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The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions.

Torto-Alalibo T, Collmer CW, Gwinn-Giglio M - BMC Microbiol. (2009)

Bottom Line: They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply.The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes.The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. trudy@vbi.vt.edu

ABSTRACT
All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology, describe the development and use of these terms.

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Parent and child terms associated with " GO:0044403 symbiosis, encompassing mutualism through parasitism".  "GO:0044403 symbiosis, encompassing mutualism through parasitism", was developed by the PAMGO consortium to emphasize the continuum of microbe-host relationships. "GO:0051701 interaction with host", a child term under GO:0044403, has several child terms that represent key processes in the interaction between diverse microbes and their host, irrespective of the symbiotic partner (mutualist or pathogen). To describe the fact that a particular symbiont-host association results in susceptibility, the term "GO:0009405 pathogenesis", a sibling of "GO:0051701 interaction with host", can be used.
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Figure 1: Parent and child terms associated with " GO:0044403 symbiosis, encompassing mutualism through parasitism". "GO:0044403 symbiosis, encompassing mutualism through parasitism", was developed by the PAMGO consortium to emphasize the continuum of microbe-host relationships. "GO:0051701 interaction with host", a child term under GO:0044403, has several child terms that represent key processes in the interaction between diverse microbes and their host, irrespective of the symbiotic partner (mutualist or pathogen). To describe the fact that a particular symbiont-host association results in susceptibility, the term "GO:0009405 pathogenesis", a sibling of "GO:0051701 interaction with host", can be used.

Mentions: The initial aim of the PAMGO consortium was to create terms associated with plant-pathogen interactions. However, it soon became apparent that creating more inclusive terms that were appropriate to both prokaryotic and eukaryotic microbes, to both plant and animal hosts, and for describing the whole range of intimate relationships between them (encompassing mutualism through parasitism), would better capture commonalities across diverse gene products involved in microbe-host interactions. After all, microbes of every domain face the same challenges in initiating an intimate association with a host. All must initially attach to the host and breach a barrier or enter through openings to gain access to a nutritional source; all must suppress, evade, or tolerate host defenses for successful invasion. In addition, it is known that microbes share strategies for invading a host, whether plant or animal. For example, bacterial pathogens of both plants and animals utilize the type III protein secretion machinery to inject effectors into host cells [9]. (Bacterial secretion systems, including the type III is reviewed in this supplement [10].) Some of those effectors target defensive signal transduction pathways common to both plant and animal hosts. Furthermore, pathogens as diverse as oomycetes (attacking plants) and protozoans (attacking animals) have been shown to share a common targeting domain in their secreted proteins that enter host cells [11,12]. Therefore we created an initial set of general terms to describe microbial activities common across the systems described above. Some of those general terms can be seen in Figure 1. In a different paper of this Gene Ontology-focused supplement, Lindeberg et al. [13] detail the GO annotation of type III effectors from both a plant pathogen, Pseudomonas syringae pv tomato DC3000 (PtoDC3000), and the animal pathogen Escherichia coli, emphasizing the similarities and differences in processes employed by these diverse pathogens in manipulating host defenses. A similar analysis reported in another paper in this series [14] extends the comparison to effectors of eukaryotic pathogens from diverse taxa, including oomycetes, fungi, and nematodes. The power of ontology-based annotation to capture common themes in such diverse pathogens is well illustrated in these two mini reviews.


The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions.

Torto-Alalibo T, Collmer CW, Gwinn-Giglio M - BMC Microbiol. (2009)

Parent and child terms associated with " GO:0044403 symbiosis, encompassing mutualism through parasitism".  "GO:0044403 symbiosis, encompassing mutualism through parasitism", was developed by the PAMGO consortium to emphasize the continuum of microbe-host relationships. "GO:0051701 interaction with host", a child term under GO:0044403, has several child terms that represent key processes in the interaction between diverse microbes and their host, irrespective of the symbiotic partner (mutualist or pathogen). To describe the fact that a particular symbiont-host association results in susceptibility, the term "GO:0009405 pathogenesis", a sibling of "GO:0051701 interaction with host", can be used.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654661&req=5

Figure 1: Parent and child terms associated with " GO:0044403 symbiosis, encompassing mutualism through parasitism". "GO:0044403 symbiosis, encompassing mutualism through parasitism", was developed by the PAMGO consortium to emphasize the continuum of microbe-host relationships. "GO:0051701 interaction with host", a child term under GO:0044403, has several child terms that represent key processes in the interaction between diverse microbes and their host, irrespective of the symbiotic partner (mutualist or pathogen). To describe the fact that a particular symbiont-host association results in susceptibility, the term "GO:0009405 pathogenesis", a sibling of "GO:0051701 interaction with host", can be used.
Mentions: The initial aim of the PAMGO consortium was to create terms associated with plant-pathogen interactions. However, it soon became apparent that creating more inclusive terms that were appropriate to both prokaryotic and eukaryotic microbes, to both plant and animal hosts, and for describing the whole range of intimate relationships between them (encompassing mutualism through parasitism), would better capture commonalities across diverse gene products involved in microbe-host interactions. After all, microbes of every domain face the same challenges in initiating an intimate association with a host. All must initially attach to the host and breach a barrier or enter through openings to gain access to a nutritional source; all must suppress, evade, or tolerate host defenses for successful invasion. In addition, it is known that microbes share strategies for invading a host, whether plant or animal. For example, bacterial pathogens of both plants and animals utilize the type III protein secretion machinery to inject effectors into host cells [9]. (Bacterial secretion systems, including the type III is reviewed in this supplement [10].) Some of those effectors target defensive signal transduction pathways common to both plant and animal hosts. Furthermore, pathogens as diverse as oomycetes (attacking plants) and protozoans (attacking animals) have been shown to share a common targeting domain in their secreted proteins that enter host cells [11,12]. Therefore we created an initial set of general terms to describe microbial activities common across the systems described above. Some of those general terms can be seen in Figure 1. In a different paper of this Gene Ontology-focused supplement, Lindeberg et al. [13] detail the GO annotation of type III effectors from both a plant pathogen, Pseudomonas syringae pv tomato DC3000 (PtoDC3000), and the animal pathogen Escherichia coli, emphasizing the similarities and differences in processes employed by these diverse pathogens in manipulating host defenses. A similar analysis reported in another paper in this series [14] extends the comparison to effectors of eukaryotic pathogens from diverse taxa, including oomycetes, fungi, and nematodes. The power of ontology-based annotation to capture common themes in such diverse pathogens is well illustrated in these two mini reviews.

Bottom Line: They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply.The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes.The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. trudy@vbi.vt.edu

ABSTRACT
All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology, describe the development and use of these terms.

Show MeSH
Related in: MedlinePlus