A Functional Genomics Study of the Primary Pathways for Carbon Metabolism in a Hyperthermophilic Archaeon

超嗜热古菌碳代谢主要途径的功能基因组学研究

• 批准号: 0129841
• 负责人: Michael Adams
• 金额: $ 48万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-06-01 至 2006-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0129841&HistoricalAwards=false
• 关键词: Functional; Genomics; Study; Primary; Pathways

Well over 200 genomic sequencing efforts have been completed ranging from pathogens and exotic microbes, to yeast, rice and human, yielding a phenomenal array of sequence information, the comprehension of which is only just beginning. Understanding how a living cell works, however, obviously requires much more than simply determining the genome sequence and the number of genes. A fundamental problem is how to find genes and assign functions to these genes. Insights can be obtained by analyzing the sequences of the proteins that the genes encode using the available databases, but by such methods less than half of the genes in a given organism can be assigned a function with any degree of confidence. Hence, the roles of about half of the genes in any given genome is essentially unknown. This suggests that half of life's biochemistry is unknown. A major effort is therefore needed to assign biological roles to these unknown genes through functional genomic approaches.The goal of this research is to identify genes involved in carbon metabolism of Pyrococcus furiosus, an archaeon (archaebacterium) that grows optimally at 100C. The research will largely focus on finding genes involved in carbon metabolism in the 'unknown' half of the microbial genome. The P. furiosus 1.908 Mb genome contains approximately 2,200 putative genes. The fundamental hypothesis to be tested is that many of the more than 1,000 genes of unknown function play key roles in primary carbon metabolism by as yet unknown mechanisms. This will be ascertained using DNA microarray analyses using all 2,200 genes in the P. furiosus genome. Preliminary data have shown that a surprisingly large number of the unknown genes are regulated by the carbon source used to grow the organism. The specific aims are a) to identify previously uncharacterized genes involved in the metabolism of carbohydrates, proteins and C-1 compounds by analyzing expression levels using cells grown under a wide variety of conditions, b) to confirm gene expression data by enzymatic assays and metabolite analyses, and c) to characterize the key enzymes by direct purification using P. furiosus biomass from 600 liter fermentations and by using recombinant proteins that are available through a complementary structural genomics effort with P. furiosus. It is anticipated that the results of this study will provide completely new insights into the metabolism of fixed carbon compounds and the role of what are currently hypothetical genes in both P. furiosus and in other organisms, including human.

从病原体和外来微生物到酵母，水稻和人类，已经完成了200多种基因组测序工作，从而产生了一系列出色的序列信息，其理解仅仅是刚刚开始的。 但是，了解生物细胞的工作原理显然需要不仅需要简单地确定基因组序列和基因数量。 一个基本问题是如何找到基因并将功能分配给这些基因。 可以通过分析使用可用数据库编码的蛋白质的序列来获得见解，但是通过这种方法，可以以任何置信度分配给定生物体中的基因的一半。 因此，大约一半基因在任何给定基因组中的作用本质上都是未知的。 这表明生命的生物化学一半是未知的。 因此，需要一项重大努力来通过功能基因组方法为这些未知基因分配生物学作用。该研究的目的是确定与Furiosus的碳代谢有关的基因，该基因是Furiosus的碳代谢，该基因是100C最佳生长的古氏菌（古菌）。 这项研究将主要集中在寻找与微生物基因组的“未知”一半中涉及碳代谢的基因。 Furiosus 1.908 MB基因组包含大约2200个假定基因。 要测试的基本假设是，未知功能的1,000多个未知功能的基因中有许多基因在原始碳代谢中扮演着关键的作用。 使用DNA微阵列分析使用所有2200个基因中的所有基因组中的DNA微阵列分析来确定这一点。 初步数据表明，大量未知基因受到生长生物体的碳源调节。 The specific aims are a) to identify previously uncharacterized genes involved in the metabolism of carbohydrates, proteins and C-1 compounds by analyzing expression levels using cells grown under a wide variety of conditions, b) to confirm gene expression data by enzymatic assays and metabolite analyses, and c) to characterize the key enzymes by direct purification using P. furiosus biomass from 600 liter fermentations and by using重组蛋白可以通过富含猪笼草的互补结构基因组学努力获得。 可以预料，这项研究的结果将为固定碳化合物的代谢以及当前假设基因在富虫和其他生物（包括人）中的假设基因的作用提供全新的见解。