We report the lipidomic response of the murine macrophage RAW cell line to Kdo 2 -lipid A, the active component of an inflammatory lipopolysaccharide functioning as a selective TLR4 agonist and compactin, a statin inhibitor of cholesterol biosynthesis. Analyses of lipid molecular species by dynamic quantitative mass spectrometry and concomitant transcriptomic measurements define the lipidome and demonstrate immediate responses in fatty acid metabolism represented by increases in eicosanoid synthesis and delayed responses characterized by sphingolipid and sterol biosynthesis. Lipid remodeling of glycerolipids, glycerophospholipids, and prenols also take place, indicating that activation of the innate immune system by inflammatory mediators leads to alterations in a majority of mammalian lipid categories, including unanticipated effects of a statin drug. Our studies provide a systems-level view of lipid metabolism and reveal significant connections between lipid and cell signaling and biochemical pathways that contribute to innate immune responses and to pharmacological perturbations.The "omics" revolution has provided significant insight into the genes, mRNAs, and proteins of mammalian cells, biological systems, and disease (1-3). An important function of these macromolecular classes is the production of metabolites that in turn are used by cells for replication and function. Lipids comprise major structural and metabolic components of cells and have essential functions in the formation of membranes, energy production, and intracellular signaling. Despite the central role of lipids in mammalian cell function, there has been no systematic effort to define the lipid "parts list" of a mammalian cell or the changes in these lipids associated with cellular function and disease. Many biochemical pathways leading to the synthesis and degradation of major lipid categories are known, but how these pathways interact under normal and pathological conditions remains unexplored. Recent advances in mass spectrometry have made it possible to qualitatively and quantitatively analyze a majority of cellular lipids (4 -8). We report here a comprehensive systems-level analysis of a mammalian cell lipidome through temporal measurements.We characterized lipidomic responses of RAW264.7 (RAW) macrophages to a highly specific ligand for Toll-like receptor 4 (TLR4) 4 that mimics aspects of bacterial infection. This model is of particular interest because of the essential roles that alterations in macrophage lipid metabolism play in innate and adaptive immune responses and the development of chronic inflammatory and cardiovascular diseases. Recent studies further suggest that TLR signaling in macrophages is not only required for innate immunity against viral and bacterial pathogens but also contributes to the pathogenesis of atherosclerosis, diabetes, arthritis, and other inflammatory diseases (9). Although TLR4 signaling is known to exert profound effects on the macrophage transcriptome (10), proteome (11), and selected lipid species that...

Supplementary key words lipidome • membrane • lipopolysaccharide • mitochondria • endoplasmic reticulum • plasmalemma • nucleusLipids regulate and modify protein function and thus various biological processes by two distinct mechanisms. Signaling lipids, including free fatty acids, eicosanoids, sphingosine-1-phosphate, and lysophosphatidic acid, may be released from the sites of their generation in membranes and can subsequently affect receptors located remotely throughout tissues and cells [e.g., see ( 1-4 ) for reviews]. Structural lipids, which represent the bulk of the lipid in the organism, affect membrane-bound enzymes, transporters, and receptors in a local fashion by altering membrane properties or by specifi c binding to target proteins [reviewed in ( 5-8 )].A fundamentally accepted general concept of cell biology is the compartmentalization of biological processes within subcellular structures, termed organelles. Detailed information about the location of biochemical reactions is crucial for understanding their roles in cellular function and dysfunction. By the same token, knowing how different signaling and structural lipids affect cellular responses requires knowledge of their subcellular distribution. Traditional lipid analysis involves organic extraction of whole Abstract Lipids orchestrate biological processes by acting remotely as signaling molecules or locally as membrane components that modulate protein function. Detailed insight into lipid function requires knowledge of the subcellular