Creatine kinase muscle type specifically interacts with saturated fatty acid- and/or monounsaturated fatty acid-containing phosphatidic acids

Distinct regions of Praja-1 E3 ubiquitin-protein ligase selectively bind to docosahexaenoic acid-containing phosphatidic acid and diacylglycerol kinase δ

1-Stearoyl-2-docosahexaenoyl (18:0/22:6)-phosphatidic acid (PA) interacts with and activates Praja-1 E3 ubiquitin-protein ligase (full length: 615 aa) to ubiquitinate and degrade the serotonin transporter (SERT). SERT modulates serotonergic system activity and is a therapeutic target for depression, autism, obsessive-compulsive disorder, schizophrenia and Alzheimer's disease. Moreover, diacylglycerol kinase (DGK) δ2 (full length: 1214 aa) interacts with Praja-1 in addition to SERT and generates 18:0/22:6-PA, which binds and activates Praja-1. In the present study, we investigated the interaction of Praja-1 with 18:0/22:6-PA and DGKδ2 in more detail. We first found that the N-terminal one-third region (aa 1-224) of Praja-1 bound to 18:0/22:6-PA and that Lys141 in the region was critical for binding to 18:0/22:6-PA. In contrast, the C-terminal catalytic domain of Praja-1 (aa 446-615) interacted with DGKδ2. Additionally, the N-terminal half of the catalytic domain (aa 309-466) of DGKδ2 intensely bound to Praja-1. Moreover, the N-terminal region containing the pleckstrin homology and C1 domains (aa 1-308) and the C-terminal half of the catalytic domain (aa 762-939) of DGKδ2 weakly associated with Praja-1. Taken together, these results reveal new functions of the N-terminal (aa 1-224) and C-terminal (aa 446-615) regions of Praja-1 and the N-terminal half of the catalytic region (aa 309-466) of DGKδ2 as regulatory domains. Moreover, it is likely that the DGKδ2-Praja-1-SERT heterotrimer proximally arranges the 18:0/22:6-PA-producing catalytic domain of DGKδ2, the 18:0/22:6-PA-binding regulatory domain of Praja-1, the ubiquitin-protein ligase catalytic domain of Praja-1 and the ubiquitination acceptor site-containing SERT C-terminal region.

Saturated fatty acid- and/or monounsaturated fatty acid-containing phosphatidic acids selectively interact with heat shock protein 27

Diacylglycerol kinase (DGK) α, which is a key enzyme in the progression of cancer and, in contrast, in T-cell activity attenuation, preferentially produces saturated fatty acid (SFA)- and/or monounsaturated fatty acid (MUFA)-containing phosphatidic acids (PAs), such as 16:0/16:0-, 16:0/18:0-, and 16:1/16:1-PA, in melanoma cells. In the present study, we searched for the target proteins of 16:0/16:0-PA in melanoma cells and identified heat shock protein (HSP) 27, which acts as a molecular chaperone and contributes to cancer progression. HSP27 more strongly interacted with PA than other phospholipids, including phosphatidylcholine, phosphatidylserine, phosphatidylglycerol, cardiolipin, phosphatidylinositol, phosphatidylinositol 4-monophosphate, and phosphatidylinositol 4,5-bisphosphate. Moreover, HSP27 is more preferentially bound to SFA- and/or MUFA-containing PAs, including 16:0/16:0- and 16:0/18:1-PAs, than PUFA-containing PAs, including 18:0/20:4- and 18:0/22:6-PA. Furthermore, HSP27 and constitutively active DGKα expressed in COS-7 cells colocalized in a DGK activity-dependent manner. Notably, 16:0/16:0-PA, but not phosphatidylcholine or 16:0/16:0-phosphatidylserine, induced oligomer dissociation of HSP27, which enhances its chaperone activity. Intriguingly, HSP27 protein was barely detectable in Jurkat T cells, while the protein band was intensely detected in AKI melanoma cells. Taken together, these results strongly suggest that SFA- and/or MUFA-containing PAs produced by DGKα selectively target HSP27 and regulate its cancer-progressive function in melanoma cells but not in T cells.

