tra-2

Gene Description

Cbr-TRA-2 is the Caenorhabditis briggsae ortholog of the sex-determining transformer protein TRA-2, a large multi-pass integral membrane protein that is a central, membrane-localized regulator of the nematode sex-determination pathway. It promotes female (oocyte) cell fates in XX animals by repressing the masculinizing FEM proteins: its intracellular domain binds and sequesters FEM-3 at the membrane, preventing FEM-3 from inhibiting the terminal transcription factor TRA-1. In XO animals the secreted male-promoting signal HER-1 binds the TRA-2 extracellular domain and antagonizes this activity, so TRA-2 also behaves as a receptor for HER-1. The intracellular MX regulatory domain additionally binds the TRA-1 transcription factor directly, and proteolytic cleavage of TRA-2 (by the calpain-like protease TRA-3) generates a feminizing fragment. Through these activities TRA-2 governs both somatic sexual differentiation and the germline sperm/oocyte decision (including hermaphrodite spermatogenesis). The FEM-3-binding region of TRA-2 is hypervariable and coevolves rapidly with FEM-3, making tra-2 a key gene for comparative study of sex-determination pathway evolution between C. briggsae and C. elegans.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005886 plasma membrane	IBA GO_REF:0000033	ACCEPT	Summary: TRA-2 is an integral multi-pass membrane protein and the UniProt subcellular location is "Membrane; Multi-pass membrane protein". An IDA membrane annotation (GO:0016020) is independently supported. Plasma membrane is the biologically expected localization for a receptor that binds the secreted HER-1 ligand and sequesters FEM proteins at the cell surface; the IBA call is consistent with the family. Accepted as the cellular location where TRA-2 acts.
GO:0004888 transmembrane signaling receptor activity	IBA GO_REF:0000033	ACCEPT	Summary: TRA-2 functions as a membrane receptor for the secreted male-promoting signal HER-1; HER-1 binding to the TRA-2 extracellular domain modulates the masculinizing output of the pathway. This receptor activity is a core molecular function of TRA-2 and is consistent across the TRA-2 family (IBA). Accepted and retained as a core molecular function.
GO:0018992 germ-line sex determination	IBA GO_REF:0000033	ACCEPT	Summary: TRA-2 controls the germline sperm/oocyte decision and hermaphrodite spermatogenesis; null mutants have masculinized germ lines producing only sperm (disruption phenotype). This is independently supported by an IMP annotation (PMID:11250902). A core biological process for tra-2. Accepted.
GO:0004888 transmembrane signaling receptor activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO (IPR032848, Ce-Tra-2) electronic annotation of the same receptor activity supported by the IBA call above. Consistent with TRA-2 acting as a receptor for HER-1. Accepted as a redundant but correct electronic annotation.
GO:0016020 membrane	IEA GO_REF:0000044	ACCEPT	Summary: Electronic mapping from the UniProt subcellular-location keyword "Membrane". Correct but more general than the supported localization; the IDA membrane and IBA plasma membrane annotations are more informative. Kept as a correct, if general, component annotation.
GO:0040021 hermaphrodite germ-line sex determination	IEA GO_REF:0000002	ACCEPT	Summary: More specific child of germ-line sex determination, appropriate for tra-2 given its required role in the hermaphrodite germline sperm/oocyte switch and hermaphrodite spermatogenesis (PMID:24098152 disruption phenotype; PMID:11250902 MX-domain control of spermatogenesis). This specificity is well justified for the gene; accepted as a core process annotation.
GO:0042001 hermaphrodite somatic sex determination	IEA GO_REF:0000002	ACCEPT	Summary: TRA-2 promotes female somatic fates in XX animals; null mutants make incomplete (masculinized) male tails, indicating a somatic sex-determination role in addition to the germline role. The hermaphrodite-specific somatic term is appropriate. Accepted.
