BB-norm+ner@ldeleger:BB-norm+ner-16990433 / 137-1580 JSONTXT

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bionlp-ost-19-BB-norm-ner-train

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Id Subject Object Predicate Lexical cue NCBI_Taxonomy OntoBiotope
T2 0-1443 Paragraph denotes 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 Map/IpgB 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.
T6 8-18 Phenotype denotes pathogenic OBT:002806
T7 30-46 Microorganism denotes Escherichia coli 562
T8 55-73 Phenotype denotes type III secretion OBT:000019
T9 109-120 Habitat denotes human cells OBT:000061
T10 109-114 Habitat denotes human OBT:002488
T11 141-156 Habitat denotes eukaryotic cell OBT:000061
T12 305-310 Microorganism denotes Sakai 386585
T13 321-338 Phenotype denotes enterohemorrhagic OBT:002806
T14 339-361 Microorganism denotes E. coli (EHEC) O157:H7 83334
T15 348-352 Phenotype denotes EHEC OBT:002806
T16 738-742 Phenotype denotes EHEC OBT:002806
T17 738-742 Microorganism denotes EHEC 386585
T18 850-855 Microorganism denotes Sakai 386585
T19 870-874 Phenotype denotes EHEC OBT:002806
T20 870-874 Microorganism denotes EHEC 562
T21 926-941 Phenotype denotes plant pathogens OBT:002732
T22 926-931 Habitat denotes plant OBT:000393
T23 973-981 Microorganism denotes Shigella 620
T24 1291-1309 Microorganism denotes lambdoid prophages 186765
T25 1317-1335 Phenotype denotes type III secretion OBT:000019
T26 1339-1346 Microorganism denotes E. coli 562
T27 1429-1442 Phenotype denotes pathogenicity OBT:002806