GO:0000285 1-phosphatidylinositol-3-phosphate 5-kinase activity

1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285) is a molecular function that catalyzes the phosphorylation of phosphatidylinositol 3-phosphate (PI3P) at the D-5 position of the inositol ring to produce phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). This lipid kinase activity is highly conserved across eukaryotes and is central to the regulation of endosomal dynamics, membrane trafficking, and cellular stress responses. In humans, the principal enzyme carrying this activity is PIKfyve, while in budding yeast it is known as Fab1. The reaction consumes ATP and releases ADP and a proton, and its product PI(3,5)P2 serves as a low-abundance but potent signaling lipid that recruits effector proteins to endosomal membranes. Researchers study GO:0000285 because perturbations in this activity have been linked to diverse physiological and pathological outcomes. For example, inhibition of PIKfyve with apilimod promotes an adipocyte-like vascular smooth muscle cell phenotype and prevents arterial calcification, suggesting a role in vascular biology. In yeast, the Fab1 kinase is required for nitrogen-regulated mitotic commitment and cell size control, connecting lipid signaling to cell cycle progression. Moreover, targeting PIKfyve with inhibitors can reverse inflammatory and neuropathic pain by modulating sodium channels Nav1.7 and Nav1.8. In plants, omics studies of cowpea under root dehydration have highlighted the importance of inositols and their derivatives, including phosphatidylinositol phosphates, in stress responses. Given its broad impact, GO:0000285 is a focal point for research in cell biology, neuroscience, and plant physiology. Understanding its regulation and downstream effects requires precise genetic and pharmacological tools, many of which are now available through CRISPR-based cell models and high-throughput screening.

According to the Gene Ontology, GO:0000285 is defined as the catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + H+. In simpler terms, it is the enzyme activity that adds a phosphate group to the fifth position of the inositol ring of phosphatidylinositol 3-phosphate, using ATP as the phosphate donor. This activity is also known as phosphatidylinositol 3-phosphate 5-kinase activity or type III PIP kinase activity. The reaction is a key step in the generation of phosphatidylinositol 3,5-bisphosphate, a signaling lipid involved in endosomal trafficking and cellular stress responses.

GO:0000285 is important because the product of this reaction, PI(3,5)P2, is a critical regulator of endosomal membrane dynamics, ion transport, and cell signaling. Dysregulation of this activity has been implicated in vascular calcification, pain sensation, and cell cycle control, making it a potential therapeutic target. Moreover, its evolutionary conservation from yeast to plants underscores its fundamental role in cellular physiology.

The following genes and proteins are directly involved in or regulate 1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285) across model organisms.

The activity of 1-phosphatidylinositol-3-phosphate 5-kinase is tightly regulated at multiple levels. In yeast, Fab1 is activated in response to nitrogen availability to control mitotic commitment and cell size, involving the Vac14-Fig4 complex. In mammals, PIKfyve activity can be modulated by growth factor signaling and is inhibited by small molecules such as apilimod, which alters vascular smooth muscle cell phenotype. Additionally, cellular stress and ion channel activity can influence the downstream effects of PI(3,5)P2, as seen in pain pathways where PIKfyve inhibition reverses neuropathic pain. Plant inositol signaling also responds to dehydration stress, suggesting conserved regulatory mechanisms.

Inhibition of PIKfyve with apilimod promotes an adipocyte-like vascular smooth muscle cell phenotype and prevents arterial calcification, indicating that GO:0000285 activity contributes to vascular pathology. This suggests that modulating this lipid kinase could be a therapeutic strategy for cardiovascular calcification.

Targeting PIKfyve with inhibitors reverses inflammatory and neuropathic pain by modulating Nav1.7 and Nav1.8 sodium channels. This links GO:0000285 activity to pain signaling and highlights PIKfyve as a potential analgesic target.

In yeast, Fab1 phosphatidylinositol-3-phosphate 5-kinase is required for nitrogen-regulated mitotic commitment and cell size control, suggesting that loss of this activity could lead to cell cycle defects. This has implications for understanding growth-related diseases.

Omics studies in cowpea under root dehydration reveal the importance of inositols and their derivatives, including phosphatidylinositol phosphates, in stress adaptation. This indicates a role for GO:0000285 in plant physiology and crop resilience.

In vitro kinase assays using recombinant PIKfyve or Fab1 and radiolabeled ATP can directly measure the conversion of PI3P to PI(3,5)P2, providing kinetic parameters.

Genome-wide CRISPR knockout screens can identify genes that modify sensitivity to PIKfyve inhibitors like apilimod, revealing pathways that interact with GO:0000285.

Fluorescently tagged PI(3,5)P2 probes or PIKFYVE-GFP knock-in cells allow visualization of endosomal dynamics and lipid distribution in real time.

Transcriptomic and metabolomic analyses of cowpea under root dehydration have highlighted inositol derivatives, offering a systems view of GO:0000285-related pathways.

Researchers studying 1-phosphatidylinositol-3-phosphate 5-kinase activity-related genes often need to determine whether a candidate gene is causally involved in lipid signaling, endosomal trafficking, or disease phenotypes. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research, from gene knockout to precise point mutations and knock-in models.

1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285) is a fundamental enzymatic function that generates the signaling lipid PI(3,5)P2, with critical roles in endosomal trafficking, cell cycle control, vascular biology, and pain signaling. Its conservation across eukaryotes and involvement in human disease make it a compelling target for both basic and translational research. Leveraging CRISPR-based models and high-throughput screening will continue to unravel its mechanisms and therapeutic potential.