We thank R. Bartenschlager (University of Heidelberg) for the Jc1 constructs, C.M. Rice (Rockefeller University) for the Huh7.5 cells, J. McLauchlan (Medical Research Council Virology Unit) for the JFH1 construct, T. Wakita (National Institute of Infectious Diseases, Japan) for the JFH1, and B. Webster and W.C. Greene (Gladstone Institute of Virology and Immunology) for the HCVcc reporter constructs. This work was supported by funds from the DFG (HE 6889/2-1 (EH), INST 337/15-1 2013, and INST 337/16-1 2013 (HS)). The Heinrich Pette Institute, Leibniz Institute for Experimental Virology is supported by the Free and Hanseatic City of Hamburg and the Federal Ministry of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

1. Preparation of Media for Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)
NOTE: Here, the SILAC Protein Quantitation Kit - DMEM supplemented with 50 mg of 13C6 L-Arginine-HCl was used for SILAC labeling. The dialyzed Fetal Calf Serum (FCS) is provided with the SILAC Protein Quantitation Kit.
<ol>
	<li>Remove 50 mL from each bottle of DMEM medium and add 50 mL of dialyzed FCS.</li>
	<li>Dissolve 50 mg of 13C6 L-Lysine-2HCl and 50 ...

<ol>
	<li>Thiam, A. R., Farese, R. V., Walther, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biophysics+and+cell+biology+of+lipid+droplets.">The biophysics and cell biology of lipid droplets.</a> Nat Rev Mol Cell Biol. 14 (12), 775-786 (2013).</li><li>Welte, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expanding+roles+for+lipid+droplets.">Expanding roles for lipid droplets.</a> Curr Biol. 25 (11), R470-R481 (2015).</li><li>Brasaemle, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thematic+review+series:+adipocyte+biology.+The+perilipin+family+of+structural+lipid+droplet+proteins:+stabilization+of+lipid+droplets+and+control+of+lipolysis.">Thematic review series: adipocyte biology. The perilipin family of structural lipid droplet proteins: stabilization of lipid droplets and control of lipolysis.</a> J Lipid Res. 48 (12), 2547-2559 (2007).</li><li>Choudhary, V., Ojha, N., Golden, A., Prinz, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+conserved+family+of+proteins+facilitates+nascent+lipid+droplet+budding+from+the+ER.">A conserved family of proteins facilitates nascent lipid droplet budding from the ER.</a> J Cell Biol. 211 (2), 261-271 (2015).</li><li>Kory, N., Farese, R. V., Walther, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+Fat:+Mechanisms+of+Protein+Localization+to+Lipid+Droplets.">Targeting Fat: Mechanisms of Protein Localization to Lipid Droplets.</a> Trends Cell Biol. 26 (7), 535-546 (2016).</li><li>Hashemi, H. F., Goodman, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+life+cycle+of+lipid+droplets.">The life cycle of lipid droplets.</a> Curr Opin Cell Biol. 33, 119-124 (2015).</li><li>Gao, Q., Goodman, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+lipid+droplet-a+well-connected+organelle.">The lipid droplet-a well-connected organelle.</a> Front Cell Dev Biol. 3, 49 (2015).</li><li>Herker, E., Ott, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emerging+role+of+lipid+droplets+in+host/pathogen+interactions.">Emerging role of lipid droplets in host/pathogen interactions.</a> J Biol Chem. 287 (4), 2280-2287 (2012).</li><li>Wedemeyer, H., Dore, G. J., Ward, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimates+on+HCV+disease+burden+worldwide+-+filling+the+gaps.">Estimates on HCV disease burden worldwide - filling the gaps.</a> J Viral Hepat. 22 Suppl 1, 1-5 (2015).</li><li>Paul, D., Madan, V., Bartenschlager, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hepatitis+C+virus+RNA+replication+and+assembly:+living+on+the+fat+of+the+land.">Hepatitis C virus RNA replication and assembly: living on the fat of the land.</a> Cell Host Microbe. 16 (5), 569-579 (2014).</li><li>Lindenbach, B. D., Rice, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ins+and+outs+of+hepatitis+C+virus+entry+and+assembly.">The ins and outs of hepatitis C virus entry and assembly.</a> Nat Rev Microbiol. 11 (10), 688-700 (2013).</li><li>Barba, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hepatitis+C+virus+core+protein+shows+a+cytoplasmic+localization+and+associates+to+cellular+lipid+storage+droplets.">Hepatitis C virus core protein shows a cytoplasmic localization and associates to cellular lipid storage droplets.