Detecting the Critical States of Type 2 Diabetes Mellitus Based on Degree Matrix Network Entropy by Cross-Tissue Analysis

Type 2 diabetes mellitus (T2DM) is a metabolic disease caused by multiple etiologies, the development of which can be divided into three states: normal state, critical state/pre-disease state, and disease state. To avoid irreversible development, it is important to detect the early warning signals before the onset of T2DM. However, detecting critical states of complex diseases based on high-throughput and strongly noisy data remains a challenging task. In this study, we developed a new method, i.e., degree matrix network entropy (DMNE), to detect the critical states of T2DM based on a sample-specific network (SSN). By applying the method to the datasets of three different tissues for experiments involving T2DM in rats, the critical states were detected, and the dynamic network biomarkers (DNBs) were successfully identified. Specifically, for liver and muscle, the critical transitions occur at 4 and 16 weeks. For adipose, the critical transition is at 8 weeks. In addition, we found some "dark genes" that did not exhibit differential expression but displayed sensitivity in terms of their DMNE score, which is closely related to the progression of T2DM. The information uncovered in our study not only provides further evidence regarding the molecular mechanisms of T2DM but may also assist in the development of strategies to prevent this disease.

Phosphatidylinositol 4,5-bisphosphate-specific phospholipase C β1 selectively binds dipalmitoyl and distearoyl phosphatidic acids via Lys946 and Lys951

Phospholipase C (PLC) β1 hydrolyzes 1-stearoyl-2-arachidonoyl (18:0/20:4)-phosphatidylinositol (PtdIns) 4,5-bisphosphate to produce diacylglycerol, which is converted to phosphatidic acid (PtdOH), in the PtdIns cycle and plays pivotal roles in intracellular signal transduction. The present study identified PLCβ1 as a PtdOH-binding protein using PtdOH-containing liposomes. Moreover, the comparison of the binding of PLCβ1 to various PtdOH species, including 14:0/14:0-PtdOH, 16:0/16:0-PtdOH, 16:0/18:1-PtdOH, 18:0/18:1-PtdOH, 18:0/18:0-PtdOH, 18:1/18:1-PtdOH, 18:0/20:4-PtdOH, and 18:0/22:6-PtdOH, indicated that the interaction of PLCβ1 with 16:0/16:0-PtdOH was the strongest. The PLCβ1-binding activity of 18:0/18:0-PtdOH was almost the same as the binding activity of 16:0/16:0-PtdOH. Furthermore, the binding of PLCβ1 to 16:0/16:0-PtdOH was substantially stronger than 16:0/16:0-phosphatidylserine, 16:0/16:0/16:0/16:0-cardiolipin, 16:0/16:0-PtdIns, and 18:0/20:4-PtdIns. We revealed that a PLCβ1 mutant whose Lys946 and Lys951 residues were replaced with Glu (PLCβ1-KE) did not interact with 16:0/16:0-PtdOH and failed to localize to the plasma membrane in Neuro-2a cells. Retinoic acid-dependent increase in neurite length and numbers was significantly inhibited in PLCβ1-expressing cells; however, this considerable attenuation was not detected in the cells expressing PLCβ1-KE. Overall, these results strongly suggest that PtdOHs containing only saturated fatty acids, including 16:0/16:0-PtdOH, which are not derived from the PtdIns cycle, selectively bind to PLCβ1 and regulate its function.

Docosahexaenoic acid-containing phosphatidic acid interacts with clathrin coat assembly protein AP180 and regulates its interaction with clathrin

The clathrin coat assembly protein AP180 drives endocytosis, which is crucial for numerous physiological events, such as the internalization and recycling of receptors, uptake of neurotransmitters and entry of viruses, including SARS-CoV-2, by interacting with clathrin. Moreover, dysfunction of AP180 underlies the pathogenesis of Alzheimer's disease. Therefore, it is important to understand the mechanisms of assembly and, especially, disassembly of AP180/clathrin-containing cages. Here, we identified AP180 as a novel phosphatidic acid (PA)-binding protein from the mouse brain. Intriguingly, liposome binding assays using various phospholipids and PA species revealed that AP180 most strongly bound to 1-stearoyl-2-docosahexaenoyl-PA (18:0/22:6-PA) to a comparable extent as phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂), which is known to associate with AP180. An AP180 N-terminal homology domain (1–289 aa) interacted with 18:0/22:6-PA, and a lysine-rich motif (K38–K39–K40) was essential for binding. The 18:0/22:6-PA in liposomes in 100 nm diameter showed strong AP180-binding activity at neutral pH. Notably, 18:0/22:6-PA significantly attenuated the interaction of AP180 with clathrin. However, PI(4,5)P₂ did not show such an effect. Taken together, these results indicate the novel mechanism by which 18:0/22:6-PA selectively regulates the disassembly of AP180/clathrin-containing cages.

Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits

DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.

The SAC1 phosphatase domain of synaptojanin-1 is activated by interacting with polyunsaturated fatty acid-containing phosphatidic acids

Although there are many phosphatidic acid (PA) molecular species based on its fatty acyl compositions, their interacting partners have been poorly investigated. Here, we identified synaptojanin-1 (SYNJ1), Parkinson's disease-related protein that is essential for regulating clathrin-mediated synaptic vesicle endocytosis via dually dephosphorylating D5 and D4 position phosphates from phosphatidylinositol (PI) (4,5)-bisphosphate, as a 1-stearoyl-2-docosahexaenoyl (18:0/22:6)-PA-binding protein. SYNJ1 failed to substantially associate with other acidic phospholipids. Although SYNJ1 interacted with 18:0/20:4-PA in addition to 18:0/22:6-PA, the association of the enzyme with 16:0/16:0-, 16:0/18:1-, 18:0/18:0-, or 18:1/18:1-PA was not considerable. 18:0/20:4- and 18:0/22:6-PAs bound to SYNJ1 via its SAC1 domain, which preferentially hydrolyses D4 position phosphate. Moreover, 18:0/20:4- and 18:0/22:6-PA selectively enhanced the D4-phosphatase activity, but not the D5-phosphatase activity, of SYNJ1.

Phosphatidic acid: Mono- and poly-unsaturated forms regulate distinct stages of neuroendocrine exocytosis

Lipids have emerged as important actors in an ever-growing number of key functions in cell biology over the last few years. Among them, glycerophospholipids are major constituents of cellular membranes. Because of their amphiphilic nature, phospholipids form lipid bilayers that are particularly useful to isolate cellular content from the extracellular medium, but also to define intracellular compartments. Interestingly, phospholipids come in different flavors based on their fatty acyl chain composition. Indeed, lipidomic analyses have revealed the presence in cellular membranes of up to 50 different species of an individual class of phospholipid, opening the possibility of multiple functions for a single class of phospholipid. In this review we will focus on phosphatidic acid (PA), the simplest phospholipid, that plays both structural and signaling functions. Among the numerous roles that have been attributed to PA, a key regulatory role in secretion has been proposed in different cell models. We review here the evidences that support the idea that mono- and poly-unsaturated PA control distinct steps in hormone secretion from neuroendocrine cells.

New Era of Diacylglycerol Kinase, Phosphatidic Acid and Phosphatidic Acid-Binding Protein

Diacylglycerol kinase (DGK) phosphorylates diacylglycerol (DG) to generate phosphatidic acid (PA). Mammalian DGK consists of ten isozymes (α–κ) and governs a wide range of physiological and pathological events, including immune responses, neuronal networking, bipolar disorder, obsessive-compulsive disorder, fragile X syndrome, cancer, and type 2 diabetes. DG and PA comprise diverse molecular species that have different acyl chains at the sn-1 and sn-2 positions. Because the DGK activity is essential for phosphatidylinositol turnover, which exclusively produces 1-stearoyl-2-arachidonoyl-DG, it has been generally thought that all DGK isozymes utilize the DG species derived from the turnover. However, it was recently revealed that DGK isozymes, except for DGKε, phosphorylate diverse DG species, which are not derived from phosphatidylinositol turnover. In addition, various PA-binding proteins (PABPs), which have different selectivities for PA species, were recently found. These results suggest that DGK–PA–PABP axes can potentially construct a large and complex signaling network and play physiologically and pathologically important roles in addition to DGK-dependent attenuation of DG–DG-binding protein axes. For example, 1-stearoyl-2-docosahexaenoyl-PA produced by DGKδ interacts with and activates Praja-1, the E3 ubiquitin ligase acting on the serotonin transporter, which is a target of drugs for obsessive-compulsive and major depressive disorders, in the brain. This article reviews recent research progress on PA species produced by DGK isozymes, the selective binding of PABPs to PA species and a phosphatidylinositol turnover-independent DG supply pathway.

