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

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bionlp-ost-19-BB-kb-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
E4 30-46 Lives_In denotes Escherichia coli
E2 30-46 Exhibits denotes Escherichia coli
E3 30-46 Exhibits denotes Escherichia coli
E5 339-361 Exhibits denotes E. coli (EHEC) O157:H7
E6 339-361 Exhibits denotes E. coli (EHEC) O157:H7
E7 738-742 Exhibits denotes EHEC
E8 870-874 Exhibits denotes EHEC
E9 1339-1346 Exhibits denotes E. coli
R3 E4 T7 Microorganism Escherichia coli,Escherichia coli
R4 E4 T10 Location Escherichia coli,human
R5 E2 T7 Microorganism Escherichia coli,Escherichia coli
R6 E2 T6 Property Escherichia coli,pathogenic
R7 E3 T7 Microorganism Escherichia coli,Escherichia coli
R8 E3 T8 Property Escherichia coli,type III secretion
R9 E5 T14 Microorganism E. coli (EHEC) O157:H7,E. coli (EHEC) O157:H7
R10 E5 T13 Property E. coli (EHEC) O157:H7,enterohemorrhagic
R11 E6 T14 Microorganism E. coli (EHEC) O157:H7,E. coli (EHEC) O157:H7
R12 E6 T15 Property E. coli (EHEC) O157:H7,EHEC
R13 E7 T17 Microorganism EHEC,EHEC
R14 E7 T16 Property EHEC,EHEC
R15 E8 T20 Microorganism EHEC,EHEC
R16 E8 T19 Property EHEC,EHEC
R17 E9 T26 Microorganism E. coli,E. coli
R18 E9 T25 Property E. coli,type III secretion