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

Review

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

Trudy Torto-Alalibo et al. BMC Microbiol. 2009.

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.

PubMed Disclaimer

Figures

Figure 1

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.

References

    1. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR. The general secretory pathway: a general misnomer? Trends Microbiol. 2004;12:306–309. doi: 10.1016/j.tim.2004.05.002. - DOI - PubMed
    1. Bailey BA. Purification of a protein from culture filtrates of Fusarium oxysporium that induces ethylene and necrosis in leaves of Erythroxylum coca. Phytopathology. 1995;85:1250–1255. doi: 10.1094/Phyto-85-1250. - DOI
    1. Fellbrich G, Romanski A, Varet A, Blume B, Brunner F, Engelhardt S, Felix G, Kemmerling B, Krzymowska M, Nurnberger T. NPP1, a Phytophthora-associated trigger of plant defense in parsley and Arabidopsis. Plant J. 2002;32:375–390. doi: 10.1046/j.1365-313X.2002.01454.x. - DOI - PubMed
    1. Qutob D, Kamoun S, Gijzen M. Expression of a Phytophthora sojae necrosis-inducing protein occurs during transition from biotrophy to necrotrophy. Plant J. 2002;32:361–373. doi: 10.1046/j.1365-313X.2002.01439.x. - DOI - PubMed
    1. Qutob D, Kemmerling B, Brunner F, Kufner I, Engelhardt S, Gust AA, Luberacki B, Seitz HU, Stahl D, Rauhut T, et al. Phytotoxicity and innate immune responses induced by Nep1-like proteins. Plant Cell. 2006;18:3721–3744. doi: 10.1105/tpc.106.044180. - DOI - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources