C. elegans Mitophagy & Mitochondrial Quality Control Project

Bottom line: mitophagy, the selective autophagy of damaged
mitochondria, is conserved in C. elegans, where the PINK-1 kinase, the
PDR-1 Parkin ligase and the DCT-1 (BNIP3L/NIX) receptor mark mitochondria
for the LGG-1/LGG-2 autophagy machinery, and ATFS-1 decides between repair
through the mitochondrial unfolded protein response and removal. We
reviewed every existing GO annotation on 17 genes in three tiers (core
mitophagy and dynamics, autophagy machinery, longevity regulators) and wrote
a pathway summary. All 17
reviews are complete: 543 rows, 408 ACCEPT, 62 KEEP_AS_NON_CORE, 12
MARK_AS_OVER_ANNOTATED, 26 MODIFY, 3 REMOVE, 9 UNDECIDED and 23 NEW
proposals. The main results are a NEW mitochondrion autophagosome adaptor
activity (GO:0140580) for DCT-1, replacement of generic protein binding
rows on LGG-1, LGG-2, BEC-1, SQST-1 and SKN-1, and new transport and fission
terms for MIRO-1. The December 2025 status notes below overstate
removals: the DRP-1 microtubule rows are marked over-annotated, and a
September 2026 re-review moved EAT-3's peroxisome-fission and microtubule
rows from REMOVE to UNDECIDED. The notes below also say fundc-1 has no
clear worm ortholog; that is out of date: fundc-1 (Q22252, the FUNDC1
ortholog) now has a completed review in genes/worm/ that proposes the
same adaptor activity (GO:0140580), but it is not counted in the 17-gene,
543-row totals. Six of the 17 genes are shared with other projects
(bec-1, lgg-1, atg-18, skn-1 and hlh-30 with proteostasis, atfs-1 with
the UPR project), so do not sum row totals across projects.

We did this because the worm is a main genetic model for Parkinson's
disease genes and for the link between mitochondrial quality control and
lifespan, and its annotations feed orthology-based inference for the human
PINK1/Parkin pathway.

Overview

Mitophagy is the selective autophagy of damaged mitochondria, essential for maintaining a healthy mitochondrial population. C. elegans has conserved mitophagy pathways and is particularly valuable for studying the interplay between mitophagy, aging, and neurodegeneration.

The PINK1-Parkin pathway, originally discovered through Parkinson's disease genetics, is well-conserved in worms. Recent work connects mitophagy to ferroptosis regulation, longevity pathways, and stress responses.

Model Species

Primary: Caenorhabditis elegans (worm)
- UniProt species code: CAEEL
- Conserved mitophagy pathways
- Parkinson's disease models
- Aging-mitophagy connections

Core Pathway Architecture

1. PINK1-Parkin Pathway

Canonical mitophagy initiation:
- pink-1 - PINK1 kinase (accumulates on damaged mito)
- pdr-1 - Parkin E3 ligase (recruited by PINK1)
- miro-1 - Miro GTPase (mitochondrial transport, Parkin substrate)

2. Mitophagy Receptors

Direct autophagosome recruitment:
- dct-1 - BNIP3L/NIX ortholog (primary receptor)
- fundc-1 - FUNDC1 ortholog (hypoxia-induced)

3. Mitochondrial Dynamics

Fission/fusion machinery (required for mitophagy):
- drp-1 - DRP1/Dynamin-related (fission)
- fzo-1 - Mitofusin (outer membrane fusion)
- eat-3 - OPA1 ortholog (inner membrane fusion)
- fis-1 - FIS1 (fission factor)
- fis-2 - MFF ortholog (fission)
- mff-1 - MFF ortholog

4. Core Autophagy Machinery

Shared with other autophagy pathways:
- bec-1 - Beclin ortholog
- lgg-1 - LC3/GABARAP
- lgg-2 - LC3/GABARAP family
- atg-18 - WIPI1/2 ortholog
- epg-5 - Autophagy gene
- sqst-1 - p62/SQSTM1 receptor

5. Mitochondrial UPR Connection

Stress response coordination:
- atfs-1 - ATFS1 (UPR-mt vs mitophagy decision)
- hsp-6 - mtHSP70
- clpp-1 - ClpP protease

6. Longevity-Mitophagy Axis

• daf-2 - Insulin receptor (reduced signaling increases mitophagy)
• daf-16 - FOXO (promotes mitophagy genes)
• skn-1 - Nrf2 ortholog
• hlh-30 - TFEB ortholog (autophagy/lysosome TF)
• sir-2.1 - SIRT1 (deacetylase)

7. Mitochondrial Import/Proteostasis

• tin-44 - TIM44 (import machinery)
• tomm-22 - TOM22 (import machinery)
• spg-7 - SPG7/Paraplegin (m-AAA protease)
• phb-1/phb-2 - Prohibitins

8. ROS and Damage Sensing

• sod-2 - Mn-SOD (mitochondrial)
• sod-3 - Fe-SOD
• clk-1 - COQ7 (ubiquinone synthesis)
• isp-1 - Rieske iron-sulfur protein

Genes for Review (Priority Order)

Priority 1: Core Mitophagy Pathway (~6 genes)

Priority 2: Autophagy Machinery (~6 genes)

Priority 3: Longevity & Regulation (~5 genes)

Note: fundc-1 was originally skipped as lacking a clear C. elegans ortholog in UniProt; this is out of date. fundc-1 (Q22252) is the FUNDC1 ortholog and now has a completed review (genes/worm/fndc-1/), not yet counted in this project's totals.

