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1.  Plasma membrane organization and function: moving past lipid rafts 
Molecular Biology of the Cell  2013;24(18):2765-2768.
“Lipid raft” is the name given to the tiny, dynamic, and ordered domains of cholesterol and sphingolipids that are hypothesized to exist in the plasma membranes of eukaryotic cells. According to the lipid raft hypothesis, these cholesterol- and sphingolipid-enriched domains modulate the protein–protein interactions that are essential for cellular function. Indeed, many studies have shown that cellular levels of cholesterol and sphingolipids influence plasma membrane organization, cell signaling, and other important biological processes. Despite 15 years of research and the application of highly advanced imaging techniques, data that unambiguously demonstrate the existence of lipid rafts in mammalian cells are still lacking. This Perspective summarizes the results that challenge the lipid raft hypothesis and discusses alternative hypothetical models of plasma membrane organization and lipid-mediated cellular function.
doi:10.1091/mbc.E13-03-0165
PMCID: PMC3771939  PMID: 24030510
2.  Identification of protein complexes with quantitative proteomics in S. cerevisiae 
Lipids are the building blocks of cellular membranes that function as barriers and in compartmentalization of cellular processes, and recently, as important intracellular signalling molecules. However, unlike proteins, lipids are small hydrophobic molecules that traffic primarily by poorly described nonvesicular routes, which are hypothesized to occur at membrane contact sites (MCSs). MCSs are regions where the endoplasmic reticulum (ER) makes direct physical contact with a partnering organelle, e.g., plasma membrane (PM). The ER portion of ER-PM MCSs is enriched in lipid-synthesizing enzymes, suggesting that lipid synthesis is directed to these sites and implying that MCSs are important for lipid traffic. Yeast is an ideal model to study ER-PM MCSs because of their abundance, with over 1000 contacts per cell, and their conserved nature in all eukaryotes. Uncovering the proteins that constitute MCSs is critical to understanding how lipids traffic is accomplished in cells, and how they act as signaling molecules. We have found that an ER called Scs2p localize to ER-PM MCSs and is important for their formation. We are focused on uncovering the molecular partners of Scs2p. Identification of protein complexes traditionally relies on first resolving purified protein samples by gel electrophoresis, followed by in-gel digestion of protein bands and analysis of peptides by mass spectrometry. This often limits the study to a small subset of proteins. Also, protein complexes are exposed to denaturing or non-physiological conditions during the procedure. To circumvent these problems, we have implemented a large-scale quantitative proteomics technique to extract unbiased and quantified data. We use stable isotope labeling with amino acids in cell culture (SILAC) to incorporate staple isotope nuclei in proteins in an untagged control strain. Equal volumes of tagged culture and untagged, SILAC-labeled culture are mixed together and lysed by grinding in liquid nitrogen. We then carry out an affinity purification procedure to pull down protein complexes. Finally, we precipitate the protein sample, which is ready for analysis by high-performance liquid chromatography/ tandem mass spectrometry. Most importantly, proteins in the control strain are labeled by the heavy isotope and will produce a mass/ charge shift that can be quantified against the unlabeled proteins in the bait strain. Therefore, contaminants, or unspecific binding can be easily eliminated. By using this approach, we have identified several novel proteins that localize to ER-PM MCSs. Here we present a detailed description of our approach.
doi:10.3791/1225
PMCID: PMC2789102  PMID: 19262458
3.  Illuminating the lipidome to advance biomedical research: peptide-based probes of membrane lipids 
Future medicinal chemistry  2013;5(8):947-959.
Systematic investigation of the lipidome will reveal new opportunities for disease diagnosis and intervention. However, lipidomic research has been hampered by the lack of molecular tools to track specific lipids of interest. Accumulating reports indicate lipid recognition can be achieved with properly constructed short peptides in addition to large proteins. This review summarizes the key developments of this area within the past decade. Select lantibiotic peptides present the best examples of low-molecular-weight probes of membrane lipids, displaying selectivity comparable to lipid-binding proteins. Designed peptides, through biomimetic approaches and combinational screening, have begun to demonstrate their potential for lipid tracking in cultured cells and even in living organisms. Biophysical characterization of these lipid-targeting peptides has revealed certain features critical for selective membrane binding, including preorganized scaffolds and the balance of polar and nonpolar interactions. The knowledge summarized herein should facilitate the development of molecular tools to target a variety of membrane lipids.
