MIM1 (also named TOM13) is a small, 113-residue integral protein of the Saccharomyces cerevisiae mitochondrial outer membrane, anchored by a single central alpha-helical transmembrane segment with its N-terminal domain facing the cytosol and its C-terminal domain facing the intermembrane space. Mim1 self-associates into an oligomer of roughly 400-450 kDa that, together with one to two copies of the small partner protein Mim2, forms the mitochondrial import (MIM) complex. The MIM complex is the outer-membrane insertase for precursor proteins that are held in the membrane by alpha-helical anchors rather than by a beta-barrel, and its substrates span three classes: multi-spanning alpha-helical proteins such as Ugo1, signal-anchored (N-terminally anchored) proteins including the import receptors Tom20 and Tom70, and a subset of tail-anchored proteins. MIM works both downstream of the TOM receptor Tom70, from which it accepts precursors, and independently of Tom70 for other single-spanning substrates, and it cooperates with the sorting and assembly machinery (SAM) during the late maturation of the beta-barrel protein Tom40. Because Tom20, Tom70 and the final assembly of Tom40 all depend on it, loss of Mim1 collapses biogenesis of the TOM translocase and secondarily compromises general mitochondrial protein import, whereas SAM-dependent insertion of porin and the translocation of matrix and inner-membrane precursors are not themselves Mim1-dependent. Purified Mim1 reconstituted into planar lipid bilayers behaves as an aqueous, strongly cation-preferring pore that closes at high membrane potentials and whose selectivity is attenuated by co-reconstituted Mim2, consistent with the MIM complex furnishing a protein-conducting conduit suited to the positively charged residues that flank alpha-helical transmembrane segments; no physiological ion flux through Mim1 has been demonstrated. Beyond protein import, the complex has been reported to anchor lipid droplets to mitochondria: the lipid metabolism enzyme Ayr1 engages MIM through a single hydrophobic segment in the manner of a substrate but is never released, and the resulting assembly promotes mitochondria-lipid droplet contact sites and raises cellular lipid droplet number. Mim1 defines a protein family (Pfam TOM13/PF08219, InterPro IPR013262, PANTHER PTHR28241) that is restricted to fungi and conserved within them, with the conservation concentrated in the transmembrane region; self-association through two GXXXG helix-dimerisation motifs in that segment is required for activity, and the segment alone is the minimal functional unit. Organisms outside fungi solve the same problem with unrelated proteins - pATOM36 in trypanosomes and MTCH1/MTCH2 in mammals - which are functionally interchangeable with MIM in both directions despite sharing neither sequence nor topology.
Definition: Enables the passage of a polypeptide chain, or of a transmembrane segment of a polypeptide chain, through a transmembrane aqueous pore. Channels of this class exhibit measurable single-channel conductance, ion selectivity and voltage-dependent closure when reconstituted into artificial bilayers, but their physiological permeant is protein rather than a solute; the ion conductance is a property of the unoccupied pore.
Justification: GO currently offers no molecular function term for the pore character of a protein translocase. Curators who wish to record the electrophysiology of a reconstituted translocase - which has been measured for Tom40, Sam50, Mdm10 and Mim1, and for translocation channels in other membranes - have only ion-channel terms available, and the resulting annotations assert a solute-transport function the proteins do not have and, through inter-ontology links, propagate that error into the biological process ontology. MIM1 is a concrete case: GO:0022832 on MIM1 generates a spurious GO:0055085 "transmembrane transport". A dedicated term would let the observation be curated faithfully while keeping the substrate honest, and would sit naturally alongside GO:0032977 "membrane insertase activity" and GO:0008320 "transmembrane protein transporter activity" as the pore-level counterpart of those activities.
Parent term: channel activity
Supporting Evidence:
Definition: A membrane contact site between the mitochondrial outer membrane and the lipid droplet monolayer, structured by a bridging complex.
Justification: GO already carries GO:0160259 "endoplasmic reticulum membrane-lipid droplet contact site" and GO:0044233 for the ER-mitochondrion apposition, but has no term for the mitochondrion-lipid droplet contact site. PMID:41748941 reports that the MIM complex, captured by Ayr1, nucleates exactly this structure in yeast, and mitochondria-lipid droplet contacts are also well described in mammalian tissue. Without the term the localisation of MIM's second function cannot be recorded at all. Proposed alongside a tether molecular function, by analogy with the GO:0160259 / GO:0170007 pair that already exists for the ER case.
Parent term: organelle membrane contact site
Supporting Evidence:
Definition: The binding activity of a molecule that brings together a lipid droplet with the mitochondrial outer membrane to establish a membrane contact site.
Justification: The molecular-function counterpart of the contact-site term above, mirroring the existing GO:0170007 "endoplasmic reticulum-lipid droplet tether activity". The MIM-Ayr1 assembly performs this role in yeast per PMID:41748941. Proposed with lower confidence than the cellular-component term: the tether is the MIM-Ayr1 assembly rather than Mim1 alone, and on the reported mechanism it is Ayr1 that supplies the lipid droplet-facing determinant while MIM supplies the mitochondrial anchor, so which partner "enables" the tether activity is not settled by the abstract alone.
