GO:0102091 phosphatidylinositol-5-phosphate phosphatase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0102091 describes the enzymatic removal of the 5-phosphate from phosphatidylinositol-5-phosphate (PI5P), converting it to phosphatidylinositol (PI).
• This activity is carried out by myotubularin-related phosphatases and other 5-phosphatases, including OCRL and TMEM55A [2,4,7].
• PI5P, the substrate of this reaction, is a low-abundance phosphoinositide with emerging roles in nuclear signaling, actin dynamics, and insulin response [6,5].
• Dysregulation of PI5P metabolism is linked to Lowe syndrome, cancer, and metabolic disorders such as diabetes [7,4].
• Studying GO:0102091 requires precise measurement of phosphoinositide levels, often using radiolabeled substrates, mass spectrometry, or fluorescent probes [2,6].
• CRISPR-based models (knockout, knock-in, overexpression) are powerful tools to dissect the physiological roles of enzymes with this activity [4,7].
Description
Phosphatidylinositol-5-phosphate phosphatase activity (GO:0102091) is a molecular function that catalyzes the hydrolysis of phosphatidylinositol-5-phosphate (PI5P) to phosphatidylinositol (PI) and inorganic phosphate. This reaction is a key step in phosphoinositide metabolism, influencing the cellular levels of PI5P and its downstream derivatives. PI5P itself is a minor but potent signaling lipid that has been implicated in diverse processes, from nuclear events to cytoskeletal reorganization. The enzyme activity defined by GO:0102091 is therefore central to controlling the abundance and duration of PI5P signals. Researchers study this activity to understand how cells regulate phosphoinositide pools and how perturbations contribute to disease. For example, mutations in the OCRL gene, which encodes a 5-phosphatase with activity toward PI5P, cause Lowe syndrome, a rare disorder affecting the eyes, brain, and kidneys. Moreover, the myotubularin family of phosphatases, which includes enzymes that dephosphorylate PI5P, are frequently mutated in neuromuscular diseases and cancers. Thus, GO:0102091 represents a critical node in lipid signaling with broad physiological and pathological relevance.
phosphatidylinositol-5-phosphate phosphatase activity At A Glance
| GO ID | GO:0102091 |
|---|---|
| GO term | phosphatidylinositol-5-phosphate phosphatase activity |
| Ontology | molecular_function |
| Synonym | phosphatidylinositol-5-phosphate 5-phosphatase activity |
| Definition | Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate. |
| Major function | Dephosphorylation of phosphatidylinositol-5-phosphate to phosphatidylinositol |
| Substrate | Phosphatidylinositol-5-phosphate (PI5P) |
| Product | Phosphatidylinositol (PI) and phosphate |
| Cellular location | Cytosol, nucleus, Golgi, and other membrane compartments [6,8] |
What Is GO:0102091?
GO:0102091 is defined as the catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate. In simpler terms, it is the enzymatic removal of the phosphate group at the 5-position of the inositol ring of phosphatidylinositol-5-phosphate, yielding phosphatidylinositol and free phosphate.
Why Is phosphatidylinositol-5-phosphate phosphatase activity Important in Cell Biology?
GO:0102091 is important because it directly controls the cellular concentration of phosphatidylinositol-5-phosphate (PI5P), a lipid messenger that regulates diverse processes including insulin signaling, actin dynamics, and gene expression [5,6]. By removing the 5-phosphate, enzymes with this activity terminate PI5P signals and generate phosphatidylinositol, which can be further phosphorylated to other phosphoinositides. Dysregulation of this activity has been linked to human diseases such as Lowe syndrome, cancer, and diabetes, making it a potential therapeutic target [7,4].
• Regulates PI5P levels, a lipid involved in nuclear signaling and chromatin remodeling.
• Controls insulin signaling by modulating PI-3,4,5-trisphosphate degradation.
• Essential for actin dynamics during bacterial infection and cell motility.
• Mutations in OCRL, a 5-phosphatase, cause Lowe syndrome.
• TMEM55A-mediated PI5P signaling regulates glucagon secretion in alpha cells.