doi:10.4155/fmc.13.66
PMCID: PMC3905809  PMID: 23682570
4.  Lipid Rafts and Alzheimer’s Disease: Protein-Lipid Interactions and Perturbation of Signaling 
Lipid rafts are membrane domains, more ordered than the bulk membrane and enriched in cholesterol and sphingolipids. They represent a platform for protein-lipid and protein–protein interactions and for cellular signaling events. In addition to their normal functions, including membrane trafficking, ligand binding (including viruses), axonal development and maintenance of synaptic integrity, rafts have also been implicated in the pathogenesis of several neurodegenerative diseases including Alzheimer’s disease (AD). Lipid rafts promote interaction of the amyloid precursor protein (APP) with the secretase (BACE-1) responsible for generation of the amyloid β peptide, Aβ. Rafts also regulate cholinergic signaling as well as acetylcholinesterase and Aβ interaction. In addition, such major lipid raft components as cholesterol and GM1 ganglioside have been directly implicated in pathogenesis of the disease. Perturbation of lipid raft integrity can also affect various signaling pathways leading to cellular death and AD. In this review, we discuss modulation of APP cleavage by lipid rafts and their components, while also looking at more recent findings on the role of lipid rafts in signaling events.
doi:10.3389/fphys.2012.00189
PMCID: PMC3381238  PMID: 22737128
AChE; Alzheimer’s disease; amyloid β peptide; APP; AICD; BACE-1; cholesterol; neprilysin
5.  Perilipin1 promotes unilocular lipid droplet formation through the activation of Fsp27 in adipocytes 
Nature Communications  2013;4:1594-.
Mature white adipocytes contain a characteristic unilocular lipid droplet. However, the molecular mechanisms underlying unilocular lipid droplet formation are poorly understood. We previously showed that Fsp27, an adipocyte-specific lipid droplet-associated protein, promotes lipid droplet growth by initiating lipid exchange and transfer. Here, we identify Perilipin1 (Plin1), another adipocyte-specific lipid droplet-associated protein, as an Fsp27 activator. Plin1 interacts with the CIDE-N domain of Fsp27 and markedly increases Fsp27-mediated lipid exchange, lipid transfer and lipid droplet growth. Functional cooperation between Plin1 and Fsp27 is required for efficient lipid droplet growth in adipocytes, as depletion of either protein impairs lipid droplet growth. The CIDE-N domain of Fsp27 forms homodimers and disruption of CIDE-N homodimerization abolishes Fsp27-mediated lipid exchange and transfer. Interestingly, Plin1 can restore the activity of CIDE-N homodimerization-defective mutants of Fsp27. We thus uncover a novel mechanism underlying lipid droplet growth and unilocular lipid droplet formation that involves the cooperative action of Fsp27 and Plin1 in adipocytes.
Adipocytes store lipid in spherical droplets whose size is determined by lipid exchange and transfer proteins. Sun et al. show that Perilipin1 promotes the growth of lipid droplets by activating the lipid transfer protein Fsp27.
doi:10.1038/ncomms2581
PMCID: PMC3615468  PMID: 23481402
6.  Reversible binding and rapid diffusion of proteins in complex with inositol lipids serves to coordinate free movement with spatial information 
The Journal of Cell Biology  2009;184(2):297-308.
Polyphosphoinositol lipids convey spatial information partly by their interactions with cellular proteins within defined domains. However, these interactions are prevented when the lipids' head groups are masked by the recruitment of cytosolic effector proteins, whereas these effectors must also have sufficient mobility to maximize functional interactions. To investigate quantitatively how these conflicting functional needs are optimized, we used different fluorescence recovery after photobleaching techniques to investigate inositol lipid–effector protein kinetics in terms of the real-time dissociation from, and diffusion within, the plasma membrane. We find that the protein–lipid complexes retain a relatively rapid (∼0.1–1 µm2/s) diffusion coefficient in the membrane, likely dominated by protein–protein interactions, but the limited time scale (seconds) of these complexes, dictated principally by lipid–protein interactions, limits their range of action to a few microns. Moreover, our data reveal that GAP1IP4BP, a protein that binds PtdIns(4,5)P2 and PtdIns(3,4,5)P3 in vitro with similar affinity, is able to “read” PtdIns(3,4,5)P3 signals in terms of an elongated residence time at the membrane.
doi:10.1083/jcb.200809073
PMCID: PMC2654307  PMID: 19153221
7.  Functional Interactions between Sphingolipids and Sterols in Biological Membranes Regulating Cell Physiology 
Molecular Biology of the Cell  2009;20(7):2083-2095.
