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Method Article
Two techniques for isolating cellular lipid droplets from 1) yeast cells and 2) human placentas are presented. The centerpiece of both procedures is density gradient centrifugation, where the resulting floating layer containing the droplets can be readily visualized by eye, extracted, and quantified by Western Blot analysis for purity.
Lipid droplets are dynamic organelles that can be found in most eukaryotic and certain prokaryotic cells. Structurally, the droplets consist of a core of neutral lipids surrounded by a phospholipid monolayer. One of the most useful techniques in determining the cellular roles of droplets has been proteomic identification of bound proteins, which can be isolated along with the droplets. Here, two methods are described to isolate lipid droplets and their bound proteins from two wide-ranging eukaryotes: fission yeast and human placental villous cells. Although both techniques have differences, the main method - density gradient centrifugation - is shared by both preparations. This shows the wide applicability of the presented droplet isolation techniques.
In the first protocol, yeast cells are converted into spheroplasts by enzymatic digestion of their cell walls. The resulting spheroplasts are then gently lysed in a loose-fitting homogenizer. Ficoll is added to the lysate to provide a density gradient, and the mixture is centrifuged three times. After the first spin, the lipid droplets are localized to the white-colored floating layer of the centrifuge tubes along with the endoplasmic reticulum (ER), the plasma membrane, and vacuoles. Two subsequent spins are used to remove these other three organelles. The result is a layer that has only droplets and bound proteins.
In the second protocol, placental villous cells are isolated from human term placentas by enzymatic digestion with trypsin and DNase I. The cells are homogenized in a loose-fitting homogenizer. Low-speed and medium-speed centrifugation steps are used to remove unbroken cells, cellular debris, nuclei, and mitochondria. Sucrose is added to the homogenate to provide a density gradient and the mixture is centrifuged to separate the lipid droplets from the other cellular fractions.
The purity of the lipid droplets in both protocols is confirmed by Western Blot analysis. The droplet fractions from both preps are suitable for subsequent proteomic and lipidomic analysis.
Cellular lipid droplets are dynamic organelles that serve multiple functions in cells. They are storage hubs for neutral lipids, which can be converted into energy or used for phospholipid synthesis. The droplets play central roles in physiological and pathological conditions including atherosclerosis, obesity and related metabolic diseases, and also infectious diseases1,2. In addition, they are intriguing sources for biodiesel fuels.
Much information on the cellular roles of lipid droplets has been obtained from proteomic and lipidomic analysis of droplets purified from wide-ranging organisms3. These organisms have included bacteria4,5, yeast6-11, plants12,13, nematodes14, and flies15,16. Given the interest in the role of lipid droplets in human metabolic diseases, droplets have also been isolated from cultured animal cells and animal tissues. Cultured cell lines have included 3T3-L1 adipocytes17, Chinese hamster ovary (CHO) K2 cells18, human hepatocyes19,20, and epithelial cell lines21. Animal tissues from which droplets have been isolated have included mouse skeletal muscle22, liver23, and mammary glands23. As mentioned above, the goal of most droplet isolation studies is to perform proteomic analysis on the bound factors and lipidomic analysis on the neutral and phospholipids.
Since neutral lipids - the most numerous component of lipid droplets - are less dense than most other cellular materials, isolation of droplets has traditionally been performed using density gradient centrifugation. That technique is the centerpiece of both preps presented here. Previous techniques6,24 are combined and modified into a visual presentation of the isolation of droplets from cultured fission yeast cells and noncultured human cells obtained from placental tissue. The goal is to show the broad applicability of this technique by choosing two vastly different cell types as starting points for the droplet isolation. This technique should be useful for those wishing to isolate droplets from most organisms.
Protocol 1 describes the isolation of lipid droplets from the fission yeast, Schizosaccharomyces pombe, which has been used as a model for observing droplet formation during eukaryotic cell division25. The budding yeast Saccharomyces cerevisiae has been used extensively as a model organism for studying lipid droplet biology. Protocol 1 is applicable to both organisms and differences in the preparations are highlighted.
Protocol 2 describes the isolation of lipid droplets from placental villous cells, which are in turn obtained from human term placentas. The collection of term placentas provides a unique opportunity to safely and ethically obtain 200-250 g of readily available human tissue26, which contains significant numbers of lipid droplets. This is in contrast to most lipid droplet isolation work in higher eukaryotes where the droplets originate from cultured cells. In those studies, fatty acids are often added to the culture to promote the synthesis of neutral lipids and thus the growth of droplets. This is in contrast to the work here where lipid droplets are formed under native conditions in placental tissue.
The purities of the lipid droplet fractions are determined by Western Blot analysis using organelle marker antibodies. These two protocols will yield lipid droplet fractions that are suitable for subsequent proteomic and lipidomic analysis.
1. Isolating Lipid Droplets from (Fission) Yeast Cells
Isolation of droplets from the popular model organism budding yeast Saccharomyces cerevisiae is almost identical to the following protocol6. Differences in the preparations are noted.
