The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69

Enteropathogenic Escherichia coli (EPEC) are an important aetiological agent in infant diarrhoea and the prototype for a family of pathogens exhibiting the unique virulence mechanism known as attaching and effacing (AE) (Nataro and Kaper, 1998). All genes necessary for AE are encoded on a 35 kb chromosomal pathogenicity island called the locus of enterocyte effacement (LEE), which contains genes encoding a type III secretion system, secreted proteins (Esp) and the adhesin intimin (McDaniel et al., 1995; McDaniel and Kaper, 1997). Study of the LEE will illuminate our understanding of the pathogenesis of EPEC and other AE pathogens and contribute to the growing body of knowledge about type III secretion systems and pathogenicity islands. We have recently sequenced the entire LEE of EPEC strain E2348/69 and describe below our initial analysis. Further details can be found in GenBank (accession number AF022236) and on the Molecular Microbiology Web site (http://www.blackwellscience.com/products/journals/mole.htm). The complete region was 35 624 bp with an average G þ C content of 38.36%, which is far below that of the E. coli chromosome (50.8%; Blattner et al., 1997), a pattern in keeping with many other pathogenicity islands (Hacker et al., 1997). The LEE contains 41 predicted open reading frames (ORFs) (of > 50 amino acids) arranged in at least five polycistronic operons, as predicted by the close spacing of co-directional genes. The LEE may be divided into at least three functional domains (Fig. 1): the central eae (encoding intimin), the region encoding the secreted Esp proteins and a large region encoding the type III secretion apparatus. Several LEE genes have been reported previously, and our final LEE sequence entry contains corrections to some of these previously reported genes and predicted proteins. Additionally, we have decided to adopt a standardized nomenclature (Bogdanove et al., 1996a; Yahr et al., 1997), which changes the name of several previously described genes comprising the type III secretion system of EPEC (Jarvis et al., 1995). Those genes homologous to Yersinia type III secretion (ysc) genes are referred to as esc (E. coli secretion) genes with the same suffix as the Yersinia homologue (e.g. sepA becomes escV, homologous with yscV; Table 1). Within the family of type III secretory genes, the LEE shares the highest level of predicted amino acid similarity and genetic organization with ssa genes from the SPI-2 pathogenicity island of Salmonella typhimurium (Shea et al., 1996). Genes that are not ysc homologues but are involved in type III secretion are named sep (secretion of E. coli proteins). The chaperone for the secretion of EspD is named cesD for chaperone for E. coli secreted protein D (Wainwright and Kaper, 1998). The remaining named genes, esp (E. coli secreted protein), eae (E. coli attaching and effacing) and orfU will retain their designations, and remaining ORFs are designated orf or rorf depending on the direction of transcription relative to eae. A brief description of selected LEE ORFs follows. More details can be found in Table 1, Fig. 1 and on the Molecular Microbiology home page (http://www.blackwell-science. com/products/journals/mole.htm. rOrf1 is similar to a protein of unknown function from E. coli K-12 and to a predicted lipoprotein that is encoded on the S. typhimurium virulence plasmid adjacent to rck (Heffernan et al., 1992), which has been shown to be important for virulence (Cirillo et al., 1996). rOrf2 is similar to the VirA protein of Shigella flexneri, a type III secreted protein that is involved in invasion and intercellular spreading (Uchiya et al., 1995). Secretion of rOrf2 has not been observed, and it is unclear what functions rOrf2 may have in EPEC, in which the role of invasion remains undefined. Molecular Microbiology (1998) 28(1), 1–4