The authors gratefully acknowledge funding from the New Zealand Marsden Fund (Grant UOO1305), and a block grant from Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (M. Niimi). They wish to thank the University of Otago for providing G. Madani with a PhD Scholarship. The authors also wish to express their gratitude to Professor Stefan Raunser and his colleagues, Dr Amir Apelbaum, and Dr Deivanayagabarathy Vinayagam, for their support and supervision during a 6-month visit of G. Madani at the Max Planck Institute of Molecular Physiology (MPIMP), Dortmund, Germany. The authors also thank the German Academic Exchange Service (DAAD) for providing G. Madani with a research grant (57381332) to visit the MPIMP.

1. Preparation of fresh or frozen stocks of transformation competent AD&#916; and AD&#916;&#916; cells
<ol>
	<li>Inoculate 25 mL of 2x YPCD [i.e., 2x YPD; 2% (w/v) yeast extract, 2% (w/v) peptone, 4% (w/v) dextrose), 0.079 % (w/v) CSM (complete supplement mixture)]35 medium with a single yeast colony and incubate overnight (o/n) for 16 h at 30 &#176;C with shaking at 200 revolutions per minute (rpm).</li>
	<li>Inoculate 225 mL of 2x YPCD medium with the 25 mL&#160;o/n culture and check the cell optical density at 600 nm (OD600); the OD600 is usually ~0.5-1.0. 
	NOTE: At this stage make sure that all materials that are required for the following transformation experiment are readily available.</li>
	<li>Grow the culture at 30 &#176;C for a further ~6-8 h with shaking at 200 rpm until the cell density reaches an OD600 of ~6-8. 
	NOTE: The following steps are performed at room temperature (RT) unless otherwise stated.</li>
	<li>Harvest these logarithmic-phase cells by centrifugation at 3,000 x g for 3 min.</li>
	<li>Resuspend the cells and wash them twice with sterile double-distilled water (ddH2O; i.e., 200 mL and then 20 mL).</li>
	<li>Harvest the cells at 3,000 x g for 3 min.</li>
	<li>Slowly (i.e., add 30 equal aliquots of frozen competent cell (FCC) solution every minute for 30 min) resuspend the cell pellet in X mL of FCC [5% (w/v) glycerol, 10% (v/v) dimethyl sulfoxide (DMSO)] on ice (where X = OD600; e.g., if OD600 = 6 resuspend in 6 mL, or if OD600 = 3 resuspend in 3 mL). 
	NOTE: The correct FCC composition is critical for the transformation success.</li>
	<li>Keep cells on ice for 2 h before transformation or store aliquots at -80 &#176;C until required. 
	NOTE: AD&#916; and AD&#916;&#916; cells are very sensitive to freezing. Thus, cells must be cooled down slowly to -80 &#176;C: place ice-cold microcentrifuge tubes containing 50-600 &#181;L cell aliquots into a plastic storage box (RT). Place the box in a larger polystyrene container (RT) and close the container with a fitting polystyrene lid. Then, put the container into the -80 &#176;C freezer. 
	&#8203;CAUTION: Slow freezing is critical for cell survival.</li>
</ol>
2. Transformation of AD&#916;&#160;and AD&#916;&#916;&#160;with CaCDR1-XLmGFPHis and confirmation of correct transformants by colony PCR and DNA sequencing
NOTE: Plasmid pABC3-CDR1-mGFPHis was created using conventional cloning strategies described in detail in Lamping et al., 201055 and is illustrated in Figure 1B. Wild-type C. albicans CDR1 was isolated as a PacI/NotI fragment from plasmid pABC3-CaCDR1A-GFP14 and cloned into pABC3-XLmGFPHis26.
<ol>
	<li>PCR amplify the entire CDR1 transformation cassette with a high-fidelity DNA polymerase and primer pair PDR5-pro/PDR5-ter35 using 1-10 ng of pABC3-CaCDR1-XLmGFPHis as a DNA template or, alternatively, digest 2 &#181;g of pABC3-CaCDR1-XLmGFPHis to completion with 10 U restriction enzyme AscI at 37 &#176;C (Figure 1A,B). 
	NOTE: The CDR1 transformation cassette (Figure 1A) comprises the PDR5 promoter - CaCDR1-mGFPHis - PGK1 terminator - URA3 selection marker - PDR5 downstream region.</li>
	<li>Perform agarose gel electrophoresis and gel extract the ~8 kb transformation cassette. 
	NOTE: Gel purification of the ~8 kb CaCDR1 transformation cassette removes any possible undigested plasmid DNA, which could lead to incorrect transformants that have the entire plasmid, rather than the linear transformation cassette, integrated at the genomic PDR5 locus.</li>
	<li>Denature the required amount of salmon sperm carrier DNA (2 mg/mL; 10 mM Tris, 1 mM EDTA; pH 7.5) for 10 min in a boiling water bath and keep on ice. Use screw-capped tubes for boiling salmon sperm DNA to avoid opening of the lid.</li>
	<li>Mix 50 &#181;L of denatured salmon sperm DNA with 14 &#181;L of the transformation cassette (500-2,000 ng) and keep the 64 &#181;L of DNA mixture on ice until further use. 
	NOTE: Use 10 ng of an E. coli-yeast shuttle plasmid (e.g., pYES2) as a positive transformation control (Figure 2B).</li>
	<li>Resuspend fresh or frozen competent cells quickly defrosted for 5 min in a 30 &#176;C water bath and divide them into 50 &#181;L aliquots in 1.5 mL microcentrifuge tubes.</li>
	<li>Harvest cells by centrifugation for 1 min in a microfuge at maximum speed (18,000 x g).</li>
	<li>Remove the supernatant and keep the cell pellet at RT.</li>
	<li>For each transformation, mix 296 &#181;L combinations (RT) of 260 &#181;L of 50% (w/v) polyethylene glycol (PEG 3350) and 36 &#181;L of 1 M lithium acetate (LiAc), by repeat pipetting, with the appropriate 64 &#181;L of ice-cold DNA mixtures.</li>
	<li>Add the appropriate mixture immediately to a 50 &#181;L competent cell pellet aliquot.</li>
	<li>Resuspend the cell pellet in the 360 &#181;L of PEG-LiAc-DNA mixture by thoroughly vortexing for about 30 s.</li>
	<li>Incubate the cell mixture in a 30 &#176;C water bath for 1 h. 
	NOTE: AD&#916; and AD&#916;&#916; cells transform better at 30 &#176;C than at 42 &#176;C35.</li>
	<li>Harvest the cells at 18,000 x g for 10 s. Discard the supernatant and resuspend the cell pellet in 80 &#181;L of ddH2O.</li>
	<li>Spread the cells onto a CSM-URA agar plate35 [i.e., 0.67% (w/v) yeast nitrogen base without amino acids, 0.077% (w/v) CSM minus uracil, 2% (w/v) glucose, and 2% (w/v) agar].</li>
	<li>Incubate the plates for 2-3 days at 30 &#176;C until uracil prototroph transformants are clearly visible. 
