, molecules which contain the essential genetic information for growth and development in plants and all other living organisms. UDP-sugars are also activated intermediates in the synthesis of certain types of lipids, as well as a major carbohydrate storage product (sucrose) and cell wall polysaccharides (cellulose, hemicellulose, pectins) in plants, accounting for much of the earth's biomass and production of food and fiber. Biochemical studies have helped to define major enzymes and pathways comprising pyrimidine metabolism, but plants remain the only major group of organisms for which basic mechanisms controlling pyrimidine metabolism have not been elucidated.A functional genomics approach will be used to study pyrimidine metabolism in the model plant, Arabidopsis. Using bioinformatics tools to "mine" information from integrated genomics databases, 146 genes encoding functionally characterized or putative enzymes in each of the major areas of pyrimidine metabolism (de novo synthesis of nucleotides, nucleotide interconversions, salvaging of preformed nucleobases/nucleosides to nucleotides, catabolic pathways) and related pathways (UDP-glucose and arginine synthesis) have been identified. The goals of this research are to 1) use DNA microarrays to characterize coordination of pathway activities, at the level of gene expression, and to identify potentially-regulated genes 2) to functionally characterize a small number of genes/enzymes in vitro (complementation of defined mutants, biochemical studies) or in planta (T-DNA knockouts, RNAi-mediated gene silencing, 35S promoter-driven overexpression in transgenic Arabidopsis lines) 3) to study expression of each gene in response to changes in pyrimidine availability in plant tissues (N-(phosphonacetyl)-L-aspartate (PALA) inhibition of de novo synthesis, exogenous pyrimidines, etc.) The proposed collaboration with The Institute for Genomic Research ensures that high-quality array data will be generated, while availability of full-length cDNAs/ESTs and Arabidopsis T-DNA knockout mutants for the enzymes to be studied will facilitate the proposed research.Broader impacts: These studies will significantly advance our understanding of the regulation of pyrimidine metabolism in plants and will provide important insights into coordination of these activities with other areas of plant metabolism. The project will provide training opportunities for undergraduate students in bioinformatics and plant functional genomics. Gene expression data from array experiments will also be used in future student investigator-driven projects in a bioinformatics course at Goucher College, expanding the educational impact of this research. Students will present their research at scientific meetings and will co-author publications. If the past trends continue, most of them will pursue post-baccalaureate training at top-ranked graduate or professional schools.