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

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.

Improved Gene Ontology Annotation for Biofilm Formation, Filamentous Growth, and Phenotypic Switching in Candida albicans

“…We worked with the GO Consortium to develop and contribute new terms to the ontology and then used these terms to annotate or reannotate specific classes of genes in CGD. Due to the concentrated efforts of the Plant-Associated Microbe Gene Ontology (PAMGO) project (30), the GO is quite well developed to cover areas related to host interactions and pathogenesis, though new GO terms were needed to more precisely capture the functions of genes related to filamentous growth and regulation of adhesion and biofilm formation. Certain biological processes, such as phenotypic switching, lacked representation in the GO altogether.…”

What we can learn about Escherichia coli through application of Gene Ontology

“…This means that the quality control in areas of GO relevant to microbiologists is connected to how actively bacterial systems are being curated with GO. The PAMGO project has focused on the interaction of bacterial and fungal pathogens with their plant hosts, leading to the addition of hundreds of appropriate GO terms 57 . Annotation of E. coli is already stimulating reexamination of other aspects of GO.…”

Ranking Gene Ontology terms for predicting non-classical secretory proteins in eukaryotes and prokaryotes

“…ontologies) that characterize individual gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. The Plant-associated Microbe Gene Ontology (PAMGO) Consortium (Torto-Alalibo et al, 2009) has developed standardized terms for describing biological processes and cellular components that play important roles in the interactions between microbes and plant and animal hosts, including bacterial secretion processes (Tseng et al, 2009). Hence, the GO annotations have a high potential in improve prediction performance when identifying non-classically secreted proteins in eukaryotes and prokaryotes.…”