localization of individual lipids. We report an analysis of the subcellular lipidome of the mammalian macrophage, a cell type that plays key roles in infl ammation, immune responses, and phagocytosis. Nuclei, mitochondria, endoplasmic reticulum (ER), plasmalemma, and cytoplasm were isolated from RAW 264.7 macrophages in basal and activated states. Subsequent lipidomic analyses of major membrane lipid categories identifi ed 229 individual/isobaric species, including 163 glycerophospholipids, 48 sphingolipids, 13 sterols, and 5 prenols. Major subcellular compartments exhibited substantially divergent glycerophospholipid profi les. Activation of macrophages by the Toll-like receptor 4-specifi c lipopolysaccharide Kdo 2 -lipid A caused significant remodeling of the subcellular lipidome. Some changes in lipid composition occurred in all compartments (e.g., increases in the levels of ceramides and the cholesterol precursors desmosterol and lanosterol). Other changes were manifest in specifi c organelles. For example, oxidized sterols increased and unsaturated cardiolipins decreased in mitochondria, whereas unsaturated ether-linked phosphatidylethanolamines decreased in the ER. We speculate that these changes may refl ect mitochondrial oxidative stress and the release of arachidonic acid from the ER in response to cell activation. Tissue cultureCells were maintained, treated, and fractionated as previously described ( 9 ). Briefl y, RAW264.7 cells were maintained between passages 4 and 24 at 37°C and 10% CO 2 . The me...

The pgsA null Escherichia coli strain, UE54, lacks the major anionic phospholipids phosphatidylglycerol and cardiolipin. Despite these alterations the strain exhibits relatively normal cell division. Analysis of the UE54 phospholipids using negativeion electrospray ionization mass spectrometry resulted in identification of a new anionic phospholipid, N-acylphosphatidylethanolamine. Staining with the fluorescent dye 10-N-nonyl acridine orange revealed anionic phospholipid membrane domains at the septal and polar regions. Making UE54 null in minCDE resulted in budding off of minicells from polar domains. Analysis of lipid composition by mass spectrometry revealed that minicells relative to parent cells were significantly enriched in phosphatidic acid and N-acylphosphatidylethanolamine. Thus despite the absence of cardiolipin, which forms membrane domains at the cell pole and division sites in wildtype cells, the mutant cells still maintain polar/septal localization of anionic phospholipids. These three anionic phospholipids share common physical properties that favor polar/septal domain formation. The findings support the proposed role for anionic phospholipids in organizing amphitropic cell division proteins at specific sites on the membrane surface.A unique lipid composition and lipid-protein interactions appear to exist at the transient membrane domain that defines the division site in bacterial cells (1). Using the cardiolipin (CL) 4 -specific fluorescent dye 10-N-nonyl acridine orange (NAO), we previously found CL-enriched membrane domains located at cell poles and near potential division sites in Escherichia coli (2). Subsequently others reported similar CL domains in Bacillus subtilis (3) and Pseudomonas putida (4). In addition, cell pole and division site enrichment in CL in E. coli was confirmed by lipid analysis of minicells spontaneously budded off from the cell poles of a ⌬minCDE mutant (5). We suggested that formation of CL domains at cell pole/division sites plays an important role in selection and recognition of the division site by amphitropic cell cycle and cell division proteins, such as DnaA (initiation of DNA replication at oriC), MinD (a part of MinCDE system preventing positioning of the divisome at cell poles in E. coli), and FtsA (bacterial actin, which is a linker protein for cytoskeletal protein FtsZ (bacterial tubulin), responsible for targeting the Z-ring to the mid-cell membrane domain). They interact directly with membrane phospholipids through specific amphipathic motifs enriched in basic amino acids, which confers the preference for anionic lipids (for references see Ref. 1). In E. coli the ATP-bound form of MinD recruits an inhibitor of Z-ring formation, MinC, to the membrane, whereas the topological regulator, MinE, induces hydrolysis of ATP bound to MinD resulting in release of MinD, and consequently MinC, from the membrane into the cytoplasm. As a result, all three proteins oscillate between the cell poles maintaining the maximum concentration of the inhibitor MinC at the cell p...