Diacylglycerol kinase η regulates C2C12 myoblast proliferation through the mTOR signaling pathway

Diacylglycerol kinase (DGK) phosphorylates diacylglycerol to produce phosphatidic acid (PA). The η isozyme of DGK is abundantly expressed in C2C12 myoblasts. However, the role of DGKη in skeletal muscle cells remains unknown. In the present study, we showed that DGKη was downregulated at an early stage of myogenic differentiation. The knockdown of DGKη by siRNAs significantly inhibited C2C12 myoblast proliferation but did not inhibit differentiation. Moreover, the suppression of DGKη expression decreased the expression levels of mammalian target of rapamycin (mTOR), which is a key regulator of cell proliferation, and fatty acid synthase (FASN), which catalyzes the de novo synthesis of fatty acids for cell proliferation and is transcriptionally regulated via mTOR signaling. Furthermore, the knockdown of mTOR or raptor, which is a component of mTOR complex 1 (mTORC1), decreased the amount of FASN. These results indicate that DGKη regulates myoblast proliferation through the mTOR (mTORC1)-FASN pathway. Interestingly, the knockdown of mTOR reduced the expression levels of DGKη, implying mutual regulation between DGKη and mTOR. In DGKη-knockdown myoblasts, C30-C36-PA species, mTOR activators, were decreased, suggesting that the modulation of mTOR activity through these PA species also plays an important role in myoblast proliferation.

Polyunsaturated fatty acid-containing phosphatidic acids selectively interact with L-lactate dehydrogenase A and induce its secondary structural change and inactivation

Phosphatidic acid (PA) consists of various molecular species that have different fatty acyl chains at the sn-1 and sn-2 positions; and consequently, mammalian cells contain at least 50 structurally distinct PA molecular species. However, the different roles of each PA species are poorly understood. In the present study, we attempted to identify dipalmitoyl (16:0/16:0)-PA-binding proteins from mouse skeletal muscle using liposome precipitation and tandem mass spectrometry analysis. We identified L-lactate dehydrogenase (LDH) A, which catalyzes conversion of pyruvate to lactate and is a key checkpoint of anaerobic glycolysis critical for tumor growth, as a 16:0/16:0-PA-binding protein. LDHA did not substantially associate with other phospholipids, such as phosphatidylcholine, phosphatidylserine, phosphatidylglycerol, phosphatidylinositol, phosphoinositides and cardiolipin at physiological pH (7.4), indicating that LDHA specifically bound to PA. Interestingly, 18:0/18:0-, 18:0/20:4- and 18:0/22:6-PA also interacted with LDHA, and their binding activities were stronger than 16:0/16:0-PA at pH 7.4. Moreover, circular dichroism spectrometry showed that 18:0/20:4- and 18:0/22:6-PA, but not 16:0/16:0- or 18:0/18:0-PA, significantly reduced the α-helical structure of LDHA. Furthermore, 18:0/20:4- and 18:0/22:6-PA attenuated LDH activity. Taken together, we demonstrated for the first time that LDHA is a PA-binding protein and is a unique PA-binding protein that is structurally and functionally controlled by associating with 18:0/20:4- and 18:0/22:6-PA.

Phosphatidic acid: an emerging versatile class of cellular mediators

Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Cellular phosphatidic acid sensor, α-synuclein N-terminal domain, detects endogenous phosphatidic acid in macrophagic phagosomes and neuronal growth cones

Phosphatidic acid (PA) is the simplest phospholipid and is involved in the regulation of various cellular events. Recently, we developed a new PA sensor, the N-terminal region of α-synuclein (α-Syn-N). However, whether α-Syn-N can sense physiologically produced, endogenous PA remains unclear. We first established an inactive PA sensor (α-Syn-N-KQ) as a negative control by replacing all eleven lysine residues with glutamine residues. Using confocal microscopy, we next verified that α-Syn-N, but not α-Syn-N-KQ, detected PA in macrophagic phagosomes in which PA is known to be enriched, further indicating that α-Syn-N can be used as a reliable PA sensor in cells. Finally, because PA generated during neuronal differentiation is critical for neurite outgrowth, we investigated the subcellular distribution of PA using α-Syn-N. We found that α-Syn-N, but not α-Syn-N-KQ, accumulated at the peripheral regions (close to the plasma membrane) of neuronal growth cones. Experiments using a phospholipase D (PLD) inhibitor strongly suggested that PA in the peripheral regions of the growth cone was primarily produced by PLD. Our findings provide a reliable sensor of endogenous PA and novel insights into the distribution of PA during neuronal differentiation.