GO:0000425 pexophagy: Selective Autophagy Pathway, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• Pexophagy (GO:0000425) is the selective autophagy process in which a peroxisome is degraded by macroautophagy.
• In mammals, pexophagy is triggered by ubiquitination of peroxisomal membrane proteins such as PEX5 and PEX13, which recruit autophagy receptors.
• BNIP3L/NIX acts as a selective autophagy receptor that regulates both mitophagy and pexophagy.
• Pexophagy is essential for peroxisome quality control and is linked to neurological diseases and cancer.
• Key experimental models include yeast and mammalian cells with fluorescent reporters, ubiquitination assays, and CRISPR knockout of PEX genes.
• Dysregulated pexophagy contributes to peroxisomal disorders, neurodegeneration, and tumorigenesis, making it a therapeutic target.
Description
Pexophagy (GO:0000425) is a selective autophagy pathway that specifically targets peroxisomes for degradation via macroautophagy. Peroxisomes are essential organelles involved in lipid metabolism, reactive oxygen species (ROS) homeostasis, and biosynthesis of ether lipids and bile acids. The selective removal of peroxisomes by pexophagy is critical for maintaining organelle quality control and adapting to metabolic stress. In mammals, pexophagy is induced by hypoxia, ROS, and nutrient deprivation, and it requires the ubiquitination of peroxisomal membrane proteins such as PEX5 and PEX13. The autophagy receptor BNIP3L/NIX has been shown to regulate both mitophagy and pexophagy, highlighting crosstalk between selective autophagy pathways. Dysregulation of pexophagy is implicated in neurological diseases, including Alzheimer's and Parkinson's, as well as in cancer. Understanding the molecular mechanisms of pexophagy is therefore crucial for developing therapeutic strategies targeting peroxisome homeostasis.
pexophagy At A Glance
| GO ID | GO:0000425 |
|---|---|
| GO term | pexophagy |
| Ontology | biological_process |
| Synonym | macropexophagy |
| Major function | Selective degradation of peroxisomes via macroautophagy |
| Trigger signals | Hypoxia, ROS, nutrient deprivation, ubiquitination of PEX proteins |
| Key receptors | BNIP3L/NIX, p62/SQSTM1, NBR1 |
| Cellular outcome | Peroxisome removal, metabolic adaptation, quality control |
What Is GO:0000425?
Pexophagy (GO:0000425) is defined as the selective autophagy process in which a peroxisome is degraded by macroautophagy. This process involves the recognition of peroxisomes by autophagy receptors, their engulfment into autophagosomes, and subsequent fusion with lysosomes for degradation. Pexophagy is distinct from general autophagy because it specifically targets peroxisomes, often through ubiquitin-dependent signals on peroxisomal membrane proteins.
Why Is pexophagy Important in Cell Biology?
Pexophagy is critical for cellular homeostasis because it controls peroxisome abundance and quality, which directly impacts lipid metabolism, ROS detoxification, and energy balance. Defects in pexophagy lead to the accumulation of damaged peroxisomes, contributing to oxidative stress and neurodegeneration. Moreover, pexophagy is a model system for studying selective autophagy, providing insights into how cells target specific organelles for degradation. In cancer, pexophagy can either promote survival or induce cell death depending on context, making it a potential therapeutic target.
• Maintains peroxisome quality control by removing damaged or excess organelles.
• Regulates lipid metabolism and ROS homeostasis.
• Implicated in neurological diseases such as Alzheimer's and Parkinson's.
• Plays a dual role in cancer, either promoting survival or cell death.
• Serves as a model for selective autophagy mechanisms.
• Involves ubiquitin-dependent signaling via PEX5 and PEX13.
• Crosstalks with mitophagy through shared receptors like BNIP3L/NIX.
• Potential target for therapies aimed at peroxisomal disorders.
• Regulated by hypoxia and nutrient-sensing pathways.
• Key to understanding organelle-specific autophagy in health and disease.
