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Flexibility of a Eukaryotic Lipidome - Insights from Yeast Lipidomics
PLOS ONE
Abstract and Figures
Mass spectrometry-based shotgun lipidomics has enabled the quantitative and comprehensive assessment of cellular lipid compositions. The yeast Saccharomyces cerevisiae has proven to be a particularly valuable experimental system for studying lipid-related cellular processes. Here, by applying our shotgun lipidomics platform, we investigated the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids. This extensive dataset allowed for a quantitative description of the intrinsic flexibility of a eukaryotic lipidome, thereby providing new insights into the adjustments of lipid biosynthetic pathways. In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism.
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... The acyl chain composition is mainly determined by de novo fatty acid synthesis, followed by acyl-CoA desaturation and elongation (Tehlivets et al, 2007;De Kroon et al, 2013). Despite this simple acyl chain composition, the yeast lipidome comprises hundreds of structurally distinct lipids (Ejsing et al. 2009;Klose et al. 2012; Danne-Rasche, Rubenzucker, and Ahrends 2020; Reinhard et al. 2020). Phospholipids are the major component of the yeast lipidome, with phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI) being the most abundant classes (Ejsing et al. 2009;Klose et al. 2012). ...
... Despite this simple acyl chain composition, the yeast lipidome comprises hundreds of structurally distinct lipids (Ejsing et al. 2009;Klose et al. 2012; Danne-Rasche, Rubenzucker, and Ahrends 2020; Reinhard et al. 2020). Phospholipids are the major component of the yeast lipidome, with phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI) being the most abundant classes (Ejsing et al. 2009;Klose et al. 2012). ...
... The first evidence for yeast lipidome adaptation in response to temperature established redistribution of the total acyl chain composition, increasing in acyl chain length and decreasing unsaturation in response to higher culture temperatures (Martin, Oh, and Jiang 2007;Suutari, Liukkonen, and Laakso 1990;Hunter and Rose 1972). Using shotgun lipidomics, Klose et al. showed that at elevated temperatures, phospholipids generally increase in monounsaturated species at the expense of diunsaturated species, and decrease in C32 species compensated by an increase in C34 species (Klose et al. 2012). Ejsing et al. used MS 2 data to determine the phospholipid molecular composition, showing that with increasing temperatures, PC mainly increases in PC 16:0_16:1, PC 16:1_18:1, and PC 16:0_18:1 at the expense of PC 16:1_16:1 (Ejsing et al. 2009). ...
The budding yeast Saccharomyces cerevisiae is a poikilothermic organism and adapts its lipid composition to the environmental temperature to maintain membrane physical properties. Studies addressing temperature-dependent adaptation of the lipidome in yeast have described changes in the phospholipid composition at the level of sum composition ( e.g. PC 32:1) and molecular composition (e.g. PC 16:0_16:1). However, to date, there is no information at the level of positional isomers ( e.g. PC 16:0/16:1 versus PC 16:1/16:0). In this study, combined Collision- and Ozone-Induced Dissociation (CID/OzID) mass spectrometry was deployed to investigate homeoviscous adaptation of PC, PE, and PS sn -molecular species composition. We determined the main species to be 16:1/16:1, 16:0/16:1, 16:1/18:1, 16:0/18:1, and 18:0/16:1. In general, at higher culture temperature, the sn -1 position is increased in saturated acyl chains, whereas the sn -2 position mainly is increased in acyl chain length. PC mainly increases in 16:0/16:1 and 16:0/18:1, at the expense of 16:1/16:1, whereas PS and PE increase in 16:1/18:1, at the expense of 16:1/16:1 and 16:0/16:1. Our data suggest distinct adaptation mechanisms of the sn -1 and sn -2 acyl chains, and different manners of sn -molecular species adaptation between PC and PE/PS.
... Only a limited number of studies have conducted comprehensive investigations into lipidomic remodeling across various physicochemical perturbations and nutrient stress (33)(34)(35)(36)(37), despite the fact that exploration of the lipidome response to these conditions would offer valuable insight into the molecular mechanisms that govern the functionality of bacterial cellular membranes, probing further the remarkable adaptability and plasticity of biological systems. Desulfatibacillum alkenivorans strain PF2803 T (38), a mesophilic sulfate-reducing bacterium, possesses the ability to synthesize a wide array of mixed ether/ester bond lipids (19,23,39,40), which allows the role of this facet of lipidome adaptation to be deciphered. ...
