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Gene Ontology Annotation (GOA) for Plant Associated Microbes

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What is Gene Ontology?

The Gene Ontology Annotation, also known as GO or GOA, is a trio of controlled vocabularies that are being developed to aid the description of the molecular functions of gene products, their placement in and as cellular components, and their participation in biological processes. (for a variety of resources and FAQ related to GO, go to the gene ontology home page)

Why do we need GO?

Comparative genomic analysis represents an important tool for gaining new insight into biological mechanisms. 

  • STRUCTURAL comparison is routinely accomplished using various tools for alignment of genes and whole genomes. 
  • FUNCTIONAL comparison is impeded by the lack of consistent terminology for describing the function of individual gene products.
Why don't existing annotation approaches allow for effective functional comparisons?
  1. Typically, gene annotation reflects only a subset of the multiple roles of any given gene product.
  2. Terminology often has specific and different meanings for people in different fields of biology.

    EXAMPLE: "adhesion", "attachment" and "pre-penetration activity" are all commonly used to refer to analogous biological processes

  3. Name assignments are made with varying degrees of evidence ranging from low levels of BLAST similarity to extensive experimental confirmation. In many cases, the nature of the supporting evidence is not indicated in the standard annotation.

Type II secretion in pathogenic bacteria as an illustration of the limitations of traditional annotation:

  • The biological process is variously referred to as “Type II secretion”, “Type II secretory pathway, “general secretion pathway”, and "main terminal branch"
  • Three letter gene and product names are as various as Xcp, Out, Xps, and Gsp
  • Many type II secretion genes are also required for type IV pilus biogenesis, but the dual function is rarely noted in individual annotations


How does GO annotation address the limitations of traditional annotation?

GO encompasses three distinct ontologies:

  1. MOLECULAR FUNCTION – what the gene product does
  2. CELLULAR COMPONENT – where it does what it does 
  3. BIOLOGICAL PROCESS – why it does what it does (what larger process is it part of)

Each of these three ontologies is composed of a hierarchical arrangement of terms whose definitions and interrelationships are precisely defined.
Each of the terms has an associated numerical ID in the form "GO:#######" which is assigned to annotated gene products.
A gene product can be annotated to broader or more specific GO terms depending on the extent to which it has been characterized.

Biological process ontology and term definition for "adhesion to host"
Note that a gene product could be annotated to a more general term "adhesion to host" or a more specific child term such as "single-species biofilm formation in or on host organism" depending on the available evidence

GO annotations are accompanied by precisely defined evidence codes such as IDA (Inferred from Direct Assay) or ISS (Inferred from Sequence or Structural Similarity) (view full list of evidence codes)

(Browse and search terms in all three ontologies at the AmiGO website)

PAMGO - project for development of biological process terms for plant associated microbes

The original developers of GO were associated with the mouse, yeast and fly genome projects and as such, early version of the ontologies were focused on eukaryotic cells.
Terms relevant to prokaryotes have been developed and integrated on a continual basis.
Recognition of the need for terms relevant to pathogenesis led to formation of the PAMGO interest group

PAMGO’s mission:

The PAMGO consortium aspires to develop precisely defined GO terms that describe biological processes involved in the interaction of microbes with their hosts. Those created will include broad terms that encompass the interactions of symbionts (from mutualists to pathogens) with their hosts (plant or animal) as well as child terms more relevant to specific host kingdoms and specific microbial symbionts (more information on PAMGO)

Who is PAMGO:

The PAMGO Consortium is made up of scientists from 6 institutions involved in genome projects for a range of prokaryotic and eukaryotic plant pathogens (more information on the people involved)

Term development by the PAMGO consortium:

2005 - broad ranging discussion about terms related to pathogenicity and symbiosis followed by developement and acceptance of 35 new terms under the parent term GO:0051701: Interaction with host (view a subset of these terms)

2006 - draft list of several hundred "child" terms of the original 35

Our long term goal:

To achieve comprehensive GO annotation of gene products for plant-associated microbes so that researchers can rapidly and comprehensively identify gene products from multiple genomes, regardless of structural similarity, that share the same biological process, molecular function, and/or cellular component.

To ask further questions or to get involved, contact the PPI site administrator



Magdalen Lindeberg
PPI Project Coordinator
Plant Pathology and Plant-Microbe Biology
Cornell University