MIRO-1 is a mitochondrial Rho GTPase that functions as an outer mitochondrial membrane adaptor/scaffold linking mitochondria to cytoskeletal motor proteins for transport along microtubules. The protein contains two GTPase domains (N- and C-terminal Miro domains) flanking two EF-hand calcium-binding motifs. MIRO-1 is tail-anchored to the outer mitochondrial membrane and integrates calcium signals with motor engagement, facilitating both anterograde (via kinesin) and retrograde (via dynein) mitochondrial transport in neurons. Beyond transport, MIRO-1 maintains mitochondrial membrane potential through interaction with VDAC-1, and participates in stress-induced mitochondrial dynamics including wound-triggered fragmentation. The protein is essential for proper mitochondrial distribution in neurons and influences organismal lifespan.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003924 GTPase activity | IBA GO_REF:0000033 | ACCEPT | Summary: MIRO-1 contains two Miro GTPase domains (N-terminal and C-terminal) with conserved GTP-binding and hydrolysis motifs. The domain architecture is confirmed by UniProt annotations showing GTP binding sites at positions 16-23, 62-66, 123-126 (first GTPase domain) and 433-440, 470-474, 537-540 (second GTPase domain). The IBA annotation is well-supported by phylogenetic inference from the mitochondrial Rho GTPase family (Aspenstrom 2024, Cells). Reason: Core enzymatic function supported by domain architecture and evolutionary conservation. The dual GTPase domain structure is characteristic of the Miro family and is essential for its function in mitochondrial transport regulation. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md MIRO proteins have tandem GTPase domains, tandem EF-hand Ca2+-binding motifs, and regulate motor/adaptor interactions |
| GO:0005525 GTP binding | IBA GO_REF:0000033 | ACCEPT | Summary: GTP binding is the prerequisite for GTPase activity. UniProt shows detailed GTP binding sites in both GTPase domains. This function is essential for the regulatory role of MIRO-1. Reason: Molecular function directly follows from domain architecture. GTP binding is confirmed by sequence analysis and is required for the GTPase cycle that regulates motor coupling. Supporting Evidence: UniProt:Q94263 BINDING 16..23 /ligand="GTP" |
| GO:0047497 mitochondrion transport along microtubule | IBA GO_REF:0000033 | ACCEPT | Summary: This is a core function of Miro proteins. In C. elegans, MIRO-1 collaborates with MTX-1/2 (metaxins) and TRAK-1 to couple mitochondria to kinesin and dynein motors for bidirectional transport. Loss of miro-1 largely immobilizes axonal mitochondria (Zhao et al. 2021, Wu et al. 2024). Reason: This is the primary biological process function of MIRO-1. Multiple C. elegans studies demonstrate that MIRO-1 is essential for mitochondrial motility in neurons via adaptor complex formation with metaxins and TRAK. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md MTX-1/2 bind MIRO-1 and kinesin light chain (KLC-1) to form adaptor complexes; MTX-2, MIRO-1, TRAK-1 form a distinct adaptor for dynein-based transport file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 promotes recruitment/enrichment of RIC-7 on mitochondria and optimizes kinesin-1-mediated anterograde transport |
| GO:0007005 mitochondrion organization | IBA GO_REF:0000033 | ACCEPT | Summary: MIRO-1 is involved in maintaining mitochondrial morphology and organization. In C. elegans, miro-1 mutants show reduced mitochondrial content (~50% of wild type) and altered mitochondrial distribution in neurons (Shen et al. 2016). Reason: Broad but accurate term capturing MIRO-1's role in mitochondrial dynamics including distribution, morphology maintenance, and transport. Supported by direct experimental evidence in C. elegans. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md miro-1(tm1966) mutants show ~50% of wild-type mitochondrial amount |
| GO:0005741 mitochondrial outer membrane | IBA GO_REF:0000033 | ACCEPT | Summary: MIRO-1 is a tail-anchored outer mitochondrial membrane protein. UniProt shows a transmembrane helix at positions 602-622 that anchors the protein to the outer membrane, with the bulk of the protein (residues 1-601) facing the cytoplasm. Reason: Subcellular localization is well-established. The C-terminal transmembrane domain is characteristic of Miro proteins and required for mitochondrial anchoring. Supporting Evidence: UniProt:Q94263 TRANSMEM 602..622 /note="Helical; Anchor for type IV membrane protein" file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 is tail-anchored to the outer mitochondrial membrane; in vivo worm studies show MIRO-1 enrichment on fragmented mitochondria during stress |
| GO:0000166 nucleotide binding | IEA GO_REF:0000043 | ACCEPT | Summary: This is a parent term of GTP binding and is technically correct but less informative than the more specific GO:0005525 (GTP binding) annotation that is already present. Reason: While redundant with more specific annotations, this general IEA annotation from UniProt keywords is not incorrect. It can be retained as a broader classification. |
| GO:0003924 GTPase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Duplicate of the IBA annotation for GTPase activity, inferred from InterPro domain annotations (IPR001806, IPR020860, IPR021181). Reason: Same as IBA annotation. Multiple evidence sources for core GTPase activity are appropriate. InterPro-based inference is consistent with the phylogenetic evidence. |
