mstE

Summary: Transport of glucose by MstE is established, but its proton coupling has never been tested. This IBA rests on the PTHR48022 family root, an IBD that does not have MstE among its seeds.

Reason: MstE descends from PTN000627328, the LUCA-level root of PTHR48022 (521 leaves), which carries the GO:0005351 IBD. That node's seeds are S. pombe SPCC548.07c, SGD:S000003521, and the A. nidulans paralogs MstA (AN8737, Q5ASJ3) and MstC (AN6669, Q5AYG1), all in other subfamilies; MstE is not among them, although the same curator used MstE as a seed for the membrane and carbohydrate-transport IBDs at the same node (mstE-bioinformatics/RESULTS.md). The family also contains low-affinity glucose facilitators such as S. cerevisiae HXT1/HXT3, so proton coupling is not a family-wide property; the PTHR48022 family review states that family-wide proton coupling is not supported. The only MstE experiment is uptake kinetics in germlings and a deletion mutant (PMID:16418173, abstract), with no uncoupler or proton-flux measurement; the CCCP-sensitivity data in PMID:24282591 concern HxtB, HxtC and HxtE, not MstE. At the TM1 position equivalent to the XylE Asp27 protonation site MstE has Ser67 (its SF92 ortholog GLT-1 has Val48), whereas the proton-coupled paralogs MstC and HxtE retain Asp. This is suggestive only, since the facilitator HXT1 also has Asp. The mechanism-agnostic GO:0055056, which is experimentally supported, is the appropriate core activity; the symporter claim is an over-specific mechanistic inference.

Summary: An AspGD IDA from the MstE-sGFP localisation study. The abstract (the only part cached) reports only cell-periphery (plasma membrane) fluorescence, so the vacuolar observation cannot be checked.

Reason: The cached copy of PMID:16418173 is abstract-only, and the full text could not be retrieved (publisher and repository routes returned 403). The abstract describes MstE-sGFP fluorescence at the periphery of conidia and hyphae, consistent with the plasma membrane, and does not mention vacuoles. A vacuolar signal for a fungal plasma-membrane sugar transporter often reflects endocytic turnover and vacuolar degradation rather than a vacuolar site of action. Without the full text I cannot tell which applies here, and the curator saw data I cannot, so this row is neither overruled nor treated as a functional location. If it reflects turnover, it is not where MstE acts and would at most be non-core.

Summary: MstE-sGFP localises to the periphery of conidia and hyphae, consistent with the plasma membrane, where it mediates uptake of extracellular glucose.

Reason: Direct localisation of a functional fusion protein in this species (PMID:16418173), in agreement with the transporter's physiological role in glucose uptake. The ortholog GLT-1 (same SF92 subfamily) also localises to the cell periphery in N. crassa (PMID:28115989).

Summary: This family-root IBD is correct for MstE, which is itself one of the seeds, but it is far broader than the D-glucose transmembrane transport that is experimentally established for MstE.

Reason: The IBD at PTN000627328 is sound. MstE descends from that node and is one of its experimental seeds, which marks experimental grounding on this gene itself and is not circular. Carbohydrate transport is nevertheless a general ancestor of GO:1904659 D-glucose transmembrane transport, a term the gene already carries by IMP and that its deletion phenotype supports directly. The specific term is preferred.

Proposed replacements: D-glucose transmembrane transport

Summary: An AspGD IDA for mannose transport. The abstract reports only glucose transport; the mannose evidence is presumably in the unavailable full text.

Reason: PMID:16418173 is cached abstract-only, and the full text could not be retrieved. The abstract describes MstE only as a low-affinity glucose transporter. In this literature the usual evidence for alternative substrates is that an excess of unlabelled sugar competes with radiolabelled-glucose uptake, as for MstA/MstC in PMID:24751997. Such data show that mannose interacts with the transporter but do not by themselves show that MstE translocates mannose. Because I cannot see what the curator saw, the row is left undecided rather than removed. Even if mannose transport is confirmed, it is a minor activity and not the core function.

