id: Q94263 gene_symbol: miro-1 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:6239 label: Caenorhabditis elegans description: 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. existing_annotations: - term: id: GO:0003924 label: GTPase activity evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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). action: ACCEPT 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO proteins have tandem GTPase domains, tandem EF-hand Ca2+-binding motifs, and regulate motor/adaptor interactions - term: id: GO:0005525 label: GTP binding evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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. action: ACCEPT 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. supported_by: - reference_id: UniProt:Q94263 supporting_text: BINDING 16..23 /ligand="GTP" - term: id: GO:0047497 label: mitochondrion transport along microtubule evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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). action: ACCEPT 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: 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 - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO-1 promotes recruitment/enrichment of RIC-7 on mitochondria and optimizes kinesin-1-mediated anterograde transport - term: id: GO:0007005 label: mitochondrion organization evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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). action: ACCEPT 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: miro-1(tm1966) mutants show ~50% of wild-type mitochondrial amount - term: id: GO:0005741 label: mitochondrial outer membrane evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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. action: ACCEPT reason: Subcellular localization is well-established. The C-terminal transmembrane domain is characteristic of Miro proteins and required for mitochondrial anchoring. supported_by: - reference_id: UniProt:Q94263 supporting_text: TRANSMEM 602..622 /note="Helical; Anchor for type IV membrane protein" - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO-1 is tail-anchored to the outer mitochondrial membrane; in vivo worm studies show MIRO-1 enrichment on fragmented mitochondria during stress - term: id: GO:0000166 label: nucleotide binding evidence_type: IEA original_reference_id: GO_REF:0000043 review: 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. action: ACCEPT 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. - term: id: GO:0003924 label: GTPase activity evidence_type: IEA original_reference_id: GO_REF:0000002 review: summary: Duplicate of the IBA annotation for GTPase activity, inferred from InterPro domain annotations (IPR001806, IPR020860, IPR021181). action: ACCEPT reason: Same as IBA annotation. Multiple evidence sources for core GTPase activity are appropriate. InterPro-based inference is consistent with the phylogenetic evidence. - term: id: GO:0005509 label: calcium ion binding evidence_type: IEA original_reference_id: GO_REF:0000002 review: 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). action: ACCEPT 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. supported_by: - reference_id: UniProt:Q94263 supporting_text: DOMAIN 188..223 /note="EF-hand 1" - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO-1 EF-hand mutation impairs mitochondrial membrane potential and stress responses, consistent with Ca2+-responsive regulation - term: id: GO:0005525 label: GTP binding evidence_type: IEA original_reference_id: GO_REF:0000120 review: summary: Duplicate annotation for GTP binding from combined automated annotation methods. action: ACCEPT reason: Same function as IBA annotation. Multiple independent evidence sources reinforce the annotation. - term: id: GO:0005741 label: mitochondrial outer membrane evidence_type: IEA original_reference_id: GO_REF:0000120 review: summary: Duplicate annotation for mitochondrial outer membrane localization from combined automated methods. action: ACCEPT reason: Same localization as IBA annotation. Consistent with domain architecture showing C-terminal transmembrane anchor. - term: id: GO:0007005 label: mitochondrion organization evidence_type: IEA original_reference_id: GO_REF:0000002 review: summary: Duplicate annotation for mitochondrion organization inferred from InterPro. action: ACCEPT reason: Same process as IBA annotation. Multiple evidence sources support this biological process role. - term: id: GO:0016787 label: hydrolase activity evidence_type: IEA original_reference_id: GO_REF:0000043 review: 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. action: ACCEPT reason: Correct but generic. Retained as it reflects the UniProt keyword mapping. The more informative GTPase activity annotations take precedence for understanding function. - term: id: GO:0046872 label: metal ion binding evidence_type: IEA original_reference_id: GO_REF:0000043 review: summary: General term that encompasses calcium ion binding. MIRO-1 binds Ca2+ through its EF-hand domains. action: ACCEPT reason: Correct but less specific than GO:0005509 (calcium ion binding). Retained as it reflects UniProt keyword mapping. - term: id: GO:0007005 label: mitochondrion organization evidence_type: IMP original_reference_id: PMID:25190516 review: 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. action: ACCEPT 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. supported_by: - reference_id: UniProt:Q94263 supporting_text: RNAi-mediated knockdown results in a hyper- connected mitochondrial network in body wall muscle cells - term: id: GO:0097345 label: mitochondrial outer membrane permeabilization evidence_type: ISS original_reference_id: GO_REF:0000024 review: 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. action: UNDECIDED 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. - term: id: GO:0005741 label: mitochondrial outer membrane evidence_type: ISS original_reference_id: GO_REF:0000024 review: summary: ISS annotation for localization transferred from human RHOT1. action: ACCEPT reason: Localization is well-conserved across species and supported by domain architecture. Multiple other evidence codes support this annotation. - term: id: GO:0019725 label: cellular homeostasis evidence_type: ISS original_reference_id: GO_REF:0000024 review: 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. action: MARK_AS_OVER_ANNOTATED 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. - term: id: GO:0047497 label: mitochondrion transport along microtubule evidence_type: ISS original_reference_id: GO_REF:0000024 review: summary: ISS annotation for microtubule-based mitochondrial transport transferred from human RHOT1. action: ACCEPT 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. - term: id: GO:0019896 label: axonal transport of mitochondrion evidence_type: IDA original_reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md review: 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. action: NEW 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: 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 - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: miro mutants show largely immobilized axonal mitochondria yet residual long-timescale anterograde movement depends on RIC-7 + kinesin-1 - term: id: GO:0019894 label: kinesin binding evidence_type: IPI original_reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md review: 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. action: NEW reason: Kinesin binding is a core molecular function enabling anterograde mitochondrial transport. Direct biochemical evidence exists in C. elegans for this interaction. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MTX-1/2 bind MIRO-1 and kinesin light chain (KLC-1) to form adaptor complexes - term: id: GO:0048312 label: intracellular distribution of mitochondria evidence_type: IMP original_reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md review: 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. action: NEW reason: This term is more specific than general mitochondrion organization and captures MIRO-1's role in establishing proper mitochondrial distribution patterns within cells. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: miro-1(tm1966) mutants have approximately half the mitochondrial amount of wild type (~50%) with only mildly reduced oxygen consumption - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO-1 influences mitochondrial numbers in a neuron-specific manner - term: id: GO:0051881 label: regulation of mitochondrial membrane potential evidence_type: IMP original_reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md review: 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. action: NEW 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: MIRO-1 physically interacts with VDAC-1 and is required to maintain mitochondrial membrane potential and ATP levels - term: id: GO:0090140 label: regulation of mitochondrial fission evidence_type: IMP original_reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md review: 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+. action: NEW 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. supported_by: - reference_id: file:worm/miro-1/miro-1-deep-research-falcon.md supporting_text: Wounding triggers rapid, reversible mitochondrial fragmentation that requires MIRO-1 and cytosolic Ca2+ references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000043 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:25190516 title: The small GTPase Arf1 modulates mitochondrial morphology and function full_text_unavailable: true findings: [] - id: file:worm/miro-1/miro-1-deep-research-falcon.md title: Deep research summary for miro-1 gene function findings: - statement: miro-1(tm1966) mutants have ~50% wild-type mitochondrial content supporting_text: miro-1(tm1966) mutants show ~50% of wild-type mitochondrial amount - statement: Reduced mitochondrial amount correlates with lifespan extension dependent on daf-16/FOXO - statement: Oxygen consumption only mildly reduced despite reduced mitochondrial content - statement: MIRO-1 physically interacts with VDAC-1 supporting_text: MIRO-1 physically interacts with VDAC-1 - statement: Required for maintaining mitochondrial membrane potential (measured by TMRE, JC-1) - statement: EF-hand mutations impair membrane potential maintenance - statement: MIRO-1 enriched on fragmented mitochondria during stress - statement: MIRO-1/MTX-1/MTX-2/KLC-1 complex for kinesin-based anterograde transport supporting_text: MTX-1/2 bind MIRO-1 and kinesin light chain (KLC-1) to form adaptor complexes - statement: MIRO-1/MTX-2/TRAK-1 complex for dynein-based retrograde transport supporting_text: MTX-2, MIRO-1, TRAK-1 form a distinct adaptor for dynein-based transport - statement: Biochemical evidence from gel filtration and immunoprecipitation - statement: Genetic evidence from PVD and DA9 neuron studies - statement: MIRO-1 promotes RIC-7 recruitment to mitochondria supporting_text: MIRO-1 promotes recruitment/enrichment of RIC-7 on mitochondria - statement: MIRO-1 optimizes but is not strictly required for anterograde transport - statement: miro-1 mutants show largely immobilized axonal mitochondria supporting_text: miro mutants show largely immobilized axonal mitochondria - statement: Neuron-specific effects on mitochondrial distribution - statement: MIRO-1 required for Ca2+-dependent mitochondrial fragmentation after wounding supporting_text: Wounding triggers rapid, reversible mitochondrial fragmentation that requires MIRO-1 and cytosolic Ca2+ - statement: Fragmentation accelerates actin-based wound repair - statement: Links MIRO-1 calcium sensing to stress response - statement: Comprehensive review of Miro domain architecture and function supporting_text: MIRO proteins have tandem GTPase domains, tandem EF-hand Ca2+-binding motifs, and regulate motor/adaptor interactions - statement: EF-hands as Ca2+ sensors regulate transport - statement: PINK1/Parkin targeting of Miro during mitophagy - statement: ER-mitochondria contact regulation core_functions: - molecular_function: id: GO:0003924 label: GTPase activity description: MIRO-1 possesses GTPase activity through its two Miro GTPase domains. This enzymatic function is essential for the regulatory cycle that controls motor protein coupling. - molecular_function: id: GO:0005509 label: calcium ion binding description: Calcium binding through tandem EF-hand domains enables MIRO-1 to sense intracellular calcium levels and regulate mitochondrial transport and dynamics accordingly. - molecular_function: id: GO:0019894 label: kinesin binding description: MIRO-1 binds kinesin light chain (KLC-1) as part of adaptor complexes that link mitochondria to kinesin-1 motors for anterograde transport. locations: - id: GO:0005741 label: mitochondrial outer membrane directly_involved_in: - id: GO:0019896 label: axonal transport of mitochondrion - molecular_function: id: GO:0005525 label: GTP binding description: MIRO-1 binds GTP through conserved motifs in both Miro GTPase domains, which is required for GTPase cycle and motor protein regulation. locations: - id: GO:0005741 label: mitochondrial outer membrane proposed_new_terms: [] suggested_questions: - question: 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. - question: 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. - question: 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. suggested_experiments: - description: 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. - description: 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. tags: - caeel-mitophagy