| GO:0005509 calcium ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: MIRO-1 contains two EF-hand calcium-binding domains (EF-hand 1 at positions 188-223 and EF-hand 2 at positions 308-343). UniProt shows detailed Ca2+ binding residues. In C. elegans, EF-hand mutation impairs mitochondrial membrane potential maintenance (Ren et al. 2023). Reason: Calcium binding through EF-hands is a core molecular function that enables calcium-dependent regulation of mitochondrial transport. Essential for the calcium-sensing function of Miro proteins. Supporting Evidence: UniProt:Q94263 DOMAIN 188..223 /note="EF-hand 1" file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 EF-hand mutation impairs mitochondrial membrane potential and stress responses, consistent with Ca2+-responsive regulation |
| GO:0005525 GTP binding | IEA GO_REF:0000120 | ACCEPT | Summary: Duplicate annotation for GTP binding from combined automated annotation methods. Reason: Same function as IBA annotation. Multiple independent evidence sources reinforce the annotation. |
| GO:0005741 mitochondrial outer membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Duplicate annotation for mitochondrial outer membrane localization from combined automated methods. Reason: Same localization as IBA annotation. Consistent with domain architecture showing C-terminal transmembrane anchor. |
| GO:0007005 mitochondrion organization | IEA GO_REF:0000002 | ACCEPT | Summary: Duplicate annotation for mitochondrion organization inferred from InterPro. Reason: Same process as IBA annotation. Multiple evidence sources support this biological process role. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | ACCEPT | Summary: This is a very broad parent term of GTPase activity. GTPases are NTP hydrolases. While technically correct, this term adds no information beyond the more specific GTPase activity annotations. Reason: Correct but generic. Retained as it reflects the UniProt keyword mapping. The more informative GTPase activity annotations take precedence for understanding function. |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: General term that encompasses calcium ion binding. MIRO-1 binds Ca2+ through its EF-hand domains. Reason: Correct but less specific than GO:0005509 (calcium ion binding). Retained as it reflects UniProt keyword mapping. |
| GO:0007005 mitochondrion organization | IMP PMID:25190516 The small GTPase Arf1 modulates mitochondrial morphology and... | ACCEPT | Summary: This IMP annotation is based on the study by Ackema et al. (2014) which primarily focused on Arf1 function in mitochondrial morphology. The study examined miro-1 RNAi knockdown effects and found hyper-connected mitochondrial networks in body wall muscle, demonstrating MIRO-1's role in mitochondrial morphology regulation. Reason: Direct experimental evidence in C. elegans showing that miro-1 knockdown alters mitochondrial morphology (hyper-connected network phenotype). This supports MIRO-1's role in mitochondrion organization. Supporting Evidence: UniProt:Q94263 RNAi-mediated knockdown results in a hyper- connected mitochondrial network in body wall muscle cells |
| GO:0097345 mitochondrial outer membrane permeabilization | ISS GO_REF:0000024 | UNDECIDED | Summary: This annotation is transferred from human RHOT1 (Q8IXI2). While Miro proteins are targeted by PINK1/Parkin during mitophagy in mammalian systems, direct evidence for MIRO-1 involvement in outer membrane permeabilization in C. elegans is limited. Reason: The ISS transfer from human RHOT1 may not fully apply to C. elegans. Outer membrane permeabilization is typically associated with apoptosis/mitophagy pathways. While Miro proteins are Parkin substrates in mammals, the worm pathway may differ. More direct evidence is needed. |
| GO:0005741 mitochondrial outer membrane | ISS GO_REF:0000024 | ACCEPT | Summary: ISS annotation for localization transferred from human RHOT1. Reason: Localization is well-conserved across species and supported by domain architecture. Multiple other evidence codes support this annotation. |
| GO:0019725 cellular homeostasis | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Very broad term transferred from human RHOT1. While MIRO-1 does contribute to cellular homeostasis through mitochondrial function, this term is too general to be informative. Reason: This term is too broad and does not capture specific MIRO-1 function. More specific process terms like mitochondrion organization and mitochondrial transport are more appropriate. Many proteins could be annotated to cellular homeostasis. |
| GO:0047497 mitochondrion transport along microtubule | ISS GO_REF:0000024 | ACCEPT | Summary: ISS annotation for microtubule-based mitochondrial transport transferred from human RHOT1. Reason: This core function is well-conserved and directly demonstrated in C. elegans through multiple studies. The ISS annotation is consistent with the IBA annotation and C. elegans experimental data. |