</a> Proc Natl Acad Sci U S A. 94 (4), 1200-1205 (1997).</li><li>Shi, S. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hepatitis+C+virus+NS5A+colocalizes+with+the+core+protein+on+lipid+droplets+and+interacts+with+apolipoproteins.">Hepatitis C virus NS5A colocalizes with the core protein on lipid droplets and interacts with apolipoproteins.</a> Virology. 292 (2), 198-210 (2002).</li><li>Herker, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+hepatitis+C+virus+particle+formation+requires+diacylglycerol+acyltransferase-1.">Efficient hepatitis C virus particle formation requires diacylglycerol acyltransferase-1.</a> Nat Med. 16 (11), 1295-1298 (2010).</li><li>Camus, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diacylglycerol+acyltransferase-1+localizes+hepatitis+C+virus+NS5A+protein+to+lipid+droplets+and+enhances+NS5A+interaction+with+the+viral+capsid+core.">Diacylglycerol acyltransferase-1 localizes hepatitis C virus NS5A protein to lipid droplets and enhances NS5A interaction with the viral capsid core.</a> J Biol Chem. 288 (14), 9915-9923 (2013).</li><li>Miyanari, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+lipid+droplet+is+an+important+organelle+for+hepatitis+C+virus+production.">The lipid droplet is an important organelle for hepatitis C virus production.</a> Nat Cell Biol. 9 (9), 1089-1097 (2007).</li><li>Boulant, S., Targett-Adams, P., McLauchlan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disrupting+the+association+of+hepatitis+C+virus+core+protein+with+lipid+droplets+correlates+with+a+loss+in+production+of+infectious+virus.">Disrupting the association of hepatitis C virus core protein with lipid droplets correlates with a loss in production of infectious virus.</a> J Gen Virol. 88 (Pt 8), 2204-2213 (2007).</li><li>Vogt, D. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipid+droplet-binding+protein+TIP47+regulates+hepatitis+C+Virus+RNA+replication+through+interaction+with+the+viral+NS5A+protein.">Lipid droplet-binding protein TIP47 regulates hepatitis C Virus RNA replication through interaction with the viral NS5A protein.</a> PLoS Pathog. 9 (4), e1003302 (2013).</li><li>Ploen, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TIP47+plays+a+crucial+role+in+the+life+cycle+of+hepatitis+C+virus.">TIP47 plays a crucial role in the life cycle of hepatitis C virus.</a> J Hepatol. 58 (6), 1081-1088 (2013).</li><li>Ploen, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TIP47+is+associated+with+the+hepatitis+C+virus+and+its+interaction+with+Rab9+is+required+for+release+of+viral+particles.">TIP47 is associated with the hepatitis C virus and its interaction with Rab9 is required for release of viral particles.</a> Eur J Cell Biol. 92 (12), 374-382 (2013).</li><li>Rosch, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+Lipid+Droplet+Proteome+Analysis+Identifies+Annexin+A3+as+a+Cofactor+for+HCV+Particle+Production.">Quantitative Lipid Droplet Proteome Analysis Identifies Annexin A3 as a Cofactor for HCV Particle Production.</a> Cell Rep. 16 (12), 3219-3231 (2016).</li><li>Kwiatkowski, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrafast+extraction+of+proteins+from+tissues+using+desorption+by+impulsive+vibrational+excitation.">Ultrafast extraction of proteins from tissues using desorption by impulsive vibrational excitation.</a> Angew Chem Int Ed Engl. 54 (1), 285-288 (2015).</li><li>Webster, B., Ott, M., Greene, W. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evasion+of+superinfection+exclusion+and+elimination+of+primary+viral+RNA+by+an+adapted+strain+of+hepatitis+C+virus.">Evasion of superinfection exclusion and elimination of primary viral RNA by an adapted strain of hepatitis C virus.</a> J Virol. 87 (24), 13354-13369 (2013).</li><li>Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In-gel+digestion+for+mass+spectrometric+characterization+of+proteins+and+proteomes.">In-gel digestion for mass spectrometric characterization of proteins and proteomes.</a> Nat Protoc. 1 (6), 2856-2860 (2006).</li><li>Ting, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Normalization+and+statistical+analysis+of+quantitative+proteomics+data+generated+by+metabolic+labeling.">Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling.</a> Mol Cell Proteomics. 8 (10), 2227-2242 (2009).</li><li>Brasaemle, D. L., Dolios, G., Shapiro, L., Wang, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+proteins+associated+with+lipid+droplets+of+basal+and+lipolytically+stimulated+3T3-L1+adipocytes.">Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes.</a> J Biol Chem. 279 (45), 46835-46842 (2004).</li><li>Tingting, P., Caiyun, F., Zhigang, Y., Pengyuan, Y., Zhenghong, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subproteomic+analysis+of+the+cellular+proteins+associated+with+the+3'+untranslated+region+of+the+hepatitis+C+virus+genome+in+human+liver+cells.">Subproteomic analysis of the cellular proteins associated with the 3' untranslated region of the hepatitis C virus genome in human liver cells.</a> Biochem Biophys Res Commun. 347 (3), 683-691 (2006).</li><li>Ariumi, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DDX3+DEAD-box+RNA+helicase+is+required+for+hepatitis+C+virus+RNA+replication.">DDX3 DEAD-box RNA helicase is required for hepatitis C virus RNA replication.</a> J Virol. 81 (24), 13922-13926 (2007).</li><li>Weinlich, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IGF2BP1+enhances+HCV+IRES-mediated+translation+initiation+via+the+3'UTR.">IGF2BP1 enhances HCV IRES-mediated translation initiation via the 3'UTR.</a> RNA. 15 (8), 1528-1542 (2009).</li></ol>

The authors have nothing to disclose.

Here, we describe a protocol to isolate lipid droplets for quantitative lipid droplet proteome analysis to compare the enrichment and depletion of proteins associated with lipid droplets under diverse culture conditions, such as viral infections. As an alternative method, the proteome analysis can be performed with label-free quantifications based on total peak intensities. This method has no dynamic range limitation and avoids metabolic problems. The advantage of the SILAC approach is that the samples are pooled prior l...

Lipid droplets are highly dynamic cytoplasmic (and nuclear) cell organelles composed of a core of neutral lipids (triglycerides (TG) and cholesterol ester (CE)) enclosed by a monolayer of phospholipids with embedded proteins1. All cell types produce lipid droplets, but they vary in size, lipid composition, and protein decoration. Lipid droplets fulfill diverse functions, including serving as energy and membrane precursor reservoirs or as protein deposits. In addition, through the uptake of lipids, they protect cells from lipotoxicity, release lipids as signaling molecules, and are involved in protein degradation and endoplasmic reticulum (ER) stress responses2. As such, a host of proteins bind to lipid droplets and govern their generation, degradation, trafficking, and interaction with other organelles. Among them are the perilipin family of bona fide lipid droplet binding proteins (PLIN1-5)3.
Lipid droplet biogenesis likely starts at the ER, where ER-resident enzymes catalyze the synthesis of neutral lipids that accumulate within the membrane bilayer, forming a lens of neutral lipids, a process that was recently visualized nicely in yeast4. Membrane bending and elevated phosphatidic acid and diacylglycerol levels are then thought to attract proteins involved in phospholipid biosynthesis, as the simultaneous synthesis of the core neutral lipids and the shielding phospholipids is required for lipid droplet generation5. Enzymes harboring transmembrane domains that reside at the ER catalyze this process. Expansion to large lipid droplets requires the activity of a different class of lipid-synthesizing enzymes that harbor an amphipathic helix and can thus travel from the ER to lipid droplets. The mobilization of lipids from lipid droplets occurs through the local activation of the triglyceride and diacylglycerol lipases adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) or by different autophagic pathways, such as macro- and microlipophagy or chaperone-mediated autophagy6. Lipid droplets interact with other cellular organelles, such as mitochondria (for beta-oxidation and lipid synthesis) and ER (for lipid synthesis and protein trafficking), but also with lysosomes, endosomes, and the vacuoles induced by intracellular bacteria7. Indeed bacteria, viruses, and even parasites target lipid droplets for replication and persistence, among them HCV8.
