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Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains.

Lindeberg M, Biehl BS, Glasner JD, Perna NT, Collmer A, Collmer CW - BMC Microbiol. (2009)

Bottom Line: The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses.In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa.GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, Cornell University, Ithaca, NY 14850, USA. ML16@cornell.edu

ABSTRACT
Genome-informed identification and characterization of Type III effector repertoires in various bacterial strains and species is revealing important insights into the critical roles that these proteins play in the pathogenic strategies of diverse bacteria. However, non-systematic discipline-specific approaches to their annotation impede analysis of the accumulating wealth of data and inhibit easy communication of findings among researchers working on different experimental systems. The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses. The application of these terms to annotate type III effector genes in different bacterial species - the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic strains of Escherichia coli - illustrates how GO can effectively describe fundamental similarities and differences among different gene products deployed as part of diverse pathogenic strategies. In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa. GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.

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Gene Ontology annotation for the Pto DC3000 Type III effector AvrPtoB. aIndicates the nearest common parent term in the GO term hierarchy. Terms sharing the specified parent are delimited by dashed lines. bIndicates the publication supporting annotation of AvrPtoB to the specified GO term. cIndicates the nature of the evidence supporting the annotation; IDA, inferred from direct evidence; IEP, inferred from expression profile; IPI, inferred from physical interaction; IMP, inferred from mutant phenotype; ISS, inferred from sequence similarity. dIndicates the Uniprot accession number of the interacting protein, where inferred from physical evidence, or of the similar protein, where inferred from sequence similarity. eIndicates the taxon ID of the host where biological processes occurred in relation to a host organism.
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Figure 1: Gene Ontology annotation for the Pto DC3000 Type III effector AvrPtoB. aIndicates the nearest common parent term in the GO term hierarchy. Terms sharing the specified parent are delimited by dashed lines. bIndicates the publication supporting annotation of AvrPtoB to the specified GO term. cIndicates the nature of the evidence supporting the annotation; IDA, inferred from direct evidence; IEP, inferred from expression profile; IPI, inferred from physical interaction; IMP, inferred from mutant phenotype; ISS, inferred from sequence similarity. dIndicates the Uniprot accession number of the interacting protein, where inferred from physical evidence, or of the similar protein, where inferred from sequence similarity. eIndicates the taxon ID of the host where biological processes occurred in relation to a host organism.

Mentions: Since their initial identification as substrates of the T3SS, research on the Pto DC3000 effectors has yielded new insights into their molecular functions, cellular destinations within the host, and the biological processes in which they participate. To date, over 300 Gene Ontology annotations have been generated for 36 effector genes as part of the PAMGO project, with the vast majority of annotations concerning processes that occur during the interaction between microbes and their host organisms. An example of the range of processes in which the effectors engage is illustrated by the Pto DC3000 effector protein AvrPtoB (HopAB2) (see the table in Figure 1). Like many other effectors, AvrPtoB is annotated to terms in all three ontologies. Within the Biological Process Ontology, terms range from the more general such as "GO:0009405 pathogenesis" and "GO:0044412 growth or development of symbiont within the host", applicable to a wide range of virulence factors in diverse pathogens, to more specific terms such as "GO:0052049 interaction with host via protein secreted by type III secretion system" that specifically identifies the Type III effectors.


Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains.

Lindeberg M, Biehl BS, Glasner JD, Perna NT, Collmer A, Collmer CW - BMC Microbiol. (2009)

Gene Ontology annotation for the Pto DC3000 Type III effector AvrPtoB. aIndicates the nearest common parent term in the GO term hierarchy. Terms sharing the specified parent are delimited by dashed lines. bIndicates the publication supporting annotation of AvrPtoB to the specified GO term. cIndicates the nature of the evidence supporting the annotation; IDA, inferred from direct evidence; IEP, inferred from expression profile; IPI, inferred from physical interaction; IMP, inferred from mutant phenotype; ISS, inferred from sequence similarity. dIndicates the Uniprot accession number of the interacting protein, where inferred from physical evidence, or of the similar protein, where inferred from sequence similarity. eIndicates the taxon ID of the host where biological processes occurred in relation to a host organism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654664&req=5

Figure 1: Gene Ontology annotation for the Pto DC3000 Type III effector AvrPtoB. aIndicates the nearest common parent term in the GO term hierarchy. Terms sharing the specified parent are delimited by dashed lines. bIndicates the publication supporting annotation of AvrPtoB to the specified GO term. cIndicates the nature of the evidence supporting the annotation; IDA, inferred from direct evidence; IEP, inferred from expression profile; IPI, inferred from physical interaction; IMP, inferred from mutant phenotype; ISS, inferred from sequence similarity. dIndicates the Uniprot accession number of the interacting protein, where inferred from physical evidence, or of the similar protein, where inferred from sequence similarity. eIndicates the taxon ID of the host where biological processes occurred in relation to a host organism.
Mentions: Since their initial identification as substrates of the T3SS, research on the Pto DC3000 effectors has yielded new insights into their molecular functions, cellular destinations within the host, and the biological processes in which they participate. To date, over 300 Gene Ontology annotations have been generated for 36 effector genes as part of the PAMGO project, with the vast majority of annotations concerning processes that occur during the interaction between microbes and their host organisms. An example of the range of processes in which the effectors engage is illustrated by the Pto DC3000 effector protein AvrPtoB (HopAB2) (see the table in Figure 1). Like many other effectors, AvrPtoB is annotated to terms in all three ontologies. Within the Biological Process Ontology, terms range from the more general such as "GO:0009405 pathogenesis" and "GO:0044412 growth or development of symbiont within the host", applicable to a wide range of virulence factors in diverse pathogens, to more specific terms such as "GO:0052049 interaction with host via protein secreted by type III secretion system" that specifically identifies the Type III effectors.

Bottom Line: The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses.In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa.GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, Cornell University, Ithaca, NY 14850, USA. ML16@cornell.edu

ABSTRACT
Genome-informed identification and characterization of Type III effector repertoires in various bacterial strains and species is revealing important insights into the critical roles that these proteins play in the pathogenic strategies of diverse bacteria. However, non-systematic discipline-specific approaches to their annotation impede analysis of the accumulating wealth of data and inhibit easy communication of findings among researchers working on different experimental systems. The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses. The application of these terms to annotate type III effector genes in different bacterial species - the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic strains of Escherichia coli - illustrates how GO can effectively describe fundamental similarities and differences among different gene products deployed as part of diverse pathogenic strategies. In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa. GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.

Show MeSH
Related in: MedlinePlus