What Happens During pexophagy?
Induction and Signaling
In simple terms: The cell receives a signal to start breaking down peroxisomes.
Pexophagy is induced by various stressors, including hypoxia, reactive oxygen species (ROS), and nutrient deprivation. In mammalian cells, hypoxia triggers the expression of BNIP3L/NIX, which acts as a selective autophagy receptor for both mitophagy and pexophagy. Additionally, ROS can cause damage to peroxisomes, leading to their ubiquitination and subsequent recognition by autophagy receptors. The induction phase involves signaling pathways such as mTOR inhibition, which activates autophagy.
Recognition and Ubiquitination
In simple terms: Damaged peroxisomes get tagged with ubiquitin so the cell knows to destroy them.
Peroxisomal membrane proteins, particularly PEX5 and PEX13, are ubiquitinated in response to stress. PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS. The ubiquitination of PEX5 serves as a signal for the recruitment of autophagy receptors such as p62/SQSTM1 and NBR1, which bind to ubiquitin and to LC3 on the autophagosome membrane. This step ensures selectivity for peroxisomes over other organelles.
Autophagosome Formation and Engulfment
In simple terms: The tagged peroxisome is wrapped in a membrane bubble called an autophagosome.
Once recognized, the peroxisome is engulfed by a double-membrane structure called the autophagosome. The autophagy receptor BNIP3L/NIX facilitates this process by linking the peroxisome to LC3 on the forming autophagosome. In yeast, the adaptor protein Atg30 recruits the autophagy machinery to peroxisomes. The autophagosome formation requires core autophagy proteins such as ATG5, ATG7, and LC3.
Fusion with Lysosomes and Degradation
In simple terms: The bubble carrying the peroxisome fuses with a lysosome, where the peroxisome is digested.
The autophagosome containing the peroxisome fuses with lysosomes to form an autolysosome, where the peroxisome is degraded by lysosomal hydrolases. This step releases breakdown products, including amino acids and lipids, back into the cytoplasm for reuse. The degradation process is essential for clearing damaged peroxisomes and maintaining cellular homeostasis.
Regulation by PEX13 and ROS
In simple terms: A protein called PEX13 acts as a brake on pexophagy by controlling ROS and PEX5 ubiquitination.
PEX13 is a peroxisomal membrane protein that prevents pexophagy by regulating the levels of ubiquitinated PEX5 and peroxisomal ROS. Loss of PEX13 leads to increased pexophagy, suggesting that PEX13 is a negative regulator. This regulation is critical for preventing excessive peroxisome degradation under normal conditions.
Key Genes Involved in GO:0000425 pexophagy
The following genes and proteins are central to the regulation and execution of pexophagy in yeast and mammals.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PEX5 | Peroxisomal matrix protein receptor; ubiquitination triggers pexophagy | Key marker for pexophagy induction; knockout leads to peroxisome loss |
| PEX13 | Peroxisomal membrane protein; prevents pexophagy by regulating ubiquitinated PEX5 and ROS | Negative regulator; knockout increases pexophagy |
| BNIP3L/NIX | Selective autophagy receptor for mitophagy and pexophagy | Links hypoxia to pexophagy; knockout impairs pexophagy |
| LC3 | Autophagosome membrane protein; binds autophagy receptors | Essential for autophagosome formation; used as marker |
| p62/SQSTM1 | Autophagy receptor; binds ubiquitinated proteins and LC3 | Mediates selective pexophagy; knockout reduces pexophagy |
| NBR1 | Autophagy receptor; similar to p62 | Contributes to pexophagy; redundant with p62 |
| ATG5 | Core autophagy protein; required for autophagosome formation | Knockout blocks pexophagy |
| ATG7 | Core autophagy protein; essential for LC3 lipidation | Knockout blocks pexophagy |
| ATG30 | Yeast peroxisome-specific autophagy adaptor | Recruits autophagy machinery to peroxisomes |
| PEX3 | Peroxisomal membrane protein; involved in pexophagy in yeast | Knockout affects pexophagy |
| PEX10 | Peroxisomal membrane protein; ubiquitination target | Potential regulator of pexophagy |
| PEX14 | Peroxisomal membrane protein; involved in pexophagy | Knockout affects peroxisome degradation |
| Stub1 | E3 ubiquitin ligase; mediates PEX5 ubiquitination | Regulates pexophagy; monitored in assays |
| mTOR | Kinase; inhibits autophagy under nutrient-rich conditions | Regulates pexophagy induction |
| HIF1A | Transcription factor; induces BNIP3L/NIX under hypoxia | Links hypoxia to pexophagy |
| MAP1LC3B | Autophagosome marker; used in pexophagy assays | Essential for autophagosome formation |
| SQSTM1 | Autophagy receptor; binds ubiquitin and LC3 | Mediates selective pexophagy |
| NBR1 | Autophagy receptor; binds ubiquitin and LC3 | Contributes to pexophagy |
How Is pexophagy Regulated?