	NOTE: Expect ~100 transformants per &#181;g of the linear ~8 kb CaCDR1 transformation cassette and ~4 x 104 transformants per &#181;g pYES2.</li>
	<li>Pick five independent transformants and spread them on a fresh CSM-URA plate to separate the uracil prototroph transformants from remnants of non-transformed host cells.</li>
	<li>Remove any possible petite mutants by growing the transformants on YPG-agar plates [1% (w/v) yeast extract, 2% (w/v) peptone, 2% (v/v) glycerol, and 2% (w/v) agar] (Figure 2D). 
	NOTE: Petite mutants have defective mitochondria and, thus, cannot grow on non-fermentable carbon sources. They are quite common in S. cerevisiae56. S. cerevisiae AD&#916; and AD&#916;&#916; are particularly prone to acquire the petite phenotype.</li>
	<li>Perform yeast colony PCR and confirm at least three independent transformants to be correctly integrated into the genomic PDR5 locus (Figure 1C) by amplifying the entire ~8 kb CaCDR1 transformation cassette with a specific DNA polymerase that is optimized for amplifying PCR products from impure DNA template sources. Use a set of primers that bind just outside the integration site and 1 &#181;L aliquots of cell suspensions (in ddH2O) derived from single colonies as DNA templates. 
	NOTE: This particular DNA polymerase reliably amplifies ~8 kb PCR fragments from intact yeast cells. However, for reliable amplification, 45 PCR cycles are required, and the yeast cells must be resuspended at OD600 1-10 in ddH2O.</li>
	<li>Confirm the correct ~8 kb PCR amplification product by DNA agarose gel electrophoresis of a 1 &#181;L portion of the PCR reaction.</li>
	<li>Remove excess amplification primers from a 10 &#181;L portion of the PCR reaction with an enzyme mixture of a single-strand DNA exonuclease and a phosphatase following the manufacturer&#39;s instructions before sequencing the entire ORF using portions of the treated DNA sample with appropriate primers.</li>
</ol>
3. Small-scale yeast plasma membrane isolation protocol
<ol>
	<li>Growing yeast cells
	<ol>
		<li>Pre-culture a single yeast colony in 10 mL of YPD at 30 &#176;C for ~7-8 h with shaking at 200 rpm.</li>
		<li>Inoculate 40 mL of YPD medium with the 10 mL pre-culture and incubate the cells at 30 &#176;C o/n (~16 h) with shaking at 200 rpm until the cell density reaches an OD600 of 1-3.</li>
	</ol>
	</li>
	<li>Harvesting yeast cells
	<ol>
		<li>Harvest 40 OD units (ODU; e.g., 1 mL at an OD600 of 1 = 1 ODU) of logarithmic-phase cells at 4,200 x g for 5 min at 4 &#176;C.</li>
		<li>Resuspend and wash cells twice with ice cold sterile ddH2O (i.e., 40 mL and then 1 mL; harvest cells in between steps by centrifugation at 4,200 x g for 5 min at 4 &#176;C).</li>
		<li>Resuspend the pellet in 1 mL of ice cold sterile ddH2O and transfer the cell suspension into a pre-cooled (on ice) 1.5 mL microcentrifuge tube.</li>
		<li>Harvest cells at 3,300 x g for 3 min at 4 &#176;C.</li>
		<li>Aspirate the supernatant.</li>
		<li>Resuspend the cell pellet in 0.5 mL homogenizing buffer [HB; 50 mM Tris, 0.5 mM EDTA, 20% (v/v) glycerol; pH 7.5] freshly supplemented with 1 mM phenylmethylsulfonyl fluoride (PMSF). 
		NOTE: Always add PMSF fresh because PMSF is inactivated quickly upon exposure to water. 
		CAUTION: PMSF is a serine protease inhibitor, which is extremely corrosive and destructive to tissues. It may cause irreversible eye damage.</li>
		<li>Store the cell suspension at -80 &#176;C or use&#160;immediately.</li>
	</ol>
	</li>
	<li>Isolation of plasma membranes
	<ol>
		<li>If frozen, defrost the cells on ice for ~1 h.</li>
		<li>Add ice-cold 0.5 mm diameter silica beads to the 0.5 mL cell suspension to reach a total volume of 1 mL.</li>
		<li>Break cells with 6 cycles of vortexing at maximum shaking intensity for 1 min interspersed with 3 min cooling periods on ice.</li>
		<li>Make a thin hole at the bottom of the tube with a heated scalpel blade.</li>
		<li>Collect the broken cell homogenate through the bottom of the tube fitted into another ice-cold 1.5 mL microcentrifuge tube with a 10 s low-speed (~200 rpm) spin. 
		NOTE: This ensures that the silica beads remain in the original tube.</li>
		<li>Centrifuge the cell homogenate at 5,156 x g for 5 min at 4 &#176;C to remove cell debris, unbroken cells, and nuclei.</li>
		<li>Transfer 450 &#181;L of supernatant into an ice cold 1.5 mL microcentrifuge tube and add an additional 1 mL of ice-cold HB supplemented with fresh PMSF (1 mM). 
		&#8203;NOTE: This dilution step is critical for the high-quality plasma membrane protein recovery.</li>
		<li>Harvest plasma membranes at 17,968 x g for 1 h at 4 &#176;C and resuspend the plasma membrane pellet, by repeat pipetting, in 100 &#181;L of HB freshly supplemented with 1 mM PMSF. Loosen the cell pellet for proper plasma membrane homogenization by stirring the cell pellet with the 100 &#181;L pipette tip before releasing the 100 &#181;L of HB and up and down pipetting.</li>
		<li>Measure the protein concentration of the plasma membrane preparation with a protein assay kit that is compatible with buffers containing reducing agent and detergent.</li>
		<li>Store the plasma membranes at -80 &#176;C or keep on ice for immediate use.</li>
	</ol>
	</li>
</ol>
4. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)
<ol>
	<li>Assemble the apparatus for preparing polyacrylamide gels.</li>
	<li>For two separating gels (7% polyacrylamide), mix 2.1 mL of 40% acrylamide/bis-acrylamide, 3 mL of 4x separating buffer (1.5 M Tris, 0.4% sodium dodecyl sulfate [SDS] (w/v); pH 8.8), and 6.9 mL of ddH2O. Add 8 &#181;L of tetramethylethylenediamine (TEMED) and 60 &#181;L of 10% ammonium persulphate (APS) to initiate polymerization of acrylamide. 
	CAUTION: Acrylamide/bis-acrylamide is very toxic. It causes skin irritation, peripheral neuropathy and is a carcinogen. TEMED is harmful if swallowed or inhaled. APS is harmful if swallowed. It causes serious eye and skin irritations.</li>
	<li>Pour ~4-5 mL of this mixture into the assembled gel apparatus, up to ~2 cm from the top.</li>
	<li>Carefully layer ~1-2 mL of 0.1% SDS on top to create a planar meniscus.</li>
