# Organelle x lifecycle-stage coverage for the ORGANELLE_LIFECYCLES project. # status: RULE_READY (eukaryote-wide, required parts hold in every lineage), # RULE_CANDIDATE (rule-shaped and eukaryote-wide, but named lineage exceptions # are not yet modelled as variants, so those lineages report gaps), # DESCRIPTIVE (exists but clade-scoped or over-required; linked as optional), # MISSING (no module usable as a eukaryote-wide stage; a clade-specific # CONCRETE module may exist and is named in the note), NOT_APPLICABLE. # For a lineage-restricted organelle (plastid, plant vacuole) the same statuses are read # within the clade named by the row's scope. organelles: - organelle: mitochondrion umbrella: mitochondrion_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: mitochondrial_protein_import, status: RULE_CANDIDATE, note: kinetoplastids replace the TIM23/TIM22 pair with a single Tim17-family translocase; needs a lineage variant_set} - {module_ref: dmel_mitochondrial_protein_import, status: DESCRIPTIVE, note: "Drosophila compendium of the same stage, not referenced by the umbrella"} - {topic: alpha-helical outer-membrane insertion (MIM/MTCH), status: MISSING} - {topic: membrane lipid supply (cardiolipin, ER contact sites), status: MISSING, note: "Drosophila-only dmel_cardiolipin_biosynthesis_remodeling exists"} division: - {module_ref: "mitochondrial_dynamics#drp1_fission", status: DESCRIPTIVE, note: requires metazoan MFF} fusion: - {module_ref: "mitochondrial_dynamics#fzo1_omm_fusion", status: DESCRIPTIVE, note: mitofusin absent from plants} - {module_ref: "mitochondrial_dynamics#eat3_imm_fusion", status: DESCRIPTIVE} function: - {module_ref: mitochondrial_complex_i_core, status: DESCRIPTIVE, note: absent from Saccharomyces; optional within respiration} - {module_ref: mitochondrial_complex_ii, status: DESCRIPTIVE} - {module_ref: mitochondrial_complex_iii, status: DESCRIPTIVE} - {module_ref: mitochondrial_complex_iv, status: DESCRIPTIVE} - {module_ref: mitochondrial_complex_v, status: DESCRIPTIVE} - {module_ref: mitochondrial_iron_sulfur_cluster_assembly, status: RULE_CANDIDATE, note: "Archamoebae such as Entamoeba replace NFS1 and ISCU with a bacterial-type NIF system (the one exception checked so far); needs NIF realizers for those steps"} - {topic: mtDNA maintenance and gene expression, status: MISSING, note: "Drosophila-only dmel_mitochondrial_dna_replisome and dmel_mitochondrial_ribosome exist"} quality_control: - {module_ref: mitochondrial_upr, status: DESCRIPTIVE, note: metazoan} turnover: - {module_ref: "mitophagy#atg8_capture", status: DESCRIPTIVE} - organelle: peroxisome umbrella: peroxisome-lifecycle stages: biogenesis_and_protein_supply: - {module_ref: peroxisomal_protein_import, status: RULE_CANDIDATE, note: "PAINT places the core peroxins at Eukaryota except Pex2 (Amniota node; placed by subfamily membership); lineage losses of Pex16 and PTS2/Pex7 are optional parts but not yet checked against proteomes; the E2 and the PEX1/PEX6 anchor are not grounded per lineage"} division: - {module_ref: "peroxisome-lifecycle#peroxisome_proliferation", status: DESCRIPTIVE, note: "PEX11-FIS1-DNM1L and MFF routes as complexes; MFF is metazoan"} function: - {module_ref: peroxisomal_beta_oxidation, status: DESCRIPTIVE} - {module_ref: ether_lipid_plasmalogen_biosynthesis, status: DESCRIPTIVE} turnover: - {topic: pexophagy, status: MISSING} - organelle: lysosome and endosome umbrella: lysosome_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: escrt_iii_intralumenal_vesicle_formation, status: RULE_CANDIDATE, note: "ESCRT-III and Vps4 core by subfamily; the Vps2/Vps24 step is met by any CHMP2/3/1-family member; ESCRT-0/I/II not yet modelled; the machinery also acts at other membranes, so passing shows scission capacity, not intralumenal vesicles"} - {module_ref: mannose_6_phosphate_lysosomal_targeting, status: DESCRIPTIVE, note: metazoan; Vps10/VSR sorting in fungi and plants not modelled} - {topic: endosome maturation and fusion (Rab7, Mon1-Ccz1, CORVET/HOPS), status: MISSING, note: "phagosome_maturation