Pexophagy is tightly regulated by multiple signaling pathways. Under nutrient-rich conditions, mTOR kinase inhibits autophagy, including pexophagy. Hypoxia induces the expression of BNIP3L/NIX through HIF1A, which then promotes pexophagy. Reactive oxygen species (ROS) generated by peroxisomes can trigger pexophagy by causing oxidative damage and ubiquitination of peroxisomal proteins. PEX13 acts as a negative regulator by controlling ROS levels and ubiquitinated PEX5. Additionally, the ubiquitin-proteasome system and autophagy receptors such as p62 and NBR1 fine-tune the selectivity and extent of pexophagy. In yeast, Atg30 is phosphorylated to regulate pexophagy under different metabolic conditions.
pexophagy and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PEX5 | Peroxisome biogenesis disorders (Zellweger spectrum) | Knockout in human fibroblasts; pexophagy reporter |
| PEX13 | Neurological dysfunction; pexophagy regulation | Knockout in HeLa cells; ubiquitination assays |
| BNIP3L/NIX | Hypoxia-induced pexophagy; cancer and neurodegeneration | Knockout in mouse embryonic fibroblasts; hypoxia treatment |
| ATG5 | Autophagy deficiency; neurodegenerative diseases | Knockout in neurons; LC3 flux assays |
| SQSTM1 | Pagetic bone disease and ALS; autophagy receptor | Knockout in osteoclasts; pexophagy induction |
Pexophagy in Neurological Diseases
Dysregulation of pexophagy has been implicated in neurological diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS). In these conditions, impaired pexophagy leads to the accumulation of damaged peroxisomes, contributing to oxidative stress and neuronal death. For example, mutations in peroxisomal genes that affect pexophagy can cause peroxisomal disorders with severe neurological phenotypes. Targeting pexophagy may offer therapeutic benefits by restoring peroxisome function.
Pexophagy in Cancer
Pexophagy plays a dual role in cancer. In some contexts, pexophagy promotes tumor cell survival by removing damaged peroxisomes and maintaining metabolic homeostasis. In other contexts, excessive pexophagy can induce cell death, making it a potential tumor suppressor mechanism. The role of pexophagy in cancer is context-dependent and influenced by factors such as hypoxia and ROS levels. Understanding how pexophagy is regulated in cancer cells could lead to novel therapeutic strategies.
Pexophagy in Metabolic Disorders
Peroxisomes are critical for lipid metabolism, and defects in pexophagy can lead to metabolic disorders. For instance, impaired pexophagy may contribute to the accumulation of very-long-chain fatty acids, which are toxic to cells. In addition, pexophagy is important for adapting to fasting and high-fat diets by regulating peroxisome abundance. Research into pexophagy in metabolic tissues such as liver and adipose could reveal new targets for metabolic diseases.
