Figuring out genetic functional systems in Prokaryotes through computational genomics and metagenomics

通过计算基因组学和宏基因组学弄清楚原核生物的遗传功能系统

• 批准号: 312480-2012
• 负责人: MorenoHagelsieb, Gabriel
• 金额: $ 2.04万
• 依托单位: Wilfrid Laurier University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2013
• 资助国家: 加拿大
• 起止时间: 2013-01-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=526531
• 关键词: Figuring; out; genetic; functional; systems

The proposed research program is concerned to two problems: (1) Since prokaryotic genomes within a species show high variability in gene content, and since such gene differences can make the difference between a harmless bacterial strain and a pathogenic one, we aim at understanding how different gene sets incorporate into the functional network of their host genome. To this end, we will examine high-quality computationally predicted associations by comparing against knowledge databases and literature, and by finding patterns revealing points of insertion into functional networks. We will concentrate on the role of transcription factors in the integration of genomic islands to their hosts. (2) Since we have developed powerful computational tools for predicting functional interactions in prokaryotic genomes, and there is an increasing abundance of semi-finished genomes, and metagenomic sequences, we aim at expanding these tools towards predicting such interactions with the same quality in any sequences, as when using complete genomes. These predictions will associate unknown genes to well understood functions and provide hints for their later characterization in the laboratory. The proposed work will benefit Canada and the world by providing instruments for finding different versions of gene modules attaining similar functions, from pathogenicity to functions of interest to industry such as cellulose degradation. Such information might help finding new ways for combating disease, or point to novel genes for biotechnological applications.

该研究计划涉及两个问题：（1）由于一个物种内的原核基因组在基因含量上表现出高度的变异性，并且由于这种基因差异可以在无害菌株和致病菌株之间产生差异，因此我们的目标是了解不同的基因集如何整合到其宿主基因组的功能网络中。为此，我们将通过与知识数据库和文献进行比较，并通过寻找揭示功能网络插入点的模式，来研究高质量的计算预测关联。我们将集中在基因组岛整合到他们的主机中的转录因子的作用。(2)由于我们已经开发出强大的计算工具来预测原核基因组中的功能相互作用，并且半成品基因组和元基因组序列越来越丰富，我们的目标是扩展这些工具，以在任何序列中以相同的质量预测此类相互作用，就像使用完整基因组时一样。这些预测将把未知基因与已被充分理解的功能联系起来，并为它们以后在实验室中的表征提供线索。拟议的工作将使加拿大和世界受益，为寻找具有相似功能的不同版本的基因模块提供工具，从致病性到工业感兴趣的功能，如纤维素降解。这些信息可能有助于找到对抗疾病的新方法，或者为生物技术应用指明新的基因。