With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (o1 per 13 000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

Chromosomes in eukaryotes are linear, whereas those of most, but not all, prokaryotes are circular. To explore the effects of possessing a linear genome on prokaryotic cells, we linearized the Escherichia coli genome using the lysogenic k-like phage N15. Linear genome E. coli were viable and their genome structure was stable. There were no appreciable differences between cells with linear or circular genomes in growth rates, cell and nucleoid morphologies, genome-wide gene expression (with a few exceptions), and DNA gyrase-and topoisomerase IV-dependent growth. However, under dif-defective conditions, only cells with a circular genome developed an abnormal phenotype. Microscopy indicated that the ends of the linear genome, but not the circular genome, were separated and located at each end of a new-born cell. When tos-the cis-element required for linearization-was inserted into different chromosomal sites, those strains with the genome termini that were more remote from dif showed greater growth deficiencies.

A monoclonal antibody (mAb) with a unique antigenic specificity against Escherichia coli O9 was produced. The O9a mAb was reactive with a part of the strains in E. coli O9. The O9a mAb did not react with LPS from the E. coli O9 test strain Bi316-42. The distribution of the antigen defined by the O9a mAb in E. coli O9 was consistent with thatof E. coli O9a present in E. coli O9 strains. The chemical structure of the repeating unit of the O-specific polysaccharide detected by the mAb was demonstrated to be a mannotetraose by two-dimensional nuclear magnetic resonance spectroscopy. It was confirmed that the mAb recognized E. coli O9a serotype in E. coli O9 serotype strains, suggesting that E. coli O9a serotype might be a dominant strain in E. coli O9.