	<li>Allow the polyacrylamide to set for ~60 min at RT.</li>
	<li>Prepare a stacking gel mixture for two gels by mixing 0.5 mL of 40% acrylamide/bis-acrylamide, 1 mL of 4x stacking buffer (0.5 M Tris, 0.4% SDS (w/v); pH 6.8), and 6.9 mL of ddH2O. Add 2 &#181;L of TEMED and 30 &#181;L of 10% APS to initiate polymerization of acrylamide.</li>
	<li>Remove the 0.1% SDS layer from the polymerized separating gel and rinse with ddH2O to remove traces of SDS.</li>
	<li>Pour the stacking gel mix onto the separating gel.</li>
	<li>Place a comb into the stacking gel and remove any air bubbles from around the comb.</li>
	<li>Allow the stacking gel to set for ~60 min at RT.</li>
	<li>Remove the comb and rinse the gel slots with water. Put the gel into the gel tank and fill the gel tank to the top with 1x running buffer (24.8 mM Tris, 190 mM glycine, 0.1% SDS). 
	NOTE: Prepare 1x running buffer from a 10x buffer stock (248 mM Tris, 1.9 M glycine, 1% SDS (w/v) in ddH2O) stored at RT.</li>
	<li>Mix 5-10 &#181;L plasma membrane samples (i.e., 10-20&#160;&#181;g protein) with equal volumes of 2x protein loading dye [120 mM Tris-HCl (pH 6.8), 20% glycerol, 0.02% bromophenol blue, 4% SDS, 200 mM dithiothreitol (DTT)] and immediately load into individual gel slots submerged in running buffer. 
	CAUTION: DTT is harmful if swallowed. It causes serious eye and skin irritations. 
	NOTE: Make a 10 mL stock of 2x protein loading dye, aliquot and store at -20 &#176;C. Do not heat the mixed samples but immediately load them into individual gel slots so that the GFP tag is not denatured, and the in-gel fluorescence signals can be detected.</li>
	<li>Load protein molecular weight markers (10-245 kDa range) into a separate slot to enable the size estimation of individual protein fragments.</li>
	<li>Perform gel electrophoresis at 200 V until the blue loading dye reaches the bottom of the gel (usually 45-55 min).</li>
	<li>Examine the gel for in-gel GFP-fluorescence with a gel imaging system (excitation and emission wavelengths are 475-485 nm and 520 nm, respectively).</li>
	<li>Following in-gel fluorescence imaging, fix proteins by gentle agitation of the gel in ~10-20 mL Protein Gel Fixing Solution (40% ethanol, 10% acetic acid) for 15 min at RT.</li>
	<li>Rinse the gel twice for 10 min with 10 mL of ddH2O and visualize protein bands by placing the gel in 10 mL colloidal Coomassie stain solution with gentle shaking for ~1 h at RT.</li>
	<li>For improved visualization of protein bands, de-stain the gel once or twice in ~20 mL of ddH2O for ~1 h before recording images with the gel imaging system.</li>
</ol>
5. Determination of Cdr1 ATPase Activities&#160;57
<ol>
	<li>Dilute plasma membrane samples &#62;2.2 mg/mL to 1-2 mg/mL in HB.</li>
	<li>Equilibrate the ATPase assay cocktail (75 mM MES-Tris, 75 mM potassium nitrate, 0.3 mM ammonium molybdate, 7.5 mM sodium azide; pH 7.5) and Mg-ATP (28.8 mM ATP disodium salt, 28.8 mM MgCl2; pH 7.0) to 30 &#176;C in a 30 &#176;C incubator. 
	CAUTION: Sodium azide is highly toxic. 
	NOTE: Ensure all buffer stocks and bottles are phosphate free; i.e., wash glassware with 1% (vol/vol) HCl and rinse it several times with ddH2O. Also, keep it separate from other glassware that likely contains traces of phosphate commonly present in detergents used to wash glassware.</li>
	<li>Add 90 &#181;L of assay cocktail with or without Cdr1-ATPase inhibitor (20 &#181;M of oligomycin) into individual wells of a 96-well microtiter plate. 
	NOTE: The assay is performed in triplicate.</li>
	<li>Add 5 &#181;L of the isolated plasma membranes (~5-10 &#181;g protein) or phosphate standards (0-100 nmoles Pi) into the appropriate wells of the microtiter plate. 
	NOTE: Keep the first and last columns for two separate sets of phosphate standards.</li>
	<li>Start the assay by adding 25 &#181;L of prewarmed 28.8 mM Mg-ATP (6 mM final concentration) with a multi-channel pipette into individual wells and incubate at 30 &#176;C for 30 min.</li>
	<li>Stop the reaction by adding 130 &#181;L of development reagent (1.6% sodium L-ascorbate, 1% SDS, 12% ammonium molybdate in 6 M sulfuric acid). 
	CAUTION: Concentrated sulfuric acid reacts violently with water. It is corrosive and may cause skin and lung damage.</li>
	<li>Incubate at RT for 10 min.</li>
	<li>Read the absorbance of the microtiter plate wells at 750 nm with a microtiter plate reader. 
	&#8203;NOTE: Sticking to the 10 min incubation time for blue dye development (i.e., a reduced phosphor-molybdenum complex) is critical for assay accuracy because the blue dye development continues with time.</li>
	<li>Obtain the Cdr1-specific ATPase activity (i.e., the oligomycin-sensitive ATPase activity) by subtracting the ATPase activity in the presence of oligomycin from the total ATPase activity in the absence of oligomycin.</li>
</ol>
6. Small scale detergent screen
<ol>
	<li>Combine the plasma membrane preparations (i.e., 2.5 mg of plasma membrane protein) of cells overexpressing Cdr1-mGFPHis with GTED-20 buffer [10 mM Tris, 0.5 mM EDTA, 20 % (w/v) glycerol; pH 7.5; freshly supplemented with 1 mM PMSF] containing 5 mg of the test detergent, to reach a total volume of 0.5 mL supplemented with 1% (w/v) detergent.</li>
	<li>Rotate the mixture at 4-8 &#176;C for 2 h, with a rotation device.</li>
	<li>Centrifuge the mixture at 141,000 x g at 4 &#176;C for 1 h.</li>
	<li>Transfer the supernatant containing solubilized material to a fresh microcentrifuge tube.</li>
	<li>Add 0.5 mL of GTED-20 buffer supplemented with 2% (w/v) SDS to the insoluble pellet fraction and incubate at 30 &#176;C o/n in a shaking incubator to extract all detergent-insoluble membrane protein.</li>
	<li>Analyze and compare the supernatant and solubilized pellet fractions by SDS-PAGE.</li>
	<li>Photograph gels containing GFP-tagged proteins for in-gel GFP-fluorescence before Coomassie staining and quantify expression levels with the imaging system.</li>
	<li>Use the soluble membrane protein fraction for downstream applications such as fluorescence size exclusion chromatography (FSEC)58 to identify suitable detergent(s).</li>
</ol>

