Trade.Information

Topic Name: 450 new terms for describing gene products involved in microbe-host interactions.

Category: Biomedical

Research persons:
Brett Tyler,
PAMGO project leader
Virginia Bioinformatics Institute
Phone: (540) 231-7318;
Email: bmtyler@vt.edu

Cheryl Dybas,
National Science Foundation,
(703) 292-7734
cdybas@nsf.gov

Location: Virginia Bioinformatics Institute
Washington Street,Blacksburg, VA 24061-0447
&
The National Science Foundation
4201 Wilson Boulevard, Arlington, Virginia 22230, United States

Details

An international group of scientists has expanded the universal language for the genes of both disease-causing and beneficial microbes and their hosts. This expanded "lingua franca," called The Gene Ontology (GO), gives researchers a common set of terms to describe the interactions between a microbe and its host. The Plant-Associated Microbe Gene Ontology (PAMGO) consortium and the GO consortium staff at the European Bioinformatics Institute approved and released more than 450 new terms for describing gene products involved in microbe-host interactions. The National Science Foundation (NSF) and the USDA's Cooperative State Research, Education and Extension Service (CSREES) support the PAMGO project through grants from their joint Microbial Genome Sequencing program. This new "common terminology" will speed development of new technologies for preventing infections by disease-causing microbes, while preserving or encouraging the presence of beneficial microbes. Scientists say the Gene Ontology will provide a powerful tool for comparing the functions of genes and proteins in a wide range of disease-related organisms. "A common set of terms for exchange of information about microbe-host interactions will help researchers communicate information, and expand concepts from studies of microbes and their hosts," says Maryanna Henkart, director of NSF's Division of Molecular and Cellular Biology. Microbes that associate with plants or animals can be pathogenic, neutral, or beneficial, but all share many common processes in their interactions with their hosts. For example, all must initially attach to the host. PAMGO, from the beginning, tailored the new terms so they would be useful for describing both benign and pathogenic microbes in plant or animal hosts. "Having a common set of terms to describe genes of pathogenic and beneficial microbes, as well as the organisms they come into contact with, is critical to understanding host-microbe-environment interactions," said Brett Tyler, PAMGO project leader at the Virginia Bioinformatics Institute (VBI) in Blacksburg, Va. Many of the early GO terms described biological functions and processes found in microbes, but very few described the functions used by microbes in their associations with hosts. PAMGO started by creating terms to describe how microbes interact with plants, but researchers soon discovered that almost all the terms were also relevant to microbes that interact with animals and humans. The Gene Ontology Consortium was organized so all users can actively contribute to the ongoing refinement of the terms. When scientists submit new terms to PAMGO, the entire community participates to synthesize a common understanding of how microbes associate with hosts. The PAMGO consortium is a collaboration between VBI, Cornell University, North Carolina State University, the University of Wisconsin-Madison, The Institute for Genomic Research (a division of the J.C. Venter Institute) and Wells College. The group works closely with the Gene Ontology Consortium.
About Researcher:

Tyler, Brett, PhD

Research Interests
* Comparative and functional genomics of oomycete plant pathogens
* Molecular analysis of oomycete virulence proteins
* Functional genomics of quantitative disease resistance and infection responses in plants * Computational prediction of gene functions
* Mathematical modeling of complex cellular responses

Professional Preparation
Monash University, Melbourne, Australia, B.Sc. in genetics, biochemistry, and mathematics, 1977
University of Melbourne, Australia, Ph.D. in molecular biology, 1981
University of Georgia, postdoctoral training, 1982-84
Selected Publications
Tyler BM, Tripathy S, Zhang X et al. (52 authors) (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (in press)
Tripathy S, Pandey VN, Fang B, Salas F, Tyler BM (2006) VMD: A community annotation database for microbial genomes. Nucl. Acids Res. 34: D379–D381.
Rehmany AP, Gordon A, Allen RL, Armstrong MR, Whisson SC, Kamoun S, Tyler BM, Birch PRJ, Beynon JL (2005) Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 genes from two Arabidopsis lines. Plant Cell 17(6): 1839–1850.
Shan W-X, Cao M, Leung D, Tyler BM (2004) The Avr1b locus of Phytophthora sojae encodes an elicitor and a regulator required for avirulence on soybean plants carrying resistance gene Rps1b. Mol. Plant-Microbe Interact. 17(4): 394–403.
Tyler BM (2002) Molecular basis of recognition between Phytophthora species and their hosts. Annu. Rev. Phytopathol. 40: 137-167.
Fundfor reesearch
The National Science Foundation (NSF) and the USDA's Cooperative State Research, Education and Extension Service (CSREES) support the PAMGO project through grants from their joint Microbial Genome Sequencing program.