From pexophagy-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X regulate pexophagy? | CRISPR knockout of gene X in HeLa or HEK293 cells, followed by pexophagy reporter assay |
| Does mutation in PEX13 affect pexophagy? | Point mutation knock-in of PEX13 variants in patient fibroblasts |
| Can a tag be used to track peroxisomes? | Knock-in of fluorescent tag (e.g., GFP) into PEX14 locus |
| Does overexpression of BNIP3L/NIX induce pexophagy? | Overexpression of BNIP3L/NIX in mammalian cells under hypoxia |
| What is the role of ubiquitination in pexophagy? | Knockout of Stub1 or PEX5 ubiquitination sites; ubiquitin pulldown |
| How does pexophagy affect lipid metabolism? | Knockout of ATG5 in hepatocytes; lipidomics |
How to Study the pexophagy Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Fluorescence microscopy | Colocalization of peroxisomes and autophagosomes | Monitoring pexophagy induction |
| Western blot | Degradation of peroxisomal proteins | Quantifying pexophagy flux |
| Ubiquitination assay | Ubiquitination of PEX5/PEX13 | Studying signaling triggers |
| Electron microscopy | Ultrastructure of peroxisomes in autophagosomes | Confirming pexophagy morphology |
| CRISPR knockout | Loss of gene function | Identifying essential pexophagy genes |
| siRNA knockdown | Transient gene silencing | Validating pexophagy regulators |
| Live-cell imaging | Real-time peroxisome degradation | Tracking pexophagy dynamics |
| Proteomics | Changes in peroxisomal protein abundance | Global analysis of pexophagy |
Fluorescence Microscopy and Reporter Assays
Pexophagy can be monitored using fluorescent reporters that label peroxisomes and autophagosomes. For example, cells expressing GFP-PTS1 (peroxisomal marker) and mCherry-LC3 (autophagosome marker) allow visualization of peroxisome engulfment by autophagosomes. Time-lapse imaging can track the degradation of peroxisomes in real time. This method is widely used to assess pexophagy induction and flux.
Western Blotting and Ubiquitination Assays
Western blotting can detect the degradation of peroxisomal proteins such as PEX5 and PEX13 during pexophagy. Ubiquitination assays, including immunoprecipitation followed by ubiquitin immunoblotting, reveal the ubiquitination status of PEX proteins. These methods are essential for studying the molecular triggers of pexophagy.
Electron Microscopy
Transmission electron microscopy (TEM) provides ultrastructural evidence of peroxisomes within autophagosomes or autolysosomes. This technique confirms the morphological hallmarks of pexophagy, such as double-membrane structures surrounding peroxisomes. TEM is often used as a gold standard for validating pexophagy.
Genetic Knockout and Knockdown
CRISPR/Cas9-mediated knockout of core autophagy genes (e.g., ATG5, ATG7) or peroxisomal genes (e.g., PEX5, PEX13) is used to dissect pexophagy pathways. siRNA knockdown provides a complementary approach for transient gene silencing. These genetic tools help establish causality between specific genes and pexophagy.
How CRISPR Can Be Used to Study GO:0000425 pexophagy
Knockout
CRISPR knockout of genes such as PEX5, PEX13, ATG5, or BNIP3L/NIX is used to determine their necessity in pexophagy. For example, PEX13 knockout increases pexophagy, confirming its role as a negative regulator. Knockout of ATG5 blocks autophagosome formation and thus pexophagy. These models are essential for establishing causal relationships.
Point Mutation
Point mutations can be introduced into peroxisomal genes to mimic disease-associated variants or to disrupt specific ubiquitination sites. For instance, mutation of lysine residues in PEX5 can prevent its ubiquitination and block pexophagy. Such models help dissect the molecular details of pexophagy signaling.
Knock-in
Knock-in of fluorescent tags (e.g., GFP, mCherry) into endogenous peroxisomal genes such as PEX14 allows real-time tracking of peroxisomes during pexophagy. Tagged knock-in models are valuable for imaging and biochemical studies. Additionally, knock-in of disease-relevant mutations can model peroxisomal disorders.