The authors have nothing to disclose.

Despite recent progress in the structural analysis of membrane proteins, no 3D structure for Cdr1, or any other PDR transporter, is currently available. So, gaining knowledge of the Cdr1 structure and its biochemical features is important, as this will not only provide insight into rational design of novel drugs to overcome efflux-mediated drug resistance, but also into the mechanism of function of an important subfamily of ABC proteins.
One of the main requirements for the structural characte...

The extraction of integral membrane proteins from their native lipid environment can dramatically affect their structure and function1,2,3,4. The complex lipid composition of biological membranes5 ensures that critically important protein-lipid interactions can occur6. Lipids maintain the structural integrity of membrane proteins, thus enabling them to function correctly in their membrane compartment destination(s)7,8. Therefore, a critical first step in the membrane protein purification is the extraction of the protein from its native environment without affecting its structure and/or function.
There are many obstacles to characterizing the structure of membrane proteins, most of which are related to their hydrophobic nature, and the difficulties of expressing properly folded and functional membrane proteins in the quantities required for X-ray crystallography or cryo-electron microscopy (cryo-EM)9,10,11,12. There are three types of membrane protein expression systems: homologous9, heterologous13,14,15, and in vitro expression systems16,17. The often-low expression levels, or the prohibitive costs, of many expression systems leave only a few hosts as the preferred option to produce membrane proteins. They include the bacterial host, Escherichia coli, the yeasts S. cerevisiae and Pichia pastoris, and higher eukaryotes such as Sf9 insect cells or mammalian cell lines18. All membrane protein expression technologies have advantages and disadvantages; however, S. cerevisiae is perhaps the best studied eukaryotic model organism suitable for membrane protein production. It is highly versatile with applications in genetic engineering, drug discovery, synthetic biology, and the expression of eukaryotic membrane proteins14,19,20,21.
In this study, a patented S. cerevisiae membrane protein expression technology21 was used, with S. cerevisiae AD&#916;14 and AD&#916;&#916;22 as the preferred hosts (Figure 1A), to overexpress and study the major C. albicans multidrug efflux pump Cdr1. Both the S. cerevisiae strains are derivatives of AD1-8u-&#160;23 that have either the ura3 (AD&#916;) or both the ura3 and his1 (AD&#916;&#916;) genes deleted to eliminate any false positive uracil or histidine prototroph transformants arising through the unwanted integration at the URA3 or the HIS1 genomic loci. The deletion of the 7 major multidrug efflux pumps23, indicated in Figure 1A, makes AD&#916;&#916; exquisitely sensitive to most xenobiotics. The gain-of-function mutant transcription factor Pdr1-3 causes the constitutive overexpression of heterologous membrane proteins such as Cdr1 (red octagons in Figure 1A) after integration of the heterologous-ORF-containing transformation cassette (Figure 1A) at the genomic PDR5 locus (blue rectangle in Figure 1A) via two homologous recombination events. Proper plasma membrane localization of C-terminally mGFPHis tagged proteins can be confirmed by confocal microscopy (Figure 1A), and the His tag can be used for nickel-affinity purification of the tagged protein. Cloning some fungal ABC transporters (e.g., Candida krusei ABC1) into pABC3-derived plasmids was, however, not possible because they could not be propagated&#160;in Escherichia coli due to cell toxicity. This prompted the development of the one-step cloning of membrane proteins14,24 tagged at either their N- or C-terminus with various affinity, epitope, or reporter tags directly into S. cerevisiae AD&#916;&#916; (Figure 1C). S. cerevisiae AD&#916;&#916; strains overexpressing various CDR1 mutants can also be created efficiently this way by using up to five individual PCR fragments that overlap by 25 bp (Figure 1C). Employing this protocol, many ORFs of interest can be cloned, expressed, and characterized at low cost and at high efficiency within a very short time span. The transformation efficiency reduces only ~2-fold with each additional PCR fragment.
If desired, expression levels can also be readily manipulated by primer design to predictably tune expression levels down to anywhere between 0.1%-50% of the usually high, constitutive expression levels25. The optimized, multifunctional, pABC314 derivative cloning vector, pABC3-XLmGFPHis26 (Figure 1B) contains a HRV-3C protease cleavage site (X; LEVLFQ|GP), a protease that performs better at 4 &#176;C than the frequently used tobacco etch virus (TEV) protease27. L is a five amino acid (GSGGS) linker, mGFP is a monomeric mutant (A206K)28,29 version of the yeast enhanced green-fluorescence protein variant yEGFP330, and His is a three amino acid linker (GGS) followed by the six-histidine (HHHHHH) nickel-affinity protein purification tag.
This expression technology has been successfully used in drug discovery and the study of membrane proteins. The first structure for a fungal azole drug target, S. cerevisiae Erg1131, was solved using this technology. It also enabled the detailed characterization of C. albicans Cdr132,33,34 and the creation of a cysteine-deficient Cdr1 molecule35 suitable for cysteine-crosslinking studies to verify any future high-resolution structure. Many other ABC transporters from major human fungal pathogens&#160;(i.e., C. albicans, Candida glabrata, Candida auris, Candida krusei, Candida utilis, Cryptococcus neoformans, Aspergillus fumigatus, Penicillium marneffei, and the Fusarium solani species complex) have also been studied in detail using this expression platform24,36,37,38,39. This has enabled the generation of a panel of S. cerevisiae strains overexpressing efflux pumps that has been used in high-throughput screens to discover the novel fluorescent efflux pump substrate Nile red40 and specific41 and broad-spectrum14,33,42,43,44&#160;efflux pump inhibitors. The use of this system also enabled the discovery of clorgyline as the first of its kind broad-spectrum fungal multidrug efflux pump inhibitor42.