Sterols and sphingolipids are limited to eukaryotic cells, and their interaction has been proposed to favor formation of lipid microdomains. Although there is abundant biophysical evidence demonstrating their interaction in simple systems, convincing evidence is lacking to show that they function together in cells. Using lipid analysis by mass spectrometry and a genetic approach on mutants in sterol metabolism, we show that cells adjust their membrane composition in response to mutant sterol structures preferentially by changing their sphingolipid composition. Systematic combination of mutations in sterol biosynthesis with mutants in sphingolipid hydroxylation and head group turnover give a large number of synthetic and suppression phenotypes. Our unbiased approach provides compelling evidence that sterols and sphingolipids function together in cells. We were not able to correlate any cellular phenotype we measured with plasma membrane fluidity as measured using fluorescence anisotropy. This questions whether the increase in liquid order phases that can be induced by sterol–sphingolipid interactions plays an important role in cells. Our data revealing that cells have a mechanism to sense the quality of their membrane sterol composition has led us to suggest that proteins might recognize sterol–sphingolipid complexes and to hypothesize the coevolution of sterols and sphingolipids.
doi:10.1091/mbc.E08-11-1126
PMCID: PMC2663937  PMID: 19225153
8.  Role of Amphipathic Helix of a Herpesviral Protein in Membrane Deformation and T Cell Receptor Downregulation 
PLoS Pathogens  2008;4(11):e1000209.
Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking. Tyrosine kinase interacting protein (Tip) of T lymphotropic Herpesvirus saimiri (HVS) is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression. Here, we report that the membrane-proximal amphipathic helix preceding Tip's transmembrane (TM) domain mediates lipid raft localization and membrane deformation. In turn, this motif directs Tip's lysosomal trafficking and selective TCR downregulation. The amphipathic helix binds to the negatively charged lipids and induces liposome tubulation, the TM domain mediates oligomerization, and cooperation of the membrane-proximal helix with the TM domain is sufficient for localization to lipid rafts and lysosomal compartments, especially the mutivesicular bodies. These findings suggest that the membrane-proximal amphipathic helix and TM domain provide HVS Tip with the unique ability to deform the cellular membranes in lipid rafts and to downregulate TCRs potentially through MVB formation.
Author Summary
Herpesvirus persists in its host by entering a latent state, periodically reactivating to produce infectious viral particles. Some of the herpesviruses have also been known to be related to cancers. Herpesvirus saimiri (HVS), an oncogenic monkey herpesvirus, persists in the T lymphocytes of its natural host, the squirrel monkey, without any apparent disease symptoms, but infection of other species of New World and Old World primates results in fulminant T cell lymphomas. Two viral oncoproteins, Saimiri Transforming Protein and Tyrosine kinase-interacting protein (Tip), are required for T cell transformation. It has been known that Tip may also play some role in viral persistency within T cells by inhibiting the activation of the host cells upon antigenic stimulation. Here, we have identified a structural domain, a putative amphipathic helical motif, preceding the transmembrane domain of Tip. We also found that the structural motif is essential for Tip's localization on specialized membrane domains, lipid rafts, and selective downregulation of antigen receptors. Furthermore, we could genetically dissect the functional roles of the amphipathic helical motif and transmembrane domain of Tip in membrane deformation and oligomerization, respectively. These findings significantly advanced our understanding of how herpesvirus modulates host lymphocytes for viral persistence and pathogenesis.
doi:10.1371/journal.ppat.1000209
PMCID: PMC2581436  PMID: 19023411
9.  Lipid raft involvement in yeast cell growth and death 
Frontiers in Oncology  2012;2:140.
The notion that cellular membranes contain distinct microdomains, acting as scaffolds for signal transduction processes, has gained considerable momentum. In particular, a class of such domains that is rich in sphingolipids and cholesterol, termed as lipid rafts, is thought to compartmentalize the plasma membrane, and to have important roles in survival and cell death signaling in mammalian cells. Likewise, yeast lipid rafts are membrane domains enriched in sphingolipids and ergosterol, the yeast counterpart of mammalian cholesterol. Sterol-rich membrane domains have been identified in several fungal species, including the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe as well as the pathogens Candida albicans and Cryptococcus neoformans. Yeast rafts have been mainly involved in membrane trafficking, but increasing evidence implicates rafts in a wide range of additional cellular processes. Yeast lipid rafts house biologically important proteins involved in the proper function of yeast, such as proteins that control Na+, K+, and pH homeostasis, which influence many cellular processes, including cell growth and death. Membrane raft constituents affect drug susceptibility, and drugs interacting with sterols alter raft composition and membrane integrity, leading to yeast cell death. Because of the genetic tractability of yeast, analysis of yeast rafts could be an excellent model to approach unanswered questions of mammalian raft biology, and to understand the role of lipid rafts in the regulation of cell death and survival in human cells. A better insight in raft biology might lead to envisage new raft-mediated approaches to the treatment of human diseases where regulation of cell death and survival is critical, such as cancer and neurodegenerative diseases.
