Special issue of microbiology journal spotlights standardized language for describing microbes
A special issue of "BMC Microbiology" highlights some of the recent achievements of scientists developing a universal language to describe the genes involved in the complex interplay between microbes and the hosts that they colonize.
Eight papers from members of the international Plant-Associated Microbe Gene Ontology (PAMGO) consortium chronicle efforts to expand The Gene Ontology to include a language that gives researchers a shared vocabulary to describe disease-related and beneficial interactions between a microbe and its host. In three years, the PAMGO consortium has created more than 700 terms that represent the myriad of interactions between microbes and their plant and animal hosts.
Trudy Torto-Alalibo, PAMGO project coordinator, remarked: “The Gene Ontology resource for more comprehensive cross-kingdom analyses will ultimately increase our knowledge of the molecular mechanisms underlying microbial interactions with their hosts. These advances in knowledge should, in time, enable many applications, including the design of novel disease-limiting strategies.”
Microbes have evolved many ingenious ways to live either peacefully with or wreak havoc on their host cells. Some microbes keep their host cells alive; others kill them quickly. Some sophisticated pathogens have even evolved to do both at different times of the infection process. The complexity and scope of these relationships have to be reflected in the Gene Ontology.
Candace Collmer of Wells College, who helped launch PAMGO in 2003, noted: “A crucial step at the beginning of the project was the realization that host pathogenesis is only one possible outcome on a continuum of symbiotic microbial-host interactions ranging from beneficial to detrimental. Since all are types of intimate interactions, and because microbes initiating these different types of interactions have common needs in approaching a host, we initially crafted broad terms for describing ‘symbiont’ gene functions in an attempt to highlight these similarities across a diverse set of microbes.”
The first paper in the “BMC Microbiology” supplement describes in detail progress made in the community-driven effort to develop this resource. Another paper looks at how effector molecules from diverse microbes get into cells, where they reside, what they do in the host, and how Gene Ontology terms were created to capture this information. Effectors are proteins that manipulate how plant cells work in such a way as to make their hosts more susceptible to infection. This article is accompanied by a review of the seven types of protein secretion systems that are used by bacteria to launch such molecules into their hosts. The power of Gene Ontology terms to reveal similarities and differences for a specific type of effector protein in very different bacterial organisms is shown by taking a close-up look at the plant pathogen Pseudomonas syringae pv tomato DC3000 and the animal pathogen Escherichia coli strains.
Many plant pathogens that draw their nutrition from living tissue have evolved sophisticated ways to interfere with programmed cell death, an in-built suicide mechanism that kills infected plant tissue so the pathogen can no longer feed on it. One of the articles in the supplement looks at the Gene Ontology terms that are useful for researchers to describe the processes involved in this subterfuge.
The series of articles is wrapped up by looking at how Gene Ontology terms can be used to describe the ways in which different microbes acquire nutrients and two further papers looking at the link between plant pathogens and disease. The PAMGO consortium has annotated gene products from diverse microbes including bacteria, oomycetes and fungi. The last paper in the supplement provides an example of how these annotations are made and showcases a whole- genome annotation of the rice blast fungus Magnaporthe oryzae using the Gene Ontology terms. Blast disease is one of the most destructive diseases of rice crop known worldwide. Gene Ontology terms will be extremely useful for scientists looking to make comparisons of the different strategies and mechanisms being used by diverse plant pathogens that cause significant disease burden worldwide.
A wide range of researchers, including many scientists who were not part of the original PAMGO consortium, are using the PAMGO terms. New research initiatives, not envisioned when the PAMGO project started, stand to benefit from this work. The National Institutes of Health has recently launched the Human Microbiome Project to acquire information about the many organisms that call the human body home and to determine how these organisms contribute to human health and disease. Dr. Michelle Giglio, assistant professor at the Institute for Genome Sciences at the University of Maryland School of Medicine and a senior scientist on the PAMGO project, commented: "At the Institute for Genome Sciences, we are responsible for the collection, coordination, and analysis of Human Microbiome Project data. The PAMGO terms will be of great benefit to our work on this project and should facilitate analysis that leads to a better understanding of how our internal inhabitants contribute to our well-being."
Brett Tyler, professor at the Virginia Bioinformatics Institute, and the PAMGO project leader, remarked: “The community-driven Gene Ontology resource is a big step forward in allowing researchers to make comparisons across microbial species of the many processes involved in microbe-host-environment interactions. We hope that readers will use these terms and create more of their own to assist in free and accurate exchange of information within the scientific research community.”
PAMGO is a consortium of researchers from Virginia Tech, Cornell University, Wells College, the University of Maryland, Baltimore, North Carolina State University, the University of Wisconsin, Madison, and the European Bioinformatics Institute in the United Kingdom. Its work is supported by grants from the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service and from the US National Science Foundation.