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...	REMOVE	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 cited work shows the binding and its genetic relevance (tra-1 dose modifies the tra-2(mx) feminization phenotype) but does not establish what the binding does to TRA-1: neither sequestration of TRA-1 nor a bridging (ternary) complex linking TRA-1 and FEM-3 is shown, so no informative MF replacement is sourced. Following the GO:0005515 policy the bare term is removed; removal does not mean the reported TRA-1/TRA-2 interaction is false. Supporting Evidence: PMID:11250902 In Caenorhabditis briggsae, we also find an MX-dependent interaction between Cb-TRA-1 and Cb-TRA-2
GO:0005515 protein binding	IPI PMID:12477393 Rapid coevolution of the nematode sex-determining genes fem-...	MODIFY	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. TRA-2 is the upstream repressor of fem-3, and binding FEM-3 prevents FEM-3 from acting, which is protein sequestering activity (GO:0140311: binding a protein to prevent it from interacting with other partners), not adaptor activity (which brings macromolecules together to function in a coordinated way). The sequestered ligand FEM-3 is a protein, so the protein-specific child of molecular sequestering activity is used. The generic term is modified to GO:0140311, as in core_functions. Proposed replacements: protein sequestering activity Supporting Evidence: PMID:12477393 the FEM-3 protein interacts with TRA-2 in each species, but in a strictly species-specific manner PMID:12477393 the male-promoting function of fem-3 and its epistatic relationship with its female-promoting upstream repressor, tra-2, are conserved
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.

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:

hermaphrodite germ-line sex determination hermaphrodite somatic 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 the masculinizing protein FEM-3, repressing it so that FEM-3 cannot promote degradation of the terminal transcription factor TRA-1; this binding-based repression of FEM-3 is the molecular basis of TRA-2 feminizing activity. The FEM-3-binding region is hypervariable and coevolves rapidly with FEM-3, so the interaction is strictly species-specific. The same intracellular region (MX regulatory domain) also binds TRA-1 directly, but the functional consequence of that binding is not established, so it is not folded into this activity.