• Myotubularin-related phosphatases with this activity are implicated in neuromuscular diseases.
• Plays a role in allelic exclusion of variant surface glycoprotein genes in Trypanosomes.
• Potential target for cancer therapy due to PI5P role in cell proliferation.
• Involved in Golgi membrane trafficking through Golgi-localized 5-phosphatases.
• Provides a mechanism to fine-tune phosphoinositide pools for cellular homeostasis.
Molecular Mechanism of phosphatidylinositol-5-phosphate phosphatase activity
Substrate recognition and binding
In simple terms: The enzyme grabs PI5P and positions it for phosphate removal.
Enzymes with phosphatidylinositol-5-phosphate phosphatase activity, such as myotubularins and OCRL, contain a conserved catalytic domain that specifically binds the inositol headgroup of PI5P. The substrate is presented in a membrane context, and the enzyme's active site accommodates the 5-phosphate for hydrolysis [2,7].
Catalytic mechanism
In simple terms: A water molecule attacks the phosphate, breaking it off.
The catalytic mechanism involves a nucleophilic water molecule that attacks the phosphorus atom of the 5-phosphate, leading to the release of inorganic phosphate and the formation of phosphatidylinositol. This reaction is dependent on conserved residues in the phosphatase domain, as shown for myotubularin-related proteins.
Cofactors and ion requirements
In simple terms: Some enzymes need metal ions to work.
Many phosphatidylinositol 5-phosphatases require magnesium or other divalent cations for optimal activity, although the exact cofactor requirements can vary among family members. The active site often coordinates a metal ion that stabilizes the transition state during catalysis.
Regulation of enzyme activity
In simple terms: The enzyme's activity can be turned on or off by other signals.
The activity of these phosphatases can be regulated by post-translational modifications, protein-protein interactions, and subcellular localization. For instance, OCRL is recruited to specific membrane compartments during infection, where it modulates actin dynamics. Additionally, PI5P levels themselves can influence the recruitment and activity of these enzymes, creating feedback loops.
Key Genes Involved in GO:0102091 phosphatidylinositol-5-phosphate phosphatase activity
The following genes encode proteins that exhibit phosphatidylinositol-5-phosphate phosphatase activity or are directly involved in its regulation.
| Gene | Major Role | Research Relevance |
|---|---|---|
| MTM1 | Myotubularin 1, a lipid phosphatase that dephosphorylates PI5P and PI3P | Mutations cause X-linked myotubular myopathy; model for studying phosphatase function |
| MTMR2 | Myotubularin-related protein 2, acts on PI5P and PI3P | Linked to Charcot-Marie-Tooth disease type 4B1 |
| OCRL | Oculocerebrorenal syndrome of Lowe protein, 5-phosphatase acting on PI5P and PI(4,5)P2 | Mutations cause Lowe syndrome; regulates actin dynamics |
| TMEM55A | Transmembrane protein 55A, a PI5P 5-phosphatase | Regulates glucagon secretion in alpha cells; potential diabetes target |
| TMEM55B | Transmembrane protein 55B, similar to TMEM55A | Less studied; may have overlapping functions with TMEM55A |
| INPP5B | Inositol polyphosphate-5-phosphatase B, acts on PI5P | Involved in Golgi function and membrane trafficking |
| INPP5E | Inositol polyphosphate-5-phosphatase E | Mutations cause Joubert syndrome; role in cilia |
| SYNJ1 | Synaptojanin 1, a polyphosphoinositide phosphatase | Implicated in Parkinson's disease and synaptic vesicle recycling |
| SYNJ2 | Synaptojanin 2 | Related to SYNJ1, involved in endocytosis |
| FIG4 | FIG4 phosphoinositide 5-phosphatase | Mutations cause Charcot-Marie-Tooth disease type 4J |
| PIP4K2A | Phosphatidylinositol-5-phosphate 4-kinase type 2 alpha | Phosphorylates PI5P to PI(4,5)P2; regulates insulin signaling |
| PIP4K2B | Phosphatidylinositol-5-phosphate 4-kinase type 2 beta | Similar to PIP4K2A; involved in metabolic regulation |
| PIP4K2C | Phosphatidylinositol-5-phosphate 4-kinase type 2 gamma | Accumulates at spindle pole; prevents microtubule depolymerization |
| PIKFYVE | Phosphatidylinositol-3-phosphate 5-kinase | Synthesizes PI(3,5)P2; indirectly affects PI5P levels |
| MTMR3 | Myotubularin-related protein 3 | Acts on PI5P and PI3P; involved in autophagy |
| MTMR4 | Myotubularin-related protein 4 | Regulates PI5P; role in TGF-beta signaling |
| MTMR6 | Myotubularin-related protein 6 | Acts on PI5P; involved in apoptosis |
| MTMR7 | Myotubularin-related protein 7 | Acts on PI5P; may regulate neuronal function |
How Is phosphatidylinositol-5-phosphate phosphatase activity Regulated?