Complete solubilization of membrane proteins and the creation of a homogeneous membrane protein-micelle preparation devoid of endogenous lipids, requires high detergent concentrations45. But unfortunately, this also often inactivates the membrane protein5,8,45,46. The properties of detergent monomers and their aggregation in solution are affected by the physical properties of the hydrophobic tail, the length and branching of the alkyl chain, the presence of an aromatic nucleus or fluoroalkyl side chain, or the number of polyoxyethylene units. Thus, detergent screening is an important first step to determine the most suitable detergent for membrane protein solubilization and purification.
C. albicans is a major human fungal pathogen of immunocompromised individuals that can cause serious, life threatening invasive infections47, and it can become resistant to azole antifungal drugs48,49. One of the main mechanisms of C. albicans multidrug resistance is the overexpression of Cdr150, which is a type II ATP-binding cassette (ABC) transporter51 of the ABCG subfamily located in the plasma membrane. Full-size fungal ABCG transporters (consisting of two nucleotide binding domains [NBDs] and two transmembrane domains [TMDs]) are more commonly known as pleiotropic drug resistance (PDR) transporters and are characterized by their unique inverted domain topology [NBD-TMD]2. PDR transporters are only found in plants52,53 and fungi54. Despite their importance, there are no structures for PDR transporters, although structures for human half-size ABCG transporters have recently been solved which helped create the first tentative model for Cdr133. Our recent experimental evidence suggests, however, that this model is flawed possibly because fungal PDR transporters have characteristic asymmetric NBDs resulting quite possibly in a unique transport mechanism. A high-resolution structure of Cdr1 is, therefore, required for both the rational design of novel efflux pump inhibitors that may help overcome efflux-mediated drug resistance, and to provide insights into the mechanism of action of this important ABC transporter family.
The objective of this study was to develop reliable protocols for the expression, solubilization, and purification of Cdr1 in the genetically modified S. cerevisiae expression host, with the ultimate aim of obtaining a high-resolution structure for Cdr1. As part of this process, a protease-cleavable mGFPHis double tag (Figure 1B) was designed with a 16-residue linker separating the tag from the C-terminus of Cdr1, which improved binding of the attached 6x His affinity tag to the nickel-affinity resin and enabled the monitoring of Cdr1 expression levels in living cells and during the entire purification process. A reproducible protocol for small-scale yeast plasma membrane protein preparations containing about 10% C. albicans Cdr1 (as estimated by Coomassie staining after SDS-PAGE) was also developed, which could be used for the biochemical characterization of Cdr1.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>2-(N-Morpholino)ethane-sulphonic acid (MES)</td>
			<td>Sigma-Aldrich</td>
			<td>M3671</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Amino-2-(hydroxymethyl)-1,3-propanediol (Tris base; ultra-pure)</td>
			<td>Merck</td>
			<td>77-86-1</td>
			<td></td>
		</tr>
		<tr>
			<td>2,2-Didecylpropane-1,3-bis-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>NG310S</td>
			<td>LMNG</td>
		</tr>
		<tr>
			<td>2,2-Dihexylpropane-1,3-bis-&#946;-D-glucopyranoside</td>
			<td>Anatrace</td>
			<td>NG311S</td>
			<td>OGNG (MNG-OG)</td>
		</tr>
		<tr>
			<td>2,2-Dioctylpropane-1,3-bis-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>NG322S</td>
			<td>DMNG</td>
		</tr>
		<tr>
			<td>4-Trans-(4-trans-propylcyclohexyl)-cyclohexyl &#945;-D-maltopyranoside</td>
			<td>Glycon Biochemicals GmbH</td>
			<td>D99019-C</td>
			<td>PCC-&#945;-M</td>
		</tr>
		<tr>
			<td>40% Acrylamide/Bis-acrylamide (37.5:1)</td>
			<td>Bio-Rad</td>
			<td>1610148</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic acid (glacial)</td>
			<td>Merck</td>
			<td>64-19-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Formedium</td>
			<td>&#160;009002-18-0</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium molybdate</td>
			<td>Sigma-Aldrich</td>
			<td>13106-76-8</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium persulphate (APS)</td>
			<td>Bio-Rad</td>
			<td>1610700</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP disodium salt</td>
			<td>sigma-Aldrich</td>
			<td>A-6419</td>
			<td></td>
		</tr>
		<tr>
			<td>Bromophenol blue</td>
			<td>SERVA Electrophoresis GmbH</td>
			<td>34725-61-6</td>
			<td></td>
		</tr>
		<tr>
			<td>CHAPS</td>
			<td>Anatrace</td>
			<td>C316S</td>
			<td></td>
		</tr>
		<tr>
			<td>CHAPSO</td>
			<td>Anatrace</td>
			<td>C317S</td>
			<td></td>
		</tr>
		<tr>
			<td>CSM</td>
			<td>Formedium</td>
			<td>DCS0019</td>
			<td></td>
		</tr>
		<tr>
			<td>CSM minus uracil</td>
			<td>Formedium</td>
			<td>DCS0161</td>
			<td></td>
		</tr>
		<tr>
			<td>Cyclohexyl-1-butyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>C324S</td>
			<td>CYMAL-4</td>
		</tr>
		<tr>
			<td>Cyclohexyl-1-heptyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>C327S</td>
			<td>CYMAL-7</td>
		</tr>
		<tr>
			<td>Cyclohexyl-methyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>C321S</td>
			<td>CYMAL-1</td>
		</tr>
		<tr>
			<td>Digitonin</td>
			<td>Sigma-Aldrich</td>
			<td>11024-24-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Dithiothreitol (DTT)</td>
			<td>Roche Diagnostics</td>
			<td>10197785103</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Merck</td>
			<td>67-68-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Merck</td>
			<td>459836</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic acid disodium salt (EDTA; Titriplex III)</td>
			<td>Merck</td>
			<td>6381-92-6</td>
			<td></td>
		</tr>
		<tr>
			<td>ExoSAP-IT PCR Product Cleanup Reagent</td>
			<td>Applied Biosystems</td>
			<td>78205</td>
			<td>A blend of exonuclease and phosphatase</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Formedium</td>
			<td>50-99-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Merck</td>
			<td>56-81-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Merck</td>
			<td>G8898</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Formedium</td>
			<td>7365-45-9</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>Merck</td>
