Lipidomics: practical aspects and applications

Lipidomics is the characterization of the molecular species of lipids in biological samples. The polar lipids that comprise the bilayer matrix of the constituent cell membranes of living tissues are highly complex and number many hundreds of distinct lipid species. These differ in the nature of the polar group representing the different classes of lipid. Each class consists of a range of molecular species depending on the length, position of attachment and number of unsaturated double bonds in the associated fatty acids. The origin of this complexity is described and the biochemical processes responsible for homeostasis of the lipid composition of each morphologically-distinct membrane is considered. The practical steps that have been developed for the isolation of membranes and the lipids there from, their storage, separation, detection and identification by liquid chromatography coupled to mass spectrometry are described. Application of lipidomic analyses and examples where clinical screening for lipidoses in collaboration with mass spectrometry facilities are considered from the user point of view.     

Identification, isolation and characterization of tetracosapolyenoic acids in lipids of marine coelenterates.

Several tetracosapolyenoic acids (TPA) were detected in lipids of different marine coelenterates. Two of these acids were isolated and their structures were confirmed by chemical and spectral methods as all-cis-6,9,12,15,18-tetracosapentaenoic and all-cis-6,9,12,15,18,21-tetracosahexaenoic acid. Their distribution among lipids of a number of species of different classes of coelenterates from the northern and tropical seas, among neutral and polar lipids of these organisms was investigated. Significant quantities of TPA were found in all of the Octacorallia species studied. In some cases the sum of TPA reaches the level of 20% of total lipid fatty acids. The fatty acid composition of different coelenterates is also discussed.     

Correlations between the thermal stability of chloroplast (thylakoid) membranes and the composition and fluidity of their polar lipids upon acclimation of the higher plant,Nerium oleander,to growth temperature

The thermal stability of excitation transfer from pigment proteins to the Photosystem II reaction center of Nerium oleander adjusts by 10 Celsius degrees when cloned plants grown at 20°C/15°C, day/night growth temperatures are shifted to 45°C/32°C growth temperature or vice versa. Concomitant with this adjustment is a decrease in the fluidity of thylakoid membrane polar lipids as determined by spin labeling. The results are consistent with the hypothesis that there is a limiting maximum fluidity compatible with maintenance of native membrane structure and function. This limiting fluidity was about the same as for a number of other species which exhibit a range of thermal stabilities. Inversely correlated shifts in lipid fluidity and thermal stability occurred during the time course of acclimation of N. oleander to new growth temperatures. Thus, the temperature at which the limiting fluidity was reached changed during acclimation while the limiting fluidity remained constant. Although the relative proportion of the major classes of membrane polar lipids remained constant during adjustments in fluidity, large changes occured in the abundance of specific fatty acids. These changes were different for the phospho- and galacto-lipids suggesting that the fatty acid composition of these two lipid classes is regulated by different mechanisms. Comparisons between membrane lipid fluidity and fatty acid composition indicate that fluidity is not a simple linear function of fatty acid composition.     

Patterns of variation in the lipid class and fatty acid composition of Nannochloropsis oculata (Eustigmatophyceae) during batch culture

Changes in the lipid and fatty acyl compositions of the marine microalga Nannochloropsis oculata Droop were examined during a batch culture growth cycle. During the early phase of batch culture the cellular proportion of triacylglycerols (TAG) increased. This was in addition to the increases in TAG observed in many microalgal species in the stationary-phase. Concomitant increases in the relative proportions of both saturated and monounsaturated fatty acids and decreases in the proportion of polyunsaturated fatty acids in total lipid were also associated with this phase. The separated individual lipid classes were found to have characteristic fatty acyl compositions. The relative proportion of lipid per cell, the relative proportions of the individual lipid classes and the fatty acyl compositions of the individual classes were all subject to variability during the growth cycle. The changing total lipid fatty acyl composition of N. oculata was found to be determined by the proportion of the total lipid present as TAG. The data suggest that the changes observed in the fatty acyl composition of N. oculata are a result of the partitioning of photosynthetically fixed carbon between polar and neutral lipid class biosynthesis and fatty acyl desaturation and elongation pathways. The effect of such a partitioning of carbon is discussed in relation to the effects of environmental variables and growth phase upon the balance of lipid class and polyunsaturated fatty acids (PUFA) synthesis in marine microalgae.     