... To date, there have been limited studies systematically characterizing the lipidomic adaptation of living cells under both physicochemical perturbation and nutrient stressors (33)(34)(35)(36)(37). To determine which parameter most significantly influences the lipidome adaptation of D. alkenivorans, we utilized molecular network analysis to assess changes in the complete lipidome under various culturing conditions. ...
Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of Desulfatibacillum alkenivorans strain PF2803T, a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an unprecedented assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen- and sulfur-containing polar head groups, moving beyond a reliance on conventional non-phospholipid types.
... S. cerevisiae is often used as a simple eukaryotic model system to unravel basic lipid metabolism questions or as an easy-to-engineer cell factory for biotechnology. Both (Klose et al., 2012;Solanko et al., 2018). PtdIns can be phosphorylated at the 3-, 4-, and 5-hydroxyls at the inositol ring and thereby lead to a set of phosphoinositide species depending on the number and arrangement of phosphorylations. ...
... DAG is mainly found in vacuolar membranes and the PM (Ganesan et al., 2019). Depending on the growth phase, carbon source used and environmental conditions such as temperature, the membrane lipid composition can vary to a certain degree (Klose et al., 2012). ...
Lipid binding domains and protein lipidations are essential features to recruit proteins to intracellular membranes, enabling them to function at specific sites within the cell. Membrane association can also be exploited to answer fundamental and applied research questions, from obtaining insights into the understanding of lipid metabolism to employing them for metabolic engineering to redirect fluxes. This review presents a broad catalog of membrane binding strategies focusing on the plasma membrane of Saccharomyces cerevisiae. Both lipid binding domains (pleckstrin homology, discoidin‐type C2, kinase associated‐1, basic‐rich and bacterial phosphoinositide‐binding domains) and co‐ and post‐translational lipidations (prenylation, myristoylation and palmitoylation) are introduced as tools to target the plasma membrane. To provide a toolset of membrane targeting modules, respective candidates that facilitate plasma membrane targeting are showcased including their in vitro and in vivo properties. The relevance and versatility of plasma membrane targeting modules are further highlighted by presenting a selected set of use cases.
... Yeast strains and growth conditions: All S. cerevisiae strains used in this study are described in Lipidomics analysis: Mass spectrometry-based lipid analysis was performed by Lipotype GmbH (Dresden, Germany) as previously described (58,59). Lipids were extracted using a chloroform/methanol procedure (60). ...
Cardiolipin (CL) is a unique, four-chain phospholipid synthesized in the inner mitochondrial membrane (IMM). The acyl chain composition of CL is regulated through a remodeling pathway, whose loss causes mitochondrial dysfunction in Barth syndrome. Yeast has been used extensively as a model system to characterize CL metabolism, but mutants lacking its two remodeling enzymes, Cld1p and Taz1p, have not recapitulated the structural and respiratory phenotypes observed in other systems. Here we show the essential role of CL remodeling in the structure and function of the IMM in yeast grown under reduced oxygenation. Microaerobic fermentation, which mimics natural yeast environments, caused the accumulation of saturated fatty acids and, under these conditions, remodeling mutants showed a loss of IMM ultrastructure. We extended this observation to HEK293 cells, where iPLA2 inhibition by bromoenol lactone resulted in respiratory dysfunction and cristae loss upon mild treatment with exogenous saturated fatty acids. In microaerobic yeast, remodeling mutants accumulated unremodeled, saturated CL, but also displayed reduced total CL levels, highlighting the interplay between saturation and CL biosynthesis and breakdown. We identified the mitochondrial phospholipase A1 Ddl1p as a regulator of CL levels, and those of its precursors phosphatidylglycerol and phosphatidic acid, under these conditions. Loss of DDL1 partially rescued IMM structure in cells unable to initiate CL remodeling and had differing lipidomic effects depending on oxygenation. These results introduce a revised yeast model for investigating CL remodeling and suggest that its structural functions are dependent on the overall lipid environment in the mitochondrion.
... The complexity of eukaryotic cell membranes is higher, featuring the evolution of steroid molecules, viewed as an adaptation to rising levels of oxygen in Earth's atmosphere [84]. Yeast cells, for example, manage their membrane fluidity and stability by producing ergosterol, indicating fungi's evolutionary adjustment to environmental shifts [85]. Eukaryotic cell membranes consist of a broad array of glycerophospholipids, including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, and phosphatidic acid. ...
Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.
... The total lipid content and composition of yeasts can be considerably impacted by changes in growth conditions, such as different growth phases, carbon sources, or oxygen availability [38][39][40][41]. For K. phaffii, significant differences between glucose and methanol conditions were seen regarding triacylglycerol (TAG) content, while over the course of a glycerol batch-phase and a methanol feed-phase, major changes in various phospholipid levels were observed [39,41]. ...
Background
Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions.
Results
By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h⁻¹. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g⁻¹ h⁻¹. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival.
Conclusions
In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
... The amounts of cholesterol and triglycerides (TG) were measured using FUJI DRI-CHEM slides (FUJIFILM, Tokyo, Japan) with FUJI DRI-CHEM 3500I (FUJIFILM). The cellular lipidomic profile was assessed using mass spectrometry-based lipid analysis performed by Lipotype GmbH (Dresden, Germany) as previously described [67]. Lipids were extracted using chloroform and methanol, and extracted samples were spiked with lipid class-specific internal standards before extraction. ...
Rationale: The gut and its accessory organ, the liver, are crucial determinants of metabolic homeostasis via the regulation of circulating lipids for cardiovascular health. In response to environmental insults, cells undergo diverse adaptation or pathophysiological processes via stress-responsive eukaryotic initiation factor 2 alpha (eIF2α) kinase signaling and subsequent cellular reprogramming. We noted that patients with inflammatory gut distress display enhanced levels of ribosomal stress-responsive eIF2α kinase, which is notably associated with lipid metabolic process genes. Based on an assumption that eukaryotic ribosomes are a promising stress-responsive module for molecular reprogramming, chemical ribosome-inactivating stressors (RIS) were assessed for their involvement in enterohepatic lipid regulation.
Methods: Experimental assessment was based on prediction using the clinical transcriptome and single-cell RNA-sequencing analysis of inflammatory bowel diseases and obesity. The prediction was verified using RIS exposure models of mice, gut organoids, and intestinal cells. The lipidomic profiling was performed to address RIS-induced intracellular fat alterations. Biochemical processes of the mechanisms were evaluated using RT-PCR, western blot analysis, luciferase reporter assays, and confocal microscopy of genetically ablated or chemically inhibited mice, organoids, and cells.
Results: Chemical RIS including deoxynivalenol promoted enterohepatic lipid sequestration while lowering blood LDL cholesterol in normal and diet-induced obese mice. Although ribosomal stress caused extensive alterations in cellular lipids and metabolic genes, the cholesterol import-associated pathway was notably modulated. In particular, ribosomal stress enhanced gut levels of the low-density lipoprotein receptor (LDLR) via both transcriptional and post-transcriptional regulation. Subsequently, LDLR facilitated enterohepatic cholesterol accumulation, leading to dyslipidemia in response to ribosomal stress. Moreover, genetic features of stress-responsive LDLR modulators were consistently proven in the inflammation- and obesity-associated gut model.
Conclusion: The elucidated ribosome-linked gut lipid regulation provides predictive insights into stress-responsive metabolic rewiring in chronic human diseases as an environmental health prediction.
... Besides, adjustments in membrane composition occur and are proposed to be involved in the inherent mechanism of the weak acids tolerance. Lipids account for about 50% of the composition of the yeast plasma membrane, mainly in the classes of glycerophospholipids, sphingolipids and sterols (Klose et al. 2012). A comparative analysis of lipid profiles of cell membrane showed alterations in lipids in response to S. cerevisiae exposed to different weak acids, depending on the properties of the acid (Guo et al. 2018). ...
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae , but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
We have identified a Saccharomyces cerevisiae gene necessary for the step in sphingolipid synthesis in which inositol phosphate is added to ceramide to form inositol-P-ceramide,
a reaction catalyzed by phosphatidylinositol:ceramide phosphoinositol transferase (IPC synthase). This step should be an effective
target for antifungal drugs. A key element in our experiments was the development of a procedure for isolating mutants defective
in steps in sphingolipid synthesis downstream from the first step including a mutant defective in IPC synthase. An IPC synthase
defect is supported by data showing a failure of the mutant strain to incorporate radioactive inositol or N-acetylsphinganine into sphingolipids and, by using an improved assay, a demonstration that the mutant strain lacks enzyme
activity. Furthermore, the mutant accumulates ceramide when fed exogenous phytosphingosine as expected for a strain lacking
IPC synthase activity. Ceramide accumulation is accompanied by cell death, suggesting the presence of a ceramide-activated
death response in yeast. A gene, AUR1 (YKL004w), that complements the IPC synthase defect and restores enzyme activity and sphingolipid synthesis was isolated.
