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.//
