A fast and efficient protocol is presented for the isolation of plastoglobule lipid droplets associated with various photosynthetic organisms. The successful preparation of isolated plastoglobules is a crucial first step that precedes detailed molecular investigations such as proteomic and lipidomic analyses.
Plastoglobule lipid droplets are a dynamic sub-compartment of plant chloroplasts and cyanobacteria. Found ubiquitously among photosynthetic species, they are believed to serve a central role in the adaptation and remodeling of the thylakoid membrane under rapidly changing environmental conditions. The capacity to isolate plastoglobules of high purity has greatly facilitated their study through proteomic, lipidomic, and other methodologies. With plastoglobules of high purity and yield, it is possible to investigate their lipid and protein composition, enzymatic activity, and protein topology, among other possible molecular characteristics. This article presents a rapid and effective protocol for the isolation of plastoglobules from chloroplasts of plant leaf tissue and presents methodological variations for the isolation of plastoglobules and related lipid droplet structures from maize leaves, the desiccated leaf tissue of the resurrection plant, Eragrostis nindensis, and the cyanobacterium, Synechocystis sp. PCC 6803. Isolation relies on the low density of these lipid-rich particles, which facilitates their purification by sucrose density flotation. This methodology will prove valuable in the study of plastoglobules from diverse species.
The current understanding of plastoglobule composition and function has emerged through detailed proteomic and lipidomic studies1,2,3,4,5. Such studies have been greatly aided by a rapid and effective method of isolation that relies on their very low density for efficient separation using sucrose gradients. Initial methods of plastoglobule isolation were achieved from species such as the beech tree (Fagus sylvatica), scotch broom (Sarothamnus scoparius), onion (Allium cepa), spinach (Spinacia oleracea), pansy (Viola tricolor), pepper (Capsicum annuum), and pea (Pisum sativum)6,7,8,9,10,11,12,13. An updated method to isolate chloroplast plastoglobules in a more efficient and better yielding manner was later presented by Ytterberg et al.3,14. While initially employed for the study of the plastoglobules of Arabidopsis thaliana leaf chloroplasts, we have successfully employed this updated method for the healthy leaf tissue of other plant species, both monocot and dicot, including maize (Zea mays), tomato (Solanum lycopersicum), lovegrass (Eragrostis nindensis), purple false brome (Brachypodium distachyon), and wild tobacco (Nicotiana benthamiana; unpublished results). Furthermore, the isolation method has been successfully adapted to the plastoglobules of cyanobacteria, including Synechocystis sp. PCC 6803 and Anabaena sp. PCC 712015, and the desiccated leaf tissue of the resurrection plant, E. nindensis.
Chloroplast plastoglobules of healthy leaf tissue are physically connected to the thylakoid membranes16. Despite this physical continuity, the two chloroplast sub-compartments maintain distinct lipid and protein compositions, although the regulated exchange of lipid and protein between the two compartments has been proposed2,4,17,18,19. In fact, an interesting hemifusion model has recently been proposed for the trafficking of neutral lipids between chloroplasts and cytosol19. Due to the physical continuity of plastoglobules and thylakoids, the isolation method with healthy leaf tissue begins with the collection of a pelleted crude thylakoid preparation, which is subsequently sonicated to separate the plastoglobules from the thylakoids, which is in contrast to methods used for isolating cytosolic lipid droplets20. Ultracentrifugation on a sucrose cushion then floats the low-density plastoglobules up through the sucrose, effectively separating them from the thylakoids, nuclei, and other high-density material. In contrast, plastoglobules in cyanobacteria, as well as those of desiccated leaf tissue, evidently exist in vivo in a free-floating form. Hence, their isolation involves directly floating on a sucrose gradient. This article demonstrates the isolation method from healthy leaf tissue and further demonstrates two variations that can be used to isolate plastoglobules from desiccated leaf tissue or cyanobacterial cultures, greatly expanding the physiological breadth and evolutionary context in which plastoglobules can be studied.
Isolated plastoglobules can subsequently be used for any number of downstream analyses to investigate molecular characteristics. We have used the isolated plastoglobules from A. thaliana leaf tissue for extensive proteomic and lipidomic analysis under differing environmental conditions or genotypes, demonstrating the selective modification of protein and lipid composition in adaptation to stress2,4,21,22. In addition, in vitro kinase assays that demonstrate trans-phosphorylation activity associated with isolated plastoglobules have been performed22, the oligomeric states of protein components has been investigated using native gel electrophoresis 21, and protease-shaving assays have been performed23.