Mutations in AUR1 had been shown previously to give resistance to the antifungal drug aureobasidin A, leading us to predict that the drug should
inhibit IPC synthase activity. Our data show that the drug is a potent inhibitor of IPC synthase with an IC50 of about 0.2 nM. Fungal pathogens are an increasing threat to human health. Now that IPC synthase has been shown to be the target for aureobasidin
A, it should be possible to develop high throughput screens to identify new inhibitors of IPC synthase to combat fungal diseases.
The growth conditions known to influence the occurrence of mitochondrial profiles and other cell membrane systems in anaerobic
cells of S. cerevisiae have been examined, and the effect of the several growth media on the lipid composition of the organism has been determined.
The anaerobic cell type containing neither detectable mitochondrial profiles nor the large cell vacuole may be obtained by
the culture of the organism on growth-limiting levels of the lipids, ergosterol, and unsaturated fatty acids. Under these
conditions, the organism has a high content of short-chain saturated fatty acids (10:0, 12:0), phosphatidyl choline, and squalene,
compared with aerobically grown cells, and it is especially low in phosphatidyl ethanolamine and the glycerol phosphatides
(phosphatidyl glycerol + cardiolipin). The high levels of unsaturated fatty acids normally found in the phospholipids of the
aerobic cells are largely replaced by the short-chain saturated acids, even though the phospholipid fraction contains virtually
all of the small amounts of unsaturated fatty acid present in the anaerobic cells. Such anaerobic cells may contain as little
as 0.12 mg of ergosterol per g dry weight of cells while the aerobic cells contain about 6 mg of ergosterol per g dry weight.
Anaerobic cell types containing mitochondrial profiles can be obtained by the culture of the organism in the presence of excess
quantities of ergosterol and unsaturated fatty acids. Such cells have increased levels of total phospholipid, ergosterol,
and unsaturated fatty acids, although these compounds do not reach the levels found in aerobic cells. The level of ergosterol
in anaerobic cells is markedly influenced by the nature of the carbohydrate in the medium; those cells grown on galactose
media supplemented with ergosterol and unsaturated fatty acids have well defined mitochondrial profiles and an ergosterol
content (2 mg per g dry weight of cells) three times that of equivalent glucose-grown cells which have poorly defined organelle
profiles. Anaerobic cells which are low in ergosterol synthesize increased amounts of squalene.
1.1. Phospholipids, total fatty acids, sterols and hydrocarbons were determined in respiratory-competent and respiratory-deficient cells of Saccharomyces cerevisiae grown aerobically and anaerobically.2.2. In a respiratory-competent strain, the previously-reported reduction in the content of phospholipids, fatty acids, and sterols of cells grown anaerobically on glucose in medium supplemented with ergosterol and Tween 80, relative to aerobically-grown cells, was confirmed. Anaerobically-grown cells from medium lacking ergosterol contained more phospholipids and fatty acids, and from medium lacking both ergosterol and Tween 80 contained more phospholipids, than cells from the supplemented medium.3.3. Changes in the lipid fractions during respiratory adaptation of anaerobically-grown respiratory-competent yeast were followed. The level of phospholipids rose during the first 2 h of adaptation, the level of other fractions rising during several hours approximately parallel with the development of respiratory activity.4.4. When anaerobically-grown respiratory-competent yeast was aerated in the presence of acriflavin or chloramphenicol, no respiratory adaptation took place. However, the content of phospholipids and of total fatty acids increased in a manner similar to that in cells during respiratory adaptation, whereas the content of sterols increased less. The cells aerated in the presence of cycloheximide had no respiratory ability, the content of phospholipids was similar to that in the cells aerated with acriflavin or chloramphenicol, the content of fatty acids was intermediate between aerobically- and anaerobically-grown cells, and the content of sterols was markedly reduced and approximated that of non-aerated anaerobically-grown cells.5.5. The respiratory-deficient mutant, derived from the competent strain, showed the same pattern of lipid composition as the original strain. The amount of lipids was reduced in anaerobically-grown cells. The lipid composition of aerobically-grown mutant cells was the same as that of aerobically-grown wild yeast, except for the phospholipid content which was lower in the mutant.