1. Growing yeast cells
2. Converting fission yeast cells into spheroplasts and subsequent lysis
3. Density gradient centrifugation
2. Isolating Lipid Droplets from Human Placental Villous Cells
Placentas were collected from healthy women with singleton pregnancies undergoing elective cesarean section delivery prior to the onset of spontaneous labor at term. Subjects gave written, informed consent for the collection of their placenta. The collection, and subsequent use, of placentas was performed with approval from the University of Tennessee and University of Tennessee Graduate School of Medicine in Knoxville Institutional Review Board (#8757B and #3338, respectively).
1. Isolating human placental villous cells
Part 1 of the protocol is a modification of an earlier published protocol by Petroff et al.26
Prepare following solutions:
2. Homogenizing placental villous cells
3. Isolating lipid droplets by ultracentrifugation
Characterizing lipid droplets fraction (Protocols 1 and 2)
The recovery and purity of the lipid droplet fraction can be verified by Western Blot combined with light or electron microscopy. In addition, aliquots after different centrifugation steps can be collected and retained for determining purification efficiency. In Western Blotting, it is more appropriate to compare a volume of the lipid droplet fraction that represents an equivalent of the whole cell lysate than comparing lipid droplets to other membrane fractions on the basis of total protein content24.
If the density gradient centrifugation worked as expected, the floating layer should contain lipid droplets and be depleted of other organelles throughout the progression of the high-speed spins.
For Protocol 1, Western Blots were performed with marker antibodies to lipid droplets (Erg6p), and organelles that have been found to interact with lipid droplets in yeast, ER (Dpm1p), mitochondria (Por1p), plasma membrane (Pma1p), and vacuoles (Vma1p).
Equal volumes of the...
Critical steps within this protocol
Make sure to be consistent with media and cell densities during growth of cultured cells. Cellular lipid droplets are unique in that their associated proteins are highly dependent upon the environment in which the cells are cultured17. Therefore, the media in which the cells are grown and the density of the cells should be closely monitored before lysis.
The protein composition of lipid...
The authors declare no competing financial interests.
This work was supported by American Heart Association award 13SDG14500046 to P.D., a Sustainable Energy Education & Research Center Award (Univ. of Tennessee) to P.D., and by the Physicians’ Medical Education and Research Foundation (Univ. of Tennessee) award to J.M. The authors thank Caroline Leplante (Yale Univ.) for the protocol for converting fission yeast to spheroplasts; Eric T. Boder (Univ. of Tennessee) for the use of his shaking incubators, tabletop centrifuge, and Western Blot analysis equipment; and the Center for Environmental Biotechnology (Univ. Tennessee) for the use of their ultra-centrifuge; Günther Daum for yeast antibodies (Graz Univ. of Technology, Austria); the personnel of the Department of Obstetrics and Gynecology (Univ. Tennessee Medical Center) for technical assistance.
Name | Company | Catalog Number | Comments |
Protocol 1 | |||
1. Growing yeast cells and converting to spheroplasts | |||
Edinburgh Minimal Media (EMM) | Sunrise Science Products | 2005 | |
Yeast extract with 5 supplements (YE5S) | Sunrise Science Products | 2011 | YE5S media with 225 mg/ml of each supplement: adeninie, histidine, leucine, lysine, uracil. The equivalent for budding yeast would be YPD. |
YPD powder | Sunrise Science Products | 1875 | For S. cerevisiae |
Sorbitol | Fisher Scientific | BP439 | |
Yeast Lytic Enzyme | MP Biomedicals | 215352610 | |
Lysing Enzymes from Trichoderma harzianum | Sigma-Aldrich | L1412 | |
Zymolayse-20T | Sunrise Science Products | N0766391 | For S. cerevisiae |
BODIPY 493/503 | Invitrogen | D-3922 | |
Microscope Slides | Fisher Scientific | 12-544-7 | |
Microscope Cover Glass | Fisher Scientific | 12-542-B | |
Plastic transfer pipette | Fisher Scientific | 137115AM | |
1 L glass bottle | |||
