Exploring autophagy with Gene Ontology

Abstract

Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of 'annotations' that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.

Keywords: Gene Ontology; Parkinson disease; annotation; autophagy; biocuration; curation; enrichment analysis; network analysis.

Figure 1.

Information associated with the GO term ‘autophagosome membrane disassembly’ (GO:0030399). The ontology stanza, in obo format, shows the term and various metadata associated with it. The textual definition labeled ‘def’ is the human-readable definition used by biocurators. The ‘intersection_of’ tags specify the necessary and sufficient conditions to define the term in a computable format. The stanza also contains other information related to a term, such as synonyms.

Figure 2.

Schematic representation of the different types of autophagy. The main autophagy-related GO terms and their corresponding IDs are indicated. The different types of autophagy are represented with different background colors: macroautophagy in pink; chaperone-mediated autophagy, green; late endosomal microautophagy, cream; and lysosomal microautophagy, blue. The major steps of macroautophagy are shown, from the formation of omegasomes to the fusion with the lysosome, via engulfment of macroautophagy targets by the phagophore, the formation of a closed autophagosome, and the maturation of the autophagosome through removal of ATG proteins such as Atg8-family proteins. The branching pathway via an amphisome is also represented. Black lines correspond to membranes (apart from the lysosomal membrane which is in red). Red dots correspond to ATG proteins such as Atg8-family protein members required for the autophagosome assembly and removed during autophagosome maturation. The scissors represent proteins such as ATG4 and the PI3P phosphatase that strip ATG proteins from the outer autophagosome membrane during the maturation step. The red arrows within the lysosome represent lysosomal breakdown of the autophagy targets. The CMA-targeting motif that is recognized by a cytosolic chaperone is indicated by a rectangle on the misfolded/unfolded protein. To distinguish between biological process and cellular component GO terms, the latter are in red italics.

Figure 3.

A view of the ontology showing the ‘is_a’ neighborhood around autophagy. This figure was generated by the Protégé ontology editing tool and shows the ‘is_a’ hierarchy of the autophagy branch of the ontology. Each indentation indicates a term that is a type of its parent. The grouping term ‘process utilizing autophagic mechanism’ is used to group conventional autophagy with the Cvt pathway, both of which use common mechanisms. General terms ‘autophagy of X’ are used to group types of autophagy that can use different mechanisms to degrade similar targets. For example, ‘mitophagy’ is a child of both ‘autophagy of mitochondrion’ and ‘macroautophagy’. Macroautophagy of specific targets are grouped under a term to describe the ‘selective autophagy’ pathway and nomenclature has been assigned to be consistent with the names that are used prominently in the literature. To view the entire structure of this branch see Table S1; for a dynamic view we also recommend the 'inferred view’ tab in the AmiGO2 browser.

Figure 4.

The GO term ‘autophagosome assembly’ showing relationships to molecular functions. A screenshot of the Protégé ontology-editing tool focusing on ‘autophagosome assembly’ (GO:0000045). The top part of the panel displays the equivalence axiom for the term ‘autophagosome assembly’ which states that the term is equivalent to a type of ‘cellular component assembly’ that results in the assembly of an ‘autophagosome’. The lower part of the panel shows the relations between this term and other terms in the ontology. The last row displays the result of computational reasoning and shows that, based on the equivalence axiom, ‘autophagosome assembly’ (GO:0000045) is a type of ‘autophagosome organization’ (GO:1905037). Rows that are not shaded in the lower part of the panel indicate relationships that have been asserted by an editor. For example, the ‘autophagosome assembly’ process has been asserted as a type of ‘organelle assembly’ (GO:0070925), and the ‘starts_with’ row indicates that the process starts with the creation of the Atg1/ULK1 complex. The ‘has_part’ rows show GO molecular functions that are necessary for autophagosome assembly to occur.

Figure 5.

Protein interactome network associated with 4 key autophagy proteins. The in silico human interactome associated with AMBRA1, BECN1, PIK3C3, ULK1 assembled with Cytoscape and analyzed with BinGO. Each node is a protein and each edge is an interaction between 2 proteins. GO terms associated with each protein are indicated by the node color (blue indicates ‘autophagy’ and red ‘regulation of autophagy’), green nodes indicate proteins that are not annotated to either of the selected GO terms. The size of each node is proportional to the number of times the interaction has been captured as an annotation. (A) BinGO analysis using the 2014 GO annotation file, 29 proteins are associated with the GO term ‘autophagy’, 18 with ‘regulation of autophagy’. (B) BinGO analysis using the 2017 GO annotation file, 45 proteins are associated with the GO term ‘autophagy’, 39 with ‘regulation of autophagy’. The black arrows indicate proteins associated with the GO terms ‘autophagy’ and ‘regulation of autophagy’ in 2014, but now associated with only ‘autophagy’ (February 2017). The blue and red arrows indicate TRIM5 and MCL1 (Q9C035 and Q07820); these proteins were not associated with any autophagy-related term in 2014 but are now associated with ‘autophagy’ or ‘regulation of autophagy’, respectively. The white arrow indicates BECN1; this remains associated with both ‘autophagy’ and ‘regulation of autophagy’ terms.