The activity of phosphatidylinositol-5-phosphate phosphatases is regulated at multiple levels. Subcellular localization determines substrate access; for example, OCRL is recruited to sites of Listeria infection to modulate actin. Post-translational modifications such as phosphorylation can alter enzyme activity. Additionally, the availability of PI5P itself, controlled by synthesis via PIP4K and PIKFYVE, influences the flux through this phosphatase reaction [5,6]. Feedback mechanisms may exist where changes in PI5P levels affect the activity or localization of the phosphatases.
phosphatidylinositol-5-phosphate phosphatase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| OCRL | Lowe syndrome | Ocrl knockout mouse, patient-derived fibroblasts, CRISPR KO in cell lines |
| TMEM55A | Diabetes, glucagon secretion | Tmem55a knockout mouse, alpha cell lines, CRISPR KO |
| MTM1 | X-linked myotubular myopathy | Mtm1 knockout mouse, CRISPR KO in myoblasts |
| MTMR2 | Charcot-Marie-Tooth disease type 4B1 | Mtmr2 knockout mouse, CRISPR KO in Schwann cells |
| PIP4K2A | Insulin resistance, cancer | Pip4k2a knockout mouse, CRISPR KO in adipocytes |
Lowe syndrome
Mutations in OCRL, which encodes a phosphatidylinositol 5-phosphatase, cause Lowe syndrome, an X-linked disorder characterized by congenital cataracts, intellectual disability, and renal Fanconi syndrome. OCRL controls actin dynamics during early steps of Listeria monocytogenes infection, and its loss leads to cytoskeletal defects.
Diabetes and metabolic disorders
TMEM55A-mediated PI5P signaling regulates alpha cell actin depolymerization and glucagon secretion, suggesting a role in glucose homeostasis. Dysregulation of this pathway may contribute to diabetes. Additionally, the PI5P 4-kinase type II enzyme controls insulin signaling by regulating PI-3,4,5-trisphosphate degradation, linking PI5P metabolism to insulin sensitivity.
Cancer
PI5P and its metabolizing enzymes are emerging as players in cancer. Nuclear PI5P has been implicated in gene regulation and chromatin remodeling, and altered expression of 5-phosphatases may affect tumor growth. Myotubularin-related phosphatases can act as tumor suppressors in some contexts.
Neuromuscular diseases
Myotubularin (MTM1) mutations cause X-linked myotubular myopathy, and MTMR2 mutations are linked to Charcot-Marie-Tooth disease, highlighting the importance of PI5P dephosphorylation in muscle and nerve function.
