Pan Genomic Discovery of Genes Toxic to Bacteria

描述(申请人提供)：临床上对新的抗菌剂的需求越来越大。抗菌素耐药性正在所有类型的病原微生物中迅速传播，但与这些新出现的威胁形成鲜明对比的是，市场上新抗生素的数量不断减少，绝大多数新抗生素是对已经在临床使用的化学抗生素类别的修改。这项提议将利用我们最近开发的一种方法来发现数千个对细菌有毒的基因，以确定潜在的新类别的抗菌剂。这种方法是基于基因组测序过程的副产品，在基因组测序过程中，初始组装总是包含间隙，这是由于DNA片段无法在细菌中成功繁殖。在对79个完成的微生物基因组的初步分析中，我们发现许多这些不可克隆的缺口是由对大肠杆菌具有复制毒性的基因引起的，包括新的抗菌肽、有毒的非编码RNA和限制性内切酶。在这项提案中，我们将分析大约1,500个已完成的微生物基因组的GAP含量，对真细菌和古生物界的所有主要门进行采样，并确定一套全面的估计对大肠杆菌有毒的~40,000个基因。功能未知的有毒基因将在以下方面进行评估：1)鉴定和研究抗菌肽和新的抗生素生物合成基因簇；2)鉴定和研究对大肠杆菌有毒的非编码RNA；3)鉴定和研究有毒基因中存在的限制性内切酶。将开发一个公共数据库，其中包括所有对大肠杆菌有毒的基因和来自1500个已分析基因组的相关功能信息。这个数据库预计将使研究抗菌剂、非编码RNA、限制性内切酶和其他导致对大肠杆菌毒性的基因功能的研究人员的广泛社区受益。 与公共卫生相关：抗生素耐药性在致病细菌中的迅速传播对公共健康构成威胁。这项提议提出了一种新的方法，有助于发现数千种对细菌有毒的基因。这种方法将被用于检测和开发新的抗菌剂，以及研究一类对细菌有毒的新型RNA分子。

DESCRIPTION (provided by applicant): There is a growing need for new antimicrobial agents in the clinic. Antimicrobial drug resistance is rapidly spreading among pathogenic microorganisms of all types, but in sharp contrast to these emerging threats, the number of new antibiotics in the market is constantly decreasing, and the vast majority of new antibiotics represent modifications on chemical antibiotic classes that are already in clinical use. This proposal will utilize a method we recently developed for the discovery of thousands of genes toxic to bacteria, in order to identify potentially new classes of antibacterial agents. The approach is based on a by-product of the process of genome sequencing, where initial assemblies invariably contain gaps due to DNA fragments that cannot be successfully propagated in bacteria. In our pilot analysis of 79 finished microbial genomes, we discovered that many of these uncloneable gaps are caused by genes that are reproducibly toxic to E. coli, including novel antimicrobial peptides, toxic non-coding RNAs, and restriction enzymes. In this proposal we will analyze the gap content of approximately 1,500 finished microbial genomes, sampling all major phyla of the eubacterial and archaeal kingdoms, and identify a comprehensive set of an estimated ~40,000 genes toxic to E. coli. Toxic genes that are of unknown function will be evaluated in assays targeted at 1) identifying and studying antimicrobial peptides and novel antibiotic biosynthesis gene clusters 2) identifying and studying non-coding RNAs that are toxic to E. coli and 3) identifying and studying restriction enzymes that are present among the toxic genes. A public database of all genes toxic to E. coli and associated functional information from the 1,500 analyzed genomes will be developed. This database is anticipated to benefit a broad community of researchers studying antimicrobials, non-coding RNAs, restriction enzymes, and other gene functions resulting in toxicity to E. coli. PUBLIC HEALTH RELEVANCE: The rapid spread of antibiotics resistance among disease-causing bacteria forms a threat to public health. This proposal presents a new approach that facilitates the discovery of thousands of genes that are toxic to bacteria. This approach will be used to detect and develop new antimicrobial agents as well as study a new class of RNA molecules that are toxic to bacteria.