SummaryThe type VI secretion system (T6SS) is a newly described apparatus for protein transport across the cell envelope of Gram-negative bacteria. Components that have been partially characterised include an IcmF homologue, the ATPase ClpV, a regulatory FHA domain protein and the secreted VgrG and Hcp proteins. The T6SS is clearly a key virulence factor for some important pathogenic bacteria and T6SS-dependent translocation of a potential effector protein into eukaryotic cells has been described for one system (Vibrio cholerae). However, T6SSs are widespread in nature and not confined to known pathogens.In accordance with the general rule that the expression of protein secretion systems is tightly regulated, expression of T6SS is controlled at both transcriptional and post-transcriptional levels.2

Several pathogenic strains of Escherichia coli exploit type III secretion to inject ''effector proteins'' into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of >60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into >20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map͞IpgB family. Genes encoding proven or predicted effectors occur in >20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage ''metagenome,'' acting as a crucible for the evolution of pathogenicity.bacterial pathogenesis ͉ bacterial protein secretion ͉ bioinformatics ͉ genomics ͉ virulence

The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KDM5 inhibitor CPI-455. The crystal structure of KDM5A revealed the mechanism of inhibition of CPI-455 as well as the topological arrangements of protein domains that influence substrate binding. CPI-455 mediated KDM5 inhibition, elevated global levels of H3K4 trimethylation (H3K4me3) and decreased the number of DTPs in multiple cancer cell line models treated with standard chemotherapy or targeted agents. These findings show that pretreatment of cancer cells with a KDM5-specific inhibitor results in the ablation of a subpopulation of cancer cells that can serve as the founders for therapeutic relapse.

ETT2 is a second cryptic type III secretion system in Escherichia coli which was first discovered through the analysis of genome sequences of enterohemorrhagic E. coli O157:H7. Comparative analyses of Escherichia and Shigella genome sequences revealed that the ETT2 gene cluster is larger than was previously thought, encompassing homologues of genes from the Spi-1, Spi-2, and Spi-3 Salmonella pathogenicity islands. ETT2-associated genes, including regulators and chaperones, were found at the same chromosomal location in the majority of genome-sequenced strains, including the laboratory strain K-12. Using a PCR-based approach, we constructed a complete tiling path through the ETT2 gene cluster for 79 strains, including the well-characterized E. coli reference collection supplemented with additional pathotypes. The ETT2 gene cluster was found to be present in whole or in part in the majority of E. coli strains, whether pathogenic or commensal, with patterns of distribution and deletion mirroring the known phylogenetic structure of the species. In almost all strains, including enterohemorrhagic E. coli O157:H7, ETT2 has been subjected to varying degrees of mutational attrition that render it unable to encode a functioning secretion system. A second type III secretion systemassociated locus that likely encodes the ETT2 translocation apparatus was found in some E. coli strains. Intact versions of both ETT2-related clusters are apparently present in enteroaggregative E. coli strain O42.The species Escherichia coli contains a wide range of commensal strains and pathogenic varieties (pathotypes) in addition to the model laboratory organism, E. coli K-12 (16). At least six pathotypes are associated with human intestinal disease: they are enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli, enteroaggregative E. coli (EAEC), and diffusely adherent E. coli. Two pathotypes are associated with extraintestinal disease in humans, namely uropathogenic E. coli (UPEC) and neonatal meningitic E. coli (NMEC). In addition, it is now clear that on phylogenetic grounds, all members of the genus Shigella belong within the species of E. coli (50). Furthermore, this dazzling phenotypic variety is matched by remarkable variations in genome size, with the largest E. coli genomes possessing more than a megabase more DNA than the smallest ones (43).Initial studies of UPEC, and later of other pathotypes, suggested that E. coli strains often acquire new complex pathogenic phenotypes in a single step by the acquisition of pathogenicity islands, which contain virulence genes clustered on the chromosome and which are acquired en bloc by horizontal gene transfer (21). Similar studies with the related bacterium Salmonella enterica have delineated several Salmonella pathogenicity islands (Spi-1, Spi-2, Spi-3, etc.) (2, 22). The horizontal transfer of DNA by mobile elements such as bacteriophages and plasmids is also known to play a role in the evolution of virulence in E. coli and S...