Measuring soil microbial community diversity using polar lipid fatty acid and denaturing gradient gel electrophoresis data

The possibility of calculating useful microbial community diversity indices from environmental polar lipid fatty acid and 16S rDNA PCR-DGGE data was investigated. First, the behavior of the species richness, Shannon's, and Simpson's diversity indices were determined on polar lipid fatty acid profiles of 115 pure cultures, communities constructed from those profiles with different numbers of species, and constructed communities with different distributions of species. Differences in the species richness of these artificial communities was detected by all three diversity indices, but they were insensitive to the evenness of the distribution of species. Second, data from a field experiment with substrate addition to soil was used to compare the methods developed for lipid- and DNA-based diversity indices. Very good agreement was found between indices calculated from environmental polar lipid fatty acid profiles and denaturing gradient gel electrophoresis profiles from matched samples (Pearson's correlation coefficient r=0.95-0.96). A method for data pre-treatment for diversity calculations is described.     

Lipid composition of developing Xenopus laevis embryos.

The total lipid content, amount of phospholipid, proportions of major polar and neutral lipid classes, and the overall fatty acid composition were examined in Xenopus laevis embryos. No obvious differences were observed in any of the parameters between fertilization and hatching or between eggs produced by different females. The average lipid content per egg was 113 mug, 31.6 mug of which was phospholipid. The major phospholipids were phosphatidylcholine and sphingomyelin. The major fatty acids were palmitic and oleic acids, but polyunsaturated fatty acids were also present in substantial amounts. The results suggest that significant de novo synthesis of lipids does not occur until after hatching.     

Occurrence of conjugated polyenoic fatty acids in seaweeds from the Indian Ocean

Three species of red marine macro algae (Rhodophyta) from the Indian Ocean were analysed for the occurrence of conjugated polyenes. The composition of different lipid classes in these seaweeds along with their fatty acid composition has also been reported. Analysis of lipid classes of these seaweeds revealed that both Acanthophora spicifera (Ceramiales, Rhodophyta) and two species of Gracilaria, viz. G. edulis and G. folifera (Gracilariales, Rhodophyta) were rich in glycolipids followed by neutral- and phospholipids. The fatty acid composition of these seaweeds revealed C16:0 as the predominant fatty acid in all three species. However, A. spicifera had significantly higher amounts of eicosapentaenoic acid (EPA) and arachidonic acid (AA) as compared to negligible amount of these fatty acids in both species of Gracilaria. The red seaweed Acanthophora spicifera contained conjugated eicosapentaenoic acid (CEPA) and conjugated arachidonic acid (CAA) in all lipid classes except glycolipids.     

Changes in the Lipid Composition of Thalassiosira pseudonana during Its Life Cycle

The lipid and fatty acid (FA) compositions of a marine diatom alga Thalassiosira pseudonana grown in culture were investigated. The relative content of separate lipid classes and their FA composition varied during of the life cycle. During the periods of active cell division and resting cell production, the proportion of polar lipids, as the structural components of cell membranes, increased. Changes in the proportion of lipid classes resulted in shifts in the FA composition of total lipids. It is suggested that the structural components of photosynthetic and cells membranes accumulate in the resting cells. Thereby, a rapid cell growth and an extensive development of the species under favorable environmental conditions is provided.     

Lipids of Pinus halepensis pollen

The total lipids of Pinus halepensis pollen were separated into individual classes of neutral and polar lipids and the components of each class were identified and determined quantitatively. Free fatty acids, waxes and triacylglycerols were found as the main constituents of neutral lipids and phosphatidylcholine and phosphatidylethanolamine of polar lipids. Glycerylether derivatives were detected in neutral and polar lipid fractions. Free and esterified volatile fatty acids were also found in pollen and its neutral lipid fraction.     

Lipid Profile Remodeling in Response to Nitrogen Deprivation in the Microalgae Chlorella sp. (Trebouxiophyceae) and Nannochloropsis sp. (Eustigmatophyceae)

Many species of microalgae produce greatly enhanced amounts of triacylglycerides (TAGs), the key product for biodiesel production, in response to specific environmental stresses. Improvement of TAG production by microalgae through optimization of growth regimes is of great interest. This relies on understanding microalgal lipid metabolism in relation to stress response in particular the deprivation of nutrients that can induce enhanced TAG synthesis. In this study, a detailed investigation of changes in lipid composition in Chlorella sp. and Nannochloropsis sp. in response to nitrogen deprivation (N-deprivation) was performed to provide novel mechanistic insights into the lipidome during stress. As expected, an increase in TAGs and an overall decrease in polar lipids were observed. However, while most membrane lipid classes (phosphoglycerolipids and glycolipids) were found to decrease, the non-nitrogen containing phosphatidylglycerol levels increased considerably in both algae from initially low levels. Of particular significance, it was observed that the acyl composition of TAGs in Nannochloropsis sp. remain relatively constant, whereas Chlorella sp. showed greater variability following N-deprivation. In both algae the overall fatty acid profiles of the polar lipid classes were largely unaffected by N-deprivation, suggesting a specific FA profile for each compartment is maintained to enable continued function despite considerable reductions in the amount of these lipids. The changes observed in the overall fatty acid profile were due primarily to the decrease in proportion of polar lipids to TAGs. This study provides the most detailed lipidomic information on two different microalgae with utility in biodiesel production and nutraceutical industries and proposes the mechanisms for this rearrangement. This research also highlights the usefulness of the latest MS-based approaches for microalgae lipid research.     

