id: pn_mapping_set:mitochondrial_proteostasis label: Mitochondrial proteostasis PN mappings references: - proteostasis-workbook-2024 - proteostasis-ms1 notes: >- Curated PN-to-GO mappings for mitochondrial proteostasis transport and chaperone entries. subject_curations: - subject_code: Mitochondrial proteostasis subject_level: branch curation_status: no_mapping rationale: Reviewed as a top-level PN branch. This is a systems/taxonomy umbrella, not a direct GO assertion; narrower child curations carry any propagating GO mappings. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone subject_level: class curation_status: no_mapping rationale: >- This PN class is too heterogeneous for a single safe GO mapping. In the workbook it mixes HSP70, HSP60, and HSP90 systems, small intermembrane-space chaperones, membrane-protein chaperones, and other mitochondrial-specific factors. references: - proteostasis-workbook-2024 - proteostasis-ms1 notes: >- Gene-level projection exposed the problem with earlier propagation to GO mitochondrial intermembrane space chaperone complex: it incorrectly pulled in mixed mitochondrial-chaperone genes such as HSPA9, HSPD1, TRAP1, PHB1, and PHB2. Keep the class explicit and unmapped rather than forcing a misleading umbrella GO target. - subject_code: Mitochondrial proteostasis|Folding enzyme subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a specific GO class. The member genes span multiple activities, complexes, or contexts, so propagation from this node would overstate the shared biology; use narrower child or gene-level curations. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Membrane protein folding subject_level: class curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a specific GO class. The member genes span multiple activities, complexes, or contexts, so propagation from this node would overstate the shared biology; use narrower child or gene-level curations. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Mitochondrial protein maturation subject_level: class curation_status: mapped target_term: id: GO:0034982 label: mitochondrial protein processing mapping_scope: ok_for_propagation_to_go rationale: This PN class groups maturation steps for mitochondrial proteins. The GO mitochondrial protein processing term captures the shared process-level semantics. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation subject_level: class curation_status: mapped target_term: id: GO:0035694 label: mitochondrial protein catabolic process mapping_scope: ok_for_propagation_to_go rationale: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Protein transport subject_level: class curation_status: mapped target_term: id: GO:0015031 label: protein transport mapping_scope: ok_for_propagation_to_go rationale: >- The PN mitochondrial Protein transport class groups protein-targeting and import pathways into mitochondria. GO protein transport is the appropriate propagation target, while the source class remains mitochondria-specific and broader than any single GO transport subtype. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|Chaperone for complex III and LETM1 subject_level: group curation_status: no_mapping rationale: Reviewed as a contextual PN bucket. The label is useful for curator triage, but no direct GO mapping is appropriate because propagation would add a process, activity, or localization not shared cleanly by all members. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP100 disaggregase subject_level: group curation_status: mapped target_term: id: GO:0140545 label: ATP-dependent protein disaggregase activity mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes mitochondrial HSP100/LON-family disaggregase activity. The GO ATP-dependent protein disaggregase activity term is the closest molecular-function target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP60 system subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a specific GO class. The member genes span multiple activities, complexes, or contexts, so propagation from this node would overstate the shared biology; use narrower child or gene-level curations. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP70 system subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a specific GO class. The member genes span multiple activities, complexes, or contexts, so propagation from this node would overstate the shared biology; use narrower child or gene-level curations. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP90 system subject_level: group curation_status: no_mapping rationale: Reviewed as a broad PN category rather than a specific GO class. The member genes span multiple activities, complexes, or contexts, so propagation from this node would overstate the shared biology; use narrower child or gene-level curations. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|Membrane protein chaperone subject_level: group curation_status: no_mapping rationale: Reviewed as a contextual PN bucket. The label is useful for curator triage, but no direct GO mapping is appropriate because propagation would add a process, activity, or localization not shared cleanly by all members. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Chaperone|Small intermembrane space chaperone subject_level: group curation_status: mapped target_term: id: GO:0042719 label: mitochondrial intermembrane space chaperone complex mapping_scope: ok_for_propagation_to_go rationale: >- This PN group captures the small intermembrane-space chaperone system that stabilizes imported proteins in the mitochondrial intermembrane space. The GO cellular-component term for the mitochondrial intermembrane space chaperone complex is an appropriate propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|small HSP subject_level: group curation_status: mapped target_term: id: GO:0044183 label: protein folding chaperone mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes mitochondrial small heat-shock chaperones. Protein folding chaperone is the appropriate shared molecular-function term. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/HSPB2/HSPB2-ai-review.yaml - file:human/HSPB3/HSPB3-ai-review.yaml - file:human/HSPB8/HSPB8-ai-review.yaml notes: >- The members projected here from proteostasis batch 5 (HSPB2, HSPB3, HSPB8) are ATP-independent small-HSP holdases whose gene-level core MF is GO:0051082 (unfolded protein binding); the broad GO:0044183 is retained as the shared propagation target. Caveat on PN placement: gene-level review localizes these sHSPs primarily to the cytosol/sarcomere (HSPB2/HSPB3 muscle, HSPB8 CASA), so the "mitochondrial" branch context should be treated as PN systems metadata rather than evidence of a mitochondrial-matrix chaperone role; the chaperone/holdase MF mapping itself is compartment-agnostic and holds. - subject_code: Mitochondrial proteostasis|Folding enzyme|Peptidyl-prolyl isomerases subject_level: group curation_status: mapped target_term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity mapping_scope: ok_for_propagation_to_go rationale: This PN group is the mitochondrial peptidyl-prolyl isomerase branch. The matching GO molecular-function term is appropriate for propagation. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Folding enzyme|Protein disulfide isomerases subject_level: group curation_status: mapped target_term: id: GO:0160203 label: mitochondrial disulfide relay system mapping_scope: ok_for_propagation_to_go rationale: This PN group contains CHCHD4/GFER mitochondrial disulfide-relay factors. The GO mitochondrial disulfide relay system process captures the shared mitochondrial folding chemistry better than a generic PDI label. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Membrane protein folding|Insertase for helical proteins into the outer membrane subject_level: group curation_status: mapped target_term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane mapping_scope: ok_for_propagation_to_go rationale: >- This PN group covers the machinery that inserts helical membrane proteins into the mitochondrial outer membrane. The corresponding GO process term protein insertion into mitochondrial outer membrane is an appropriate propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Membrane protein folding|MICOS complex subject_level: group curation_status: mapped target_term: id: GO:0061617 label: MICOS complex mapping_scope: ok_for_propagation_to_go rationale: This PN group denotes MICOS-complex components. The GO MICOS complex cellular-component term is the direct target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Membrane protein folding|Sorting and assembly machinery outer membrane subject_level: group curation_status: mapped target_term: id: GO:0005741 label: mitochondrial outer membrane mapping_scope: ok_for_propagation_to_go rationale: >- This PN group denotes the SAM outer-membrane assembly system. The GO mitochondrial outer membrane cellular-component term is a conservative propagation target for this assembly-focused bucket. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Mitochondrial protein maturation|Methionine deformylation subject_level: group curation_status: mapped target_term: id: GO:0042586 label: peptide deformylase activity mapping_scope: ok_for_propagation_to_go rationale: This PN group captures mitochondrial N-terminal methionine deformylation. The shared catalytic activity is peptide deformylase activity. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Mitochondrial protein maturation|Processing peptidase subject_level: group curation_status: mapped target_term: id: GO:0017087 label: mitochondrial processing peptidase complex mapping_scope: ok_for_propagation_to_go rationale: >- This PN group captures the mitochondrial processing peptidase machinery that removes targeting presequences from imported mitochondrial proteins. The GO cellular-component term for the mitochondrial processing peptidase complex is the best supported propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation|Degradation of mitochondrial membrane proteins that fail targeting subject_level: group curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket that is already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Organelle-specific protein degradation|Intermembrane space protease subject_level: group curation_status: mapped target_term: id: GO:0005758 label: mitochondrial intermembrane space mapping_scope: ok_for_propagation_to_go representative_genes: - NLN - ATP23 - HTRA2 rationale: >- This PN group captures proteases assigned specifically to the mitochondrial intermembrane space. The source bucket is compartmental and mechanistic rather than a single shared enzymatic GO class, so the mitochondrial intermembrane space cellular-component term is the conservative propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease subject_level: group curation_status: mapped target_term: id: GO:0005759 label: mitochondrial matrix mapping_scope: ok_for_propagation_to_go rationale: >- This PN group identifies matrix-local protease systems. The source is a compartmental proteostasis bucket, so the mitochondrial matrix cellular-component term is the conservative propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation|Vms pathway subject_level: group curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket that is already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation|mitoCPR pathway subject_level: group curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket that is already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Organelle-specific protein degradation|mitoTAD pathway subject_level: group curation_status: no_mapping rationale: Reviewed as a narrower taxonomy bucket that is already covered by a curated parent mapping or by gene-level annotations. No additional direct GO mapping is appropriate from this node. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Protein transport|Cytosolic mitochondria import stimulation factor subject_level: group curation_status: mapped target_term: id: GO:0015031 label: protein transport mapping_scope: ok_for_propagation_to_go rationale: >- This PN group captures cytosolic factors that stimulate mitochondrial import before TOM/TIM route commitment. The source is broader than a specific matrix-import pathway, so the conservative propagation target is GO protein transport. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Protein transport|Inner membrane import subject_level: group curation_status: context_only target_term: id: GO:0044743 label: protein transmembrane import into intracellular organelle mapping_scope: too_broad_to_propagate rationale: >- In `4.3.11`, inner-membrane import is a group that covers TIM22, TIM17/23, PAM-associated matrix import, and related inner-membrane sorting routes. The source is useful context for mitochondrial protein import, but protein insertion into mitochondrial inner membrane is too specific for all descendants because reviewed TIM23/PAM components include matrix-import motor and gatekeeper roles. Propagation should come from narrower child nodes such as TIM22 complex, TIM23 complex, or OXA1L-mediated insertion. references: - proteostasis-workbook-2024 - proteostasis-ms1 - file:human/PAM16/PAM16-ai-review.yaml - file:human/TIMM44/TIMM44-ai-review.yaml - subject_code: Mitochondrial proteostasis|Protein transport|Outer membrane import subject_level: group curation_status: mapped target_term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane mapping_scope: ok_for_propagation_to_go rationale: >- This PN group covers the outer-membrane entry route for mitochondrial protein import. The matching GO process protein insertion into mitochondrial outer membrane is the best conservative propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP60 system|HSP10 subject_level: type curation_status: mapped target_term: id: GO:0044183 label: protein folding chaperone mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes mitochondrial HSP10/HSPE co-chaperonins. The shared GO function is protein folding chaperone. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP60 system|HSP60 subject_level: type curation_status: mapped target_term: id: GO:0140662 label: ATP-dependent protein folding chaperone mapping_scope: ok_for_propagation_to_go rationale: >- The mitochondrial HSP60 PN category corresponds to canonical chaperonins that carry out ATP-dependent protein folding. The source label denotes the family/system member type rather than the GO molecular-function class itself, so propagation scope is the better fit. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Protein transport|Inner membrane import|For assembly of inner membrane complexes subject_level: type curation_status: mapped target_term: id: GO:0032977 label: membrane insertase activity mapping_scope: ok_for_propagation_to_go rationale: This PN leaf is represented by OXA1L, the mitochondrial inner-membrane insertase for assembly of membrane complexes. Membrane insertase activity is the best-supported molecular-function target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Protein transport|Inner membrane import|TIMM17/23 complex subject_level: type curation_status: mapped target_term: id: GO:0005744 label: TIM23 mitochondrial import inner membrane translocase complex mapping_scope: ok_for_propagation_to_go rationale: This PN type denotes TIMM17/23 import-complex components. The GO TIM23 mitochondrial import inner membrane translocase complex term is the direct cellular-component target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Protein transport|Inner membrane import|TIMM22 complex subject_level: type curation_status: mapped target_term: id: GO:0042721 label: TIM22 mitochondrial import inner membrane insertion complex mapping_scope: ok_for_propagation_to_go rationale: >- This PN type captures TIMM22-complex components responsible for a specific inner-membrane import route. The GO cellular-component term for the TIM22 insertion complex is an appropriate propagation target. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: >- Mitochondrial proteostasis|Protein transport|Outer membrane import|TOMM complex subject_level: type curation_status: mapped target_term: id: GO:0005742 label: mitochondrial outer membrane translocase complex mapping_scope: ok_for_propagation_to_go rationale: >- This PN subtype denotes TOMM-complex component membership for outer- membrane import. The source is a component-role category that maps naturally to the GO cellular-component term for the mitochondrial outer membrane translocase complex. references: - proteostasis-workbook-2024 - proteostasis-ms1 - subject_code: Mitochondrial proteostasis|Chaperone|HSP70 system|HSP70 nucleotide exchange factor|GRPE subtype subject_level: subtype curation_status: mapped target_term: id: GO:0001405 label: PAM complex, Tim23 associated import motor mapping_scope: ok_for_propagation_to_go rationale: This mitochondrial GRPE subtype is represented by GRPEL1/GRPEL2, PAM import-motor nucleotide-exchange factors. The GO PAM complex term is the direct complex-membership target. references: - proteostasis-workbook-2024 - proteostasis-ms1