Parent term: protein-membrane adaptor activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0140595 MIM complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (PAINT) propagation from node PANTHER:PTN002000670 in the MITOCHONDRIAL IMPORT PROTEIN 1 family (PTHR28241) asserting that MIM1 orthologues are constituents of the MIM complex. The GO:0140595 definition (an outer-membrane insertase complex that inserts alpha-helical proteins from the cytosol) is exactly what the Mim1-Mim2 assembly is, and MIM1's own SGD annotation (SGD:S000005386) appears in the WITH/FROM because the yeast protein is one of the experimentally characterised descendants the PAINT curator used to place the IBD -- expected grounding, not circularity. Reason: The node placement is sound. Mim1 oligomers are the bulk of the complex (PMID:28916712) and the direct Mim1-Mim2 interaction that defines it is experimentally established (PMID:22467864). Complex membership is a core cellular-component statement for this gene and is independently supported by IPI evidence in the same GOA. Supporting Evidence: PMID:28916712 Mim1 oligomers form the major constituent of the MIM complex PMID:22467864 Mim2 physically and genetically interacts with Mim1, and both proteins form the MIM complex. |
| GO:0045040 protein insertion into mitochondrial outer membrane | IBA GO_REF:0000033 | MODIFY | Summary: PAINT propagation from PANTHER:PTN002000670 asserting that the ancestral function of the MIM1/TOM13 family is participation in insertion of proteins into the mitochondrial outer membrane. This is the correct level of specificity: it names the membrane, the direction and the substrate class without over-committing to a particular client protein. Reason: Re-termed to the alpha-helical child. The 2026 mitochondrial-import reorganization (geneontology/go-ontology#31711, closed and largely landed) split GO:0045040 into GO:7770059 alpha helical protein insertion into mitochondrial outer membrane and GO:7770063 beta barrel protein insertion into mitochondrial outer membrane. MIM1 belongs unambiguously on the alpha-helical branch: GO:7770059's own definition names this complex - "In yeast, the insertase is the mitochondrial import (MIM) complex, composed of Mim1 and Mim2". Choosing the child encodes rather than obscures the conclusion recorded throughout this review that MIM1's contribution to the beta-barrel Tom40 is indirect - MIM1 belongs on GO:7770059 and explicitly NOT on its sibling GO:7770063. The parent is now an unnecessarily general grouping for this gene. Note the GOA gap this exposes: Q08176 has no GO:7770059 annotation at all, although S. pombe mim1 (Q9C1W7) and mim2 (G2TRP0) already carry PomBase IMPs to it (PMID:33138913), as do fly and human MTCH proteins. The term is being populated in other clades while the budding-yeast protein its definition is written around is absent. The underlying IBD node placement is itself well supported - the yeast protein has direct experimental evidence (PMID:32348752 IDA in the same GOA) and the family is functionally homogeneous - so this is a family-level re-term that should move with the node, not a yeast-only correction. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002000670 Β· MIM1/TOM13 family ancestral node (PTHR28241) SUPPORTS TRANSFER Node placement is sound and is not what is being corrected. The whole fungal clade descending from this node is alpha-helical-specific, so the re-term to GO:7770059 applies at the node, not just to S. cerevisiae. SGD:S000005386 Β· MIM1 (S. cerevisiae), the target's own experimental annotation SUPPORTS TRANSFER The target appearing in its own WITH/FROM is expected: MIM1's experimental annotations are among the descendant evidences the PAINT curator used to place the IBD. Not circular. PomBase:SPBC1289.15 Β· mim1 (S. pombe, UniProtKB:Q9C1W7) SUPPORTS TRANSFER Independent fungal member already annotated to the replacement term GO:7770059 by IMP (PMID:33138913), which is direct evidence that the alpha-helical child is the right granularity for this clade. Proposed replacements: alpha helical protein insertion into mitochondrial outer membrane Supporting Evidence: PMID:32348752 the mitochondrial import (MIM) complex inserts precursors of multi-spanning Ξ±-helical proteins PMID:22467864 Some of the single-span proteins and all known multiple-span proteins are inserted into the membrane in a pathway that depends on the MOM protein Mitochondrial Import 1 (Mim1). |
| GO:0005741 mitochondrial outer membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Automated combined-IEA assignment from InterPro:IPR013262 (OMP_MIM1/TOM13_mt) and the UniProt subcellular-location keyword SL-0172. The inference is trivially correct here: the family signature is defined on a protein whose outer-membrane residence has been demonstrated directly. Reason: Redundant with, but fully consistent with, three independent IDA annotations in the same GOA. Protease-protection and alkaline-carbonate extraction of isolated mitochondria place Mim1 as an integral protein of the outer membrane (PMID:15326197, PMID:15608614). The IEA is at the right level of granularity and needs no modification. Supporting Evidence: PMID:15608614 Thus, Mim1 is an outer-membrane protein. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000108 | REMOVE | Summary: A purely logical by-product: GOC generated this BP from the MF annotation GO:0022832 via an inter-ontology link (the WITH/FROM field is literally GO:0022832). GO:0055085 is defined as "the process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other". No solute transport by Mim1 has ever been demonstrated in vivo; the only underlying observation is an in vitro bilayer conductance measurement on recombinant protein, and the authors themselves interpret that pore as a conduit for precursor polypeptide segments rather than for ions. Reason: The term asserts a physiological role (solute translocation across the outer membrane) that no evidence supports, and it does so at a level of generality that conveys nothing about MIM1. Mim1's genuine transport-related process is already captured precisely and with experimental evidence by GO:0045040 "protein insertion into mitochondrial outer membrane", which is not a descendant of GO:0055085 because insertion terminates in the bilayer rather than crossing it. Removing this annotation loses no information and prevents MIM1 from being retrieved as a solute transporter. Note that the annotation will regenerate for as long as GO:0022832 remains on the gene product, so the durable fix is at the MF (see the GO:0022832 entry below). Supporting Evidence: PMID:28916712 We conclude that the Mim1βMim2 complex forms a channel with cation preference and is thus conducive to the translocation of precursor segments carrying positive charges. |