Incorporation into phospholipid classes and metabolism via desaturation and elongation of various 14C-labelled (n-3) and (n-6) polyunsaturated fatty acids in trout astrocytes in primary culture

The incorporation and metabolism of [1-14C]18:3(n-3), [1-14C]20:5(n-3), [1-14C]18:2(n-6), and [1-14C]20:4(n-6) were studied in primary cultures of trout brain astrocytes. There were no significant differences between the amounts of individual fatty acids incorporated into total lipid at 22 degrees C, with greater than 90% of all the fatty acids being incorporated into polar lipid classes. The distributions of 18:2(n-6), 18:3(n-3), and 20:5(n-3) in individual phospholipid classes at 22 degrees C were very similar, with 57-63 and 18-24% being incorporated into phosphatidylcholine and phosphatidylethanolamine, respectively. Approximately equal amounts of 20:4(n-6), approximately 30% of the total, were incorporated into each of phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. The metabolism of the (n-3) fatty acids to longer-chain and more unsaturated species was significantly greater than that of (n-6) acids, but delta 4-desaturase activity was very low. A culture temperature of 10 degrees C increased the incorporation of all the fatty acids into total lipid and that of C20 fatty acids into polar lipid. At 10 degrees C, the incorporation of C20 fatty acids into phosphatidylethanolamine and phosphatidylinositol was increased, and the incorporation into phosphatidylcholine and phosphatidylserine was decreased. The distribution of C18 fatty acids was unchanged at the lower temperature, as was the desaturation and elongation of all the polyunsaturated fatty acids incorporated.     

Analysis of interspecific variation in relative fatty acid composition: use of flow cytometry to estimate unsaturation index and relative polyunsaturated fatty acid content in microalgae

Relative polyunsaturated fatty acid content and unsaturation index are very important composition variables in the use of microalgae both for animal and human nutrition and biofuel production. A readily available technique to rapidly and inexpensively estimate relative fatty acid composition is very important for mass screening of new strains for the production of different types of oil. This study demonstrates the validity of Nile Red staining and flow cytometry for quick estimation of unsaturation index and relative fatty acid content in microalgae. Nile Red staining allows polar and neutral lipid contents to be estimated, and in this study a significant correlation was observed between polar/neutral ratio and fatty acid content in the species studied, corresponding to higher polyunsaturated fatty acid content in the polar lipid fraction of microalgae. This technique enables quick estimation of relative polyunsaturated fatty acid content and interspecific variation, as well as variations caused by culture conditions. In the species studied, most variability in fatty acid composition was due to variation in monounsaturated and polyunsaturated fatty acids, with less variation observed in saturated fatty acid content.     

Polar lipid and fatty acid profiles – Re-vitalizing old approaches as a modern tool for the classification of mycoplasmas?

A set of 20 Mollicutes strains representing different lines of descent, including the type species of the genus Mycoplasma, Mycoplasma mycoides, Acholeplasma laidlawii and a strain of Mesoplasma, were subjected to polar lipid and fatty acid analyses in order to evaluate their suitability for classification purposes within members of this group. Complex polar lipid and fatty acid profiles were detected for each examined strain. All strains contained the polar lipids phosphocholine-6'-alpha-glucopyranosyl-(1'-3)-1, 2-diacyl-glycerol (MfGL-I), 1-O-alkyl/alkenyl-2-O-acyl-glycero-3-phosphocholine (MfEL), sphingomyelin (SphM), 1-O-alkyl/alkenyl-glycero-3-phosphocholine (lysoMfEL), the unknown aminophospholipid APL1 and the cholesterol Chol2. A total of 19 strains revealed the presence of phosphatidylethanolamine (PE) and/or phosphatidylglycerol (PG), and the presence of diphosphatidylglycerol (DPG) was detected in 13 strains. The unknown aminolipid AL1 was found in the extracts of 17 strains. Unbranched saturated and unsaturated compounds predominated in the fatty acid profiles. Major fatty acids were usually C16:0, C18:0, C18:1 omega9c and 'Summed feature 5' (C18:2 omega6, 9c/C18:0 anteiso). Our results demonstrated that members of the M. mycoides cluster showed rather homogenous polar lipid and fatty acid profiles. In contrast, each of the other strains was characterized by a unique polar lipid profile and significant quantitative differences in the presence of certain fatty acids. These results indicate that analyses of both polar lipid and fatty acid profiles could be a useful tool for classification of mycoplasmas.     

