The Analysis of Multiple Genome Comparisons in Genus Escherichia and Its Application to the Discovery of Uncharacterised Metabolic Genes in Uropathogenic Escherichia coli CFT073

Abstract

A survey of a complete gene synteny comparison has been carried out between twenty fully sequenced strains from the genus Escherichia with the aim of finding yet uncharacterised genes implicated in the metabolism of uropathogenic strains of E. coli (UPEC). Several sets of adjacent colinear genes have been identified which are present in all four UPEC included in this study (CFT073, F11, UTI89, and 536), annotated with putative metabolic functions, but are not found in any other strains considered. An operon closely homologous to that encoding the L-sorbose degradation pathway in Klebsiella pneumoniae has been identified in E. coli CFT073; this operon is present in all of the UPEC considered, but only in 7 of the other 16 strains. The operon's function has been confirmed by cloning the genes into E. coli DH5alpha and testing for growth on L-sorbose. The functional genomic approach combining in silico and in vitro work presented here can be used as a basis for the discovery of other uncharacterised genes contributing to bacterial survival in specific environments.

Figure 1

Structure of the pSC-B plasmid with the putative L-sorbose operon insert from CFT073.

Figure 2

Positions of the SACs identified in the genome sequence of E. coli CFT073, as labelled in Table 2.

Figure 3

Phylogenetic tree of L-sorbose operons (both confirmed and putative) in the genus Escherichia and in two Klebsiella strains. The scale is in units of substitutions per site. Unless otherwise stated, the strain is Escherichia coli.

Figure 4

Growth curves for DH5α containing plasmid pQR793, compared to CFT073 and DH5α with an empty pUC-19 plasmid. DH5α with pQR793 is represented by ∘ and •, DH5α with pUC19 by Δ and ▴ and CFT073 by □ and ▪ where empty symbols represent growth on glucose and filled symbols represent growth on L-sorbose. Where duplicate samples were taken, readings varied by less than 0.01 OD₆₀₀ units using a CO8000 Cell Density Meter (WPA).