| GO:0019896 axonal transport of mitochondrion | IDA file:worm/miro-1/miro-1-deep-research-falcon.md | NEW | Summary: MIRO-1 is essential for axonal mitochondrial transport in C. elegans neurons. Studies in PVD and DA9 neurons demonstrate that MIRO-1 forms adaptor complexes with metaxins and TRAK-1 to couple mitochondria to kinesin and dynein motors for bidirectional axonal transport. Reason: This is a more specific term than GO:0047497 that captures the neuronal axonal transport function which is well-documented in C. elegans studies. The existing annotations do not specifically capture the axonal context of mitochondrial transport. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 binds MTX-1/MTX-2 and KLC-1, forming adaptor assemblies; MIRO-1 with MTX-2 and TRAK-1 also forms an adaptor complex for dynein-based transport. Genetic and biochemical data in PVD and DA9 neurons support motor-specific adaptor roles file:worm/miro-1/miro-1-deep-research-falcon.md miro mutants show largely immobilized axonal mitochondria yet residual long-timescale anterograde movement depends on RIC-7 + kinesin-1 |
| GO:0019894 kinesin binding | IPI file:worm/miro-1/miro-1-deep-research-falcon.md | NEW | Summary: MIRO-1 interacts with kinesin light chain (KLC-1) as part of the mitochondrial transport adaptor complex. Biochemical pull-down and gel filtration experiments demonstrate MIRO-1/MTX-1/MTX-2/KLC-1 complex formation. Reason: Kinesin binding is a core molecular function enabling anterograde mitochondrial transport. Direct biochemical evidence exists in C. elegans for this interaction. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md MTX-1/2 bind MIRO-1 and kinesin light chain (KLC-1) to form adaptor complexes |
| GO:0048312 intracellular distribution of mitochondria | IMP file:worm/miro-1/miro-1-deep-research-falcon.md | NEW | Summary: MIRO-1 is required for proper subcellular distribution of mitochondria. Loss of miro-1 alters mitochondrial density in neurons and causes mitochondrial network alterations in muscle cells. Reason: This term is more specific than general mitochondrion organization and captures MIRO-1's role in establishing proper mitochondrial distribution patterns within cells. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md miro-1(tm1966) mutants have approximately half the mitochondrial amount of wild type (~50%) with only mildly reduced oxygen consumption file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 influences mitochondrial numbers in a neuron-specific manner |
| GO:0051881 regulation of mitochondrial membrane potential | IMP file:worm/miro-1/miro-1-deep-research-falcon.md | NEW | Summary: MIRO-1 interacts with VDAC-1 and is required to maintain mitochondrial membrane potential in C. elegans. Loss of MIRO-1 or EF-hand mutations significantly reduce membrane potential as measured by TMRE and JC-1 assays. Reason: This is a key biological process function distinct from transport that is directly demonstrated in C. elegans. The existing annotations do not capture this regulatory role. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md MIRO-1 physically interacts with VDAC-1 and is required to maintain mitochondrial membrane potential and ATP levels |
| GO:0090140 regulation of mitochondrial fission | IMP file:worm/miro-1/miro-1-deep-research-falcon.md | NEW | Summary: MIRO-1 is required for calcium-dependent mitochondrial fragmentation after epidermal wounding. Wounding triggers rapid, reversible mitochondrial fragmentation that requires MIRO-1 and cytosolic Ca2+. Reason: MIRO-1's role in regulating mitochondrial fission during stress responses is documented in C. elegans and represents a distinct function from steady-state transport. Supporting Evidence: file:worm/miro-1/miro-1-deep-research-falcon.md Wounding triggers rapid, reversible mitochondrial fragmentation that requires MIRO-1 and cytosolic Ca2+ |
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Download this section (compressed HTML)Q: What is the relationship between MIRO-1's transport function and its role in maintaining mitochondrial membrane potential through VDAC-1 interaction? These appear to be independent functions, but the mechanistic connection and relative importance under different physiological conditions is unclear.
Q: Does C. elegans have a functional PINK1/Parkin pathway that targets MIRO-1 for degradation during mitophagy, as occurs in mammals? The ISS annotation for mitochondrial outer membrane permeabilization is transferred from human RHOT1 but the relevance of this pathway in C. elegans is uncertain.
Q: What determines the neuron-specific effects on mitochondrial density observed in miro-1 mutants (increased in AIY, decreased in DA9)? Understanding this heterogeneity could reveal cell-type-specific regulatory mechanisms.
Experiment: Test GTPase activity of purified MIRO-1 domains in vitro to confirm enzymatic function directly in the C. elegans protein. Current GTPase annotations are based on domain conservation rather than direct biochemical demonstration in the worm protein.
Hypothesis: Purified MIRO-1 GTPase domains will show measurable GTP hydrolysis activity comparable to mammalian Miro proteins.
Experiment: Examine whether C. elegans PINK1/Parkin orthologs (pink-1, pdr-1) target MIRO-1 for degradation during mitochondrial stress. This would clarify whether the outer membrane permeabilization annotation transferred from human RHOT1 is applicable to C. elegans.
Hypothesis: MIRO-1 protein levels will decrease upon mitochondrial depolarization in a pink-1 and pdr-1 dependent manner if the PINK1/Parkin pathway is conserved.
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