| GO:0005515 protein binding | IPI PMID:22467864 A crucial role for Mim2 in the biogenesis of mitochondrial o... | MARK AS OVER ANNOTATED | Summary: IntAct-derived IPI recording the direct Mim1-Mim2 interaction (WITH/FROM UniProtKB:Q3E798). The underlying interaction is real, reproducible (IntAct NbExp=3) and biologically important - it is the interaction that constitutes the MIM complex. Reason: "Protein binding" is uninformative as a molecular function: it names no activity and, by project convention, is not retained as a functional statement. The entire informative content of this annotation - that Mim1 binds Mim2 and that the two form a complex - is already captured, with the same reference, by the GO:0140595 "MIM complex" part_of annotations. Retain the interaction record in IntAct/ComplexPortal, but it should not stand as MIM1's molecular function; the molecular function that is missing is the insertase activity of the complex (see the proposed GO:0032977 entry). Supporting Evidence: PMID:22467864 Mim2 physically and genetically interacts with Mim1, and both proteins form the MIM complex. |
| GO:0005741 mitochondrial outer membrane | IDA PMID:28916712 Identification of new channels by systematic analysis of the... | ACCEPT | Summary: SGD IDA with the stronger is_active_in qualifier, from the systematic survey of yeast outer-membrane channels. The paper isolated outer-membrane vesicles from purified mitochondria, and treats Mim1 throughout as an outer-membrane protein with a defined topology (cytosolic N-terminus, intermembrane-space C-terminus) whose activity belongs to that membrane. Reason: Correct, and the is_active_in qualifier is justified: Mim1's demonstrated activities - insertion of alpha-helical precursors and, in reconstitution, pore formation - are activities of the outer membrane, not merely activities of a protein that happens to reside there. Localisation itself is independently established by carbonate extraction and protease protection in two other studies. Supporting Evidence: PMID:28916712 The 13-kD protein Mim1 contains a predicted central Ξ±-helical transmembrane segment and exposes its N-terminal domain to the cytosol and its C-terminal domain to the intermembrane space PMID:28916712 Mim1 promotes the biogenesis of several Ξ±-helical precursor proteins of the mitochondrial outer membrane by an unknown mechanism |
| GO:0022832 voltage-gated channel activity | IDA PMID:28916712 Identification of new channels by systematic analysis of the... | MARK AS OVER ANNOTATED | Summary: SGD IDA from a systematic electrophysiological screen of the yeast mitochondrial outer membrane. The measurement itself is strong: recombinant full-length Mim1, purified from inclusion bodies and reconstituted into planar lipid bilayers, gave a reproducible main conductance state of ~580 pS that closed at high positive or negative membrane potentials; the activity was abolished by Mim1-specific antibodies, reproduced with protein made in a second (wheat-germ) expression system, strongly cation selective (PK+/PCl- = 23.5:1), and modulated by co-reconstitution of the physiological partner Mim2 (PK+/PCl- falling to 11:1). What is at issue is not the observation but what molecular function should be ascribed on the basis of it. Reason: GO:0022832 is not factually wrong, but as MIM1's molecular function it over-reads an in vitro biophysical property. Two problems. (i) The "voltage-gated" element describes closure of the pore at high absolute membrane potential, the generic behaviour shared by every protein-conducting channel of this membrane (Tom40, Sam50 and Mdm10 all behave this way in the same study), not the operation of a voltage sensor gating a conductance pathway for signalling; nothing in the paper claims Mim1 responds to physiological changes in outer-membrane potential, and the outer membrane is not a potential-bearing membrane. (ii) The physiological cargo is polypeptide, not ions. The authors' own conclusion is explicitly that the cation preference makes the pore conducive to the translocation of precursor segments carrying positive charges, and the article's summary line describes Mim1 as forming a channel for protein import. No ion flux through Mim1 in intact mitochondria has been shown. I deliberately do NOT propose MODIFY to GO:0022843 "voltage-gated monoatomic cation channel activity", even though it is the substrate-correct child of the measured selectivity, for two reasons. First, moving to the more specific child makes the claim stronger in exactly the direction the biology does not support: it commits GO to the assertion that MIM1's function is to conduct monoatomic cations, whereas the parent term's vagueness at least leaves the substrate open. Second, it would make the downstream inter-ontology damage worse rather than better - GO:0022832 already spawns the spurious GO:0055085 "transmembrane transport" BP, and GO:0022843 would spawn a more specific and more definitely wrong cation-transport process. KEEP_AS_NON_CORE is also the wrong shape: it implies a genuine secondary job, but there is no second activity here - the pore that was measured is the same conduit that performs the insertase function, viewed through an electrode. MARK_AS_OVER_ANNOTATED keeps the experimental record attached to the gene while signalling that this is not MIM1's molecular function; the function that belongs in that slot is membrane insertase activity (GO:0032977), proposed below. Supporting Evidence: PMID:28916712 Upon reconstitution into planar lipid bilayers, Mim1 exhibited a characteristic channel activity that was inhibited by Mim1-specific antibodies PMID:28916712 that closed upon application of high positive or negative voltages PMID:28916712 The Mim1 channel was cation selective with a ratio of PK+/PClβ of 23.5:1 based on a positive reversal potential of 53 mV PMID:28916712 We conclude that the Mim1βMim2 complex forms a channel with cation preference and is thus conducive to the translocation of precursor segments carrying positive charges. |
| GO:0045040 protein insertion into mitochondrial outer membrane | IMP PMID:15608614 Mim1, a protein required for the assembly of the TOM complex... | MODIFY | Summary: SGD IMP from the study that named Mim1. Conditional depletion of Mim1 (GAL10-regulated allele) abrogates assembly of the TOM complex and causes Tom40 to accumulate as a low-molecular-mass species; the block is downstream of TOB/SAM-mediated insertion of Tom40, and is specific, since biogenesis of the TOB/SAM and porin complexes is unaffected. Reason: Re-termed to the alpha-helical child, for the reasons given on the IBA row for this term: geneontology/go-ontology#31711 split GO:0045040 into GO:7770059 (alpha helical) and GO:7770063 (beta barrel), and MIM1 belongs on the alpha-helical branch, whose definition names the Mim1-Mim2 complex. This row keeps its existing caveat as well. One caveat worth recording for the curator: as of 2005 the direct evidence in this particular paper concerns TOM complex assembly at a step after insertion - the authors state explicitly that the Mim1-requiring steps are located after the TOB-complex-dependent insertion of Tom40 - so this reference is a weaker support for GO:0045040 than for GO:0070096, which SGD also annotated from it. The insertase reading of the phenotype was established later, when Mim1 was shown to be required for membrane insertion of the signal-anchored receptors Tom20 and Tom70 (PMID:17974559) and then directly as the MIM translocase (PMID:32348752). Since a stronger IDA for the same term from PMID:32348752 is present in the same GOA, the term stands; no change is needed. Proposed replacements: alpha helical protein insertion into mitochondrial outer membrane Supporting Evidence: PMID:15608614 Depletion of Mim1 abrogates assembly of the TOM complex and results in accumulation of Tom40 PMID:15608614 The steps in the assembly of the TOM complex requiring Mim1 are located after the TOB-complex-dependent insertion of Tom40 into the outer membrane. |