Improved high-performance liquid chromatographic method for the separation and quantification of lipid classes: application to fish lipids

An improved straight-phase HPLC method for the separation and quantification of lipid classes is described. Two binary gradient solvent systems were used, one for polar and one for neutral lipids, and detection was performed with a light-scattering detector. The developed HPLC methods were highly reproducible and allowed base-line separation of all investigated polar lipid classes (phosphatidic acid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingomyelin, phosphatidylserine, phosphatidylinositol and lysophosphatidylcholine) and neutral lipid classes (triacylglycerol, free fatty acid, diacylglycerol, cholesterol and monoacylglycerol) except of cholesterol ester and wax ester. Application of the chromatographic systems demonstrated that the methods are suitable for quantitative analysis of the major lipid classes present in lipid extracts from livers and eggs of Atlantic salmon (Salmo salar).     

Composition, accumulation and utilization of yolk lipids in teleost fish

Lipid reserves in teleost eggs are stored in lipoprotein yolk and, in some species, a discrete oil globule. Lipoprotein yolk lipids are primarily polar lipids, especially phosphatidylcholine and phosphatidylethanolamine (PE), and are rich in (n–3) polyunsaturated fatty acids, especially 22:6(n–3) (docosahexaenoic acid, DHA). Oil consists of neutral lipids and is rich in monounsaturated fatty acids (MUFA). Egg lipids are derived from dietary fatty acid, fatty acid mobilized from reserves and possibly fatty acid synthesized de novo. There is selective incorporation of essential fatty acids, particularly DHA, into yolk lipids and discrimination against incorporation of 22:1(n–11). Lipid is delivered to the oocyte by vitellogenin, which is rich in polar lipids, and likely also by other lipoproteins, especially very low density lipoprotein, which is rich in triacylglycerol (TAG). All classes of lipid may be used as fuel during embryonic and larval development and MUFA are preferred fatty acids for catabolism by embryos. Catabolism of oil globules is frequently delayed until latter stages of development. In some species, DHA derived from hydrolysis of phospholipid may be conserved by transfer to the neutral lipid. Recent work has expanded knowledge of the role of DHA in membrane structure, especially in neural tissue, and molecular species analysis has indicated that PE containing sn-1 oleic acid is a prime contributor to membrane fluidity. The results of this type of study provide an explanation for the selection pressures that influence yolk lipid composition. Future work ought to expand knowledge of specific roles of individual fatty acids in embryos along with knowledge of the ecological physiology of ovarian recrudescence, environmental influences on vitellogenin and yolk lipid composition, and the control of yolk lipid accumulation and utilization.     

Biodegradation of solar by Candida guilliermondii strain 1

Summary Candida guilliermondii strain 1 was grown on solar as a sole carbon source for 14 days, and the lipid classes were investigated. The yeast showed high affinity towards hydrocarbons of short chain length, and within 6 days the cellular lipid classes represented 39.69%, 27.50%, 15.35%, 2.23%, 16.20% of hydrocarbons, neutral lipids, free fatty acids, sterols and polar lipids respectively. Undecanoic and hexadecanoic acids were the major fatty acids of the cellular neutral lipids and oleic acid was the major component of the polar lipids.     

Lipids and fatty acids of two pelagic cottoid fishes (Comephorus spp) endemic to Lake Baikal

