Peroxisome lifecycle

Peroxisomes grow by importing membrane and matrix proteins, divide, carry out lineage- and tissue-specific metabolism, and are removed by pexophagy. This umbrella module composes the modules for those stages by reference. Protein import is required in every eukaryote with peroxisomes or peroxisome-derived organelles; division, metabolism and turnover vary between lineages or are not yet written as eukaryote-wide rules.

MODULE:peroxisome_lifecycleDRAFTCONCRETEOrganelle Lifecyclemodules/peroxisome-lifecycle.yaml
peroxisome organizationGO:0007031 peroxisomeGO:0005777
file:modules/peroxisomal_protein_import.yaml
Peroxisomal protein import machinery
Eukaryote-wide import core split out of this module, with per-subunit family selectors.
file:modules/peroxisome-lifecycle-deep-research-falcon.md
Peroxisome lifecycle and matrix protein import module deep research
Falcon deep research synthesis used to refine the module boundaries, importomer/exportomer distinction, lineage variants, and 2023-2024 mechanistic updates.
DOI:10.1016/j.tcb.2023.08.005
Towards solving the mystery of peroxisomal matrix protein import
Supports the coupled import-receptor recycling cycle and the current PEX13/YG-repeat meshwork model for matrix protein import.
DOI:10.1007/s00418-023-02259-5
The peroxisome: an update on mysteries 3.0
Supports the current conserved peroxin skeleton, lineage-specific peroxin variants, peroxisome proliferation/division machinery, and organelle contact-site context.
PMID:28765278
Supports treating the peroxisomal docking/translocation machinery as an importomer module.
PMID:35768507
Supports a distinct ATP-dependent matrix import receptor recycling/extraction module.

Organelle lifecycle umbrella (see projects/ORGANELLE_LIFECYCLES.md); stage roles follow the shared skeleton. Read as a satisfiability rule, only protein import is required. Division is optional because its module still requires lineage-specific routes (the metazoan MFF adaptor, and PEX11-FIS1-dynamin units not yet grounded per subunit); metabolism is optional because resident peroxisomal pathways vary by lineage and tissue; turnover (pexophagy) is an interface not yet modelled as a module. The import stages moved into MODULE:peroxisomal_protein_import with their annotons and evidence; the importomer, RING peroxin and PEX1/PEX6 complexes became per-subunit family annotons, and the one-of route and receptor choices became a required core plus optional parts (see that module's notes).

9Nodes
6Parts
1Variant Sets
2Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • peroxisome-lifecycle-deep-research-falcon.md (falcon)

Leaf nodes lacking representative members

1 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

1 gene-function check(s) reflected in core functions · 0 conflict(s) · 6 evidence or coverage gap(s) (10 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
pex11_like_membrane_remodeling human PEX11A
UniProtKB:O75192
Family Representative 		peroxisome membrane remodeling for elongation and division
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
pex11_like_membrane_remodeling human PEX11B
UniProtKB:O96011
Family Representative 		peroxisome membrane remodeling for elongation and division
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
pex11_like_membrane_remodeling human PEX11G (PANTHER family PTHR20990)
UniProtKB:Q96HA9
Family Representative 		peroxisome membrane remodeling for elongation and division
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
pex11_fis1_dynamin_division_unit PROTEIN_COMPLEX
Gene 		peroxisome membrane scission after elongation
No function ID 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
mff_drp1_division_unit PROTEIN_COMPLEX
Gene 		DRP1-mediated peroxisome membrane scission
No function ID 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
mff_drp1_division_unit/mff_division_adaptor_unit human MFF
UniProtKB:Q9GZY8
Family Representative 		protein-membrane adaptor activity (DRP1 receptor)
GO:0043495 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ubiquitin_linked_pexophagy_interface ANY_PARTICIPANT
Gene 		selective autophagy signaling for peroxisome turnover
No function ID 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
pex11_like_membrane_remodeling Pex11-like membrane remodeling family
PANTHER:PTHR12652
Family 		peroxisome membrane remodeling for elongation and division
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
pex11_like_membrane_remodeling Pex11-like membrane remodeling family
PANTHER:PTHR20990
Family 		peroxisome membrane remodeling for elongation and division
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
mff_division_adaptor_unit MFF-like fission adaptor family
PANTHER:PTHR16501:SF17
Family 		protein-membrane adaptor activity (DRP1 receptor)
GO:0043495 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16501:SF17.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

