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PORPHYROMONAS GINGIVALIS GENOME PROJECT

牙龈卟啉单胞菌基因组计划

基本信息

批准号：
2770267
负责人：
ROBERT D FLEISCHMANN
金额：
$ 62.16万
依托单位：
INSTITUTE FOR GENOMIC RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
1997
资助国家：
美国
起止时间：
1997-09-01 至 2001-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/2770267
关键词：
PORPHYROMONAS GINGIVALIS GENOME PROJECT

项目摘要

DESCRIPTION (Adapted from the Investigator's Abstract): The long-term objective of the proposed research is to develop a comprehensive molecular understanding of the organism Porphyromonas gingivalis, a species strongly associated with human periodontal diseases. P. gingivalis is a small genome representative of the little studied Cytophaga/Flavobacteria/Bacteroides phylum, a phylogenetically and medically important group of organisms. The complete genome sequence of virulent strain W83, about 2.2 Mb, will be determined (Aim 1). For sequencing, a 2.0 kb average insert size library will be prepared in the pUC18 vector and an 18. kb average insert size library in lambda DashII. Approximately 35,200 sequences from both ends of 17,600 pUC clones will yield approximately 8-fold coverage of the genome. The ends of 1,000 lambda DashII clones will also be sequenced to create a genome scaffold, and to verify the orientation and integrity of the contigs formed from the assembly of sequences from the plasmid library. The genome sequence will be assembled from the collection of randomly sequenced fragments; sequencing gaps will be closed by walking appropriate clones, and physical gaps by polymerase chain reaction. The sequence will be analyzed and annotated (Aim 2). Open reading frames (Orfs) will be identified related to proteins of known and unknown function. The sequence will be analyzed to identify a number of features, including metabolic pathways, virulence factors, and exported proteins. DNA structural motifs (such as promoters, replication origins and repeat elements) and genes for rRNA, and small RNAs, such as tRNA, 4.5S, 6S, 10S, and RNAse P, will be identified. The information from the annotated sequence will be integrated with experimental data from the P. gingivalis research community, including in vivo expression technology (Aim 3). The genome sequence and annotation data will be made available on the TIGR Microbial Database web site, as well as deposited in GenBank and other appropriate databases (Aim 4). The sequence information generated in this proposal will accelerate ongoing P. gingivalis research to identify and characterize virulence factors and to develop an effective P. gingivalis vaccine. Periodontal disease affects one in five Americans, and therefore, advances in prevention and therapy will have a significant effect on the health of the American people, and the cost of dental care.

描述(改编自《调查者摘要》)：长期拟议研究的目标是开发一种全面的分子对牙龈卟啉单胞菌的认识与人类牙周病有关。牙龈假单胞菌是一个很小的基因组研究较少的细胞吞噬/黄杆菌/类杆菌的代表门：在系统发育和医学上具有重要地位的一类生物。这个强毒株W83的完整基因组序列约为2.2Mb，将已确定(目标1)。对于测序，2.0kb的平均插入大小的文库将在pUC18载体中制备，平均插入大小为18.kb 位于Lambda DashII的图书馆。两端的大约35,200个序列 17,600个PUC克隆将产生大约8倍的基因组覆盖率。还将对1,000个lambda DashII克隆的末端进行测序，以创建基因组支架，并验证重叠群的方向和完整性由来自质粒文库的序列组装而成。基因组序列将从随机排序的集合中组装而成片段；测序差距将通过行走适当的克隆来弥合，以及聚合酶链式反应产生的体格差异。将对序列进行分析和注解(目标2)。将确定开放阅读框架(ORF) 与已知和未知功能的蛋白质有关的。该序列将是分析以确定一些特征，包括代谢途径，毒力因子，以及出口的蛋白质。DNA结构基序(如启动子、复制起点和重复元件)和rRNA的基因，以及将识别小RNA，如tRNA、4.5S、6S、10S和RNaseP。来自带注释的序列的信息将与牙龈假单胞菌研究社区的实验数据，包括在活体表达技术(AIM 3)。基因组序列和注释数据将在TIGR微生物数据库网站以及存入GenBank和其他适当的数据库(AIM 4)。该序列这项提案中产生的信息将加速正在进行的牙龈假单胞菌研究确定和表征毒力因子，并开发一种有效的牙龈假单胞菌疫苗。五分之一的人患牙周病因此，预防和治疗方面的进步将对对美国人民的健康产生重大影响，以及牙科护理。