A total of 39 type III effectors have been identified in E. coli 0157:H7 strain Sakai through a combination of bioinformatics, “”secretome”" analysis, and translocation assays with Cya fusions [5]. However, the absence of a convenient model host system for E. coli O157:H7 has impeded in vivo characterization of host interaction phenotypes on the level conducted in P. syringae, with the result Metabolism inhibitor that annotation of E. coli O157:H7 effectors has relied more extensively on inferences made from sequence similarity. Among the O157:H7 effectors studied in greater depth is the Translocated Intimin Receptor protein (Tir), which plays a key role in bacterial

attachment to host cells [12–15]. Given that attachment has proven a tractable process for studying in cell culture models, it is possible to assign GO annotations to Tir with a specificity comparable to that of AvrPtoB. Tir is secreted into host cells via the LEE (locus of enterocyte effacement) T3SS and then trafficked to the host cell plasma membrane (GO:0020002), where it binds the (also LEE-encoded) intimin protein on the bacterial cell surface.

This binding activity is captured by the combination of Molecular Function ontology terms “”GO:0051635 bacterial cell surface binding”" and “”GO:0005515 protein binding”" using the IPI evidence code and “”with”" qualifier to specify the interacting partner as intimin. The role of Tir in bacterial attachment is reflected by the Biological Process term Cell Cycle inhibitor “”GO:0044406 adhesion to host”", with subsequent effects of Tir on the cascade of host signaling, described by “”GO:0052027 modulation by symbiont of defense-related host MAP kinase-mediated signal transduction pathway”" and major host cytoskeletal remodeling captured by “”GO:0052039 modification

by symbiont of host cytoskeleton”" easily accommodated by child terms of “”GO:0051701 interaction with host”". The term “”GO:0052057 modification by symbiont of host morphology or physiology via protein secreted by type III secretion system”" links Tir to other T3SS effectors, while “”GO:0009405 crotamiton pathogenesis”" indicates its role in disease. The Tir effector also highlights some of the challenges inherent to cross-genome term assignments. Given that transitive annotation based on sequence and structural similarity forms the basis of most annotations in the GO database, discussion of the limitations of such annotations is warranted. Specifically, similar gene products involved in the interaction between organisms can have very different properties depending on both their source organism and the host with which they are interacting. For example, Tir has been shown to have different molecular functions depending on whether it is produced by enterohemorrhagic (EHEC) O157:H7 or enteropathogenic (EPEC) strains of E. coli.