HCV infection is one of the leading causes of liver-related morbidity and mortality worldwide, accounting for approximately 0.5 million deaths per year9. The true number of HCV infections is unknown, but recent estimates suggest that 130 - 150 million people are chronically infected. No vaccine exists, but the recently approved direct-acting antivirals dramatically increase therapeutic responses compared to the standard interferon-based therapy. However, worldwide, the treatment of patients will likely be restricted due to the extremely high costs of the new therapeutics. About half of all individuals chronically infected with HCV develop fatty liver disease (steatosis), a condition characterized by the excessive accumulation of lipid droplets in hepatocytes. Intriguingly, lipid droplets also emerged as vital cellular organelles for HCV replication, putatively serving as viral assembly sites10,11.
In HCV-infected cells, the viral protein core and NS5A localize to lipid droplets in a process that depends on triglyceride biosynthesis, as inhibitors of diacylglycerol acyltransferase-1 (DGAT1) impair trafficking to lipid droplets and subsequent HCV particle production12,13,14,15. In addition, mutations in the lipid droplet-binding domains of either core or NS5A suppress HCV assembly16,17. Core and NS5A then recruit all other viral proteins, as well as viral RNA replication complexes, to membranes closely associated with lipid droplets16. A concerted action of all viral proteins is required for the successful production of infectious viral progeny10,11. The structural proteins are part of the virions, and the nonstructural proteins promote the protein-protein interactions required for this process. Intriguingly, the bona fide lipid droplet-binding protein PLIN3/TIP47 is required for both HCV RNA replication and the release of virions18,19,20. Despite these recent advances, the mechanistic details, especially of virus-host interactions during the late stages of HCV replication, remain ill-defined, and the precise function of the lipid droplets is unknown.
Here, we describe a method to isolate lipid droplets for the quantitative mass spectrometry of associated proteins. Using this method, we found profound changes in the lipid droplet proteome during HCV infection and identified annexin A3 as a host protein that co-fractionates with lipid droplets and is required for efficient HCV maturation21.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>SILAC Protein Quantitation Kit - DMEM</td>
			<td>Thermo Fisher</td>
			<td>89983&#160;</td>
		</tr>
		<tr>
			<td>13C6 L-Arginine-HCl 50 mg</td>
			<td>Thermo Fisher</td>
			<td>88210&#160;</td>
		</tr>
		<tr>
			<td>Roti-Load 1</td>
			<td>Roth GmbH</td>
			<td>K929.1</td>
		</tr>
		<tr>
			<td>Roti-Blue 5x-Concentrate</td>
			<td>Roth GmbH</td>
			<td>A152.2&#160;</td>
		</tr>
		<tr>
			<td>10x SDS-Tris-Glycine - Buffer&#160;</td>
			<td>Geyer Th. GmbH &#38; Co.KG&#160;</td>
			<td>A1415,0250&#160;</td>
		</tr>
		<tr>
			<td>GlutaMAX (100x)</td>
			<td>Life Technologies GmbH&#160;</td>
			<td>350500038&#160;</td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin Solution for Cell Culture</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>P4333-100ml&#160;</td>
		</tr>
		<tr>
			<td>PBS 1x Dulbeccos Phosphate Buffered Saline</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>D8537&#160;</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>T3924-100ML&#160;</td>
		</tr>
		<tr>
			<td>Sodium Chloride BioChemica</td>
			<td>AppliChem GmbH</td>
			<td>A1149,1000</td>
		</tr>
		<tr>
			<td>Tris Ultrapure&#160;&#160;</td>
			<td>AppliChem GmbH</td>
			<td>A1086,5000A&#160;</td>
		</tr>
		<tr>
			<td>EDTA BioChemica</td>
			<td>AppliChem GmbH</td>
			<td>A1103,0250</td>
		</tr>
		<tr>
			<td>Protease Inhibitor Cocktail 5ml</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>P8340-5ML&#160;</td>
		</tr>
		<tr>
			<td>D(+)-Sucrose BioChemica</td>
			<td>AppliChem GmbH</td>
			<td>A3935,1000</td>
		</tr>
		<tr>