Overexpression
Overexpression of BNIP3L/NIX or other autophagy receptors induces pexophagy even under nutrient-rich conditions. Overexpression of PEX13 can suppress pexophagy, further confirming its regulatory role. These models are useful for gain-of-function studies and for testing therapeutic interventions.
How EDITGENE Supports pexophagy Research
Researchers studying pexophagy-related genes often need to determine whether a candidate gene is causally involved in peroxisome degradation, how specific mutations affect pexophagy flux, or whether a gene product can be tracked in live cells. EDITGENE provides a comprehensive suite of CRISPR-based services to address these questions with precision and reproducibility.
Contact EDITGENE today to design your custom CRISPR model for pexophagy research.
Frequently Asked Questions About pexophagy
What is pexophagy?
Pexophagy (GO:0000425) is the selective autophagy process in which a peroxisome is degraded by macroautophagy.
What genes are involved in pexophagy?
Key genes include PEX5, PEX13, BNIP3L/NIX, ATG5, ATG7, LC3, p62/SQSTM1, and NBR1.
How is pexophagy induced?
Pexophagy is induced by hypoxia, reactive oxygen species, nutrient deprivation, and ubiquitination of peroxisomal proteins such as PEX5.
What is the role of PEX13 in pexophagy?
PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS.
How does BNIP3L/NIX regulate pexophagy?
BNIP3L/NIX acts as a selective autophagy receptor that links peroxisomes to LC3 on the autophagosome, promoting pexophagy under hypoxia.
What diseases are associated with pexophagy?
Pexophagy dysregulation is linked to neurological diseases such as Alzheimer's and Parkinson's, as well as cancer and metabolic disorders.
How can I study pexophagy in the lab?
Common methods include fluorescence microscopy with peroxisome and autophagosome markers, western blotting for peroxisomal protein degradation, and electron microscopy.
What is the difference between pexophagy and mitophagy?
Pexophagy specifically targets peroxisomes, while mitophagy targets mitochondria; however, they share receptors such as BNIP3L/NIX.
Can CRISPR be used to study pexophagy?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are powerful tools to dissect pexophagy pathways.
What is the GO term for pexophagy?
The Gene Ontology term for pexophagy is GO:0000425, under biological_process.
Conclusion
Pexophagy (GO:0000425) is a vital selective autophagy pathway that maintains peroxisome homeostasis and protects cells from oxidative stress. Its dysregulation is implicated in neurological diseases, cancer, and metabolic disorders, making it an important area of research. Advances in CRISPR-based models and imaging techniques continue to unravel the molecular mechanisms of pexophagy, offering potential therapeutic targets. EDITGENE provides comprehensive services to support pexophagy research, from knockout and knock-in models to library screening and bioinformatics.
References
- 1. Bajdzienko J et al.. 2024. Mammalian pexophagy at a glance.. J Cell Sci 137(9) PMID: 38752931
- 2. Demers ND et al.. 2023. PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS.. Autophagy 19(6):1781-1802 PMID: 36541703
- 3. Germain K et al.. 2020. Pexophagy: A Model for Selective Autophagy.. Int J Mol Sci 21(2) PMID: 31963200
- 4. Xu W et al.. 2024. Peroxisome and pexophagy in neurological diseases.. Fundam Res 4(6):1389-1397 PMID: 39734532
- 5. Wilhelm LP et al.. 2022. BNIP3L/NIX regulates both mitophagy and pexophagy.. EMBO J 41(24):e111115 PMID: 36215693
- 6. Li J et al.. 2021. Mechanisms and Functions of Pexophagy in Mammalian Cells.. Cells 10(5) PMID: 34063724
- 7. Chen BH et al.. 2023. Monitoring Stub1-Mediated Pexophagy.. J Vis Exp PMID: 37246878
- 8. Eberhart T et al.. 2018. Pexophagy in yeast and mammals: an update on mysteries.. Histochem Cell Biol 150(5):473-488 PMID: 30238155