Key Biological Concepts

PINK1-Parkin Mechanism

1. PINK1 accumulates on depolarized mitochondria
2. PINK1 phosphorylates ubiquitin and Parkin
3. Parkin ubiquitinates outer membrane proteins
4. Autophagy receptors recognize ubiquitin chains
5. Autophagosome engulfs mitochondrion

DCT-1/BNIP3L Receptor Pathway

• Direct receptor on mitochondrial outer membrane
• LIR motif binds LC3/LGG-1
• Regulated by phosphorylation
• Important in hypoxia

Mitophagy vs UPR-mt Decision

• ATFS-1 normally imported into mitochondria and degraded
• Mitochondrial damage prevents import
• ATFS-1 translocates to nucleus
• Activates either repair (UPR-mt) or elimination (mitophagy)

Heat Shock Induces Mitophagy

• Acute heat shock (37C) causes mitochondrial fragmentation
• DCT-1, PINK-1, PDR-1 dependent process
• Clears damaged mitochondria

Key Phenotypes

• Mitophagy reporters - mito-GFP/mCherry flux
• Parkinson's model - Dopaminergic neuron loss
• Mitochondrial morphology - Fragmentation/hyperfusion
• Lifespan - Often extended by mild mitochondrial stress
• Rotenone sensitivity - Complex I inhibitor sensitivity

Key References

• Palikaras K et al. (2015) Nature - DCT-1 receptor discovery
• Springer & Bharat (2017) eLife - PINK-1/PDR-1 in worms
• Schiavi A et al. (2015) Cell Rep - Mitophagy and longevity
• Luz AL & Bharat T (2020) Redox Biol - Mitophagy in aging
• Bratic I & Trifunovic A (2010) - Mitochondrial aging

Disease Relevance

• Parkinson's disease - PINK1/Parkin mutations
• Aging - Mitochondrial dysfunction accumulation
• Neurodegeneration - General mitochondrial quality control
• Cardiomyopathy - Tissue-specific mitophagy requirements

Project Status

• [x] Create gene folders and fetch UniProt/GOA data
• [x] Priority 1 genes review (core mitophagy)
• [x] Priority 2 genes review (autophagy machinery)
• [x] Priority 3 genes review (longevity regulation)
• [x] Pathway summary and integration (see CAEEL_MITOPHAGY-pathway.md)

STATUS

2025-12-27 - Priority 1 COMPLETE

All 6 core mitophagy genes reviewed:

Priority 1 Summary:

• pink-1 (Q09298): PINK1 kinase - 26 annotations reviewed, 21 ACCEPT, 6 KEEP_AS_NON_CORE. Core mitophagy initiator and kinase.
• pdr-1 (Q9XUS3): Parkin E3 ligase - 37 annotations reviewed, 24 ACCEPT, 6 KEEP_AS_NON_CORE, 3 MODIFY, 2 MARK_AS_OVER_ANNOTATED. Works with PINK-1 in mitophagy pathway.
• dct-1 (Q09969): BNIP3L/NIX receptor - 26 annotations reviewed, 14 ACCEPT, 8 KEEP_AS_NON_CORE, 1 NEW (GO:0140580 mitochondrion autophagosome adaptor activity). Key mitophagy receptor with LIR-like motif.
• drp-1 (Q8WQC9): DRP1 fission GTPase - 28 annotations reviewed, 22 ACCEPT, 4 KEEP_AS_NON_CORE, 2 REMOVE (microtubule annotations). Required for isolating damaged mitochondria.
• fzo-1 (Q23424): Mitofusin - 13 annotations reviewed, all ACCEPT/KEEP. Outer membrane fusion GTPase.
• eat-3 (Q18965): OPA1 ortholog - 26 annotations reviewed, 14 ACCEPT, 6 KEEP_AS_NON_CORE, 5 REMOVE (peroxisome, microtubule), 1 NEW (GO:1990627 inner membrane fusion). Inner membrane fusion, cristae maintenance.