doi:10.3389/fonc.2012.00140
PMCID: PMC3467458  PMID: 23087902
lipid rafts; membrane domains; ergosterol; yeast; S. cerevisiae; ion homeostasis; nutrient transporters; cell death
10.  Imaging lipid domains in cell membranes: the advent of super-resolution fluorescence microscopy 
The lipid bilayer of model membranes, liposomes reconstituted from cell lipids, and plasma membrane vesicles and spheres can separate into two distinct liquid phases to yield lipid domains with liquid-ordered and liquid-disordered properties. These observations are the basis of the lipid raft hypothesis that postulates the existence of cholesterol-enriched ordered-phase lipid domains in cell membranes that could regulate protein mobility, localization and interaction. Here we review the evidence that nano-scaled lipid complexes and meso-scaled lipid domains exist in cell membranes and how new fluorescence microscopy techniques that overcome the diffraction limit provide new insights into lipid organization in cell membranes.
doi:10.3389/fpls.2013.00503
PMCID: PMC3859905  PMID: 24376453
lipid rafts; membrane microdomains; super-resolution; fluorescence; cell membranes
11.  It’s a lipid’s world: Bioactive lipid metabolism and signaling in neural stem cell differentiation 
Neurochemical Research  2012;37(6):1208-1229.
Lipids are often considered membrane components whose function is to embed proteins into cell membranes. In the last two decades, studies on brain lipids have unequivocally demonstrated that many lipids have critical cell signaling functions; they are called “bioactive lipids”. Pioneering work in Dr. Robert Ledeen’s laboratory has shown that two bioactive brain sphingolipids, sphingomyelin and the ganglioside GM1 are major signaling lipids in the nuclear envelope. In addition to derivatives of the sphingolipid ceramide, the bioactive lipids discussed here belong to the classes of terpenoids and steroids, eicosanoids, and lysophospholipids. These lipids act mainly through two mechanisms: 1) direct interaction between the bioactive lipid and a specific protein binding partner such as a lipid receptor, protein kinase or phosphatase, ion exchanger, or other cell signaling protein; and 2) formation of lipid microdomains or rafts that regulate the activity of a group of raft-associated cell signaling proteins. In recent years, a third mechanism has emerged, which invokes lipid second messengers as a regulator for the energy and redox balance of differentiating neural stem cells (NSCs). Interestingly, developmental niches such as the stem cell niche for adult NSC differentiation may also be metabolic compartments that respond to a distinct combination of bioactive lipids. The biological function of these lipids as regulators of NSC differentiation will be reviewed and their application in stem cell therapy discussed.
doi:10.1007/s11064-011-0698-5
PMCID: PMC3343224  PMID: 22246226
sphingolipids; eicosanoids; lysophospholipids; steroids; embryonic stem cells; neural progenitor cells; differentiation
12.  A New N-terminal Recognition Domain in Caveolin-1 Interacts with Sterol Carrier Protein-2 (SCP-2)† 
Biochemistry  2007;46(28):8301-8314.
Although plasma membrane domains such as caveolae provide an organizing principle for signaling pathways and cholesterol homeostasis in the cell, relatively little is known regarding specific mechanisms whereby intracellular lipid binding proteins are targeted to caveolae. Therefore, the interaction between caveolin-1 and sterol carrier protein-2 (SCP-2), a protein that binds and transfers both cholesterol and signaling lipids (e.g. phosphatidylinositides, sphingolipids), was examined by yeast two-hybrid, in vitro binding, and fluorescence resonance energy transfer analyses (FRET). Results of the in vivo and in vitro assays identified for the first time the N-terminal aa1-32 amphipathic α-helix of SCP-2 functionally interacted with caveolin-1. This interaction was independent of the classic caveolin-1 scaffolding domain in which many signaling proteins interact. Instead, SCP-2 bound caveolin-1 through a new domain identified in the N-terminal domain of caveolin-1 between amino acids 32-55. Modeling studies suggested that electrostatic interactions between the SCP-2 N-terminal aa1-32 amphipathic α-helical domain (cationic, positively charged face) and the caveolin-1 N-terminal aa33-59 α-helix (anionic, negatively charged face) may significantly contribute to this interaction. These findings provide new insights on how SCP-2 enhances cholesterol retention within the cell as well as regulates the distribution of signaling lipids such as phosphoinositides and sphingolipids at plasma membrane caveolae.