  • peroxisomal_import ⊣ peroxisome_quality_control [closed]
    peroxisomal_import is regulated by peroxisome_proliferation: feedback loop closed

Gene-review completeness (5/5 grounded genes reviewed)

4 complete review(s) · 3 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
DNM1L O00429 ✓ 144/153 ✗
MFF Q9GZY8 ✓ ✓ ✗
PEX11A O75192 ✓ ✓ ✓
PEX11B O96011 ✓ ✓ ✓
PEX11G Q96HA9 ✓ ✓ ✓

Details

Context
EukaryotaNCBITaxon:2759
conserved eukaryotic organelle lifecycle conserved peroxin core with lineage-specific additions
Peroxisome lifecycleOrganelle Lifecycleperoxisome_lifecycle
peroxisome organizationGO:0007031 peroxisomeGO:0005777
Context
EukaryotaNCBITaxon:2759
conserved eukaryotic organelle lifecycle conserved peroxin core with lineage-specific additions

Connections

Proliferation and membrane biogenesis are coupled in peroxisome growth and maintenance.
Matrix import provides enzymes required for mature peroxisome metabolic function.
Functional matrix import helps maintain organelle identity; import failure or unresolved ubiquitin signals can shift peroxisomes toward pexophagy and quality-control routes.
DOI:10.1038/s41467-023-44005-4
Supports cross-talk between import defects, pexophagy, and selective autophagy capacity.
Part 1: biogenesis and protein supply
Peroxisomal protein import (see MODULE:peroxisomal_protein_import)peroxisomal_import

Growth of peroxisomes by import of membrane and matrix proteins.

Realized by module peroxisomal_protein_import

Part 2: division (optional)
Peroxisome elongation and divisionOrganelle Lifecycleperoxisome_proliferation
peroxisome organizationGO:0007031

Annotons

Pex11-like peroxisome membrane remodeling
pex11_like_membrane_remodeling
Participant: Family: Pex11-like membrane remodeling family
Family:
Pex11-like membrane remodeling familyPANTHER:PTHR12652 Eukaryotic peroxisomal membrane factors that promote peroxisome elongation, constriction, or division; paralog copy number and naming differ by lineage. PANTHER splits these paralogs across two families that share this membrane-remodeling role: PTHR12652 (PEX11A/PEX11B) and PTHR20990 (PEX11G); the ancestral_nodes below record the IBD node for each.
Representative Members: human PEX11AUniProtKB:O75192 human PEX11BUniProtKB:O96011 human PEX11G (PANTHER family PTHR20990)UniProtKB:Q96HA9

Function

peroxisome membrane remodeling for elongation and division Membrane-shaping role that promotes peroxisome elongation and proliferation.

Locations

peroxisomal membraneGO:0005778
PMID:20826455
Supports PEX11 family involvement in peroxisome elongation and division.
DOI:10.1007/s00418-023-02259-5
Supports PEX11-family membrane remodeling and peroxisome division route variation.
Variant set: Peroxisome division route variants by fission adaptor and membrane-remodeling route (One Or More)
PEX11-FIS1-supported division routeOrganelle Lifecyclepex11_fis1_division_route

Potentially ancient route coupling PEX11-family membrane remodeling to FIS1-supported dynamin-related scission.

DOI:10.1007/s00418-023-02259-5
Supports a PEX11/FIS1-associated division route and its evolutionary interpretation.

Annotons

PEX11/FIS1/dynamin-related division unit
pex11_fis1_dynamin_division_unit
Participant: Protein Complex: PEX11-FIS1-dynamin-related peroxisome division unit
Protein Complex:
PEX11-FIS1-dynamin-related peroxisome division unit
Active units:
PEX11-family membrane remodeling unit
Participant: Family: PEX11-like membrane remodeling family
Family:
PEX11-like membrane remodeling familyPANTHER:PTHR12652
Representative Members: human PEX11AUniProtKB:O75192 human PEX11BUniProtKB:O96011
Role: membrane elongation and constriction support
FIS1-family division adaptor unit
Participant: Family: FIS1-like fission adaptor family
Family:
FIS1-like fission adaptor family
Role: dynamin-related GTPase recruitment or support
dynamin-related scission GTPase unit
Participant: Family: dynamin-related organelle scission GTPase family
Family:
dynamin-related organelle scission GTPase familyPANTHER:PTHR11566
Representative Members: human DNM1L (DRP1)UniProtKB:O00429
Role: membrane scission

Function

peroxisome membrane scission after elongation
MFF-dependent DRP1 division routeOrganelle Lifecyclemff_dependent_division_route

Metazoan route in which MFF helps recruit DRP1/DNM1L to execute scission of elongated peroxisomal membranes.