Matured females of two Lake Baikal endemic fish species, Comephorus baicalensis and Comephorus dybowski, have been investigated for lipid of the whole body and specific tissues (liver, muscles, ovaries), phospholipid classes and fatty acids of neutral and polar lipids. Total lipid in the body (38.9% fresh weight), liver (23.5%) and muscles (14.5%) of C. baicalensis were greater than those of C. dybowski (4.7, 8.7 and 2.6%, respectively); only their ovaries were similar (5.3 and 5.6% lipid, respectively). In both species, phosphatidylcholine and phosphatidylethanolamine were the major phospholipids, ranging from 60.7 to 75.1% of total phospholipid and 14.5–25.7%, respectively. In most cases, monounsaturated fatty acids (MUFA) were the major fatty acid group in C. baicalensis, whereas polyunsaturated fatty acids (PUFA) were the major group in C. dybowski. The MUFA 18:1(n-9) prevailed over other fatty acids in C. baicalensis and varied from 19% in polar lipids of muscles to 56.1% in neutral lipids of muscles. In polar lipid of C. dybowski, the PUFA 22:6(n-3) prevailed over other fatty acids in muscles and ovaries, while 16:0 dominated polar liver lipids and neutral lipids of all tissues. Other major fatty acids included 16:1(n-7), 18:1(n-7), and 20:5(n-3). Values of the (n-3)/(n-6) fatty acid ratio for neutral lipids of C. baicalensis (0.5–0.9) are well below the range of values characteristic either for marine or freshwater fish, while these values for polar lipids (1.6–1.8) are in the range typical of freshwater fish. Neutral lipid fatty acid ratios in C. dybowski (2.5–3.1) allow it to be assigned to freshwater fish, but polar lipids (2.8–3.7) leave it intermediary between freshwater and marine fish.     

Analysis of molecular species of plant polar lipids by high-performance and gas liquid chromatography

Total lipid extracts from potato tubers and tobacco leaves are separated into lipid classes by two step HPLC using a silicic column. Elution is first performed for 20 min with a programmed linear gradient of two mixed solvents running from 100% of solution A (isopropanol-hexane, 4:3) to 100% of solution B (isopropanol-hexane-water, 8:6:1.5); the column is then eluted with pure solution B in an isocratic mode for 20 min more. The main polar lipids (MGDG, DGDG, PC, PE, PG) from both plant tissues can be collected and further separated into component molecular species on a simplified HPLC system with a C₁₈ column eluted in an isocratic mode with a polar solvent. Molecular species separations are achieved within 35 min; quantifications are made through GLC analysis of attached fatty acids. Three to five main molecular species are thus clearly identified in each lipid class. In potato tuber, phospholipids (PC, PE) 18:2/18:2 species are predominant. In tobacco leaf, six double bond species (18:3/18:3 and 16:3/18:3) are predominant in galactolipids, whereas PC contains a greater number of molecular species varying by their degree of unsaturation (from 18:3/18:3 to 16:0/18:2). Only certain molecular species of PG contain Δ³-trans-hexadecenoic acid.     

Lipid content in 19 brackish and marine microalgae: influence of growth phase, salinity and temperature

Algal lipids provide essential fatty acids for higher trophic levels in the marine food web, and understanding the fatty acid composition in phytoplankton is critical for evaluating its value as a diet. Nineteen microalgal species, mainly originating from the Baltic Sea, covering major algal classes were grown in different growth conditions. Samples were taken during both the exponential and stationary growth phases and analysed regarding their fatty acid methyl esters and free fatty acids. Our results show that across all screened species, total fatty acids increased significantly from exponential to stationary growth phase. Furthermore, it was observed that warm-water species contained more lipids and differed in their lipid profile as compared with the cold-water species. Brackish water species also showed a slightly higher lipid content than the marine species, but their lipid profile was not significantly different. Plotting changes in lipids against changes in cell nitrogen revealed a significant dependency between decrease in cell nitrogen and increase in lipids across all tested species.     

The Chemical Nature of the Polar Functional Group of Oxidized Acyl Chain Uniquely Modifies the Physicochemical Properties of Oxidized Phospholipid-Containing Lipid Particles

Oxidative modification of phospholipids generates a variety of oxidized phospholipid (Ox-PL) species which differ considerably in their chemical compositions and molecular structures. Recent results suggest that even closely related Ox-PL species can have considerably different biological effects. However, the molecular mechanism for this is not yet clear. In truncated Ox-PLs (tOx-PLs) the fatty acyl chain is shorter in length than the parent nonoxidized phospholipid molecules and contains a polar functional group(s). In a previous study we showed that two closely related tOx-PL species having a similar polar functional group and differing only in the length of the oxidized fatty acyl chain exerts significantly different effects on the physicochemical properties of the nonoxidized phospholipid particles containing these lipids (Kar et al., Chem Phys Lipids 164:54–61, 2011). In this study we have characterized the effect of polar functional groups of oxidized fatty acyl chain on the physicochemical properties of the nonoxidized phospholipid particles containing these lipids. Our results show that Ox-PL species differing only in the chemical nature of polar functional groups in their oxidized fatty acyl chain modify the properties of nonoxidized phospholipid particles containing them in a distinctive way. These results indicate that different species of Ox-PLs induce unique changes in the physicochemical properties of lipid particles/membranes containing them and that this may lead to their different biological effects.