| GO:0045040 protein insertion into mitochondrial outer membrane | IDA PMID:32348752 The Mitochondrial Import Complex MIM Functions as Main Trans... | MODIFY | Summary: ComplexPortal IDA from the study that defined the MIM complex as the main translocase for alpha-helical outer-membrane proteins. Beyond the multi-spanning substrates already known, this work showed that MIM inserts both N-terminally (signal-anchored) and C-terminally (tail-anchored) single-spanning precursors, described three dynamic populations of the complex (TOM-associated, free, SAM-coupled), and concluded that MIM is a major and versatile protein translocase of the outer membrane. Reason: Re-termed to the alpha-helical child, for the reasons given on the IBA row for this term: geneontology/go-ontology#31711 split GO:0045040 into GO:7770059 (alpha helical) and GO:7770063 (beta barrel), and MIM1 belongs on the alpha-helical branch, whose definition names the Mim1-Mim2 complex. This is the strongest and most direct evidence in the GOA for MIM1's core biological process, and it is the row a curator should re-term first: the paper reports insertion of signal-anchored and tail-anchored precursors and of multi-spanning alpha-helical proteins, every one of them an alpha-helical client. Nothing in it supports the beta-barrel sibling. Before the 2026 split the parent's granularity was right; now the child is strictly better. Proposed replacements: alpha helical protein insertion into mitochondrial outer membrane Supporting Evidence: PMID:32348752 We report that the yeast MIM complex promotes the insertion of proteins with N-terminal (signal-anchored) or C-terminal (tail-anchored) membrane anchors. PMID:32348752 We conclude that the MIM complex is a major and versatile protein translocase of the mitochondrial outer membrane. |
| GO:0140595 MIM complex | IPI PMID:22467864 A crucial role for Mim2 in the biogenesis of mitochondrial o... | ACCEPT | Summary: Direct interaction evidence that Mim1 is a subunit of the MIM complex. Two GOA rows carry this assertion from the same reference (ComplexPortal, and SGD with WITH/FROM SGD:S000007618 = MIM2); they are collapsed here into a single review entry. The complex is a bona fide, stoichiometrically defined entity - Mim1 oligomers plus one to two copies of Mim2 - and is registered as ComplexPortal CPX-2281. Reason: Well supported and core. This is the annotation that carries the real content of the Mim1-Mim2 interaction (and makes the separate GO:0005515 "protein binding" annotation redundant). The complex is distinct from both TOM and TOB/SAM by size-exclusion chromatography, so the CC assignment is not merely a restatement of outer-membrane residence. Supporting Evidence: PMID:22467864 Mim2 physically and genetically interacts with Mim1, and both proteins form the MIM complex. PMID:28916712 A second subunit, the 10-kD protein Mim2, possesses the same topology as Mim1 yet is present in the MIM complex in lower abundance (one to two copies per complex; Dimmer et al., 2012). PMID:15608614 Mim1 was present in a high-molecular-mass complex of a molecular size of about 400β450 kDa, which is distinct from that of the TOM and TOB complexes. |
| GO:0005741 mitochondrial outer membrane | IDA PMID:15608614 Mim1, a protein required for the assembly of the TOM complex... | ACCEPT | Summary: SGD IDA. Mim1 fractionates with mitochondria; it is degraded by low concentrations of proteinase K applied to intact mitochondria (while the intermembrane-space marker cytochrome b2 is protected, confirming the outer membrane was intact), and it resists alkaline carbonate extraction, behaving like the integral outer-membrane proteins Tom40 and Tom70. A His-tagged allele further showed the N-terminus is cytosolic. Reason: Textbook-quality localisation evidence combining protease accessibility with carbonate extraction. One of the best-supported facts about this protein and the basis of the UniProt ECO:0000269 subcellular-location assignment. Supporting Evidence: PMID:15608614 Mim1 was recovered in the membrane fraction like known outer membrane proteins, Tom40 and Tom70 PMID:15608614 Hence, the N terminus of the protein is exposed to the cytosol. |
| GO:0005741 mitochondrial outer membrane | IDA PMID:15326197 Two novel proteins in the mitochondrial outer membrane media... | ACCEPT | Summary: SGD IDA from the independent discovery of the same protein under the name Tom13. Protease treatment and alkaline extraction of isolated mitochondria carrying a C-terminally tagged allele showed Tom13 to be an integral protein of the mitochondrial outer membrane, behaving like Tom70 and Tim23 and unlike the peripheral protein Tom38/Sam35. Reason: Independent replication of the outer-membrane localisation by a different laboratory using a differently tagged construct. Note only that this study, using a C-terminal tag, concluded that the C-terminus is cytosolic, whereas the later consensus (from an N-terminally tagged allele and from subsequent topology work) places the N-terminus in the cytosol and the C-terminus in the intermembrane space. The topology discrepancy does not affect the outer-membrane assignment, which both studies agree on. Supporting Evidence: PMID:15326197 Tom13 was, like integral membrane proteins Tom70 and Tim23, not extracted by alkaline treatment of mitochondria, but was solubilized by treatment of mitochondria with Triton X-100 PMID:15326197 These results indicate that Tom13 and Tom38 are an integral membrane protein and a peripheral membrane protein, respectively, of the mitochondrial outer membrane |
| GO:0070096 mitochondrial outer membrane translocase complex assembly | IMP PMID:15608614 Mim1, a protein required for the assembly of the TOM complex... | KEEP AS NON CORE | Summary: SGD IMP. Depletion of Mim1 causes a massive deficiency of assembled TOM complex, with Tom40 stalled as a low-molecular-mass species; the defect is in assembly rather than stability, and it is downstream of TOB/SAM-mediated insertion of the Tom40 beta-barrel. The specificity of the phenotype is established by the fact that the TOB/SAM and porin complexes assemble normally without Mim1. Reason: This is the phenotype through which the gene was characterised, and the loss-of-function evidence is sound, with an appropriate specificity control so it is not an artefact of a general import collapse. What has changed is its status as a core process rather than its validity as an observation. There is an open GO obsoletion request against this term (geneontology/go-ontology#32108, opened May 2026, 21 EXP annotations affected; MIM1's two IMPs are almost certainly among them). Its rationale, from the parent reorganization issue #31711, is that "Assembly of TOM isn't a separate assembly process, assembly is only affected