The primary benefit of this method is the relative speed of the procedure. In our experience, the protocols outlined below can be fully completed within approximately 4 h. An alternate method to isolate plastoglobules from leaf tissue has been described, which allows the simultaneous isolation of other chloroplast sub-compartments24. This alternative method offers some clear advantages when quantitative comparison to the other chloroplast sub-compartments is necessary or desired. However, this alternative method is also more tedious and will provide a significantly lower yield of isolated plastoglobules from comparable quantities of leaf tissue. When a focused study of plastoglobules is the aim, the methodology outlined here is the optimal choice. Nonetheless, total leaf and crude thylakoid aliquots can be collected during the sample preparation, and it is highly recommended to do so, to have reference samples for subsequent comparison.
1. Crude plastoglobule isolation
2. Harvesting pure plastoglobules
Upon completion of step 1 of the protocol, one should be able to readily see a considerable amount of plastoglobule/lipid droplet material floating on (or near) the top layer of the sucrose cushion (Figure 1B–C). Other fractions could also be collected at this stage. For example, the thylakoids will be pelleted and can be re-suspended with medium R 0.2 for subsequent analyses. After subsequent centrifugation, purified plastoglobules will be obtained at or near the surface of the sucrose gradient, as shown in Figure 1A,C. It has been seen in certain circumstances (e.g., specific genotypic lines or environmental conditions) that the plastoglobules will isolate as two distinct sub-populations separating at different layers in the gradient: a low-density fraction on the gradient surface and a second, denser fraction that settles at the interface between the top two gradient layers. While a careful comparative analysis of the separating fractions has not previously been performed, it seems likely that these sub-populations represent differently sized plastoglobules, in which those with smaller diameter (and hence greater surface area to volume ratio and protein to lipid ratio) will settle lower in the gradient.
In an unsuccessful attempt, one will see little or no visible plastoglobules on the surface of the sucrose cushion after the first round of centrifugation. Failure to successfully isolate enough plastoglobules can depend on several factors that may need to be optimized. In particular, the sonication technique (when using healthy leaf tissue) can have a significant impact on the success. Additionally, the necessary amount of plant/cyanobacterial material will be dependent on the specific species and its stress condition.
After the successful isolation of plastoglobules, it is possible to validate the purity of the isolated plastoglobules using immunoblotting of the marker proteins for plastoglobules and thylakoids (the primary contaminating compartment). In Figure 1D, representative immunoblots are seen using antibodies raised against A. thaliana FBN1a, as a marker for plastoglobules2, and against A. thaliana photosystem II subunit D1, as a marker of thylakoids27. The FBN homologs in Synechocystis sp. PCC 6803 associate primarily with thylakoids rather than plastoglobules.
One should also carefully consider the manner of storage, which may depend on the intended downstream studies. Especially for downstream analyses of prenyl-lipid pigment lipids, it is crucial to minimize exposure of the samples to direct light to avoid damage of the photo-labile compounds. Purified plastoglobules can be used for downstream experiments such as lipidomic- or proteomic-based experiments. Plastoglobules are characterized by a very low protein to lipid ratio, which manifests in their low density and capacity to float on the sucrose; thus, a low protein concentration of the plastoglobule samples is normal. For this reason, it is advisable to remove lipids prior to protein separation by SDS-PAGE using acetone protein precipitation or chloroform/methanol extraction.
Figure 1: Isolation and immunoblotting of plastoglobules and thylakoids. (A) A representative purified plastoglobule sample from Z. mays prior to extraction from the sucrose gradient. (B) A representative crude plastoglobule sample from desiccated E. nindensis prior to extraction from the sucrose cushion. (C) A representative crude (left) and pure (right) plastoglobule sample from Synechocystis sp. PCC 6803, showing both before and after ultracentrifugation of the loaded sucrose cushion and gradient, respectively. (D) Anti-fibrillin1a antibody (α-FBN1a) was used to monitor the accumulation of fibrillin, a marker protein of plastoglobules in higher plants. The fibrillin ortholog accumulates predominantly in the isolated thylakoids of cyanobacteria (Synecho, Syenchocystis sp. PCC 6803). Anti-photosystem II subunit D1 (α-PsbA) was used to validate the depletion of thylakoids from plastoglobule isolations. In each lane, 5 µg of thylakoids and 10 µg of plastoglobule protein were loaded. Abbreviations: PG = plastoglobules; Thy = thylakoids. Please click here to view a larger version of this figure.
