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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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Comparative Gene Ontology annotation for selected Type III effectors from Pto DC3000 and animal pathogenic genera. Black indicates the identity of effectors annotated to the specified GO term; green, effectors from plant pathogenic bacteria; orange, effectors from animal pathogenic bacteria.
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Figure 2: Comparative Gene Ontology annotation for selected Type III effectors from Pto DC3000 and animal pathogenic genera. Black indicates the identity of effectors annotated to the specified GO term; green, effectors from plant pathogenic bacteria; orange, effectors from animal pathogenic bacteria.

Mentions: A further illustration of GO-highlighted similarities is shown for a select group of effectors from multiple pathosystems in the table in Figure 2. In both plant and animal systems, complex signaling pathways mediate the response to detected pathogens, with elements of the intervening signaling pathways representing the most common targets for effector-mediated suppression of the immune response. This property is reflected by annotation of AvrPtoB as well as effectors AvrPto, HopAO1, and HopAI1 (P. syringae); IpaH9.8, OspF (Shigella); SspH1 (Salmonella); and YopP/J (Yersinia) to the term "GO:0052027 modulation by symbiont of host signal transduction pathway". For some effectors from both plant and animal pathosystems, the nature of this process has been more intensively characterized, supporting annotation to more specific child terms such as "GO:0052078 negative regulation by symbiont of defense-related host MAP kinase-mediated signal transduction pathway" and "GO:0052034 negative regulation by symbiont of pathogen-associated molecular pattern-induced host innate immunity". In other cases, the effectors in question await in depth evaluation.


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)

Comparative Gene Ontology annotation for selected Type III effectors from Pto DC3000 and animal pathogenic genera. Black indicates the identity of effectors annotated to the specified GO term; green, effectors from plant pathogenic bacteria; orange, effectors from animal pathogenic bacteria.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Comparative Gene Ontology annotation for selected Type III effectors from Pto DC3000 and animal pathogenic genera. Black indicates the identity of effectors annotated to the specified GO term; green, effectors from plant pathogenic bacteria; orange, effectors from animal pathogenic bacteria.
Mentions: A further illustration of GO-highlighted similarities is shown for a select group of effectors from multiple pathosystems in the table in Figure 2. In both plant and animal systems, complex signaling pathways mediate the response to detected pathogens, with elements of the intervening signaling pathways representing the most common targets for effector-mediated suppression of the immune response. This property is reflected by annotation of AvrPtoB as well as effectors AvrPto, HopAO1, and HopAI1 (P. syringae); IpaH9.8, OspF (Shigella); SspH1 (Salmonella); and YopP/J (Yersinia) to the term "GO:0052027 modulation by symbiont of host signal transduction pathway". For some effectors from both plant and animal pathosystems, the nature of this process has been more intensively characterized, supporting annotation to more specific child terms such as "GO:0052078 negative regulation by symbiont of defense-related host MAP kinase-mediated signal transduction pathway" and "GO:0052034 negative regulation by symbiont of pathogen-associated molecular pattern-induced host innate immunity". In other cases, the effectors in question await in depth evaluation.

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