by import pathways so the correct way to annotate this would be to add TOM subunits as targets of the appropriate import pathways." That argument is the same one this review reached independently from the primary literature: the TOM-assembly phenotype is a downstream consequence of the insertase acting on Tom20 and Tom70, and the Tom40 arm of it is indirect besides. Demoted from core accordingly. KEEP_AS_NON_CORE rather than REMOVE or MODIFY, deliberately: the term is still live and non-obsolete in the current release, the underlying loss-of-function evidence is sound, and the obsoletion request is open rather than decided. Pre-empting a GO decision that has not been taken would be worse than recording the position. If #32108 is accepted, the destination is GO:7770059 with the affected TOM subunits carried as targets/has_input rather than a re-term to another assembly term. One mechanistic caveat that post-dates this paper: the requirement for the beta-barrel Tom40 is now understood to be indirect - Mim1 does not act on Tom40 itself but on the small Tom proteins that Tom40 assembly needs (reviewed in PMID:21825073, citing Becker et al., 2010). PMID:18187149 reached the same conclusion independently and earlier by a different route: mim1-delta mitochondria import less Tom40 because they contain less functional Tom20, yet the Tom40 that arrives progresses normally through both assembly intermediates. That specific observation is in tension with this paper, which reported the second intermediate reduced on depletion; the disagreement is about how much of the Tom40 defect is import versus assembly, not about whether Mim1 is required for TOM biogenesis. This does not affect the term or the action, since GO:0070096 is about involvement in assembling the complex and Mim1's involvement is not in doubt; it only means the Tom40 arm of the phenotype should not be read as direct beta-barrel handling. Supporting Evidence: PMID:15608614 Our data show that a primary function of Mim1 is to facilitate assembly of the TOM complex. PMID:15608614 The biogenesis of other outer membrane complexes containing Ξ²-barrel proteins, such as TOB/SAM and porin complexes, was not affected by the lack of Mim1. PMID:21825073 a recent study showed that Mim1 does not directly promote the biogenesis of Tom40 but functions via the import of small Tom proteins that are needed for Tom40 assembly (Becker et al., 2010) PMID:18187149 but does not diminish the overall rate of Tom40 assembly PMID:18187149 This is consistent with the known role of Tom20 as a receptor for Tom40 import: |
| GO:0070096 mitochondrial outer membrane translocase complex assembly | IMP PMID:17974559 Biogenesis of the mitochondrial TOM complex: Mim1 promotes i... | KEEP AS NON CORE | Summary: SGD IMP from the study that resolved which TOM subunits depend on Mim1. Mim1 is required for efficient membrane insertion and assembly of the signal-anchored receptors Tom20 and Tom70 but not of the tail-anchored Tom22, and Mim1 associates with SAM(core) components in a large SAM complex, which accounts for its role in the late steps of Tom40 assembly. Disruption reduces TOM complex levels while leaving the respiratory chain intact. Reason: Independent IMP for the same process from a second laboratory, and the most mechanistically informative of the two: it converts a generic "TOM assembly" defect into a substrate-resolved statement (Tom20 and Tom70 yes, Tom22 no) and connects Mim1 to SAM. That substrate selectivity is itself the strongest argument that the underlying activity is insertion of alpha-helical anchors rather than a general chaperoning of TOM - which is precisely why the process is better captured by the insertion term than by an assembly term, and why this row is demoted from core alongside the other GO:0070096 annotation. This paper is in fact the best illustration of the GO argument: the named substrates Tom20 and Tom70 are exactly the "TOM subunits as targets of the appropriate import pathways" that #31711 proposes annotating instead. There is an open GO obsoletion request against this term (geneontology/go-ontology#32108, opened May 2026, 21 EXP annotations affected; MIM1's two IMPs are almost certainly among them). Its rationale, from the parent reorganization issue #31711, is that "Assembly of TOM isn't a separate assembly process, assembly is only affected by import pathways so the correct way to annotate this would be to add TOM subunits as targets of the appropriate import pathways." That argument is the same one this review reached independently from the primary literature: the TOM-assembly phenotype is a downstream consequence of the insertase acting on Tom20 and Tom70, and the Tom40 arm of it is indirect besides. Demoted from core accordingly. KEEP_AS_NON_CORE rather than REMOVE or MODIFY, deliberately: the term is still live and non-obsolete in the current release, the underlying loss-of-function evidence is sound, and the obsoletion request is open rather than decided. Pre-empting a GO decision that has not been taken would be worse than recording the position. If #32108 is accepted, the destination is GO:7770059 with the affected TOM subunits carried as targets/has_input rather than a re-term to another assembly term. Supporting Evidence: PMID:17974559 We report that Mim1 is required for efficient membrane insertion and assembly of Tom20 and Tom70, but not Tom22. PMID:17974559 We show that Mim1 associates with SAM(core) components to a large SAM complex, explaining its role in late steps of the assembly pathway of Tom40. PMID:18177669 Here we show that Mim1 is required for the integration of the import receptor Tom20 into the outer membrane. PMID:18187149 Mutations in the transmembrane segment that destabilize Tom20, or deletion of Mim1, prevent Tom20 from functioning as a receptor for protein import into mitochondria. |
| GO:0032977 membrane insertase activity | IDA PMID:32348752 The Mitochondrial Import Complex MIM Functions as Main Trans... | NEW | Summary: Proposed new annotation, not present in the GOA. GO:0032977 is defined as binding transmembrane domain-containing proteins and mediating their integration into a membrane - a precise description of what the Mim1-Mim2 complex does. MIM binds and inserts multi-spanning alpha-helical precursors, signal-anchored precursors (Tom20, Tom70) and a subset of tail-anchored precursors into the mitochondrial outer membrane, accepting some of them from the TOM receptor Tom70. Reason: Both halves of the GO:0032977 definition are now directly evidenced rather than inferred: PMID:21825073 shows that multispanning precursor proteins interact with Mim1 directly (the binding half) and that the Mim1 complex promotes their insertion and assembly into the outer membrane (the integration half). PMID:18187149 adds the property that distinguishes an insertase from a structural subunit: Mim1 is not among the prominent cross-linking partners of docked Tom20, so it acts on the client and is released rather than remaining part of the assembled product. MIM1 currently has no molecular function annotation that describes what the protein does. Its only two MF annotations are GO:0005515 "protein binding" (uninformative) and