Buffer compositions a | |
Grinding Buffer | 50 mM HEPES-KOH (pH 8.0) |
5 mM MgCl2 | |
100 mM sorbitol | |
5 mM ascorbic acid b | |
5 mM reduced cysteine b | |
0.05 % (w/v) BSA b | |
Medium R | 50 mM HEPES-KOH (pH 8.0) |
5 mM MgCl2 | |
Medium R 0.2 | 50 mM HEPES-KOH (pH 8.0) |
5 mM MgCl2 | |
0.2 M sucrose | |
Medium R 0.7 | 50 mM HEPES-KOH (pH 8.0) |
5 mM MgCl2 | |
0.7 M sucrose | |
Buffer A | 25 mM HEPES-KOH (pH 7.8) |
250 mM sucrose | |
a Final concentrations of each buffer component are provided. | |
b Must be added fresh on the day of the isolation. While buffers can be prepared the day before the isolation, these certain ingredients must be added fresh on the day of the isolation, as well as any phosphatase and protease inhibitors. |
Table 1: Buffer recipes for plastoglobule isolation from plant leaf tissue or cyanobacteria.
Phosphatase Inhibitor Cocktail b | |
Inhibitor | Final Conc. (mM) |
Na-Fluoride | 50 |
β-Glycerophosphate⋅2Na⋅5H2O | 25 |
Na-OrthoVanadate | 1 |
Na-Pyrophosphate⋅10H2O | 10 |
b Phosphatase inhibitors must be added fresh the day of the isolation. |
Table 2: Phosphatase inhibitor cocktail.
Protease Inhibitor Cocktail a | ||||
Inhibitor | Stock (mg/mL) | Stock medium | Dilution factor | Final conc. (mg/mL) |
Antipain⋅2HCl | 20 | water | 400x | 50 |
Bestatin | 1 | 0.15 M NaCl | 25x | 40 |
Chymostatin | 20 | DMSO | 2000x | 10 |
E-64 | 20 | water | 2000x | 10 |
Leupeptin (hemisulfate) | 20 | water | 4000x | 5 |
P-ramidon⋅2Na | 20 | water | 2000x | 10 |
AEBSF | 50 | water | 1000x | 50 |
Aprotinin | 10 | water | 5000x | 2 |
a The protease stock solutions must be stored at -20 °C in small aliquots for long term storage. Thaw and add fresh to appropriate buffer immediately prior to isolation. |
Table 3: Protease inhibitor cocktail.
To minimize physiological/biochemical changes to the material and protect certain photo- and thermo-labile prenyl-lipid pigments that are a rich component of plastoglobules, it is critical to perform the isolation at 4 °C and protected from light. As indicated above, the initial steps are performed in the cold room under a safety lamp using a green-emitting light bulb. The subsequent steps performed in the laboratory are under dimmed lights and use ice or refrigerated centrifugation. For similar reasons, the inclusion of fresh protease inhibitors (and phosphatase inhibitors if there is an interest in studying the phospho-regulation of proteins) is critical (Table 2 and Table 3).
While other methods (e.g., a Dounce homogenizer, freeze-thaw cycles) could, in principle, be employed to release plastoglobules from thylakoids in higher plant chloroplasts, sonication has been found to be far superior in providing the best yield and purity (unpublished results). Sonication may create artificial vesicles from thylakoid lamellae or endoplasmic reticulum; however, these vesicles would be very protein-rich and, hence, dense, precluding their flotation on the sucrose gradient.
When extracting the floating pad of pure plastoglobules from the sucrose gradient, it is beneficial to extract them in the smallest amount of medium R as possible. Acquiring concentrated plastoglobules in this manner facilitates downstream studies by minimizing the necessary volumes of sample. The use of a syringe and 22 G needle is the most effective strategy to extract the plastoglobules. Due to their hydrophobic, lipid-rich nature, they are extremely sticky, and the use of pipette tips or a spatula should be avoided at all costs. It has been found that the loss of plastoglobules due to sticking is best minimized with a syringe and needle, although it does not seem possible to completely prevent some loss during extraction.
