Genome Evolution in Bacteria

提出的研究将探讨促进细菌染色体大小和组织变化的因素。通过分析大肠杆菌和其他已知遗传和系谱关系的肠道细菌的分离株，他将研究发生在个体基因位点水平之上的许多类型的进化事件。本研究将探讨以下问题：(1)自然种群中水平基因交换、重组和大规模DNA重排的发生率；(2)大肠杆菌染色体物理图谱的变异；(3)染色体DNA的插入和删除程度导致自然分离株之间基因组大小的变异；(4)染色体转座元件的位置和稳定性；(5)肠道细菌遗传和染色体变化的速率和进化历史。为了在自然分离株中分析这些事件，Ochman博士将：(1)评估位于大肠杆菌染色体周围的大量基因的核苷酸变异，以寻找受重组影响的区域，这可以从基于特定基因的菌株之间系统发育关系的不一致性中看出。(2)为许多大肠杆菌菌株制作染色体物理图谱。由限制性内切酶产生的具有很少识别序列的大片段DNA可以通过脉冲场凝胶电泳等技术进行解析，并通过印迹和杂交程序进行定位。(3)比较不同分类群的同源性状——核苷酸序列和物理图谱。总之，这些方法为研究细菌基因组的动力学提供了广泛的途径

The proposed research will investigate the factors promoting variation in the size and organization of the bacterial chromosome. By analysing isolates of Escherichia coli and other enteric bacteria of known genetic and genealogical relationships, he will examine many types of evolutionary events occurring above the level of individual gene loci. This research will address questions concerning: (1) the incidence of horizontal gene exchange, recombination and large-scale DNA rearrangements in natural populations, (2) variation in the physical maps of the E. coli chromosome, (3) the extent of insertion and deletion of chromosomal DNA causing variation in genome size among natural isolates, (4) the chromosomal location and stability of transposable elements, and (5) the rate and evolutionary history of genetic and chromosomal changes in enteric bacteria. To analyse these events among natural isolates, Dr. Ochman will: (1) Assess the nucleotide variation in a large number of genes positioned around the E. coli chromosome to search for regions that have been affected by recombination, as evident by inconsistencies in the phylogenetic relationships among strains based on a particular gene. (2) Produce physical maps of the chromosome for many strains of E. coli. Large DNA fragments generated by restriction enzymes with very infrequent recognition sequences are resolved by techniques such as pulsed-field gel electrophoresis and mapped by blot and hybridization procedures. (3) Compare homologous traits- nucleotide sequences and physical maps - among divergent taxa. In total, these methods provide a broad approach to studying the dynamics of the bacterial genome.//