doi:10.1021/bi7002636
PMCID: PMC3658303  PMID: 17580960
sterol carrier protein-2; caveolae; caveolin-1; caveolae; cholesterol; signaling
13.  A systems-level approach to mapping the telomere length maintenance gene circuitry 
The ends of eukaryotic chromosomes are protected by telomeres, nucleoprotein structures that are essential for chromosomal stability and integrity. Understanding how telomere length is controlled has significant medical implications, especially in the fields of aging and cancer. Two recent systematic genome-wide surveys measuring the telomere length of deleted mutants in the yeast Saccharomyces cerevisiae have identified hundreds of telomere length maintenance (TLM) genes, which span a large array of functional categories and different localizations within the cell. This study presents a novel general method that integrates large-scale screening mutant data with protein–protein interaction information to rigorously chart the cellular subnetwork underlying the function investigated. Applying this method to the yeast telomere length control data, we identify pathways that connect the TLM proteins to the telomere-processing machinery, and predict new TLM genes and their effect on telomere length. We experimentally validate some of these predictions, demonstrating that our method is remarkably accurate. Our results both uncover the complex cellular network underlying TLM and validate a new method for inferring such networks.
doi:10.1038/msb.2008.13
PMCID: PMC2290934  PMID: 18319724
network inference; telomere
14.  Inositol Phosphorylceramide Synthase Is Located in the Golgi Apparatus of Saccharomyces cerevisiae 
Molecular Biology of the Cell  2000;11(7):2267-2281.
The plasma membrane of eukaryotic cells differs in lipid composition from most of the internal organelles, presumably reflecting differences in many of its functions. In particular, the plasma membrane is rich in sphingolipids and sterols, one property of which is to decrease the permeability and increase the thickness of lipid bilayers. In this paper, we examine the length of transmembrane domains throughout the yeast secretory pathway. Although the transmembrane domains of cis and medial Golgi residents are similar to those of endoplasmic reticulum proteins, these domains lengthen substantially beyond the medial Golgi, suggesting a thickening of the bilayer. Yeast sphingolipids have particularly long acyl chains, and Aur1p, the inositol phosphorylceramide synthase that initiates yeast sphingolipid synthesis, was found to be located in the Golgi apparatus by both immunofluorescence and membrane fractionation, with its active site apparently in the Golgi lumen. Thus, it appears that sphingolipid synthesis in yeast takes place in the Golgi, separated from glycerophospholipid synthesis in the endoplasmic reticulum. A similar separation has been found in mammalian cells, and this conservation suggests that such an arrangement of enzymes within the secretory pathway could be important for the creation of bilayers of different thickness within the cell.
PMCID: PMC14918  PMID: 10888667
15.  Membrane Organization and Lipid Rafts 
Hundreds of different lipid species are present in eukaryotic cell membranes. Some of them aggregate with specific membrane proteins to form specialized domains that concentrate and control cellular trafficking and signaling events.
Cell membranes are composed of a lipid bilayer, containing proteins that span the bilayer and/or interact with the lipids on either side of the two leaflets. Although recent advances in lipid analytics show that membranes in eukaryotic cells contain hundreds of different lipid species, the function of this lipid diversity remains enigmatic. The basic structure of cell membranes is the lipid bilayer, composed of two apposing leaflets, forming a two-dimensional liquid with fascinating properties designed to perform the functions cells require. To coordinate these functions, the bilayer has evolved the propensity to segregate its constituents laterally. This capability is based on dynamic liquid–liquid immiscibility and underlies the raft concept of membrane subcompartmentalization. This principle combines the potential for sphingolipid-cholesterol self-assembly with protein specificity to focus and regulate membrane bioactivity. Here we will review the emerging principles of membrane architecture with special emphasis on lipid organization and domain formation.
doi:10.1101/cshperspect.a004697
PMCID: PMC3179338  PMID: 21628426
16.  Extensive In vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses 
Cell  2010;143(4):639-650.