			<td>Hydrochloric acid 37% pure Ph. Eur., NF</td>
			<td>AppliChem GmbH</td>
			<td>A0625</td>
		</tr>
		<tr>
			<td>DC Protein Assay&#160;</td>
			<td>Bio-Rad Laboratoris GmbH&#160;</td>
			<td>500-0116&#160;</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>AppliChem GmbH</td>
			<td>151339</td>
		</tr>
		<tr>
			<td>SDS Ultrapure</td>
			<td>AppliChem GmbH</td>
			<td>A1112</td>
		</tr>
		<tr>
			<td>Bromophenol blue</td>
			<td>AppliChem GmbH</td>
			<td>A2331</td>
		</tr>
		<tr>
			<td>&#946;-Mercaptoethanol&#160;</td>
			<td>AppliChem GmbH</td>
			<td>A4338</td>
		</tr>
		<tr>
			<td>Blasticidin</td>
			<td>Invivogen</td>
			<td>ant-bl-1&#160;</td>
		</tr>
		<tr>
			<td>Potassium Chloride&#160;</td>
			<td>AppliChem GmbH</td>
			<td>A1039</td>
		</tr>
		<tr>
			<td>Phenylmethanesulfonyl Fluoride&#160;</td>
			<td>AppliChem GmbH</td>
			<td>A0999</td>
		</tr>
		<tr>
			<td>Potassium Phosphate Monobasic</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>221309</td>
		</tr>
		<tr>
			<td>Dipotassium Hydrogenphosphate</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>P3786&#160;</td>
		</tr>
		<tr>
			<td>DTT&#160;</td>
			<td>AppliChem GmbH</td>
			<td>A2948</td>
		</tr>
		<tr>
			<td>NP-40</td>
			<td>AppliChem</td>
			<td>A1694</td>
		</tr>
		<tr>
			<td>TWEEN 20</td>
			<td>AppliChem</td>
			<td>A4974</td>
		</tr>
		<tr>
			<td>Nonfat dried milk powder</td>
			<td>AppliChem</td>
			<td>A0830</td>
		</tr>
		<tr>
			<td>Anti-ADFP/ ADRP&#160;</td>
			<td>abcam</td>
			<td>ab52355</td>
		</tr>
		<tr>
			<td>M6PRB1/TIP47 100&#181;g&#160;</td>
			<td>abcam</td>
			<td>ab47639</td>
		</tr>
		<tr>
			<td>Calreticulin, pAb 200 &#181;g</td>
			<td>Enzo Life Science GmbH&#160;</td>
			<td>ADI-SPA-600-F&#160;</td>
		</tr>
		<tr>
			<td>Anti-&#223;-Tubulin&#160;</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>T6074 200&#181;l &#160;</td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>Geyer Th. GmbH &#38; Co.KG&#160;</td>
			<td>A3678,0250 &#160;</td>
		</tr>
		<tr>
			<td>Anti-MnSOD</td>
			<td>Enzo Life Science GmbH&#160;</td>
			<td>ADI-SOD-110-F</td>
		</tr>
		<tr>
			<td>Anti-mouse HRP</td>
			<td>Thermo Fisher Pierce</td>
			<td>32430</td>
		</tr>
		<tr>
			<td>Anti-rabbit HRP</td>
			<td>Thermo Fisher&#160; Pierce</td>
			<td>32460</td>
		</tr>
		<tr>
			<td>Amersham Hyperfilm ECL</td>
			<td>GE Healthcare</td>
			<td>28906836</td>
		</tr>
		<tr>
			<td>Lumi-Light Western Blotting Substrate</td>
			<td>Sigma-Aldrich Chemie GmbH&#160;</td>
			<td>12015196001</td>
		</tr>
		<tr>
			<td>96 Well Cell Culture Plate</td>
			<td>Greiner Bio-One GmbH&#160;</td>
			<td>655 180&#160;</td>
		</tr>
		<tr>
			<td>Terumo Syringe 1 ml</td>
			<td>Terumo</td>
			<td>SS-01T</td>
		</tr>
		<tr>
			<td>Filtropur BT 50, 500 ml, 0.45 &#181;m&#160;</td>
			<td>SARSTEDT&#160;</td>
			<td>83.1823.100&#160;</td>
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			<td>Bio-Rad Laboratoris GmbH&#160;</td>
			<td>456-9034&#160;</td>
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			<td>6 Well Cell Culture Plate</td>
			<td>Greiner Bio-One GmbH&#160;</td>
			<td>657160&#160;</td>
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			<td>Dishes Nunclon 150/20&#160;</td>
			<td>Fisher Scientific GmbH&#160;</td>
			<td>10098720 - 168381&#160;</td>
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			<td>Cell Scraper</td>
			<td>neoLab Migge GmbH&#160;</td>
			<td>C-8120&#160;</td>
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			<td>Tube, 50 ml</td>
			<td>Greiner Bio-One GmbH&#160;</td>
			<td>227261&#160;</td>
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			<td>SafeSeal Tube RNase-free&#160;</td>
			<td>SARSTEDT&#160;</td>
			<td>72.706.400&#160;</td>
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			<td>Ultra Clear Centrifuge Tubes 11 x 60 mm</td>
			<td>Beckman Coulter GmbH&#160;</td>
			<td>344062&#160;</td>
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			<td>Suction Needles</td>
			<td>Transcodent</td>
			<td>6482</td>
