Fewer structures

needed: the case of necrotrophic pathogens Many symbionts of animal and plant hosts employ a necrotrophic strategy in order to make nutrients available for uptake, by killing the host tissue prior to drawing nutrition from it, e.g. “”GO: 0001907 killing by symbiont of host cells”" [10]. Some necrotrophs utilize well-differentiated structures for penetration of host tissue, for example appressoria used by fungi and oomycetes [59]. However, differentiated structures such as haustoria are not utilized for nutrition. Instead, emphasis is placed on production of enzymes and toxins for host cell killing [60] and transporters for uptake of catabolized host cell products, e.g. “”GO: 0022857 Torin 1 manufacturer transmembrane transporter activity”" and child terms (Figure 17-AAG nmr 2). Toxins produced by necrotrophic phytopathogens may act by triggering programmed cell death in host plant cells, e.g. “”GO: 0052042 positive regulation by symbiont of host programmed cell

death”" (Figure 2). Many GO terms exist to annotate gene products involved in the production, transport, or activity of toxins including: “”GO: 0009403 toxin biosynthetic process”", “”GO: 0015643 toxin binding”", “”GO: 0019534 toxin transporter activity”", “”GO: 0009636 response to toxin”", “”GO: 0010046 response to mycotoxin”", and “”GO: 0009404 toxin metabolic process”" [10]. Furthermore, many GO terms are available for annotating gene products involved in symbiont-induced programmed cell death (see

[19] in this supplement). Necrotrophic phytopathogens, including bacteria, fungi and oomycetes, also produce enzymes such as cellulases, xylanases, and pectin-degrading Ergoloid endopolygalacturonases that catalyze degradation of the plant cell wall, e.g. “”GO: 0052009 disassembly by symbiont of host cell wall”" [61]. In an interesting Epoxomicin mouse contrast, necrotrophic animal pathogens such as the oomycete fish pathogen Saprolegnia parasitica appear to emphasize secretion of protease inhibitors and proteolytic enzymes [62]. Summary An extraordinary diversity of organisms engage in symbiotic interactions, ranging from pathogenic to mutualistic. However, many common themes for fulfilling nutritional requirements have emerged among both hosts and their symbionts. A large number of Gene Ontology terms created by the PAMGO Consortium can be used to identify these commonalities. The more that these terms are used and refined by the community, the more that they will enhance our understanding of multi-organism processes, including mechanisms of nutrient exchange. Acknowledgements The authors would like to thank the editors at The Gene Ontology Consortium, in particular Jane Lomax and Amelia Ireland, and the members of the PAMGO Consortium for their collaboration in developing many PAMGO terms. This work was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number 2005-35600-16370 and by the U.S.