Key Findings:

1. PINK-1/PDR-1/DCT-1 form the core mitophagy signaling axis
2. DRP-1 fission is required to isolate damaged mitochondria
3. FZO-1/EAT-3 fusion opposes fission for mitochondrial morphology balance
4. Several incorrect annotations inherited from other dynamins (microtubule-related) were removed from drp-1 and eat-3
5. DCT-1 acts as the primary mitophagy receptor via its LIR-like WXXL motif

NOTES

2025-12-27

• Project initiated
• Fetched data for all 6 Priority 1 genes
• Ran deep research (falcon provider) for all genes
• Completed systematic annotation review for all Priority 1 genes
• Key pathway connections established between genes

2025-12-28 - Priority 2 COMPLETE

All 6 autophagy machinery genes reviewed:

Priority 2 Summary:

• bec-1 (O16351): Beclin ortholog - VPS34 complex subunit for PI3P generation at phagophores. Required for autophagy, endocytic sorting, and apoptotic cell clearance.
• lgg-1 (Q9XYN3): GABARAP family - Ubiquitin-like modifier conjugated to phagophore membrane. Operates upstream of LGG-2 in autophagosome formation.
• lgg-2 (O02053): LC3 family - Autophagosome membrane protein. Acts downstream of LGG-1, directly binds VPS-39/HOPS for lysosome tethering.
• sqst-1 (G5ECN6): p62/SQSTM1 ortholog - Selective autophagy receptor with UBA and LIR domains. Links ubiquitinated cargo to LGG-1.
• atg-18 (O16466): WIPI1/2 ortholog - PROPPIN family PI3P effector with FRRG motif. Distinct from EPG-6 in autophagosome formation. Functions in apoptotic cell clearance, xenophagy.
• epg-5 (Q18892): Metazoan-specific autophagy factor - RAB-7 effector that promotes autophagosome-lysosome fusion. SNARE binding coordinates trans-SNARE complex assembly.

Key Findings:

1. LGG-1 (GABARAP) acts upstream of LGG-2 (LC3) in C. elegans - opposite order to some mammalian models
2. LGG-2 directly binds VPS-39/HOPS for lysosome tethering, specialized maturation role
3. ATG-18 and EPG-5 both function in LAP (LC3-associated phagocytosis) for apoptotic cell clearance
4. EPG-5 is a RAB-7 effector that coordinates SNAREs for autophagosome-lysosome fusion specificity
5. SQST-1 is the primary selective autophagy receptor, potentially targets paternal mitochondria

2025-12-28 - Priority 3 COMPLETE

All 5 longevity & regulation genes reviewed (fundc-1 omitted at the time as lacking a clear C. elegans ortholog; since reviewed as Q22252, see note above):

Priority 3 Summary:

• atfs-1 (Q23272): ATFS1 transcription factor - Master regulator of UPR-mt. Dual targeting (MTS+NLS) allows import-efficiency sensing. Under stress, accumulates in nucleus to activate mitochondrial chaperones, proteases, and immune genes. Degraded by LONP-1 in healthy mitochondria.
• hlh-30 (H2KZZ2): TFEB ortholog - bHLH transcription factor for autophagy/lysosome biogenesis and longevity. Required for lifespan extension in 6 distinct paradigms. Activated by starvation, infection (S. aureus), heat stress. Drives ~80% of host defense response.
• skn-1 (P34707): Nrf1/Nrf2 ortholog - CNC/bZIP transcription factor for oxidative stress and xenobiotic responses. Activates phase II detoxification genes. Nuclear localization regulated by phosphorylation; GSK-3 and IIS pathway suppress activity.
• miro-1 (Q94263): Miro GTPase - Outer mitochondrial membrane adaptor linking mitochondria to kinesin/dynein motors. Contains 2 GTPase domains and 2 calcium-sensing EF-hands. Parkin substrate; degradation arrests mitochondrial transport to quarantine damaged organelles.
• spg-7 (Q9N3T5): m-AAA protease subunit - Actually ortholog of AFG3L2 (not human SPG7/paraplegin). Inner membrane metalloprotease for respiratory chain assembly and protein quality control. RNAi triggers UPR-mt via ATFS-1 activation.

Key Findings:

1. ATFS-1 import-efficiency model: mitochondrial damage reduces import → nuclear accumulation → UPR-mt activation
2. HLH-30 integrates longevity, autophagy, lysosome biogenesis, and innate immunity in a unified transcriptional program
3. SKN-1 is the hub for oxidative stress response; overlaps with DAF-16/FOXO and HIF-1 networks
4. MIRO-1 serves as both mitochondrial transport adaptor AND mitophagy switch (degraded by Parkin to halt transport)
5. SPG-7 nomenclature is misleading - it's AFG3L2, not SPG7 ortholog; true SPG7 ortholog is ppgn-1

Project Complete!

All 17 genes (6 + 6 + 5) across 3 priority levels have been reviewed. Only pathway summary integration remains.

Slides

• Slides (Marp source: CAEEL_MITOPHAGY-slides.md) — AI generated