Summary: A logical inference from the mannose transmembrane transporter activity IDA, which is itself unverified.

Reason: This row follows mechanically from GO:0015578, which is UNDECIDED above because the full text of PMID:16418173 is unavailable and the abstract reports only glucose transport. It should follow whatever decision is reached on that row.

Summary: MstE is a polytopic membrane protein, and this family-root IBD (with MstE as a seed) is correct. The specific compartment, the plasma membrane, is established experimentally.

Reason: Membrane is true but general. MstE-sGFP localises to the plasma membrane (PMID:16418173), and the gene already carries GO:0005886 by IDA, a descendant of membrane. The specific term is preferred.

Proposed replacements: plasma membrane

Summary: An automated membrane annotation from sugar-transporter InterPro signatures and transmembrane-helix predictions. It is correct but general.

Reason: Twelve transmembrane helices are predicted, and the protein matches the sugar-transporter signatures. The experimentally determined compartment is the plasma membrane (PMID:16418173; the gene carries GO:0005886 by IDA), so the more specific term is preferred. This action is consistent with the IBA membrane row.

Proposed replacements: plasma membrane

Summary: An InterPro2GO annotation from the MFS and sugar-transporter domains. It is correct but uninformative, because the specific substrate (D-glucose) is established experimentally.

Reason: MstE's activity as a low-affinity glucose transporter is supported by IDA and IMP in this species (PMID:16418173), and the gene already carries GO:0055056, a descendant of transmembrane transporter activity.

Proposed replacements: D-glucose transmembrane transporter activity

Summary: Glucose uptake assays support this term, but D-glucose transmembrane transport (already annotated) is the specific process shown.

Reason: The uptake measurements in PMID:16418173 were made with glucose. GO:1904659 D-glucose transmembrane transport is a descendant of carbohydrate transmembrane transport and is already annotated to this gene by IMP from the same paper. The specific term is preferred.

Proposed replacements: D-glucose transmembrane transport

Summary: MstE is the low-affinity glucose transporter of A. nidulans, characterised by uptake kinetics in germinating conidia. This is its core activity.

Reason: PMID:16418173 identifies MstE as the transporter responsible for low-affinity glucose uptake in germinating conidia. Later A. nidulans work treats it as the reference low-affinity system (PMID:24751997). The term does not commit to a coupling mechanism, which is appropriate because the energetics have not been measured.

Summary: Deleting mstE abolishes low-affinity glucose uptake kinetics, which supports MstE as the low-affinity glucose transporter.

Reason: Loss of the low-affinity kinetic component in the deletion strain, leaving only a high-affinity system, assigns that component to MstE. Taken alone a mutant phenotype shows necessity rather than activity, but combined with the IDA row, the sugar-porter domain architecture and the plasma-membrane localisation, it supports MstE as the transporter itself.

Summary: An InterPro2GO process term from the MFS domains. It is correct but general, and the specific process (D-glucose transmembrane transport) is established.

Reason: GO:1904659 D-glucose transmembrane transport is a descendant of transmembrane transport and is already annotated to this gene by IMP (PMID:16418173).

Proposed replacements: D-glucose transmembrane transport

Summary: A logical inference from the IBA carbohydrate:proton symporter activity, which is itself an over-specific mechanistic inference for MstE.

Reason: This row exists only because of the GO:0005351 IBA (see that row). Proton co-transport by MstE has never been measured. The paralogs shown to be CCCP-sensitive (HxtB, HxtC, HxtE; PMID:24282591) lie in other PANTHER subfamilies, and MstE lacks the acidic TM1 residue that marks proton-coupled sugar porters (mstE-bioinformatics/RESULTS.md).

Summary: The mstE deletion loses low-affinity glucose uptake. MstE directly carries out this transport step and is the core process.

Reason: MstE is the transporter, so it performs the transmembrane step itself rather than acting upstream of it. The deletion phenotype, together with the transport activity and the plasma-membrane location, supports direct participation in D-glucose transmembrane transport.