Summary
Natural small compounds comprise most cellular molecules and bind proteins as substrates, products, cofactors and ligands. However, a large scale investigation of in vivo protein-small metabolite interactions has not been performed. We developed a mass spectrometry assay for the large scale identification of in vivo protein-hydrophobic small metabolite interactions in yeast and analyzed compounds that bind ergosterol biosynthetic proteins and protein kinases. Many of these proteins bind small metabolites; a few interactions were previously known, but the vast majority are novel. Importantly, many key regulatory proteins such as protein kinases bind metabolites. Ergosterol was found to bind many proteins and may function as a general regulator. It is required for the activity of Ypk1, a mammalian AKT/SGK1 kinase homolog. Our study defines potential key regulatory steps in lipid biosynthetic pathways and suggests small metabolites may play a more general role as regulators of protein activity and function than previously appreciated.
doi:10.1016/j.cell.2010.09.048
PMCID: PMC3005334  PMID: 21035178
17.  Distinct Roles of Cellular Lck and p80 Proteins in Herpesvirus Saimiri Tip Function on Lipid Rafts 
Journal of Virology  2003;77(16):9041-9051.
Lipid rafts are proposed to function as platforms for both receptor signaling and trafficking. Following interaction with antigenic peptides, the T-cell receptor (TCR) rapidly translocates to lipid rafts, where it transmits signals and subsequently undergoes endocytosis. The Tip protein of herpesvirus saimiri (HVS), which is a T-lymphotropic tumor virus, interacts with cellular Lck tyrosine kinase and p80, a WD domain-containing endosomal protein. Interaction of Tip with p80 induces enlarged vesicles and recruits Lck and TCR complex into these vesicles for trafficking. We report here that Tip is constitutively present in lipid rafts and that Tip interaction with p80 but not with Lck is necessary for its efficient localization in lipid rafts. The Tip-Lck interaction was required for recruitment of the TCR complex to lipid rafts, and the Tip-p80 interaction was critical for the aggregation and internalization of lipid rafts. These results suggest the potential mechanism for Tip-mediated TCR downregulation: Tip interacts with Lck to recruit TCR complex to lipid rafts, and it subsequently interacts with p80 to initiate the aggregation and internalization of the lipid raft domain and thereby downregulate the TCR complex. Thus, the signaling and targeting functions of HVS Tip rely on two functionally and genetically separable mechanisms that independently target cellular Lck tyrosine kinase and p80 endosomal protein.
doi:10.1128/JVI.77.16.9041-9051.2003
PMCID: PMC167239  PMID: 12885920
18.  Synthesis and Biosynthetic Trafficking of Membrane Lipids 
Eukaryotic cells can synthesize thousands of different lipid molecules that are incorporated into their membranes. This involves the activity of hundreds of enzymes with the task of creating lipid diversity. In addition, there are several, typically redundant, mechanisms to transport lipids from their site of synthesis to other cellular membranes. Biosynthetic lipid transport helps to ensure that each cellular compartment will have its characteristic lipid composition that supports the functions of the associated proteins. In this article, we provide an overview of the biosynthesis of the major lipid constituents of cell membranes, that is, glycerophospholipids, sphingolipids, and sterols, and discuss the mechanisms by which these newly synthesized lipids are delivered to their target membranes.
Most of the thousands of different membrane lipids in cells are synthesized by enzymes in the ER. Glycerophospholipid, sphingolipid, and sterol transfer proteins and transport them to the compartments where they reside.
doi:10.1101/cshperspect.a004713
PMCID: PMC3140686  PMID: 21482741
19.  SNARE-catalyzed Fusion Events Are Regulated by Syntaxin1A–Lipid Interactions 
Molecular Biology of the Cell  2008;19(2):485-497.