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			<td>Biosphere Fil. Tip 1000&#160;</td>
			<td>SARSTEDT&#160;</td>
			<td>70.762.211&#160;</td>
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			<td>Biosphere Fil. Tip 200</td>
			<td>SARSTEDT&#160;</td>
			<td>70.760.211&#160;</td>
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			<td>Biosphere Fil. Tip 10</td>
			<td>SARSTEDT&#160;</td>
			<td>70.1130.210&#160;</td>
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			<td>Dounce Tissue Grinder</td>
			<td>Fisher Scientific GmbH&#160;</td>
			<td>11883722</td>
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			<td>Pestles For Dounce All-Glass Tissue Grinders</td>
			<td>Fisher Scientific GmbH&#160;</td>
			<td>10389444</td>
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			<td>Orbitrap Fusion</td>
			<td></td>
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			<td>Branson Sonifier 450</td>
			<td></td>
			<td></td>
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			<td>Thermomixer comfort, with Thermoblock 1.5 ml</td>
			<td>Eppendorf</td>
			<td>5355&#160;000.127</td>
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			<td>Mini-PROTEAN Tetra Cell, Mini Trans-Blot Module, and PowerPac Basic Power Supply,&#160;</td>
			<td>BioRad</td>
			<td>165-8033</td>
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			<td>Mini-PROTEAN 3 Multi-Casting Chamber</td>
			<td>BioRad</td>
			<td>165-4110</td>
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			<td>PowerPac HC Power Supply</td>
			<td>Biorad</td>
			<td>164-5052</td>
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			<td>Centrifuge&#160;</td>
			<td>Eppendorf</td>
			<td>5424R</td>
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			<td>Centrifuge&#160;</td>
			<td>Eppendorf</td>
			<td>5424</td>
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			<td>Optima L-90K</td>
			<td>Beckman Coulter GmbH&#160;</td>
			<td>365670</td>
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			<td>SW 60 Ti Rotor</td>
			<td>Beckman Coulter GmbH&#160;</td>
			<td>335649</td>
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			<td>Infinite M1000 PRO</td>
			<td>Tecan</td>
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lipid droplet isolation for quantitative mass spectrometry analysis

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of virion morphogenesis. Quantitative lipid droplet proteome analysis can be used to identify proteins that localize to or are displaced from lipid droplets under conditions such as virus infections. Here, we describe a protocol that has been successfully used to characterize the changes in the lipid droplet proteome following infection with HCV. We use Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) and thus label the complete proteome of one population of cells with &#34;heavy&#34; amino acids to quantitate the proteins by mass spectrometry. For lipid droplet isolation, the two cell populations (i.e.&#160;HCV-infected/&#34;light&#34; amino acids and uninfected control/&#34;heavy&#34; amino acids) are mixed 1:1 and lysed mechanically in hypotonic buffer. After removing the nuclei and cell debris by low speed centrifugation, lipid droplet-associated proteins are enriched by two subsequent ultracentrifugation steps followed by three washing steps in isotonic buffer. The purity of the lipid droplet fractions is analyzed by western blotting with antibodies recognizing different subcellular compartments. Lipid droplet-associated proteins are then separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Coomassie staining. After tryptic digest, the peptides are quantified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Using this method, we identified proteins recruited to lipid droplets upon HCV infection that might represent pro- or antiviral host factors. Our method can be applied to a variety of different cells and culture conditions, such as infection with pathogens, environmental stress, or drug treatment.

