Peroxisome Biogenesis Project

MATURE BIOLOGY_DOMAIN

Species: human

Genes: PEX1 PEX2 PEX3 PEX5 PEX6 PEX7 PEX10 PEX11A PEX11B PEX11G PEX12 PEX13 PEX14 PEX16 PEX19 PEX26

Peroxisome Biogenesis Project

Bottom line: peroxisomes are built and maintained by the PEX proteins
(peroxins), which insert membrane proteins, import matrix enzymes through a
receptor-docking-recycling cycle, and divide the organelle; their loss causes
Zellweger spectrum disorders. We reviewed every existing GO annotation on the
16 human peroxins, in three phases: import and recycling, the RING ligases and
docking complex, then membrane biogenesis and proliferation. All 16 reviews
are in the repo (828 annotations: 579 accepted, 51 kept as non-core, 93 marked
over-annotated, 28 modified, 64 removed, 11 NEW, 2 undecided). PEX39, a
recently characterized PTS2-import factor that binds PEX7, has its own review
but is outside this set. Generic protein binding was
the dominant problem: 35 of PEX19's 37 removals and 17 of PEX5's 19
over-annotations are protein binding IPI rows. The other recurring pattern
was guilt by cargo or phenotype, where a peroxin is annotated to the metabolic
process of the enzymes it imports or to a downstream knockout phenotype; these
rows were mostly kept as non-core (PEX7 ether lipid biosynthesis, PEX13 neuron
migration) rather than removed. The
conserved machinery is modelled in the
peroxisome lifecycle module, and the
obsoletion of the targeting-signal binding terms that affects PEX5, PEX7 and
PEX19 is tracked separately.

Overview

Peroxisomes are single-membrane-bound organelles found in virtually all eukaryotic cells.
They perform essential metabolic functions including fatty acid beta-oxidation (especially
very long-chain fatty acids), ether lipid (plasmalogen) synthesis, bile acid synthesis,
and reactive oxygen species metabolism. The peroxisome biogenesis machinery is encoded by
PEX (peroxin) genes, mutations in which cause Zellweger spectrum disorders (ZSD) and
other peroxisomal biogenesis disorders (PBDs).

Model Species

Primary: Homo sapiens (human)
- Zellweger spectrum disorders provide clinical relevance
- Comprehensive proteomics data available
- Well-characterized import pathways

Functional Architecture of the PEX Machinery

1. Membrane Protein Insertion (Class I)

2. Matrix Protein Import - Receptors (Class II)

3. Docking Complex (Class III)

4. RING Complex / Ubiquitination (Class IV)

5. Receptor Recycling / AAA ATPase Complex (Class V)

6. Peroxisome Proliferation / Division (Class VI)

Evolutionary Conservation

The PEX machinery shows tiered conservation:
- Deeply conserved (yeast to human): PEX1, 2, 3, 5, 6, 7, 10, 12, 13, 14, 19
- Metazoan innovations: PEX11 family expansion (1 in yeast -> 3 in human)
- Vertebrate-specific: PEX26 (replaces yeast PEX15, convergent evolution)
- Recently characterized: PEX5L (PEX5-related), PEX39

Key reference: Jansen et al. (2021) "Comparative Genomics of Peroxisome Biogenesis Proteins:
Making Sense of the PEX Proteins" Front Cell Dev Biol 9:654163.

Disease Relevance

Disease OMIM Key Genes
Zellweger syndrome (most severe) 214100 PEX1, PEX2, PEX3, PEX5, PEX6, PEX10, PEX12, PEX13, PEX14, PEX16, PEX19, PEX26
Neonatal adrenoleukodystrophy 202370 PEX1, PEX5, PEX10, PEX13, PEX26
Infantile Refsum disease 266510 PEX1, PEX2, PEX26
Rhizomelic chondrodysplasia punctata type 1 215100 PEX7
Heimler syndrome 234580 PEX1, PEX6

PEX1 is the most commonly mutated gene (~65% of ZSD cases), followed by PEX6 (~16%) and PEX26 (~5%).

Candidate Genes - Priority Order

Priority is based on: (1) disease prevalence in ZSD, (2) functional centrality,
(3) evolutionary conservation depth.

Phase 1: Core Import/Recycling (highest priority)

Gene UniProt Function ZSD Frequency
PEX1 O43933 AAA+ ATPase, receptor recycling ~65%
PEX5 P50542 PTS1 receptor ~4%
PEX6 Q13608 AAA+ ATPase, receptor recycling ~16%
PEX7 O00628 PTS2 receptor RCDP1
PEX14 O75381 Docking complex Rare
PEX26 Q7Z412 PEX1/PEX6 anchor ~5%

Phase 2: RING Complex & Docking

Gene UniProt Function ZSD Frequency
PEX2 P28328 RING E3 ligase ~3%
PEX10 O60683 RING E3 ligase ~3%
PEX12 O00623 RING E3 ligase ~4%
PEX13 Q92968 Docking complex, SH3 Rare

Phase 3: Membrane Biogenesis & Proliferation

Gene UniProt Function
PEX3 P56589 PMP membrane anchor
PEX16 Q9Y5Y5 PMP membrane receptor
PEX19 P40855 PMP chaperone/receptor
PEX11A O75192 Proliferation (inducible)
PEX11B O96011 Proliferation (constitutive)
PEX11G Q96HA9 Proliferation (tissue-specific)

STATUS

Phase 1 Genes

Phase 2 Genes

Phase 3 Genes

NOTES

2026-03-05

2026-05-01

2026-03-05 (initial)

Slides