			<td>1003172510</td>
			<td></td>
		</tr>
		<tr>
			<td>KOD Fx Neo</td>
			<td>TOYOBO Co</td>
			<td>KFX-201</td>
			<td>Use for reliable colony PCR</td>
		</tr>
		<tr>
			<td>lithium acetate (LiAc)</td>
			<td>Sigma-Aldrich</td>
			<td>546-89-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium chloride hexa-hydrate</td>
			<td>sigma-Aldrich</td>
			<td>M2393</td>
			<td></td>
		</tr>
		<tr>
			<td>MES</td>
			<td>Formedium</td>
			<td>145224-94-8</td>
			<td></td>
		</tr>
		<tr>
			<td>n-Decanoyl-N-hydroxyethyl-glucamide</td>
			<td>Anatrace</td>
			<td>H110S</td>
			<td>HEGA-10</td>
		</tr>
		<tr>
			<td>n-Decanoyl-N-methyl-glucamide</td>
			<td>Anatrace</td>
			<td>M320S</td>
			<td>MEGA-10</td>
		</tr>
		<tr>
			<td>n-Decyl-phosphocholine</td>
			<td>Anatrace</td>
			<td>F304S</td>
			<td>Fos-choline-10</td>
		</tr>
		<tr>
			<td>n-Decyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>D322S</td>
			<td>DM</td>
		</tr>
		<tr>
			<td>n-Dodecyl-N,N-dimethyl-3-ammonio-1-propanesulphonate</td>
			<td>Anatrace</td>
			<td>AZ312S</td>
			<td>Anzergent 3-12</td>
		</tr>
		<tr>
			<td>n-Dodecyl-N,N-dimethylamine-N-oxide</td>
			<td>Anatrace</td>
			<td>D360S</td>
			<td>LDAO</td>
		</tr>
		<tr>
			<td>n-Dodecyl-&#945;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>D310HA</td>
			<td>&#945;-DDM</td>
		</tr>
		<tr>
			<td>n-Dodecyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>D310S</td>
			<td>&#946;-DDM</td>
		</tr>
		<tr>
			<td>n-Nonyl-&#946;-D-glucopyranoside</td>
			<td>Anatrace</td>
			<td>N324S</td>
			<td>NG</td>
		</tr>
		<tr>
			<td>n-Nonyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>N330S</td>
			<td>NM</td>
		</tr>
		<tr>
			<td>n-Octadecyl-N,N-dimethyl-3-ammonio-1-propanesulphonate</td>
			<td>Anatrace</td>
			<td>AZ318S</td>
			<td>Anzergent 3-18</td>
		</tr>
		<tr>
			<td>n-Octyl-N,N-dimethyl-3-ammonio-1-propanesulphonate</td>
			<td>Anatrace</td>
			<td>AZ308S</td>
			<td>Anzergent 3-8</td>
		</tr>
		<tr>
			<td>n-Octyl-phosphocholine</td>
			<td>Anatrace</td>
			<td>F300S</td>
			<td>Fos-choline-8</td>
		</tr>
		<tr>
			<td>n-Octyl-&#946;-D-glucopyranoside</td>
			<td>Anatrace</td>
			<td>O311S</td>
			<td>OG</td>
		</tr>
		<tr>
			<td>n-Tetradecyl-phosphocholine</td>
			<td>Anatrace</td>
			<td>F312S</td>
			<td>Fos-choline-14</td>
		</tr>
		<tr>
			<td>n-Tetradecyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>T315S</td>
			<td>TDM</td>
		</tr>
		<tr>
			<td>n-Tridecyl-phosphocholine</td>
			<td>Anatrace</td>
			<td>F310S</td>
			<td>Fos-choline-13</td>
		</tr>
		<tr>
			<td>n-Tridecyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>T323S</td>
			<td>-</td>
		</tr>
		<tr>
			<td>n-Undecyl-&#946;-D-maltopyranoside</td>
			<td>Anatrace</td>
			<td>U300S</td>
			<td>UM (UDM)</td>
		</tr>
		<tr>
			<td>N,N,N&#8217;,N&#8217;-tetramethyl-ethylenediamine (TEMED)</td>
			<td>Sigma-Aldrich</td>
			<td>T9281</td>
			<td></td>
		</tr>
		<tr>
			<td>Octylphenoxypolyethoxyethanol</td>
			<td>Sigma-Aldrich</td>
			<td>9002-93-1</td>
			<td>TRITON X-100</td>
		</tr>
		<tr>
			<td>Oligomycin</td>
			<td>Sigma-Aldrich</td>
			<td>75351</td>
			<td></td>
		</tr>
		<tr>
			<td>Peptone</td>
			<td>Formedium</td>
			<td>3049-73-7</td>
			<td></td>
		</tr>
		<tr>
			<td>phenylmethylsulfonyl fluoride (PMSF)</td>
			<td>Roche Diagnostics</td>
			<td>329-98-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Phusion&#160;Hot Start Flex DNA Polymerase</td>
			<td>New England Biolabs</td>
			<td>M0535S</td>
			<td>High-fidelity DNA polymerase</td>
		</tr>
		<tr>
			<td>polyethylene glycol (PEG 3350)</td>
			<td>Sigma-Aldrich</td>
			<td>25322-68-3</td>
			<td></td>
		</tr>
		<tr>
			<td>polyoxyethylenesorbitan monooleate</td>
			<td>Sigma-Aldrich</td>
			<td>9005-65-6</td>
			<td>TWEEN 80</td>
		</tr>
		<tr>
			<td>Potassium nitrate</td>
			<td>Sigma-Aldrich</td>
			<td>P8394</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein Assay Kit</td>
			<td>Bio-Rad</td>
			<td>5000122</td>
			<td>RC DC Protein Assay Kit II</td>
		</tr>
		<tr>
			<td>QC Colloidal Coomassie Stain</td>
			<td>Bio-Rad</td>
			<td>1610803</td>
			<td></td>
		</tr>
		<tr>
			<td>Prism Ultra Protein Ladder (10-245 kDa)</td>
			<td>Abcam</td>
			<td>AB116028</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium azide</td>
			<td>Sigma-Aldrich</td>
			<td>71289</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulphate</td>
			<td>Sigma-Aldrich</td>
			<td>151-21-3</td>
			<td>SDS</td>
		</tr>
		<tr>
			<td>Sodium L-ascorbate BioXtra</td>
			<td>Sigma-Aldrich</td>
			<td>11140</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose Monododecanoate</td>
			<td>Anatrace</td>
			<td>S350S</td>
			<td>DDS</td>
		</tr>
		<tr>
			<td>Sulphuric acid</td>
			<td>Sigma-Aldrich</td>
			<td>339741</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>Formedium</td>
			<td>008013-01-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast nitrogen base without amino acids</td>
			<td>Formedium</td>
			<td>CYN0402</td>
			<td></td>
		</tr>
		<tr>
			<td>&#160;Equipment (type)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge&#160; (Eppendorf 5804)</td>
			<td>Eppendorf</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge (Beckman Ultra)</td>
			<td>Beckman</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge (Sorvall RC6)</td>
			<td>Sorvall</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>FSEC apparatus (NGC Chromatography Medium Pressure system equipped with a fluorescence detector, an autosampler, a fractionator)</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gel imaging (GelDoc EZ Imager)</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate reader (Synergy 2 Multi-Detection)</td>
			<td>BioTek Instruments</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PCR thermal cycler (C1000 Touch)</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Power supply (PowerPac)</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SDS PAGE (Mini-PROTEAN Tetra)</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Shaking incubator (Multitron)</td>
			<td>Infors HT, Bottmingen</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Superose 6 Increase 10/300 GL</td>
			<td>GE Healthcare Life Sciences</td>
			<td>GE17-5172-01</td>
			<td></td>
		</tr>
		<tr>
			<td>UV/Visible spectrophotometer (Ultraspec 6300 pro)</td>
			<td colspan="2">Amersham BioSciences UK Ltd</td>
			<td></td>
		</tr>
	</tbody>
</table>