Lipid droplets are vital to HCV&#160;infection as the putative sites of virion assembly, but the molecular mechanisms of morphogenesis and egress of virions are largely unknown. To identify novel host dependency factors involved in that process, we performed quantitative lipid droplet proteome analysis of HCV-infected cells21 (Figure 1A). We established a protocol for purifying lipid droplets and routinely detected a strong enrichment of the lipid ...

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Lipid Droplet Isolation for Quantitative Mass Spectrometry Analysis

Lipid droplets are important organelles for the replication of several pathogens, including the Hepatitis C Virus (HCV). We describe a method to isolate lipid droplets for quantitative mass spectrometry of associated proteins; it can be used under a variety of conditions, such as virus infection, environmental stress, or drug treatment.

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of ...

The overall goal of isolating lipid droplets for quantitative mass spectrometry is to understand the function of these organelles, for example, in the replication of pathogens such as the hepatitis C virus. This method can answer key questions in the infectious disease field such as why pathogens tie to the droplets for replication. The isolation of lipid droplets can be done in six to seven hours.And during this procedure, it's important to avoid the contamination of keratin. To begin, remove 50 milliliters from each bottle of DMEM medium and add 50 milliliters of dialyzed fetal calf serum. Next, dissolve 50 milligrams of carbon 13 labeled lysine and 50 milligrams of carbon 13 labeled arginine in one milliliter of medium.Mix thoroughly, and add the amino acids to the DMEM plus FCS medium. Then add PenStrep and glutamine substitute. Sterile filter the medium using a 0.45 micron filter, and label the bottle as heavy SILAC medium.To prepare the light medium, repeat these steps using 50 milligrams of arginine and 50 milligrams of lysine. Label the bottle as light SILAC medium. Trypsinize the cells, and split into two wells of a six well culture plate.One well should contain two milliliters of the heavy SILAC medium, and the other, two milliliters of the light SILAC medium. Culture the cells for at least six passages. After six passages, the incorporation of the heavy amino acids should be more than 95%Harvest one million cells of the heavy and light labeled cell populations to analyze the incorporation efficacy.After the washing the cells in 1X PBS, pellet them by centrifugation for five minutes at 160 times g and four degrees Celsius. Re-suspend the cell pellets in 150 microliters of MS-buffer. Next, incubate the cells on ice for 30 minutes.Then, lyse the cells by sonication at four degrees Celsius. Remove the cell debris by centrifugation for 10 minutes at 11, 000 times g and four degrees Celsius. Transfer the supernatant to a new tube, and determine the protein concentration with a detergent compatible protein assay.Then, mix 75 micrograms of protein with six x sample buffer. After boiling at 95 degrees Celsius for five minutes, separate the proteins by SDS-PAGE in SDS running buffer at 180 bolts for approximately one hour. After Coomassie staining, excise the same protein band and analyze the incorporation efficacy by MS analysis.Infect the light population of cells with the hepatitis C reporter virus by incubating them with fibrous stocks for four hours at 37 degrees Celsius. Expand HCV infected light cells and non-infected heavy cells as described in the text protocol. If using an HCV strain that carries a blasticidin resistance gene, add 10 micrograms per milliliter of blasticidin S to the light medium to select for HCV positive cells.One day prior to lipid droplet isolation, wash the cells with PBS, tryspinize, and re-suspend in the corresponding light or heavy medium. Count the cells using a Neubauer counting chamber. Then, seed seven million cells of each population in a 150 square centimeter cell culture dish.Prepare at least five dishes per light and heavy cell population. Culture the cells in 30 milliliters of medium per dish overnight. The next day, remove the medium, and wash the cells in 1X PBS.Detach the cells in 1X PBS using a cell scraper. After counting both cell populations as before, pull equal cell numbers in 50 milliliter centrifuge tubes. Pellet the cells by centrifugation for five minutes at 160 times g and four degrees Celsius.Remove the PBS, and re-suspend the cell pellet in one milliliter of sucrose buffer. Transfer the cell suspension to