From phosphatidylinositol-5-phosphate phosphatase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the effect of losing phosphatidylinositol-5-phosphate phosphatase activity on PI5P levels? | Knockout of specific phosphatase gene (e.g., OCRL, TMEM55A) using CRISPR [4,7] |
| How does a disease-associated point mutation affect enzyme activity? | Point mutation knock-in using CRISPR to introduce the mutation |
| What are the interacting partners of the phosphatase? | Tagged knock-in (e.g., GFP or HA tag) followed by immunoprecipitation |
| What happens when the phosphatase is overexpressed? | Overexpression via lentiviral or CRISPR activation |
| How does the phosphatase regulate actin dynamics? | Knockout or overexpression in combination with live-cell imaging of actin |
| Does the phosphatase affect insulin signaling? | Knockout in insulin-responsive cells (e.g., adipocytes) and measure Akt phosphorylation |
How to Study the phosphatidylinositol-5-phosphate phosphatase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Radiolabeled substrate assay | Phosphatase activity | In vitro enzyme kinetics |
| Malachite green assay | Released phosphate | High-throughput screening of inhibitors |
| Mass spectrometry lipidomics | PI5P and other phosphoinositide levels | Quantifying changes in knockout cells |
| Fluorescent PI5P probe imaging | Subcellular localization of PI5P | Live-cell imaging of actin dynamics |
| CRISPR knockout screen | Genes affecting PI5P levels | Identifying novel regulators |
| Co-immunoprecipitation | Protein-protein interactions | Finding binding partners of phosphatases |
| Western blot | Protein expression and phosphorylation | Validating knockout or overexpression |
| qPCR | mRNA expression | Checking gene expression changes |
Measuring phosphatase activity
Enzymatic activity of phosphatidylinositol-5-phosphate phosphatases can be measured using radiolabeled PI5P as a substrate, followed by separation of products by thin-layer chromatography or HPLC. Alternatively, malachite green assays can detect released phosphate.
Quantifying phosphoinositides
Mass spectrometry-based lipidomics allows quantification of PI5P and other phosphoinositides from cell extracts. This is crucial to assess the impact of genetic manipulations on lipid pools.
Imaging phosphoinositide dynamics
Genetically encoded fluorescent probes, such as GFP-tagged PI5P-binding domains, enable real-time visualization of PI5P distribution in live cells. This helps link phosphatase activity to cellular processes like actin remodeling.
Genetic screens and CRISPR libraries
CRISPR knockout libraries can be used to identify genes that modulate PI5P levels or phosphatase activity. For example, a genome-wide screen could reveal synthetic lethal interactions with phosphatase loss.
How CRISPR Can Be Used to Study GO:0102091 phosphatidylinositol-5-phosphate phosphatase activity
Knockout
CRISPR knockout of genes encoding phosphatidylinositol-5-phosphate phosphatases (e.g., OCRL, TMEM55A) allows researchers to study the consequences of losing enzyme activity on PI5P levels and downstream processes. For instance, TMEM55A knockout in alpha cells affects glucagon secretion, and OCRL knockout impairs actin dynamics.
Point Mutation
Introducing disease-associated point mutations (e.g., in OCRL) using CRISPR base editing or homology-directed repair can reveal how specific amino acid changes affect phosphatase activity and cellular function. This is particularly useful for modeling Lowe syndrome mutations.
Knock-in
Tagged knock-in (e.g., GFP or HA) of phosphatase genes enables visualization and purification of the enzyme for interaction studies. This approach can also be used to introduce regulatory elements for conditional expression.
Overexpression
CRISPR activation (CRISPRa) or lentiviral overexpression of phosphatases can be used to increase enzyme levels, allowing study of gain-of-function effects on PI5P signaling and cellular phenotypes such as insulin sensitivity.
How EDITGENE Supports phosphatidylinositol-5-phosphate phosphatase activity Research
Researchers studying phosphatidylinositol-5-phosphate phosphatase activity-related genes often need to determine whether a candidate gene is causally involved in a specific cellular process or disease. This requires precise genetic manipulation, which can be achieved through CRISPR-based technologies. EDITGENE provides a comprehensive suite of services to support such investigations, from knockout to knock-in and overexpression models.
Contact EDITGENE today to design your custom CRISPR model for phosphatidylinositol-5-phosphate phosphatase activity research.
Frequently Asked Questions About phosphatidylinositol-5-phosphate phosphatase activity
What is phosphatidylinositol-5-phosphate phosphatase activity?
It is the enzymatic removal of the 5-phosphate from phosphatidylinositol-5-phosphate (PI5P), producing phosphatidylinositol and phosphate, as defined by GO:0102091.
