Special issue: Gene Ontology for microbiologists Describing commonalities in microbial effector delivery using the Gene Ontology Marcus C. Chibucos 1, 2* , Tsai-Tien Tseng 1, 3* and Joa ˜ o C. Setubal 1, 4 1 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA 2 current address: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA 3 current address: School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA 4 Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA Myriad symbiotic microbes, ranging from mutualistic through to pathogenic, deliver ‘effector’ molecules into the cytoplasm or cellular milieu of their hosts to facilitate colonization. Among ecologically and evolutionarily diverse taxa, analogous processes and structures exist to facilitate effector delivery. These include syringe-like injection (bacteria and nematodes), common host-tar- geting signals (oomycetes and protozoans) and special- ized intercellular structures (fungi and oomycetes). Here, we briefly introduce readers to the Gene Ontology (GO), a controlled vocabulary to facilitate comparative geno- mics of diverse taxa. We also summarize and compare selected mechanisms of effector delivery from various organisms and show how careful annotation of gene products with GO can reveal underlying similarities among diverse taxa. Microbial effector delivery and the Gene Ontology The Gene Ontology facilitates comparative genomics of diverse organisms Comparative studies of gene products among closely related taxa often rely on sequence similarity comparison. Yet, over great evolutionary distances where sequence similarity can be low or nonexistent, these approaches might be uninformative. One tool developed to provide insights into the biology of diverse taxa is the Gene Ontol- ogy (GO) (Box 1) [1]. Annotating gene products with GO terms allows researchers to perform text searches to locate gene products using standardized descriptive terms, to obtain functional summaries of genomic, cDNA or micro- array data, to group gene products into functional classes, and to discover commonalities among species not revealed by sequence similarity. The Plant-Associated Microbe Gene Ontology Consor- tium (PAMGO), a GO interest group, has developed many specialized GO terms that describe biological processes central to symbiotic interactions (Box 2) [2]. These GO terms can be used to annotate gene products of both hosts and symbionts in interactions that range from mutualistic through to parasitic. Review Glossary Analogous : analogous structures are morphological features or cellular components of taxonomically divergent organisms that are functionally equivalent, and could even share a superficial resemblance, such as a bacterial type III secretion system and a nematode stylet. Annotation : to annotate simply means to add information to something. Gene annotation is the art of adding specific information to describe a gene or gene product, and can refer to structural or functional annotation. GO annotation is functional gene annotation using GO terms, in which a specific reference is cited that describes the analysis or work performed to associate a particular gene product and GO term. Each GO annotation must include an evidence code. Apoplast : the free diffusional space outside the plasma membrane of a plant cell that includes the cell wall and extracellular spaces. Biotroph : a symbiont that avoids eliciting host cell death as a mode of infection, often forming specialized intercellular structures that facilitate nutrient uptake from the host. Effector : a molecule delivered by a symbiotic microorganism into the cellular milieu or cytoplasm of its host that can induce a change in host morphology, physiology, biochemistry or genomic content [3–5]. Although historically restricted to proteins, here effectors can also include RNA- or DNA-containing nucleoproteins [67]. In the context of plant defenses, most resistance (R)-gene products detect the action of effector proteins, either directly or indirectly. Historically, genes encoding effectors recognized by R-genes have been called ‘avirulence’ (Avr) genes [68]. Extracellular space : ‘that part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid’ (‘GO:0005615 extracellular space’). The location of the microbe with respect to the host cell requires special attention in the use of GO terms, as there are two additional, related terms. ‘GO:0005576 extracellular region’ is defined as ‘the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.’ The other term is ‘GO:0043655 extracellular space of host,’ defined as ‘the space within a host but external to the plasma membrane of host cells, e.g. within host bloodstream.’ Hemibiotroph : a symbiont that initially lives as a biotroph, but eventually transitions to a necrotrophic lifestyle, whereby it kills host cells and obtains their nutrients. Host-targeting signal (HTS) : a small motif of several amino acids within a secreted protein that directs secretion of the protein into the host. Pathogenesis : defined in the Gene Ontology as ‘the set of specific processes that generate the ability of an organism to cause disease in another’ (http:// amigo.geneontology.org). This broad level term should only be used to annotate symbiont-derived gene products that function in pathogenesis, and not host gene products involved in response to pathogenesis. Secreted protein : a protein actively transported via a secretion system. In contrast, an exoprotein is any protein found in the extracellular milieu [69]. Secretion : active transport of a substrate from the interior of a cell to its exterior; related, but distinct, terms as defined by reference [69] include: ‘export’ (i.e. active transport from the cytoplasm), ‘translocation’ (i.e. active transport across a lipid bilayer that results in a change of location) and the ‘secretome’ (i.e. all the components of translocation systems and their substrates). Translocon : a complex of proteins that translocates proteins across a membrane. Type III secretion system (T3SS) : a secretion system often found in Gram- negative bacteria with a needle-like structure for secretion of effectors. Corresponding author: Setubal, J.C. (setubal@vbi.vt.edu) * The authors contributed equally to this work. 312 0966-842X/$ – see front matter ß 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.tim.2009.05.001 Available online 1 July 2009