a tight-fitting Ounce homogenizer before the lysing the cells with 200 strokes on ice. Then, transfer the lysate into a 1.5 milliliter microfuge tube, and spin down the nuclei and cell debris for 10 minutes at 1, 000 times g and four degrees Celsius.After centrifugation, store an aliquot of 25 microliters of the post-nuclear fraction, or PNS, at minus 20 degrees Celsius as an input control. Place the rest of the PNS fraction at the bottom of the centrifuge tube, and overlay with approximately three milliliters of the lipid droplet wash buffer. Centrifuge for two hours at 100, 000 times g and four degrees Celsius.Following centrifugation, harvest the floating lipid droplet fraction from the top of the tube using a bent blunt cannula. Then, place the lipid droplet fraction in a centrifuge tube, overlay with lipid droplet wash buffer, and repeat the centrifugation step. Harvesting the lipid droplets from top of the gradient requires experience.And is easier the bigger the fraction is. You can use fat cells for practice. Or you can feed your cells with oleate to increase the amount of lipid droplets.Once again, harvest the floating lipid droplet fraction using a bent blunt cannula from the top of the tube. Transfer the lipid droplets to a new 1.5 milliliter microfuge tube, and add 500 microliters of lipid droplet wash buffer. Then, spin the sample for 20 minutes at 21, 000 times g and four degrees Celsius.Remove the subjacent wash buffer using a gel loading pipette tip, and repeat the washing step three times. After the final removal of the washing buffer, mix five microliters of lipid droplet fractions with 10 microliters of NP 40 lysis buffer for determination of the protein content. Incubate the sample on ice for one hour to inactivate the virus if working with infectious material.At this point, the lipid droplet fractions can be stored at minus 20 degrees Celsius. Next, mix the volume that corresponds to at least 35 micrograms of protein with 4x loading dye. Incubate the mixture on ice for one hour to inactivate the virus if working with infectious material.Boil the sample at 95 degrees Celsius for five minutes. Then, perform SDS-PAGE followed by Coomassie staining to prepare the sample for liquid chromatogrophy couple to tandem mass spectronomy as described in the text protocol. To analyze the lipid droplet purity, dilute aliquots of lipid droplet fractions, one to two, with NP 40 lysis buffer.Dilute input control fractions one to ten with the same buffer. Incubate the samples on ice for one hour to inactivate the virus if working with infectious material. Next, determine the protein level with a detergent compatible protein assay.Then, mix equal amount of protein with 6x sample buffer, and incubate the samples on ice for one hour to inactivate the virus if working with infectious material. Finally, proceed with SDS-PAGE, and transfer the proteins to onto a nitrocellulose membrane by tank blotting at 80 volts for 90 minutes. Shown here is a representative western blot analysis of post-nuclear and lipid droplet fractions.The western blot clearly shows an enrichment that the lipid droplet marker proteins perilipin two and perilipin three in lipid droplet fractions, and the depletion of markers of other cellular compartments. Post-nuclear and lipid droplet fractions can be additionally analyzed by Coomassie blue and silver staining. This heat map illustrates the number of peptides and percentage of protein coverage of proteins identified in lipid droplet fractions of the analyzed cells.The final heat map depicts how HCV infection changes the lipid droplet per diem. Enriched lipid droplet-associated proteins are indicated in red, and depleted lipid droplet-associated proteins are indicated in blue. The main advantage of this method is that we mix the cells prior isolation and prior lipid droplet isolation, and thus we can minimize errors that can happen during the cell lysis and during the isolation steps.

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JoVE Journal

Biochemistry

9.9K Views.  Leibniz Institute for Experimental Virology. The overall goal of isolating lipid droplets for quantitative mass spectrometry is to understand the function of these organelles, for example, in the replication of pathogens such as the hepatitis C virus. This method can answer key questions in the infectious disease field such as why pathogens tie to the droplets for replication. The isolation of lipid droplets can be done in six to seven hours.And during this procedure, it's important to avoid the contamination of keratin. To begin...