Context
metazoan lineagesNCBITaxon:33208
DOI:10.1007/s00418-023-02259-5
Supports MFF-dependent peroxisome fission as a metazoan route.
DOI:10.26508/lsa.202402608
Supports current DRP1 imaging tools relevant to mitochondrial and peroxisomal fission dynamics.

Annotons

MFF/DRP1 peroxisome division unit
mff_drp1_division_unit
Participant: Protein Complex: MFF-DRP1 peroxisome division unit
Protein Complex:
MFF-DRP1 peroxisome division unit
Active units:
MFF-family division adaptor unit
Participant: Family: MFF-like fission adaptor family
Family:
MFF-like fission adaptor familyPANTHER:PTHR16501:SF17
Representative Members: human MFFUniProtKB:Q9GZY8
Role: DRP1 recruitment to peroxisomal membrane
Function:
protein-membrane adaptor activity (DRP1 receptor)GO:0043495 Tail-anchored MFF tethers cytosolic DRP1/DNM1L to the peroxisomal (and mitochondrial outer) membrane, matching the core function in the completed human MFF review.
DRP1/DNM1L-family scission GTPase unit
Participant: Family: DRP1/DNM1L dynamin-related GTPase family
Family:
DRP1/DNM1L dynamin-related GTPase familyPANTHER:PTHR11566:SF39
Representative Members: human DNM1L (DRP1)UniProtKB:O00429
Role: GTP-dependent membrane scission

Function

DRP1-mediated peroxisome membrane scission
Part 4: function (optional)
Peroxisomal matrix metabolic operationBiological Processperoxisome_matrix_metabolism

Resident peroxisomal metabolism is treated as a module interface rather than a fixed universal pathway. Beta-oxidation, reactive oxygen metabolism, ether lipid metabolism, glyoxylate-cycle functions, or specialized biosynthetic pathways can be attached as lineage-, tissue-, or environment-specific submodules.

peroxisomal matrixGO:0005782
DOI:10.1186/s13062-024-00458-1
Supports tissue-specific expression and functional specialization of peroxisomal metabolism.

Recent expression meta-analysis supports keeping metabolic operation modular rather than universal: heart, liver, and other tissues can retain similar biogenesis machinery while emphasizing different peroxisomal metabolic programs.

Part 1: fatty acid beta-oxidation (optional)
Peroxisomal beta-oxidation (see MODULE:peroxisomal_beta_oxidation)beta_oxidation

Realized by module peroxisomal_beta_oxidation

Part 2: ether lipid synthesis (optional)
Ether lipid and plasmalogen biosynthesis (see MODULE:ether_lipid_plasmalogen_biosynthesis)ether_lipid_synthesis

Realized by module ether_lipid_plasmalogen_biosynthesis

Part 6: turnover (optional)
Peroxisome quality control and turnover interfaceOrganelle Lifecycleperoxisome_quality_control

Pexophagy and ubiquitin-linked peroxisome quality control regulate organelle abundance and remove import-defective or damaged peroxisomes. This is an interface to the lifecycle rather than part of the core matrix import mechanism.

pexophagyGO:0030242

Annotons

Ubiquitin-linked pexophagy signaling
ubiquitin_linked_pexophagy_interface
Participant: Any Participant: ubiquitinated peroxisomal membrane proteins or import-defective peroxisomes
ubiquitinated peroxisomal membrane proteins or import-defective peroxisomes

Function

selective autophagy signaling for peroxisome turnover
Targets: damaged or import-defective peroxisome
DOI:10.1038/s41467-023-44005-4
Supports pexophagy as a quality-control route connected to peroxisome import defects and cellular autophagy capacity.