Contributes to

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Definition

A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.

Range

The 'contributes_to' qualifier can only be used with GO Molecular Function terms.

Child Terms

None

Usage guidance

  • The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier.
  • In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.

Multiple subunits required for a molecular function

  • All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine.
  • For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'.

Examples

1. ATP citrate lyase (ACL) in Chlorobaculum tepidum : a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Annotation for ATP citrate lyase subunit 1:

  Object: UniProt:Q8KDG1 (CT1089)    
  Relation: contributes_to
  GO term: GO:0003878 ATP citrate synthase activity
  Evidence code: IDA
  PMID:16952946


2. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. Annotation for S. pombe RNA polymerase II large subunit Rpb1:

  Object:  SPBC28F2.12
  Relation: contributes_to
  GO term: GO:0001055 RNA polymerase II activity
  Evidence code: EXP
  PMID:9325316

3. Subunits of ATP synthase complex : The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. Annotation for ATP8 ATP synthase complex subunit:

  Object: SGD:S000007267 (ATP8)
  Relation: contributes_to
  GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
  Evidence code: IDA
  PMID:20691145

Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known

  • If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.

When NOT to use 'contributes_to': single subunit required for a molecular function

  • Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.
  • If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.

Examples Annotate the catalytic subunit, without the contributes_to qualifier.

  • eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850).
    • eIF2gamma is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are not annotated to GTPase activity [1]
  • STT3 [2]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.
  • PIGM-PIGX complex: The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [3].
    • Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.
  • Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) RGD:3388: PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role.
    • annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".
  • Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) RGD:3387 is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.

Specific cases

Other common functions for protein complex members:

Regulatory subunits

  • If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.
  • Need examples.

Adaptor subunits

  • If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.
  • Need examples.

Quality Control Checks

Relations Ontology

contributes to

  • if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]

Review Status

Last reviewed: January 30, 2020

Back to: Annotation Relations