MCH2 (YKL221W) is a 473-residue polytopic plasma/endo-membrane protein of the Major Facilitator Superfamily (MFS), classified in the monocarboxylate porter (MCT/SLC16-like; TC 2.A.1.13) family by sequence homology. It is one of five paralogous "monocarboxylate transporter homologues" (MCH1-MCH5) in budding yeast. It adopts the canonical 12-transmembrane- helix MFS fold with cytoplasmic N- and C-termini, but has no demonstrated transport substrate, no measured transport activity, and no defined physiological role. Experimental analysis of the whole Mch family showed that these proteins do not transport monocarboxylic acids (lactate, pyruvate, acetate) across the plasma membrane, and only the paralog Mch5p has an assigned substrate (riboflavin/vitamin B2). MCH2 diverges from characterized transporting MCTs at key residues (it lacks the conserved TM1 lysine and a recognizable MFS motif A), so no substrate can be inferred from homology; its transported substrate, transport direction and mechanism, and biological process remain unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic (IBA) assignment of plasma-membrane localization from the SLC16/MCT tree. MFS transporters of this family are typically at the plasma membrane, and the only paralog with a demonstrated location, Mch5p, is a plasma-membrane protein; but MCH2's own localization is not directly demonstrated, and the one study of Mch cellular distribution indicated at least some Mch proteins reside in intracellular membranes. Kept as a plausible, phylogenetically supported localization but not treated as a solved core fact. Reason: Localization is inferred by phylogeny, not directly measured for MCH2; the family study explicitly noted some Mch proteins are intracellular, so the plasma-membrane call is plausible but not established for this paralog. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: SGD:S000005833 · MCH5 SUPPORTS SOURCE BUT NOT TARGET Mch5p (riboflavin transporter) is plasma-membrane, but PMID:16204239 states the other MCH paralogs "appear to have unrelated functions"; PMID:11536335 places at least some Mch proteins in intracellular membranes, so PM localization is not firmly transferable to MCH2. Supporting Evidence: PMID:11536335 intracellular localization studies indicated that at least some of the Mch proteins reside in intracellular membranes. PMID:16204239 localize the protein to the plasma membrane |
| GO:0022857 transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: Generic transmembrane-transporter molecular function, assigned by phylogenetic inference from the MFS/SLC16 tree. This is well supported by the confirmed 12-TMS MFS fold and is the most specific molecular function that can be defended: MCH2 diverges from transporting MCTs at key functional residues and its substrate is unknown, so a more specific "monocarboxylate transmembrane transporter activity" term is NOT supported. Accepted at this generic level. Reason: The 12-TMS MFS fold supports a generic transporter molecular function; but no substrate is assignable (MCH2 lacks the conserved TM1 lysine and MFS motif A of transporting MCTs and is distant from all characterized transporters), so the annotation must stay generic and must not be specialized to a monocarboxylate term. Supporting Evidence: file:yeast/MCH2/MCH2-bioinformatics/RESULTS.md MCH2 is a bona fide polytopic MFS membrane protein of the monocarboxylate-porter (SLC16/MCT-like) family. PMID:11536335 We could not find any evidence that the monocarboxylate transporter-homologous (Mch) proteins of S. cerevisiae are involved in the uptake or secretion of monocarboxylates such as lactate, pyruvate or acetate across the plasma membrane. |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Broad membrane localization from the UniProt Subcellular Location mapping. Correct and consistent with the experimentally constrained multi-pass topology; retained as a general, non-core localization statement (the more informative membrane identity is the still-unresolved plasma vs. intracellular question addressed above). Reason: MCH2 is unambiguously an integral multi-pass membrane protein (12 TMS, N/C-in topology experimentally constrained), so the generic membrane term is directly supported and correct; it is broad but accurately captures the compartment in which this transporter acts. Supporting Evidence: PMID:16847258 present experimentally constrained topology models for 546 proteins |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: Same generic transmembrane-transporter molecular function, reached independently via the InterPro (MFS, IPR011701) to GO mapping. Correct at this generality and consistent with the IBA route above; substrate/direction remain unknown, so it stays generic. Reason: InterPro MFS-domain evidence justifies a generic transporter molecular function; the annotation is appropriately unspecific given that no substrate is inferable for MCH2. Supporting Evidence: file:yeast/MCH2/MCH2-bioinformatics/RESULTS.md Domain assignments already in UniProt/InterPro (MFS PF07690 / IPR011701; CDD MFS_MCT_SLC16 cd17352; PANTHER PTHR11360 Proton-linked MCT) are consistent with this. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | ACCEPT | Summary: Generic transmembrane-transport biological process from the InterPro (MFS) to GO mapping. Consistent with the fold; the specific substrate and direction of transport are unknown, so the annotation is kept at this generic BP level. Reason: A generic transmembrane-transport process is the appropriate BP for a confirmed MFS transporter whose substrate is undetermined; specializing it would over-annotate. Supporting Evidence: file:yeast/MCH2/MCH2-bioinformatics/RESULTS.md the molecular function is defensible only at the generic "transmembrane transporter" level; the substrate and biological process remain genuine knowledge gaps. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | REMOVE | Summary: Root molecular_function placeholder (No Data) assigned by SGD. It is superseded by the generic but informative transmembrane transporter activity (GO:0022857) annotations already present from the IBA and InterPro routes, so the uninformative root term should be removed. Reason: ND root-term placeholder that is now redundant: the molecular-function aspect is already covered, more informatively, by the GO:0022857 transmembrane transporter activity annotations. |
| GO:0008150 biological_process | ND GO_REF:0000015 | REMOVE | Summary: Root biological_process placeholder (No Data) assigned by SGD. It is superseded by the generic transmembrane transport (GO:0055085) biological-process annotation already present from the InterPro route, so the uninformative root term should be removed. Reason: ND root-term placeholder that is now redundant: the biological-process aspect is already covered by the GO:0055085 transmembrane transport annotation. |
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Download this section (compressed HTML)Q: What is the physiological substrate of MCH2, given that monocarboxylic acids are excluded and riboflavin is transported by the paralog Mch5p?