GO:0022832 "voltage-gated channel activity" (an in vitro biophysical property that misstates the physiological cargo). This leaves a gene whose biological process and cellular component are precisely curated but whose activity is invisible to any MF-based query. The qualifier is contributes_to rather than enables because insertase activity is delivered by the Mim1-Mim2 heterocomplex; Mim1 is the major constituent and the pore-forming subunit, but Mim2 is required in vivo for the biogenesis of MIM substrates and it demonstrably modifies the conduction properties of the pore, so the activity is properly assigned at the complex level with Mim1 contributing to it. Supporting Evidence: PMID:32348752 We report that the yeast MIM complex promotes the insertion of proteins with N-terminal (signal-anchored) or C-terminal (tail-anchored) membrane anchors. PMID:32348752 the mitochondrial import (MIM) complex inserts precursors of multi-spanning Ξ±-helical proteins PMID:22467864 Some of the single-span proteins and all known multiple-span proteins are inserted into the membrane in a pathway that depends on the MOM protein Mitochondrial Import 1 (Mim1). PMID:17974559 We report that Mim1 is required for efficient membrane insertion and assembly of Tom20 and Tom70, but not Tom22. PMID:21825073 The critical component for the subsequent import into the outer membrane is Mim1, and the precursor proteins directly interact with Mim1. PMID:21825073 The Mim1 complex cooperates with the receptor Tom70 in binding of precursor proteins and promotes their insertion and assembly into the outer membrane. PMID:21825074 Conversely, the multifunctional outer membrane protein mitochondrial import 1 (Mim1) plays a central role in mediating the insertion of Ugo1. PMID:18187149 Mim1 is not one of the prominent cross-linked partners of Tom20. PMID:18187149 or else Mim1 catalyzes Tom20 assembly with known subunits of the TOM complex |
| GO:0034389 lipid droplet organization | IMP PMID:41748941 Mitochondria contact lipid droplets through the mitochondria... | NEW | Summary: Proposed new annotation, not present in the GOA - the reporting study is from 2026. The MIM complex is reported to have a second function unrelated to protein insertion: the lipid metabolism enzyme Ayr1 captures MIM and thereby nucleates mitochondria-lipid droplet contact sites, and lipid droplet number in cells depends on both MIM and Ayr1. Mechanistically the capture is substrate mimicry - Ayr1 engages MIM through a single hydrophobic segment as a precursor would, but is never released - so the second function is a subverted insertase reaction rather than a separate activity, and it is carried by a distinct MIM-Ayr1 population rather than by the same complexes that insert precursors. Reason: GO:0034389 is the closest existing term that can carry this: the paper reports a cellular-level effect on lipid droplet number, which is within "the assembly, arrangement of constituent parts, or disassembly of a lipid particle". It is deliberately the general process term rather than anything contact-site specific, because GO has no mitochondrion-lipid droplet contact site term - GO:0160259 exists for the ER-lipid droplet apposition and GO:0044233 for ER-mitochondrion, but the mitochondrion-lipid droplet combination is absent. Two terms are proposed in proposed_new_terms to fill that gap; until they exist, this annotation records the biology at the only granularity the ontology currently supports. Flagged as provisional for two reasons a curator should weigh. First, this is a single 2026 study with no independent replication, and the cached record is abstract-only, so the underlying experiments have not been examined here. Second, the qualifier is involved_in rather than anything stronger because the activity belongs to the MIM-Ayr1 assembly; whether Mim1 or Ayr1 is the determining partner is not resolved by the abstract. If a curator prefers to wait for replication before annotating, the reference and findings are recorded either way. Supporting Evidence: PMID:41748941 Here we report that the MIM complex performs a second major function in lipid-droplet homeostasis. PMID:41748941 MIM and Ayr1 enhance the lipid droplet number in cells. PMID:41748941 The lipid metabolism enzyme Ayr1 captures the MIM complex, promoting the formation of mitochondria-lipid droplet contact sites. PMID:41748941 Ayr1 binds to MIM via its single hydrophobic segment in a substrate-mimicry mechanism but remains bound and is not released into the outer membrane. |
| GO:7770059 alpha helical protein insertion into mitochondrial outer membrane | IDA PMID:32348752 The Mitochondrial Import Complex MIM Functions as Main Trans... | NEW | Summary: Proposed new annotation, not present in the GOA. GO:7770059 was created in the 2026 mitochondrial-import reorganization (geneontology/go-ontology#31711) as the alpha-helical child of GO:0045040, alongside the beta-barrel sibling GO:7770063. Its definition names this complex directly: "In yeast, the insertase is the mitochondrial import (MIM) complex, composed of Mim1 and Mim2." Reason: This is a straightforward GOA gap. Q08176 carries no GO:7770059 annotation, even though the term's definition is written around the Mim1-Mim2 complex. Meanwhile the term already has manual annotations in other clades: PomBase IMPs on S. pombe mim1 (UniProtKB:Q9C1W7) and mim2 (UniProtKB:G2TRP0) from PMID:33138913, and FlyBase IMPs on Drosophila Mtch and human MTCH1/MTCH2 from PMID:38428433 and PMID:41576035. Of the ~286 annotations to the term, only seven are manual; the rest are Ensembl orthology IEA. So the budding-yeast protein the definition describes is the conspicuous absence. Evidence is IDA from PMID:32348752, mirroring the ComplexPortal GO:0045040 IDA already in the GOA and drawn from the same experiments - that study reports MIM-mediated insertion of signal-anchored, tail-anchored and multi-spanning alpha-helical precursors, all of them alpha-helical clients. This entry and the three MODIFY recommendations on GO:0045040 describe the same curation change from two directions; a curator acting on the MODIFYs would satisfy this entry too, and should not create a duplicate. Supporting Evidence: PMID:32348752 the mitochondrial import (MIM) complex inserts precursors of multi-spanning Ξ±-helical proteins PMID:32348752 We report that the yeast MIM complex promotes the insertion of proteins with N-terminal (signal-anchored) or C-terminal (tail-anchored) membrane anchors. PMID:22467864 Some of the single-span proteins and all known multiple-span proteins are inserted into the membrane in a pathway that depends on the MOM protein Mitochondrial Import 1 (Mim1). |
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Download this section (compressed HTML)Q: Do the three soluble-domain findings actually conflict? PMID:18177669 found the N- and C-terminal domains dispensable for growth and TOM assembly, while PMID:19345216 assigned the N-terminal domain a discrete role in regulating the SAM-mediated early reaction of Tom40 assembly. Is this a quantitative contribution visible to an in vitro kinetic assay but invisible to an in vivo complementation assay, or a genuine disagreement?
