Elucidating the ticking of an in vitro circadian clockwork.

A biochemical oscillator can be reconstituted in vitro with three purified proteins, that displays the salient properties of circadian (daily) rhythms, including self-sustained 24-h periodicity that is temperature compensated. We analyze the biochemical basis of this oscillator by quantifying the time-dependent interactions of the three proteins (KaiA, KaiB, and KaiC) by electron microscopy and native gel electrophoresis to elucidate the timing of the formation of complexes among the Kai proteins. The data are used to derive a dynamic model for the in vitro oscillator that accurately reproduces the rhythms of KaiABC complexes and of KaiC phosphorylation, and is consistent with biophysical observations of individual Kai protein interactions. We use fluorescence resonance energy transfer (FRET) to confirm that monomer exchange among KaiC hexamers occurs. The model demonstrates that the function of this monomer exchange may be to maintain synchrony among the KaiC hexamers in the reaction, thereby sustaining a high-amplitude oscillation. Finally, we apply the first perturbation analyses of an in vitro oscillator by using temperature pulses to reset the phase of the KaiABC oscillator, thereby testing the resetting characteristics of this unique circadian oscillator. This study analyzes a circadian clockwork to an unprecedented level of molecular detail.

Glycerophospholipid identification and quantitation by electrospray ionization mass spectrometry.

Glycerophospholipids are the structural building blocks of the cellular membrane. In addition to creating a protective barrier around the cell, lipids are precursors of intracellular signaling molecules that modulate membrane trafficking and are involved in transmembrane signal transduction. Phospholipids are also increasingly recognized as important participants in the regulation and control of cellular function and disease. Analysis and characterization of lipid species by mass spectrometry (MS) have evolved and advanced with improvements in instrumentation and technology. Key advances, including the development of "soft" ionization techniques for MS such as electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI), and tandem mass spectrometry (MS/MS), have facilitated the analysis of complex lipid mixtures by overcoming the earlier limitations. ESI-MS has become the technique of choice for the analysis of multi-component mixtures of lipids from biological samples due to its exceptional sensitivity and capacity for high throughput. This chapter covers qualitative and quantitative MS methods used for the elucidation of glycerophospholipid identity and quantity in cell or tissue extracts. Sections are included on the extraction, MS analysis, and data analysis of glycerophospholipids and polyphosphoinositides.

Lipid profiling reveals glycerophospholipid remodeling in zymosan-stimulated macrophages.

Comprehensive lipid profiling by mass spectrometry provides comparative data on the relative distribution of individual glycerophospholipids within each of the major classes. Application of this method to the analysis of glycerophospholipid remodeling in murine primary resident peritoneal macrophages (RPMs) during zymosan phagocytosis reveals significant decreases in the levels of every major arachidonic acid (20:4)-containing species of phosphatidylcholine (GPCho) and in selected 20:4-containing phosphatidylinositol (GPIns) and phosphatidylglycerol (GPGro) species. No net changes in 20:4-containing phosphatidylethanolamine (GPEtn) species were detected. Pretreatment of RPMs with LPS resulted in subtle changes in the magnitude and kinetics of the response but had no effect on the overall pattern of zymosan-induced glycerophospholipid remodeling. Inhibition of prostaglandin (PG) synthesis with indomethacin reduced the magnitude of the changes in 20:4-containing diacyl but not alkyl acyl species. Blockade of 20:4 reacylation with thimerosal had no effect on the magnitude of the zymosan-induced changes in GPCho, GPIns, or GPGro species but revealed decreases in the level of alkyl acyl GEtn species. RAW264.7 cells contain much lower levels of phospholipid 20:4 than do RPMs and synthesize PGs poorly in response to zymosan. Pretreatment with granulocyte-macrophage colony stimulating factor, lipopolysaccharide, and interferon-gamma substantially increased the extent of 20:4 mobilization and PG synthesis in these cells. However, under conditions of maximal zymosan-dependent PG synthesis, the only glycerophospholipid that exhibited a significant change was a 20:4-containing plasmenyl GPEtn. These results suggest that GPCho is the major ultimate source of 20:4 that is mobilized in zymosan-stimulated RPMs but that 20:4 mobilization may involve the intermediate turnover of alkyl acyl GPEtn species.

Lipid profiling reveals arachidonate deficiency in RAW264.7 cells: Structural and functional implications.

Glycerophospholipids containing arachidonic acid (20:4) serve as the precursors for an array of biologically active lipid mediators, most of which are produced by macrophages. We have applied mass spectrometry-based lipid profiling technology to evaluate the glycerophospholipid structure and composition of two macrophage populations, resident peritoneal macrophages and RAW264.7 cells, with regard to their potential for 20:4-based lipid mediator biosynthesis. Fatty acid analysis indicated that RAW264.7 cells were deficient in 20:4 (10 +/- 1 mol %) compared to peritoneal macrophages (26 +/- 1 mol %). Mass spectrometry of total glycerophospholipids demonstrated a marked difference in the distribution of lipid species, including reduced levels of 20:4-containing lipids, in RAW264.7 cells compared to peritoneal macrophages. Enrichment of RAW264.7 cells with 20:4 increased the fatty acid to 20 +/- 1 mol %. However, the distribution of the incorporated 20:4 remained different from that of peritoneal macrophages. RAW264.7 cells pretreated with granulocyte-macrophage colony stimulating factor followed by lipopolysaccharide and interferon-gamma mobilized similar quantities of 20:4 and produced similar amounts of prostaglandins as peritoneal macrophages treated with LPS alone. LPS treatment resulted in detectable changes in specific 20:4-containing glycerophospholipids in peritoneal cells, but not in RAW264.7 cells. 20:4-enriched RAW264.7 cells lost 88% of the incorporated fatty acid during the LPS incubation without additional prostaglandin synthesis. These results illustrate that large differences in glycerophospholipid composition may exist, even in closely related cell populations, and demonstrate the importance of interpreting the potential for lipid-mediator biosynthesis in the context of overall glycerophospholipid composition.