Membrane fusion is a process that intimately involves both proteins and lipids. Although the SNARE proteins, which ultimately overcome the energy barrier for fusion, have been extensively studied, regulation of the energy barrier itself, determined by specific membrane lipids, has been largely overlooked. Our findings reveal a novel function for SNARE proteins in reducing the energy barrier for fusion, by directly binding and sequestering fusogenic lipids to sites of fusion. We demonstrate a specific interaction between Syntaxin1A and the fusogenic lipid phosphatidic acid, in addition to multiple polyphosphoinositide lipids, and define a polybasic juxtamembrane region within Syntaxin1A as its lipid-binding domain. In PC-12 cells, Syntaxin1A mutations that progressively reduced lipid binding resulted in a progressive reduction in evoked secretion. Moreover, amperometric analysis of fusion events driven by a lipid-binding–deficient Syntaxin1A mutant (5RK/A) demonstrated alterations in fusion pore dynamics, suggestive of an energetic defect in secretion. Overexpression of the phosphatidic acid–generating enzyme, phospholipase D1, completely rescued the secretory defect seen with the 5RK/A mutant. Moreover, knockdown of phospholipase D1 activity drastically reduced control secretion, while leaving 5RK/A-mediated secretion relatively unaffected. Altogether, these data suggest that Syntaxin1A–lipid interactions are a critical determinant of the energetics of SNARE-catalyzed fusion events.
doi:10.1091/mbc.E07-02-0148
PMCID: PMC2230580  PMID: 18003982
20.  Regulation of AMPA receptor localization in lipid rafts 
Lipid rafts are special microdomains enriched in cholesterol, sphingolipids and certain proteins, and play important roles in a variety of cellular functions including signal transduction and protein trafficking. We report that in cultured cortical and hippocampal neurons the distribution of lipid rafts is development-dependent. Lipid rafts in mature neurons exist on the entire cell-surface and display a high degree of mobility. AMPA receptors co-localize and associate with lipid rafts in the plasma membrane. The association of AMPARs with rafts is under regulation; through the NOS–NO pathway, NMDA receptor activity increases AMPAR localization in rafts. During membrane targeting, AMPARs insert into or at close proximity of the surface raft domains. Perturbation of lipid rafts dramatically suppresses AMPA receptor exocytosis, resulting in significant reduction in AMPAR cell-surface expression.
doi:10.1016/j.mcn.2008.02.010
PMCID: PMC2734417  PMID: 18411055
21.  A protein interaction map for cell polarity development 
The Journal of Cell Biology  2001;154(3):549-576.
Many genes required for cell polarity development in budding yeast have been identified and arranged into a functional hierarchy. Core elements of the hierarchy are widely conserved, underlying cell polarity development in diverse eukaryotes. To enumerate more fully the protein–protein interactions that mediate cell polarity development, and to uncover novel mechanisms that coordinate the numerous events involved, we carried out a large-scale two-hybrid experiment. 68 Gal4 DNA binding domain fusions of yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases were used to screen an array of yeast transformants that express ∼90% of the predicted Saccharomyces cerevisiae open reading frames as Gal4 activation domain fusions. 191 protein–protein interactions were detected, of which 128 had not been described previously. 44 interactions implicated 20 previously uncharacterized proteins in cell polarity development. Further insights into possible roles of 13 of these proteins were revealed by their multiple two-hybrid interactions and by subcellular localization. Included in the interaction network were associations of Cdc42 and Rho1 pathways with proteins involved in exocytosis, septin organization, actin assembly, microtubule organization, autophagy, cytokinesis, and cell wall synthesis. Other interactions suggested direct connections between Rho1- and Cdc42-regulated pathways; the secretory apparatus and regulators of polarity establishment; actin assembly and the morphogenesis checkpoint; and the exocytic and endocytic machinery. In total, a network of interactions that provide an integrated response of signaling proteins, the cytoskeleton, and organelles to the spatial cues that direct polarity development was revealed.
doi:10.1083/jcb.200104057
PMCID: PMC2196425  PMID: 11489916
cytoskeleton; Rho proteins; secretion; cell polarity; endocytosis
22.  Lipid Raft in Cardiac Health and Disease 
Current Cardiology Reviews  2009;5(2):105-111.
Lipid rafts are sphingolipid and cholesterol rich micro-domains of the plasma membrane that coordinate and regulate varieties of signaling processes. Lipid rafts are also present in cardiac myocytes and are enriched in signaling molecules and ion channel regulatory proteins. Lipid rafts are receiving increasing attention as cellular organelles contributing to the pathogenesis of several structural and functional processes including cardiac hypertrophy and heart failure. At present, very little is known about the role of lipid rafts in cardiac function and dysfunction. This review will discuss the possible role of lipid rafts in cardiac health and disease.
doi:10.2174/157340309788166660
PMCID: PMC2805812  PMID: 20436850
23.  The Adeno-Associated Virus Type 2 Regulatory Proteins Rep78 and Rep68 Interact with the Transcriptional Coactivator PC4 
Journal of Virology  1999;73(1):260-269.