LipidXplorer is the open source software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra. LipidXplorer processes spectra acquired on any type of tandem mass spectrometers; it identifies and quantifies molecular species of any ionizable lipid class by considering any known or assumed molecular fragmentation pathway independently of any resource of reference mass spectra. It also supports any shotgun profiling routine, from high throughput top-down screening for molecular diagnostic and biomarker discovery to the targeted absolute quantification of low abundant lipid species. Full documentation on installation and operation of LipidXplorer, including tutorial, collection of spectra interpretation scripts, FAQ and user forum are available through the wiki site at: https://wiki.mpi-cbg.de/wiki/lipidx/index.php/Main_Page.
The activities of integral membrane proteins are often affected by the structures of the lipid molecules that surround them in the membrane. One important parameter is the hydrophobic thickness of the lipid bilayer, defined by the lengths of the lipid fatty acyl chains. Membrane proteins are not rigid entities, and deform to ensure good hydrophobic matching to the surrounding lipid bilayer. The structure of the lipid headgroup region is likely to be important in defining the structures of those parts of a membrane protein that are located in the lipid headgroup region. A number of examples are given where the conformation of the headgroup-embedded region of a membrane protein changes during the reaction cycle of the protein; activities of such proteins might be expected to be particularly sensitive to lipid headgroup structure. Differences in hydrogen bonding potential and hydration between the headgroups of phosphatidycholines and phosphatidylethanolamines could be important factors in determining the effects of these lipids on protein activities, as well as any effects related to the tendency of the phosphatidylethanolamines to form a curved, hexagonal HII phase. Effects of lipid structure on protein aggregation and helix–helix interactions are also discussed, as well as the effects of charged lipids on ion concentrations close to the surface of the bilayer. Interpretations of lipid effects in terms of changes in protein volume, lipid free volume, and curvature frustration are also described. Finally, the role of non-annular, or ‘co-factor’ lipids, tightly bound to membrane proteins, is described.
Phosphatidylcholine (PC) is a very abundant membrane lipid in most eukaryotes, including yeast. The molecular species profile of PC, i.e. the ensemble of PC molecules with acyl chains differing in number of carbon atoms and double bonds, is important for membrane function. Pathways of PC synthesis and turnover maintain PC homoeostasis and determine the molecular species profile of PC. Studies addressing the processes involved in establishing the molecular species composition of PC in yeast using stable isotope labelling combined with detection by MS are reviewed.
The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture, briey sketch how new nodes can be incorporated, and highlight some of the new features of version 2.0.
This study compares the effect of the growth phase on the phospholipid composition and the activity of several phospholipid biosynthetic enzymes in a wild-type yeast grown in fermentable (glucose) and non-fermentable (lactate) semi-synthetic and complete synthetic media. Several distinct differences as well as similarities were found. The cellular phosphatidylcholine: phosphatidylethanolamine (PC:PE) ratio was found to vary with the growth phase, with increases in PC levels at the expense of PE during the transition to stationary phase. The variation was most pronounced in semi-synthetic lactate medium, which is routinely used for the isolation of mitochondria, where the PC:PE ratio changed from 0.9 to 2.2 during this transition. Similar growth phase-dependent changes in PC and PE content were observed in isolated organelles such as mitochondria, mitochondria-associated membranes and microsomes. Phosphatidylinositol (PI) levels were much higher in cells grown on lactate compared to cells grown on glucose (20% vs. 5–10%). Irrespective of the medium, PI levels increased upon entering stationary phase. The activities of the phospholipid biosynthetic enzymes phosphatidylserine synthase and the phospholipid-N-methyltransferases were found to be maximal at the end of logarithmic growth and to decrease upon entering stationary phase in all media. Cells grown on lactate displayed a significantly higher phospholipid:protein ratio than cells grown on glucose. The results are discussed in terms of regulation of phospholipid biosynthesis and membrane biogenesis in response to growth phase and carbon source. Copyright © 2000 John Wiley & Sons, Ltd.