Suggested experts: Rapaport D, Lithgow T
Q: Is the MIM-Ayr1 lipid droplet function conserved, and is it really a second function of the same machine rather than a moonlighting role of Ayr1 that happens to use MIM as an anchor? Note that Ayr1 was independently identified as an NADPH-regulated outer-membrane channel in the same screen that found the Mim1 channel (PMID:28916712) - is the channel activity of either protein related to the contact-site role?
Suggested experts: Becker T, Pfanner N, Bohnert M
Q: If Ayr1 occupies the precursor-binding site without being released, does the MIM-Ayr1 population compete with protein insertion? Does lipid droplet load or lipid status modulate outer-membrane protein biogenesis through this competition?
Suggested experts: Becker T, den Brave F
Q: Is the reconstituted Mim1 conductance a physiologically meaningful ion pathway in the intact outer membrane, or is it strictly the unoccupied state of a protein-conducting conduit? Does loss of MIM1 change outer-membrane permeability to ions in vivo?
Suggested experts: Kruger V, Wagner R, Meisinger C
Q: The reported size of the Mim1-containing complex differs by method: ~180 kDa by glycerol gradient, ~300 kDa by BN-PAGE, 400-450 kDa by gel filtration, plus a separate report of association with SAM(core). PMID:18187149 notes the Mim1 complex needs more digitonin to solubilise than TOM does. Do these correspond to the three dynamic MIM populations later described (free MIM, TOM-coupled MIM, SAM-coupled MIM), or to differences in detergent, tagging and chromatographic method?
Suggested experts: Rapaport D, Becker T, Endo T
Q: If the transmembrane segment of Mim1 is the minimal functional domain and the N- and C-terminal domains are dispensable for both function and biogenesis, what do those soluble domains actually do? Their poor conservation across fungi contrasts sharply with the near-invariant transmembrane region, yet they are retained in every orthologue.
Suggested experts: Rapaport D, Popov-Celeketic J
Q: How do the two GXXXG motifs build a functional conduit? Do they generate a defined oligomer with a fixed subunit count and a lipid-lined or protein-lined pore, and is the ~580 pS conductance a property of that same oligomer? Where does Mim2 sit relative to the GXXXG interfaces?
Suggested experts: Rapaport D, Wagner R, Becker T
Q: How does the MIM complex recognise an alpha-helical transmembrane anchor, and what distinguishes a MIM-dependent tail-anchored substrate from a MIM-independent one such as Tom22?
Suggested experts: Doan KN, Becker T, Rapaport D
Q: The Tom40 requirement is now agreed to be indirect, but two different indirect routes have been proposed and they are not the same: PMID:18187149 attributes it to reduced functional Tom20 lowering Tom40 import, while PMID:20026336 and PMID:21825073 attribute it to Mim1-dependent insertion of the small Tom proteins that Tom40 assembly needs. Do both contribute, and in what proportion? A related loose end is that PMID:18187149 found Tom40 assembly rate undiminished in mim1-delta whereas PMID:15608614 found the second assembly intermediate reduced on depletion.
Suggested experts: Pfanner N, Wiedemann N, Becker T, Lithgow T
Q: The non-homologous counterparts are now identified - pATOM36 in trypanosomes and MTCH1/MTCH2 in mammals, with pATOM36 and Mim1/Mim2 reciprocally interchangeable. Do any of them share the pore-forming, cation-preferring architecture measured for Mim1, or is a proteinaceous conduit only one of several ways to solve alpha-helical insertion? No plant counterpart has yet been named.
Suggested experts: Rapaport D, Schneider A, Wagner R
Experiment: Resolve the soluble-domain disagreement directly by applying both readouts to the same allele set: take the Mim1(deltaN), Mim1(deltaC) and Mim1(TM) variants and assay them side by side with the in vivo complementation and steady-state readouts of PMID:18177669 and the in vitro multi-step Tom40 assembly kinetics of PMID:19345216, in one genetic background.
Hypothesis: The N-terminal domain makes a quantitative contribution to the rate of the SAM-mediated early reaction that is fully compensated in vivo, so both published results are correct at their own resolution.
Experiment: Test whether the MIM-Ayr1 and MIM-preprotein populations compete. Titrate Ayr1 levels and measure insertion of a panel of MIM substrates (a multi-span such as Ugo1, a signal-anchored such as Tom20, a tail-anchored client), and conversely ask whether precursor overload displaces Ayr1 and reduces mitochondria-lipid droplet contacts.
Hypothesis: Because Ayr1 occupies the precursor-binding site by substrate mimicry, the two functions draw on one pool of complexes and are reciprocally limiting.
Experiment: Ask whether the reconstituted Mim1 channel conductance is altered by bound Ayr1, using the planar-bilayer setup of PMID:28916712 with co-reconstituted Ayr1 instead of Mim2.
Hypothesis: If Ayr1 occupies the conduit as a non-released pseudo-substrate, it should occlude or substantially alter the 580 pS conductance, which would also test whether the measured pore is the physiological precursor path.
Experiment: Measure outer-membrane ion permeability directly in mitochondria and outer-membrane vesicles from mim1-delta and wild-type cells, in a por1-delta background so that the dominant VDAC conductance does not mask the signal, and compare with the conductance predicted from Mim1 copy number.
Hypothesis: The Mim1 conductance measured in reconstitution is the empty state of a protein-translocation conduit and makes no contribution to outer-membrane ion permeability in vivo.
Type: electrophysiology
Experiment: Trap a precursor in transit - for example a Ugo1 or Tom20 fusion arrested by a tightly folded C-terminal domain or by a bound ligand - and test whether the arrested substrate blocks the Mim1 conductance in reconstituted planar bilayers.