The adeno-associated virus type 2 (AAV-2) Rep78/Rep68 regulatory proteins are pleiotropic effectors of viral and cellular DNA replication, of cellular transformation by viral and cellular oncogenes, and of homologous and heterologous gene expression. To search for cellular proteins involved in mediating these functions, we used Rep68 as bait in the yeast two-hybrid system and identified the transcriptional coactivator PC4 as a Rep interaction partner. PC4 has been shown to mediate transcriptional activation by a variety of sequence-specific transcription factors in vitro. Rep amino acids 172 to 530 were sufficient and amino acids 172 to 224 were absolutely necessary for the interaction with PC4. The PC4 domains required for interaction were mapped to the C-terminal single-stranded DNA-binding domain of PC4. In glutathione S-transferase (GST) pull-down assays, in vitro-transcribed and -translated Rep78 or Rep68 proteins were bound specifically by GST-PC4 fusion proteins. Similarly, PC4 expressed in Escherichia coli was bound by GST-Rep fusion proteins, confirming the direct interaction between Rep and PC4 in vitro. Rep was found to have a higher affinity for the nonphosphorylated, transcriptionally active form of PC4 than for the phosphorylated, transcriptionally inactive form. The latter is predominant in nuclear extracts of HeLa or 293 cells. In the yeast system, but not in vitro, Rep-PC4 interaction was disrupted by a point mutation in the putative nucleotide-binding site of Rep68, suggesting that a stable interaction between Rep and PC4 in vivo is ATP dependent. This mutation has also been shown to impair Rep function in AAV-2 DNA replication and in inhibition of gene expression and inducible DNA amplification. Cytomegalovirus promoter-driven overexpression of PC4 led to transient accumulation of nonphosphorylated PC4 with concomitant downregulation of all three AAV-2 promoters in the absence of helper virus. In the presence of adenovirus, this effect was relieved. These results imply an involvement of the transcriptional coactivator PC4 in the regulation of AAV-2 gene expression in the absence of helper virus.
PMCID: PMC103830  PMID: 9847329
24.  Genome-Wide Identification and Functional Annotation of Dual Specificity Protein- and Lipid-Binding Modules That Modulate Protein Interactions at the Membrane 
Molecular cell  2012;46(2):226-237.
Emerging evidence indicates that membrane lipids regulate protein networking by directly interacting with protein-interaction domains (PIDs). As a pilot study to identify and functionally annodate lipid-binding PIDs on a genomic scale, we performed experimental and computational studies of PDZ domains. Characterization of 70 PDZ domains showed that 40% had submicromolar membrane affinity. Using a computational model built from these data, we predicted the membrane binding properties of 2000 PDZ domains from 20 species. The accuracy of the prediction was experimentally validated for 26 PDZ domains. We also subdivided lipid-binding PDZ domains into three classes based on the interplay between membrane and protein binding sites. For different classes of PDZ domains, lipid binding regulates their protein interactions by different mechanisms. Functional studies of a PDZ domain protein, rhophilin2 suggest that all classes of lipid binding PDZ domains serve as genuine dual-specificity modules regulating protein interactions at the membrane under physiological conditions.
doi:10.1016/j.molcel.2012.02.012
PMCID: PMC3431187  PMID: 22445486
25.  Plant Lipid Rafts 
Plant Signaling & Behavior  2007;2(6):508-511.
Lipid rafts in plasma membranes are hypothesized to play key roles in many cellular processes including signal transduction, membrane trafficking and entry of pathogens. We recently documented the biochemical characterization of lipid rafts, isolated as detergent-insoluble membranes, from Medicago truncatula root plasma membranes. We evidenced that the plant-specific lipid steryl-conjugates are among the main lipids of rafts together with free sterols and sphingolipids. An extensive proteomic analysis showed the presence of a specific set of proteins common to other lipid rafts, plus the presence of a redox system around a cytochrome b561 not previously identified in lipid rafts of either plants or animals. Here, we discuss the similarities and differences between the lipids and proteins of plant and animal lipid rafts. Moreover we describe the potential biochemical functioning of the M. truncatula root lipid raft redox proteins and question whether they may play a physiological role in legume-symbiont interactions.
PMCID: PMC2634352  PMID: 19704542
plasma membrane; Medicago; root; legume-Rhizobium symbiosis; redox; sterol; sphingolipid

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