250 ml flask | |||
2.8 L flasks | |||
2. Yeast lipid droplet isolation | |||
Tris-HCl | Fisher Scientific | BP153 | |
EDTA | Fisher Scientific | BP120 | |
Ficoll 400 | Fisher Scientific | BP525 | |
12-14k Spectra/Por Dialysis Membrane | SpectrumLabs | 132680 | |
EDTA-free Protease Inhibitor Cocktail Tablets | Roche Diagnostics | 11873580001 | irritant |
Dounce Homogenizer | Sigma-Aldrich | D9938 | |
Ultracentrifuge Tubes 25 mm x 89 mm (for SW28) | Beckman-Coulter | 355642 | |
12-14k Spectra/Por Dialysis Membrane | SpectrumLabs | 132680 | |
Temperature-controlled shaker | New Brunswick Scientific | C25KC | |
Thermo Sorvall Legend XTR centrifuge | Thermo-Scientific | 75004521 | |
Swinging Bucket Centrifuge Rotor | Thermo-Scientific | 75003607 | |
Fiberlite* F15-6x100y Fixed-Angle Rotor | Thermo-Scientific | 75003698 | |
Ultracentrifuge LB-M | Beckman-Coulter | ||
SW28 Ultracentrifuge Rotor | Beckman-Coulter | 342204 | |
Protocol 2 | |||
1. Placental villous cells isolation | |||
Disposable underpads | Fisher Scientific | 23666062 | |
Autoclavable pan (container), 3 L | Fisher Scientific | 1336110 | |
Fine scissors, sharp-sharp, straight | Fine Science Tools | 1406011 | |
London Forceps | Fine Science Tools | 1108002 | |
Dumont #7b Forceps | Fine Science Tools | 1127020 | |
Razor blades | Fisher Scientific | S65921 | |
Screen cup for CD-1 | Fisher Scientific | S1145 | |
40 mesh screen | Fisher Scientific | S0770 | |
Fisherbrand cell stainers 100 μm | Fisher Scientific | 22363549 | |
150 mm Petri Dishes | Fisher Scientific | NC9054771 | |
NaCl | Fisher Scientific | S642 | |
KCl | Fisher Scientific | P333 | |
KH2PO4 | Fisher Scientific | P386 | |
Na2HPO4 | Fisher Scientific | S374 | |
D-Glucose | Fisher Scientific | D16 | |
HEPES | Fisher Scientific | BP310 | |
2.5% Trypsin 10x | Invitrogen | 15090046 | |
DNase I grade II, from bovine pancreas | Roche Applied Science | 10104159001 | |
Sodium bicarbonate solution | Sigma-Aldrich | S8761 | |
500 ml Erlenmeyer flasks | |||
250 ml Beakers | |||
15 ml Centrifuge tubes | |||
10 ml Serological pipettes | |||
50 ml Centrifuge tubes | |||
DMEM | Invitrogen | 11965084 | |
2. Lipid droplets isolation from villous placental cells | |||
Tris-HCl | Fisher Scientific | BP153 | |
EDTA | Fisher Scientific | BP120 | |
D-Sucrose | Fisher Scientific | BP220 | |
Sodium Carbonate | Fisher Scientific | BP357 | |
EDTA-free protease inhibitor cocktail tablets | Roche Diagnostics | 11873580001 | irritant |
Dounce homogenizer | Sigma-Aldrich | D9938 | |
Ultracentrifuge tubes 25 mm x 89 mm (for SW28) | Beckman-Coulter | 355642 | |
Ultra-Clear centrifuge tubes 14 mm x 89 mm (for SW41) | Beckman-Coulter | 344059 | |
Disposable borosilicate glass Pasteur pipets | Fisher Scientific | 1367820C | |
Biological safety hood | Thermo-Scientific | ||
Waterbath | Fisher Scientific | ||
Temperature-controlled shaker | New Brunswick Scientific | C25KC | |
Thermo Sorvall Legend XTR centrifuge | Thermo-Scientific | 75004521 | |
Swinging Bucket Centrifuge Rotor | Thermo-Scientific | 75003607 | |
Ultracentrifuge LB-M | Beckman-Coulter | ||
SW28 Ultracentrifuge Rotor | Beckman-Coulter | 342204 | |
SW41 Ti Ultracentrifuge Rotor | Beckman-Coulter | 331336 | |
Western blot | |||
IRDye 680 Goat Anti-Rabbit IgG | LI-COR | 926-68071 | dilution 1:15,000 |
IRDye 800CW Goat Anti-Mouse IgG | LI-COR | 926-32210 | dilution 1:5,000 |
NuPAGE Novex 12% Bis-Tris gels | Invitrogen | NP0341 | |
Primary antibodies for Protocol 1 | |||
Erg6p | gift from Dr. G. Daum | Graz University of Technology, Austria | dilution 1:5,000 |
Dpm1p | Abcam | ab113686 | 4 μg/ml |
Por1p | gift from Dr. G. Daum | Graz University of Technology, Austria | dilution 1:5,000 |
Pma1p | gift from Dr. G. Daum | Graz University of Technology, Austria | dilution 1:10,000 |
Vma1p (anti-ATP6V1A) | Abcam | ab113745 | 0.5 μg/ml |
Primary antibodies for Protocol 2 | |||
Perilipin 2 (anti-ADFP) | Abcam | ab52355 | 2 μg/ml |
Calnexin | Cell Signaling Technology | 2679 | dilution 1:1,000 |
GM130 | Biorbyt | orb40533 | dilution 1:25 |
COX IV | Cell Signaling Technology | 4850 | dilution 1:1,000 |
MEK1 | Biorbyt | orb38775 | dilution 1:50 |
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