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 or small set of subunits of a complex.
- 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.
- Checklist: useful questions:
- Can the activity occur without this subunit? In this case maybe the 'contributes_to' annotation is not appropriate.
- Can the protein be annotated to another term? Ideally each protein would have a MF.
- If the qualifier is omitted, is the annotation still acceptable? (this is to avoid annotating for example regulatory subunits)
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'.
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: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet a subset form the catalytic core (PMID:22365827) - these subunits should be annotated with "contributes_to DNA-dependent RNA polymerase activity". Nuclear RNA polymerase complex subunits outside the catalytic core serve other functions - these subunits should therefore 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.
Out of scope
Note that not all proteins that are part of a complex should be annotated using 'contributes to'
Single subunit required for a molecular function
- 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.
- 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 
- STT3 : "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 .
- Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.
Complexes containing regulatory and catalytic subunits
Some complexes are composed of regulatory and catalytic subunits; for example of some kinases, heterotrimeric G proteins, etc. These are respectively represented by a regulator activity term, under the GO:0030234 enzyme regulator activity node, and an enzyme activity term, under the catalytic activity node. The 'has input' annotation context relation should be used to describe which gene product is being regulated.
- 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.
- 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.
Substrate specificity subunits
- Need examples.
Complexes with individual catalytic activity for each member
In some complexes, individual subunits have different catalytic activity, and the product of one activity is channeled to the next enzyme where it is being used as a substrate. These are represented by individual MF annotations for each protein.
- Need examples.
- Last reviewed: February 22, 2023, Pascale Gaudet
- Reviewed February 25, 2022 by Paul Thomas, Pascale Gaudet, Patrick Masson