covers these in a metazoan context"} function: - {module_ref: vacuolar_atpase_acidification, status: RULE_CANDIDATE, note: "one PANTHER family per V1/V0 subunit; families also hold prokaryotic A/V-type subunits; not yet checked against proteomes"} - {module_ref: glycosphingolipid_lysosomal_degradation, status: DESCRIPTIVE} - {module_ref: lysosomal_glycoprotein_degradation, status: DESCRIPTIVE} - {module_ref: heparan_sulfate_lysosomal_degradation, status: DESCRIPTIVE} - {module_ref: keratan_chondroitin_sulfate_lysosomal_degradation, status: DESCRIPTIVE} - {module_ref: lysosomal_glycogen_degradation, status: DESCRIPTIVE} turnover: - {topic: lysosome repair and lysophagy, status: MISSING} - organelle: endoplasmic reticulum umbrella: endoplasmic_reticulum_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: er_cotranslational_translocation, status: RULE_CANDIDATE, note: "SRP, SRP receptor and Sec61 alpha/gamma; plastid paralogs can satisfy SRP54 and Sec61 alpha; no plant SRalpha subfamily locally; SRbeta's PANTHER placement disputed (PTHR45909 vs PTHR11485); SRP RNA and Sec61 beta not modelled; Drosophila-only dmel_sec61_translocon and dmel_srp_cotranslational_targeting cover Sec61 beta"} - {topic: ER shaping (reticulons, Yop1/DP1, atlastin/Sey1), status: MISSING} function: - {module_ref: er_oxidative_protein_folding, status: RULE_CANDIDATE, note: "BiP and PDI required, selectors over-match their families; Ero1 optional (other PDI oxidants not modelled); calnexin cycle optional"} - {module_ref: oligosaccharyltransferase_complex, status: DESCRIPTIVE} quality_control: - {module_ref: er_unfolded_protein_response, status: DESCRIPTIVE, note: metazoan} - {topic: ERAD, status: MISSING, note: "Hrd1's PANTHER family has no local entries table; Cdc48 and Hrd3/Sel1 split into lineage-specific subfamilies; Derlin not in local entries"} turnover: - {topic: ER-phagy, status: MISSING} - organelle: autophagosome umbrella: autophagosome_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: autophagosome_core_biogenesis, status: RULE_CANDIDATE, note: "Atg1/ULK-Atg13, Vps34-Vps15-Atg6, Atg9, Atg2, Atg18/WIPI and the Atg12/Atg8 conjugation systems; Atg14 and Atg16 optional (selectors miss plants and fungi respectively); Atg1/ULK and PROPPIN selectors over-match; no Dictyostelium Atg13 or Atg2 listed; FIP200/Atg17, ATG101 and Atg10 not modelled"} - {module_ref: metazoan_autophagosome_biogenesis, status: DESCRIPTIVE} - {module_ref: phagophore_assembly_site, status: DESCRIPTIVE} turnover: - {topic: phagophore closure and autophagosome-lysosome fusion, status: MISSING} - organelle: phagosome umbrella: phagosome_maturation - organelle: synaptic vesicle umbrella: synaptic_vesicle_cycle - organelle: cilium umbrella: primary_cilium_life_cycle - organelle: Golgi apparatus umbrella: golgi_apparatus_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: dmel_copii_coat, status: DESCRIPTIVE, note: "Drosophila only; eukaryote-wide COPII not groundable locally (SEC24A, SEC31A and PREB have no local PANTHER entry; SAR1 and SEC23 families have no PAINT table)"} function: - {module_ref: golgi_copi_vesicle_coat, status: RULE_CANDIDATE, note: "GBF1/Gea, Arf1 and the seven coatomer subunits; the Arf selector over-matches the Arf/Arl family; no Dictyostelium member in the GBF1 subfamily; a fission-yeast IRD in the alpha/beta' family is bounded; ArfGAPs not modelled"} - {topic: Golgi tethers and SNAREs (golgins, TRAPP, COG), status: MISSING} - {topic: Golgi glycosylation, status: MISSING} - {topic: trans-Golgi network exit (clathrin, AP-1), status: MISSING} turnover: - {topic: mitotic Golgi disassembly and reassembly, status: MISSING, note: not universal} - organelle: nucleus and nuclear envelope umbrella: nucleus_lifecycle stages: biogenesis_and_protein_supply: - {topic: interphase nuclear pore insertion, status: MISSING} function: - {module_ref: nuclear_pore_transport_core, status: RULE_CANDIDATE, note: "partial: Nup98-96, Nup88, Seh1, Sec13, Ran, NTF2, Crm1 and Cse1 only; importins, RCC1, RanGAP and most nucleoporins have no local PANTHER