Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology

Abstract

SUMMARY Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.

Mechanisms and Evolution of Virulence in Oomycetes

“…The common theme in each case is the suppression of PAMP-and effector-triggered immune responses, especially suppression of cell death associated with these responses (108,109). PiAvr3a could suppress cell death triggered by the PAMP INF1 (11).…”

“…Successful pathogens, including oomycetes, must avoid, suppress, or tolerate these defenses, as well as gain nutrition from the host (108). Inducible plant defenses consist of two overlapping modules identified by the microbial molecules that induce them (45,102).…”

Entry of oomycete and fungal effectors into plant and animal host cells

“…A major weapon used against plant and animal immunity machinery by cellular pathogens, including bacteria, fungi and oomycetes, are secreted effector and toxin proteins that can enter into the cytoplasm of host cells (reviewed in Torto‐Alalibo et al ., 2009; 2010). Effectors characterized to date, mostly from bacteria, target numerous host proteins associated with innate immunity including PRR signalling domains, MAP kinases, the host cytoskeleton, the host programmed cell death machinery, the host ubiquitination machinery, the host poly(ADP)‐ribosylation machinery and the host transcriptional machinery (Torto‐Alalibo et al ., 2009; 2010).…”

Effectors of root sedentary nematodes target diverse plant cell compartments to manipulate plant functions and promote infection

“…17 In this regard, the nematode stylet may in some ways be considered as functionally analogous to the type II or type III secretion systems of pathogenic bacteria that inject directly effectors into host cells. 18 However, the direct observation of nematode secretions in the plant cell cytoplasm is technically challenging due to the low quantity of nematode secreted proteins present in the enlarged feeding cells. In addition, the inability to transform plant parasitic nematodes makes it impossible to use reporter fusions to trace nematode secretions in vivo.…”