Hypothesis: The pore whose conductance was measured is the physical path taken by a translocating precursor, so an arrested substrate should occlude it.
Type: single-channel electrophysiology with substrate trapping
Experiment: Determine the structure of the detergent- or nanodisc-solubilised Mim1-Mim2 complex, ideally with a trapped substrate, by cryo-EM, settling the oligomeric state of Mim1, the stoichiometry of Mim2, and whether insertion proceeds through a continuous aqueous pore or a lipid-thinning site.
Hypothesis: The Mim1-Mim2 complex admits transmembrane helices through a defined lumen or lipid-facing groove whose architecture can be resolved.
Type: cryo-EM structure determination
Experiment: Use site-specific photo-crosslinking with unnatural amino acids placed along the transmembrane segment of a signal-anchored substrate to map the sequence of Mim1 and Mim2 contacts during in organello insertion.
Hypothesis: A substrate transmembrane segment contacts Mim1 and Mim2 in a defined order during insertion.
Type: site-specific photo-crosslinking
Experiment: Separate the populations by affinity purification via Tom70, via SAM(core) and via free Mim1, and assay each preparation in vitro for insertion of a signal-anchored, a tail-anchored and a multi-spanning substrate.
Hypothesis: The three reported MIM populations (TOM-coupled, free, SAM-coupled) are functionally specialised for different substrate classes.
Type: affinity purification with in vitro insertion assay
Experiment: Reconstitute purified Mim1-Mim2 into proteoliposomes and assay insertion of a radiolabelled alpha-helical precursor by carbonate resistance and protease protection, providing the direct in vitro basis for a GO:0032977 membrane insertase annotation with an enables rather than contributes_to qualifier.
Hypothesis: The Mim1-Mim2 complex is sufficient, without other mitochondrial components, to insert an alpha-helical precursor into a membrane.
Type: reconstitution into proteoliposomes
Experiment: Swap the positively charged flanking residues of a MIM-dependent substrate for negatively charged ones (and the converse for a MIM-independent substrate such as Tom22) and measure insertion efficiency in vivo and in organello in wild-type and mim1-delta mitochondria.
Hypothesis: Positive charges flanking a transmembrane segment are what make a precursor MIM-dependent, matching the cation preference of the pore.
Type: charge-swap mutagenesis with import assay
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The mechanism by which Mim1 integrates an alpha-helical transmembrane anchor is undetermined. It is not established whether the substrate helix passes through a proteinaceous conduit formed by the Mim1 oligomer, is handed to the lipid phase at a protein-lipid interface, or is thinned/destabilised into the bilayer by the complex - nor what, if anything, makes the reaction directional and releases the client.
NARROWING BIOLOGY MF_DARK
What is known: Firmly established: Mim1 is required for insertion of multi-span, signal-anchored and a subset of tail-anchored clients; it binds precursors directly (PMID:21825073); it self-associates through two GXXXG motifs and this oligomerisation is necessary for activity (PMID:18177669); the purified protein forms a cation-selective ~580 pS pore in bilayers (PMID:28916712); and it is not a stable neighbour of the finished product, so it acts catalytically (PMID:18187149). What is missing is the path the substrate takes between those endpoints. No experimental structure of Mim1 or of the MIM complex exists.
Significance: This is the gap that makes the central curation call in this review hard. Whether GO:0022832 is an over-annotation or an under-specified description of the real conduit, and whether the proposed "protein-conducting channel activity" term is warranted, both turn on it. It is also why GO:0032977 has to be asserted with contributes_to rather than enables.
What would resolve it: A structure of the Mim1-Mim2 complex, ideally with a trapped substrate (cryo-EM on nanodisc-reconstituted complex); site-specific photo-crosslinking along a substrate transmembrane segment to map the path; and testing whether the bilayer conductance is occluded when a client or Ayr1 occupies the complex.
Provenance (the field's own admissions):
Gap: What determines whether a given alpha-helically anchored outer-membrane protein requires the MIM complex is unknown. There is no sequence or biophysical rule that predicts MIM dependence, and no substrate-recognition determinant on either the client or the complex has been identified.
OPEN BIOLOGY BP_DARK
What is known: Established: MIM is the main route for this protein class, credited with more than 90% of integral outer-membrane precursors (PMID:41748941), yet dependence is demonstrably partial - only "some" single-span proteins need it (PMID:31945731) and even the multi-span client Om14 is inserted without it, if less efficiently (PMID:35262629). Tom22 is a long-standing MIM-independent exception (PMID:17974559). Hydrophobicity, flanking charge and membrane fluidity have each been implicated, but none has been shown to be the determinant.
Significance: Affects how strongly GO:0045040 should be read for this gene, and whether MIM-dependence can be predicted for uncharacterised outer-membrane proteins rather than tested case by case. A rule would also let the annotation be propagated to client genes with confidence.
What would resolve it: Systematic insertion assays across a designed panel of clients varying hydrophobicity, helix length and flanking charge in a mim1-delta background; crosslinking to identify the recognition surface on the complex.
Provenance (the field's own admissions):
Gap: Why the Neurospora crassa orthologue only partially complements yeast mim1-delta, while the more distant Schizosaccharomyces pombe orthologue complements fully, is unexplained. It is therefore not established that MIM function is uniform across the fungal clade over which it is phylogenetically propagated.
OPEN BIOLOGYCURATION RESIDUAL_SUBGAP
What is known: Established: the family is fungi-specific (PMID:29923829); conservation is concentrated in the transmembrane segment (PMID:15608614); and the cross-species complementation result itself is solid, with expression confirmed by immunoblot so the weak rescue is not an expression artefact (PMID:18177669). The authors state plainly that they cannot account for the difference.
Significance: Bears directly on the safety of the IBA propagation from node PANTHER:PTN002000670. The N. crassa orthologue Q8X0G8 receives GO:0140595 and GO:0045040 by descent from this gene, yet the only functional test of that orthologue shows it behaving differently. A curator propagating MIM function across fungi should know the one experiment that exists is equivocal.
What would resolve it: Domain-swap complementation between the S. cerevisiae, N. crassa and S. pombe proteins to localise the determinant of the rescue difference; and a MIM-dependence assay for endogenous clients in N. crassa itself.
Provenance (the field's own admissions):
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