GO:0016020 membrane	IDA PMID:10783162 Proteolysis in Caenorhabditis elegans sex determination: cle...	ACCEPT	Summary: Direct experimental (IDA) membrane localization. Sokol & Kuwabara show that the membrane protein TRA-2A is a substrate of the TRA-3 protease, working with the membrane-associated form of TRA-2. The membrane localization is central to TRA-2 function (HER-1 reception, FEM sequestration). Accepted as experimentally supported localization.
GO:0005515 protein binding	IPI PMID:11250902 The TRA-1 transcription factor binds TRA-2 to regulate sexua...	MARK AS OVER ANNOTATED	Summary: IPI annotation (with UniProtKB:Q17308, Cbr-TRA-1) capturing the direct, MX-domain-dependent binding of TRA-2 to the TRA-1 transcription factor, demonstrated in C. briggsae as well as C. elegans. "protein binding" is uninformative on its own; the specific molecular function is better captured as protein-macromolecule adaptor/sequestration activity (see core_functions). The underlying interaction is real and experimentally supported, so the binding-partner information is retained, but the generic GO:0005515 term is marked over-annotated per curation guidance to avoid bare "protein binding".
GO:0005515 protein binding	IPI PMID:12477393 Rapid coevolution of the nematode sex-determining genes fem-...	MARK AS OVER ANNOTATED	Summary: IPI annotation (with UniProtKB:Q8I8U6, Cbr-FEM-3) capturing the direct, species-specific binding of TRA-2 to FEM-3; this interaction sequesters FEM-3 and is the molecular basis of TRA-2 feminizing activity, and the FEM-3-binding region of TRA-2 is hypervariable and rapidly coevolving with FEM-3. The interaction is well supported, but the bare "protein binding" term is uninformative. The specific adaptor/sequestration function is captured in core_functions; the generic term is marked over-annotated.
GO:0018992 germ-line sex determination	IMP PMID:11250902 The TRA-1 transcription factor binds TRA-2 to regulate sexua...	ACCEPT	Summary: Experimental (IMP) annotation. Genetic interactions between tra-1 and tra-2(mx) mutations, and the requirement of the MX domain for the onset of hermaphrodite spermatogenesis, establish tra-2 involvement in the germline sex-determination decision. A core biological process for tra-2, experimentally supported. Accepted.
GO:0030674 protein-macromolecule adaptor activity	IPI PMID:12477393 Rapid coevolution of the nematode sex-determining genes fem-...	NEW	Summary: Proposed new, more-informative molecular function replacing the bare "protein binding" IPI annotations. TRA-2's intracellular domain directly binds and sequesters FEM-3 at the membrane (PMID:12477393) and also binds TRA-1 via the MX domain (PMID:11250902), physically tethering pathway components; this adaptor/ sequestration activity is the molecular basis of TRA-2 feminizing function. Added as a NEW annotation to capture the specific function.

Core Functions

TRA-2 is a large multi-pass integral membrane protein that acts as the cell-surface receptor for the secreted male-promoting signal HER-1. HER-1 binding to the TRA-2 extracellular domain antagonizes TRA-2's feminizing activity, switching the sex-determination pathway toward the male fate in XO animals. This receptor activity is conserved across the TRA-2 family.

Molecular Function:

transmembrane signaling receptor activity

Directly Involved In:

sex determination

Supporting Evidence:

GO_REF:0000033
IBA annotation from PANTHER phylogenetic analysis assigning transmembrane signaling receptor activity to the TRA-2 family (PANTHER:PTN002217563).

Through its intracellular domain TRA-2 directly binds and sequesters the masculinizing protein FEM-3 at the membrane, preventing FEM-3 from blocking the terminal transcription factor TRA-1; the same intracellular region (MX regulatory domain) also binds TRA-1 directly. This membrane-tethering/sequestration activity links the FEM-3 and TRA-1 components of the pathway and is the molecular basis of TRA-2 feminizing function. The FEM-3-binding region is hypervariable and coevolves rapidly with FEM-3.