A New Platform to Identify Utilized Coding Sequences

识别已使用编码序列的新平台

• 批准号: 1042335
• 负责人: Igor Libourel
• 金额: $ 25.69万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1042335&HistoricalAwards=false
• 关键词: New; Platform; Identify; Utilized; Coding

Intellectual Merit: The rapid development of inexpensive, high fidelity, and high-throughput sequencing technologies has facilitated the determination of countless genomes. Sequencing data have led to valuable insights into the descent of species and have played a key role in the annotation of genes in related organisms. However, the elucidation of the direct relationship between a gene and its precise function is still laborious. Similarly, although functional domains in proteins are often known, determining which amino acids are essential and which amino acid substitutions are allowed still requires an enormous time investment. This project leverages high-throughput sequencing technology to measure genome-wide utilization of genes at the nucleotide level. Bacterial cells will be grown under well-defined experimental conditions in the continual presence of a strong mutagen. This treatment will result in the accumulation of mutations in unutilized genes or in parts of utilized genes coding for replaceable amino acids. The introduced variation will be detected by DNA sequencing and the results should distinguish utilized genes from unutilized ones, and replaceable amino acids from those required for protein function.Broader Impacts: This platform will be widely applicable, both for industrial and academic purposes to enable protocol-driven gene discovery. The method does not require much upfront knowledge about metabolism, and uses biocomputing for assessing gene function. The project will provide educational opportunities for a postdoctoral fellow and for undergraduate students.

智力优点：廉价，高保真度和高通量测序技术的快速发展促进了无数基因组的确定。测序数据已导致对物种下降的宝贵见解，并在相关生物体的基因注释中发挥了关键作用。但是，阐明基因与其精确功能之间的直接关系仍然很费力。 同样，尽管蛋白质中的功能结构域通常是已知的，但确定哪些氨基酸是必不可少的，并且允许哪些氨基酸取代仍然需要大量的时间投资。 该项目利用高通量测序技术来测量核苷酸水平基因组的全基因组利用。在持续存在强诱变剂的情况下，细菌细胞将在定义明确的实验条件下生长。这种治疗方法将导致突变在未利用的基因或用来替换氨基酸的一部分基因中积累。引入的变化将通过DNA测序检测，结果应将所利用的基因与未利用的基因区分开，并可更换氨基酸与蛋白质功能所需的氨基酸。BOADER的影响：该平台将广泛适用于工业和学术目的，以启用协议驱动的基因发现。该方法不需要太多关于新陈代谢的预先知识，并且使用生物计算来评估基因功能。该项目将为博士后研究员和本科生提供教育机会。