small-scale plasma membrane preparation for the analysis of candida albicans cdr1-mgfphis

The successful biochemical and biophysical characterization of ABC transporters depends heavily on the choice of the heterologous expression system. Over the past two decades, we have developed a yeast membrane protein expression platform that has been used to study many important fungal membrane proteins. The expression host Saccharomyces cerevisiae AD&#916;&#916; is deleted in seven major endogenous ABC transporters and it contains the transcription factor Pdr1-3 with a gain-of-function mutation that enables the constitutive overexpression of heterologous membrane protein genes stably integrated as single copies at the genomic PDR5 locus. The creation of versatile plasmid vectors and the optimization of one-step cloning strategies enables the rapid and accurate cloning, mutagenesis, and expression of heterologous ABC transporters. Here, we describe the development and use of a novel protease-cleavable mGFPHis double tag (i.e., the monomeric yeast enhanced green fluorescent protein yEGFP3 fused to a six-histidine affinity purification tag) that was designed to avoid possible interference of the tag with the protein of interest and to increase the binding efficiency of the His tag to nickel-affinity resins. The fusion of mGFPHis to the membrane protein ORF (open reading frame) enables easy quantification of the protein by inspection of polyacrylamide gels and detection of degradation products retaining the mGFPHis tag. We demonstrate how this feature facilitates detergent screening for membrane protein solubilization. A protocol for the efficient, fast, and reliable isolation of the small-scale plasma membrane preparations of the C-terminally tagged Candida albicans multidrug efflux transporter Cdr1 overexpressed in S. cerevisiae AD&#916;&#916;, is presented. This small-scale plasma membrane isolation protocol generates high-quality plasma membranes within a single working day. The plasma membrane preparations can be used to determine the enzyme activities of Cdr1 and Cdr1 mutant variants.

A high frequency of transformation of S. cerevisiae AD&#916;&#916; (~4 x 104 transformants/&#181;g) was achieved with pYES2 (Figure 2B). As expected, the no DNA (i.e., ddH2O only) control gave no transformants, and 1 &#181;g of the linear CDR1-mGFPHis transformation cassette (Figure 1A) gave ~50 transformants (Figure 2C)&#160;with the optimized AD&#916;&#916; transformation protocol. ...

Watch this Scientific Journal Video about Small-Scale Plasma Membrane Preparation for the Analysis of Candida albicans Cdr1-mGFPHis at JoVE.com

Small-Scale Plasma Membrane Preparation for the Analysis of Candida albicans Cdr1-mGFPHis

This article presents a small-scale plasma membrane isolation protocol for the characterization of Candida albicans ABC (ATP-binding cassette) protein Cdr1, overexpressed in Saccharomyces cerevisiae. A protease-cleavable C-terminal mGFPHis double tag with a 16-residue linker between Cdr1 and the tag was designed to facilitate the purification and detergent-screening of Cdr1.

Small-Scale Plasma Membrane Preparation for the Analysis of Candida albicans Cdr1-mGFPHis

The successful biochemical and biophysical characterization of ABC transporters depends heavily on the choice of the heterologous expression system. Over ...

small-scale-plasma-membrane-preparation-for-analysis-candida-albicans

Research

JoVE Journal

Biology

2.6K Views.  University of Otago. This article presents a small-scale plasma membrane isolation protocol for the characterization of Candida albicans ABC (ATP-binding cassette) protein Cdr1, overexpressed in Saccharomyces cerevisiae. A protease-cleavable C-terminal mGFPHis double tag with a 16-residue linker between Cdr1 and the tag was designed to facilitate the purification and detergent-screening of Cdr1.

Video: Small-Scale Plasma Membrane Preparation for the Analysis of Candida albicans Cdr1-mGFPHis

Quantitative Measurement of GLUT4 Translocation to the Plasma Membrane by Flow Cytometry

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces glucose uptake by insulin-sensitive tissues, most notably the brain, skeletal muscle, and adipocytes. Patients suffering from type-2 diabetes and/or obesity often develop insulin resistance and are unable to control their glucose homeostasis. New insights into the mechanisms of insulin resistance may provide new treatment strategies for type-2 diabetes.
The GLUT family of glucose transporters consists of thirteen members distributed on different tissues throughout the body1. Glucose transporter type 4 (GLUT4) is the major transporter that mediates glucose uptake by insulin sensitive tissues, such as the skeletal muscle. Upon binding of insulin to its receptor, vesicles containing GLUT4 translocate from the cytoplasm to the plasma membrane, inducing glucose uptake. Reduced GLUT4 translocation is one of the causes of insulin resistance in type-2 diabetes2,3.
The translocation of GLUT4 from the cytoplasm to the plasma membrane can be visualized by immunocytochemistry, using fluorophore-conjugated GLUT4-specific antibodies.
Here, we describe a technique to quantify total amounts of GLUT4 translocation to the plasma membrane of cells during a chosen duration, using flow cytometry. This protocol is rapid (less than 4 hours, including incubation with insulin) and allows the analysis of as few as 3,000 cells or as many as 1 million cells per condition in a single experiment. It relies on anti-GLUT4 antibodies directed to an external epitope of the transporter that bind to it as soon as it is exposed to the extracellular medium after translocation to the plasma membrane.

