BB-norm+ner@ldeleger:BB-norm+ner-16990433 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
T1 0-136 Title denotes An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination.
T2 137-1580 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.
T3 27-45 Phenotype denotes type III secretion OBT:000019
T4 59-80 Microorganism denotes Escherichia coli O157 1045010
T5 97-112 Microorganism denotes lambdoid phages 186765
T6 145-155 Phenotype denotes pathogenic OBT:002806
T7 167-183 Microorganism denotes Escherichia coli 562
T8 192-210 Phenotype denotes type III secretion OBT:000019
T9 246-257 Habitat denotes human cells OBT:000061
T10 246-251 Habitat denotes human OBT:002488
T11 278-293 Habitat denotes eukaryotic cell OBT:000061
T12 442-447 Microorganism denotes Sakai 386585
T13 458-475 Phenotype denotes enterohemorrhagic OBT:002806
T14 476-498 Microorganism denotes E. coli (EHEC) O157:H7 83334
T15 485-489 Phenotype denotes EHEC OBT:002806
T16 875-879 Phenotype denotes EHEC OBT:002806
T17 875-879 Microorganism denotes EHEC 386585
T18 987-992 Microorganism denotes Sakai 386585
T19 1007-1011 Phenotype denotes EHEC OBT:002806
T20 1007-1011 Microorganism denotes EHEC 562
T21 1063-1078 Phenotype denotes plant pathogens OBT:002732
T22 1063-1068 Habitat denotes plant OBT:000393
T23 1110-1118 Microorganism denotes Shigella 620
T24 1428-1446 Microorganism denotes lambdoid prophages 186765
T25 1454-1472 Phenotype denotes type III secretion OBT:000019
T26 1476-1483 Microorganism denotes E. coli 562
T27 1566-1579 Phenotype denotes pathogenicity OBT:002806