If an easily visible, yellow-creamy layer of plastoglobules is not seen floating on or near the surface of the sucrose gradient, insufficient plant/cyanobacterial material may have been used for the isolation. It has been found that monocots give higher plastoglobule yields than dicots from comparable amounts of plant tissue (unpublished results). While proper amounts of starting biological material are indicated for the specific isolations exemplified in this article, the necessary amounts of tissue for efficient extraction must be determined empirically based on the species, tissue, and environmental conditions of the organism. In general, stressed (but not necrotic) leaf tissue or cyanobacterial cultures will give higher yields of plastoglobules. When using A. thaliana leaf tissue, two flats of A. thaliana plants (nearly 140 individual plants) from the mid-vegetative growth stage are typically sufficient for the isolation of plastoglobules, especially when the plant material is mildly stressed, for example, by a light stress treatment2,4. As an alternative explanation for poor yields, the initial homogenization of the leaf tissue with the blender may have been too vigorous and separated the plastoglobules from the thylakoids prematurely, or the sonication of the crude thylakoid material may have been insufficiently vigorous to effectively release the plastoglobules before flotation (these points are not an issue when extracting from cyanobacteria, which are free-floating in situ).
It is important to keep in mind that plastoglobule isolation will represent the bulk population of plastoglobules from a tissue sample. Hence, any possible heterogeneity in lipid, protein, or function would not be discernible from subsequent studies. Due to this limitation, it has not been possible to gauge how much heterogeneity may exist among individual plastoglobule lipid droplets. However, transmission electron micrographs of plant leaf tissue from multiple organisms reveal differential staining patterns amongst plastoglobules, even within the same chloroplast28,29,30,31. This strongly suggests heterogeneity in the lipid content, although the nature or purpose of this remains unclear. Significantly, electron micrographs of isolated A. thaliana plastoglobules demonstrate that this method of isolation is not biased for the isolation of larger or smaller plastoglobules2.
The isolation of pure plastoglobules represents the initial step toward their detailed molecular characterization. Numerous downstream applications can subsequently be carried out depending on the specific interests and purpose of the investigator. For example, to investigate the lipid or protein composition, the isolated sample is readily amenable to proteomic or lipidomic studies. The in-gel digestion approach is favored for bottom-up proteomics studies of plastoglobules samples. However, because lipids are in vast excess relative to protein, the lipid can interfere with the SDS-PAGE separation. The initial precipitation of protein using acetone, with subsequent resuspension in Laemmli solubilization buffer, eliminates most lipids, thereby allowing an efficient separation of protein in the SDS-PAGE separating gel. Initial resuspension of the protein pellet in 100 mM tris-HCl buffer and 2% SDS allows accurate determination of the protein content by the bicinchoninic acid method before the addition of reductant, dye, and glycerol. Likewise, lipid purification using liquid-liquid phase separation methods, such as the Bligh and Dyer method, is suitable for downstream lipidomic analyses32.
The authors have nothing to disclose.
Research in the Lundquist lab group is supported by grants from the NSF (MCB-2034631) and USDA (MICL08607) to P.K.L. The authors thank Dr. Carrie Hiser (MSU) for support in the development of the cyanobacterial plastoglobule isolation method.
AEBSF | Milipore Sigma | P7626 | |
Antipain.2HCl | Bachem | H-1765.0050BA | |
Aprotinin | Milipore Sigma | A6106 | |
Ascorbate | BDH | BDH9242 | |
Bestatin | Sigma Aldrich | B8385 | |
Beta-Glycerophosphate. 2Na5H2O | EMD Millipore | 35675 | |
Bovine Serum Albumin | Proliant Biological | 68700 | |
Chymostatin | Sigma Aldrich | C7268 | |
Eragrostis nindensis | N/A | N/A | |
E-64 | Milipore Sigma | E3132 | |
French Pressure cell (model FA-079) | SLM/Aminco | N/A | |
HEPES | Sigma Aldrich | H3375 | |
Leupeptin | Sigma Aldrich | L2884 | |
Magnesium Chloride | Sigma Aldrich | M8266 | |
Multitron shaking incubator | Infors HT | N/A | |
Phospho-ramidon.2 Na | Sigma Aldrich | R7385 | |
Potassium Hydroxide | Fisher Chemicals | M16050 | |
Reduced Cysteine | MP Biochemicals | 101444 | |
Sodium Fluoride | Sigma Aldrich | S7920 | |
Sodium Ortho-vanadate | Sigma Aldrich | 450243 | |
Sodium Pyrophosphate · 10H2O | Sigma Aldrich | 3850 | |
Sorbitol | Sigma Aldrich | S3889 | |
Sucrose | Sigma Aldrich | S9378 | |
Sylvania 15 W fluorescent Gro-Lux tube light bulb, 18" | Walmart | N/A | |
Synechocystis sp. PCC 6803 | N/A | N/A | |
Optima MAX-TL Ultracentrifuge | Beckman Coulter | A95761 | |
Waring Blender (1.2 L) | VWR | 58977-227 | Commercial blender |
Zea mays | N/A | N/A |