Q: Does MCH2 reside in the plasma membrane, an endomembrane, or both, and does its location change with growth condition?
Q: Are the five MCH paralogs functionally redundant, and does MCH2 contribute to the reduced chemostat biomass phenotype seen in the mch1-5 quintuple mutant?
Experiment: Heterologously express and purify MCH2 (or use tightly controlled overexpression in yeast) and perform substrate-agnostic transport/uptake screens and comparative metabolomics of mch2 deletion vs. overexpression strains to identify candidate substrates.
Hypothesis: MCH2 transports a small solute other than a monocarboxylic acid; loss and gain of MCH2 will shift the intracellular/extracellular pool of that solute.
Experiment: Construct combinatorial mch single and multiple deletions (including a jen1 background) and phenotype them across carbon, nitrogen, and vitamin conditions and in glucose-limited chemostats to resolve paralog redundancy and MCH2's contribution.
Hypothesis: The MCH paralogs are partially redundant, and MCH2 contributes to the mch1-5 chemostat biomass phenotype only in combination with other paralogs.
Experiment: Determine the subcellular localization of endogenously tagged MCH2 (GFP) under multiple growth conditions, with plasma-membrane and endomembrane markers.
Hypothesis: MCH2 localizes at least partly to intracellular membranes rather than exclusively to the plasma membrane.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The transported substrate, transport direction (uniport/symport/antiport), driving force (proton-coupled vs. facilitated diffusion), and physiological/biological role of MCH2 are all undetermined. It is one of the "dark" conserved yeast transporters: a bona fide MFS transporter with no assignable cargo and no dedicated phenotype.
OPEN BIOLOGY WHOLLY_DARK
What is known: MCH2 is firmly established as a 12-TMS MFS membrane protein of the monocarboxylate-porter (SLC16/MCT-like) family with an experimentally constrained N/C-in topology. What is excluded: transport of monocarboxylic acids across the plasma membrane (shown for the Mch family as a whole). What is known for a paralog only: Mch5p transports riboflavin, and the remaining MCH proteins "appear to have unrelated functions". The one functional phenotype (strongly reduced biomass in glucose-limited chemostats) is of the mch1-5 quintuple mutant, not of mch2 alone, and no direct mitochondrial transport role was demonstrated (pyruvate uptake into isolated mitochondria was unaffected).
Significance: MCH2 is a conserved, ORF-named MFS transporter that has resisted functional assignment for decades; closing this gap would remove a dark node from yeast solute-transport metabolism and clarify whether the five MCH paralogs are functionally redundant or specialized.
What would resolve it: Substrate-agnostic transport/metabolomic screening of mch2 loss- and gain-of-function strains; individual (not just quintuple) mch deletion phenotyping under diverse carbon, nitrogen and vitamin conditions to resolve paralog redundancy with MCH1/MCH3/MCH4/MCH5 and JEN1; direct GFP localization to settle plasma-membrane vs. endomembrane residence.
Provenance (the field's own admissions):
Gap: Whether MCH2 contributes to the mch1-5 quintuple-mutant chemostat biomass phenotype, and whether the five MCH paralogs (and JEN1) act redundantly, is unresolved. No mch2-single phenotype has been established.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: The only reported Mch loss-of-function phenotype (strongly reduced biomass yield in aerobic glucose-limited chemostat cultures) is from the mch1-5 quintuple deletion, interpreted as a possible role in mitochondrial metabolism; however, direct pyruvate uptake into isolated mitochondria was not affected in that strain, so no direct mitochondrial transport role was demonstrated, and the contribution of MCH2 specifically is unknown.
Significance: Distinguishing paralog redundancy from specialization is required before any MCH2-specific biological process can be annotated, and before the family's link to central carbon metabolism can be interpreted.
What would resolve it: Combinatorial mch single/double/triple deletions (with and without jen1) scored for the chemostat biomass and metabolic phenotypes; complementation of the mch1-5 phenotype by MCH2 alone.
Provenance (the field's own admissions):
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