entry; Seh1 and Sec13 also work outside the pore; no Dictyostelium Nup88/Seh1 or Arabidopsis Sec13 listed"} - {module_ref: karyopherin_nuclear_protein_import, status: DESCRIPTIVE, note: "importin-alpha/beta import and the RCC1-RanGAP Ran cycle, grounded on UniProt accessions rather than PANTHER families"} - {module_ref: dmel_nuclear_pore_complex, status: DESCRIPTIVE} - {module_ref: mrna_nuclear_export, status: DESCRIPTIVE, note: human} turnover: - {topic: "nuclear envelope sealing (CHMP7, LEM2, ESCRT-III)", status: MISSING, note: "local CHMP7 subfamily is vertebrate-only, LEMD2 subfamily mammal-only"} - {topic: mitotic envelope disassembly and reassembly, status: MISSING, note: absent from closed mitosis} - {topic: nuclear lamina, status: MISSING, note: not universal} - organelle: lipid droplet umbrella: lipid_droplet_lifecycle stages: biogenesis_and_protein_supply: - {module_ref: lipid_droplet_neutral_lipid_storage, status: RULE_CANDIDATE, note: "DGAT1 or DGAT2 (ONE_OR_MORE); DGAT1 and DGAT2 each by the three subfamilies their family reviews allow, no yeast DGAT1 listed; FIT optional (opisthokont); seipin (no local BSCL2 entry) and PDAT not modelled"} - {module_ref: triacylglycerol_biosynthesis, status: DESCRIPTIVE} - {module_ref: seed_triacylglycerol_biosynthesis, status: DESCRIPTIVE, note: plant} - {topic: seipin-dependent nucleation, status: MISSING} turnover: - {module_ref: triacylglycerol_lipolysis, status: DESCRIPTIVE, note: human} - {topic: lipophagy, status: MISSING} - organelle: plastid umbrella: plastid_lifecycle scope: Embryophyta stages: biogenesis_and_protein_supply: - {module_ref: plastid_protein_import, status: RULE_CANDIDATE, note: "Toc34 and Toc159 receptors, Toc75, Tic236, Tic20, Tic110, ClpC, cpHsc70 and the stromal processing peptidase by subfamily; Tic214, Tic56, Tic100, Tic40, Hsp90C, FtsHi, Tic21, Tic22, Tic62, Tic32 and Tic55 optional; Embryophyta, as Chlamydomonas TOC34 falls in the Toc159-family subfamily; Ycf2 not modelled"} - {topic: plastid gene expression and envelope and thylakoid biogenesis, status: MISSING} division: - {module_ref: plastid_division, status: RULE_CANDIDATE, note: "FtsZ1, FtsZ2, ARC6 and ARC5 by Arabidopsis-only subfamilies; MinD optional (its subfamily also holds bacterial MinD) and PDV1/PDV2 optional (Streptophyta node)"} function: - {module_ref: photosynthesis, status: DESCRIPTIVE} - {module_ref: thylakoid_light_reactions, status: DESCRIPTIVE} - {module_ref: calvin_benson_bassham_cycle, status: DESCRIPTIVE} - {module_ref: photorespiration_c2_cycle, status: DESCRIPTIVE, note: Embryophyta} quality_control: - {topic: FtsH and Clp proteases, status: MISSING} turnover: - {topic: chlorophagy and CHLORAD, status: MISSING} - organelle: plant vacuole umbrella: plant_vacuole_lifecycle scope: Viridiplantae stages: biogenesis_and_protein_supply: - {module_ref: escrt_iii_intralumenal_vesicle_formation, status: RULE_CANDIDATE, note: eukaryote-wide rule shared with lysosome_lifecycle} - {module_ref: plant_vacuolar_sorting_receptor_cycle, status: RULE_CANDIDATE, note: "VSR (UniProt PTHR22702 and PANTHER-file PTHR24034 placements) and retromer Vps35, Vps26 (whole family), Vps29; RMR optional; PTHR22702:SF1 also holds animal PRADC1, so human also meets this module"} fusion: - {module_ref: plant_vacuole_fusion, status: RULE_CANDIDATE, note: "Mon1-Ccz1, RabG3, Vps41 and Vps39, SYP22 and VTI11 by subfamily; HOPS core (VPS11/16/18/33), SYP51 and VAMP713 not modelled; Rab7 and SNARE selectors list plant members only; chlorophyte and cotton Rab7 sit in the pan-eukaryotic PTHR47981:SF20, so the Rab7 step fails there"} function: - {module_ref: vacuolar_atpase_acidification, status: RULE_CANDIDATE, note: eukaryote-wide rule shared with lysosome_lifecycle} - {module_ref: plant_tonoplast_transport, status: RULE_CANDIDATE, note: "V-PPase (AVP1), TIP1 aquaporin and vacuolar NHX required; TPC1, TPK1, CLC-a and ALMT9 optional; CLC-a selector Arabidopsis-only; CLC-a, TPC1 and ALMT9 untyped"} turnover: - {topic: storage-vacuole conversion and vacuolar cell death, status: MISSING}