What genes are involved in phosphatidylinositol-5-phosphate phosphatase activity?
Genes include OCRL, MTM1, MTMR2, TMEM55A, TMEM55B, INPP5B, and others that encode 5-phosphatases acting on PI5P [2,4,7].
What diseases are associated with phosphatidylinositol-5-phosphate phosphatase activity?
Mutations in OCRL cause Lowe syndrome, MTM1 mutations cause myotubular myopathy, and TMEM55A is linked to diabetes [7,4,2].
How is phosphatidylinositol-5-phosphate phosphatase activity measured?
It can be measured using radiolabeled PI5P substrate assays, malachite green phosphate detection, or mass spectrometry of lipid products [2,6].
What is the role of PI5P in the cell?
PI5P is a signaling lipid involved in nuclear processes, actin dynamics, and insulin signaling [6,5].
Which enzyme removes the 5-phosphate from PI5P?
Myotubularin-related phosphatases and OCRL are examples of enzymes with this activity [2,7].
How does phosphatidylinositol-5-phosphate phosphatase activity affect insulin signaling?
By regulating PI5P levels, these enzymes indirectly influence PI-3,4,5-trisphosphate degradation and insulin sensitivity.
Can CRISPR be used to study phosphatidylinositol-5-phosphate phosphatase activity?
Yes, CRISPR knockout, knock-in, and overexpression models are widely used to dissect the function of these enzymes [4,7].
What is the subcellular localization of phosphatidylinositol-5-phosphate phosphatases?
They can localize to the cytosol, nucleus, Golgi, and other membranes depending on the specific enzyme [6,8].
What are the synonyms for phosphatidylinositol-5-phosphate phosphatase activity?
The synonym is phosphatidylinositol-5-phosphate 5-phosphatase activity.
Conclusion
Phosphatidylinositol-5-phosphate phosphatase activity (GO:0102091) is a fundamental enzymatic function that controls the cellular levels of PI5P, a critical signaling lipid. Through the action of myotubularin-related proteins, OCRL, TMEM55A, and other phosphatases, this activity impacts diverse processes including insulin signaling, actin dynamics, and gene expression. Dysregulation of these enzymes is linked to Lowe syndrome, diabetes, cancer, and neuromuscular disorders. Continued research using CRISPR-based models and advanced lipidomics will further illuminate the therapeutic potential of targeting this activity.
References
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- 2. Schaletzky J et al.. 2003. Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases.. Curr Biol 13(6):504-9 PMID: 12646134
- 3. Cestari I et al.. 2019. Nuclear Phosphatidylinositol 5-Phosphatase Is Essential for Allelic Exclusion of Variant Surface Glycoprotein Genes in Trypanosomes.. Mol Cell Biol 39(3) PMID: 30420356
- 4. Liu X et al.. 2025. TMEM55A-mediated PI5P signalling regulates alpha cell actin depolymerisation and glucagon secretion.. Diabetologia 68(7):1509-1523 PMID: 40140059
- 5. Carricaburu V et al.. 2003. The phosphatidylinositol (PI)-5-phosphate 4-kinase type II enzyme controls insulin signaling by regulating PI-3,4,5-trisphosphate degradation.. Proc Natl Acad Sci U S A 100(17):9867-72 PMID: 12897244
- 6. Poli A et al.. 2019. Phosphatidylinositol 5 Phosphate (PI5P): From Behind the Scenes to the Front (Nuclear) Stage.. Int J Mol Sci 20(9) PMID: 31035587
- 7. Kühbacher A et al.. 2012. Phosphatidylinositol 5-phosphatase oculocerebrorenal syndrome of Lowe protein (OCRL) controls actin dynamics during early steps of Listeria monocytogenes infection.. J Biol Chem 287(16):13128-36 PMID: 22351770
- 8. Merlot S et al.. 2003. A PTEN-related 5-phosphatidylinositol phosphatase localized in the Golgi.. J Biol Chem 278(41):39866-73 PMID: 12878591