This protocol describes a rapid technique to quantify the translocation of GLUT4 from the cytoplasm to the plasma membrane of cells by flow cytometry.

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces ...

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)

Our goal is to obtain a comprehensive description of molecular processes occurring at cellular membranes in different biological functions. We aim at characterizing the complex organization and dynamics of the plasma membrane at single-molecule level, by developing analytic tools dedicated to Single-Particle Tracking (SPT) at high density: Multiple-Target Tracing (MTT)1. Single-molecule videomicroscopy, offering millisecond and nanometric resolution1-11, allows a detailed representation of membrane organization12-14 by accurately mapping descriptors such as cell receptors localization, mobility, confinement or interactions.
We revisited SPT, both experimentally and algorithmically. Experimental aspects included optimizing setup and cell labeling, with a particular emphasis on reaching the highest possible labeling density, in order to provide a dynamic snapshot of molecular dynamics as it occurs within the membrane. Algorithmic issues concerned each step used for rebuilding trajectories: peaks detection, estimation and reconnection, addressed by specific tools from image analysis15,16. Implementing deflation after detection allows rescuing peaks initially hidden by neighboring, stronger peaks. Of note, improving detection directly impacts reconnection, by reducing gaps within trajectories. Performances have been evaluated using Monte-Carlo simulations for various labeling density and noise values, which typically represent the two major limitations for parallel measurements at high spatiotemporal resolution.
The nanometric accuracy17 obtained for single molecules, using either successive on/off photoswitching or non-linear optics, can deliver exhaustive observations. This is the basis of nanoscopy methods17 such as STORM18, PALM19,20, RESOLFT21 or STED22,23, which may often require imaging fixed samples. The central task is the detection and estimation of diffraction-limited peaks emanating from single-molecules. Hence, providing adequate assumptions such as handling a constant positional accuracy instead of Brownian motion, MTT is straightforwardly suited for nanoscopic analyses. Furthermore, MTT can fundamentally be used at any scale: not only for molecules, but also for cells or animals, for instance. Hence, MTT is a powerful tracking algorithm that finds applications at molecular and cellular scales.

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT

Multiple-Target Tracing is a homemade algorithm developed for tracking individually labeled molecules within the plasma membrane of living cells. Efficiently detecting, estimating and tracing molecules over time at high-density provide a user-friendly, comprehensive tool to investigate nanoscale membrane dynamics.

Our goal is to obtain a comprehensive description of molecular processes occurring at cellular membranes in different biological functions. We aim at ...

Small-scale Nuclear Extracts for Functional Assays of Gene-expression Machineries

A great deal of progress in understanding gene expression has been made using in vitro systems. For most studies, functional assays are carried out using extracts that are prepared in bulk from 10-50 or more liters of cells grown in suspension. However, these large-scale preparations are not amenable to rapidly testing in vitro effects that result from a variety of in vivo cellular treatments or conditions. This journal video article shows a method for preparing functional small-scale nuclear extracts, using HeLa cells as an example. This method is carried out using as few as three 150 mm plates of cells grown as adherent monolayers. To illustrate the efficiency of the small-scale extracts, we show that they are as active as bulk nuclear extracts for coupled RNA Polymerase II transcription/splicing reactions. To demonstrate the utility of the extract protocol, we show that splicing is abolished in extracts prepared from HeLa cells treated with the splicing inhibitor drug E7107. The small-scale protocol should be generally applicable to any process or cell type that can be investigated in vitro using cellular extracts. These include patient cells that are only available in limited quantities or cells exposed to numerous agents such as drugs, DNA damaging agents, RNAi, or transfection, which require the use of small cell populations. In addition, small amounts of freshly grown cells are convenient and/or required for some applications.

A protocol for preparation of robust, small-scale HeLa nuclear extracts is described. This protocol is valuable for assays that require use of small populations of cells, such as cells treated with drugs or RNAi. The method should be applicable to a wide variety of gene expression assays and other cell types, including patient cells.

A great deal of progress in understanding gene expression has been made using in vitro systems.  For most studies, functional assays are carried out using ...

Imaging Plasma Membrane Deformations With pTIRFM

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during the fusion of vesicle and plasma membranes. These rapid and localized changes are achieved by dynamic interactions between lipids and specialized proteins that control membrane curvature. The absence of such interactions would not only have devastating consequences for vesicle fusion, but a host of other cellular functions that involve control of membrane shape. In recent years, the identity of a number of proteins with membrane-shaping properties has been determined. What remains missing is a roadmap of when, where, and how they act as fusion and content release progress.
Our understanding of the molecular events that enable membrane remodeling has historically been limited by a lack of analytical methods that are sensitive to membrane curvature or have the temporal resolution to track rapid changes. PTIRFM satisfies both of these criteria. We discuss how pTIRFM is implemented to visualize and interpret rapid, submicron changes in the orientation of chromaffin cell membranes during dense core vesicle (DCV) fusion. The chromaffin cells we use are isolated from bovine adrenal glands. The membrane is stained with a lipophilic carbocyanine dye,1,1&#39;-dioctadecyl-3,3,3&#39;,3&#39;-tetramethylindodicarbocyanine, 4-chlorobenzenesulfonate, or&#160;diD. DiD intercalates in the membrane plane with a &#34;fixed&#34; orientation and is therefore sensitive to the polarization of the evanescent field. The diD-stained cell membrane is sequentially excited with orthogonal polarizations of a 561&#160;nm laser (p-pol, s-pol). A 488&#160;nm laser is used to visualize vesicle constituents and time the moment of fusion. Exocytosis is triggered by locally perfusing cells with a depolarizing KCl solution. Analysis is performed offline using custom-written software to understand how diD emission intensity changes relate to fusion pore dilation.

Polarization-based Total Internal Reflection Fluorescence Microscopy (pTIRFM) enables real-time detection of cell membrane dynamics. This article describes the implementation of pTIRFM for the study of membrane remodeling during regulated exocytosis. The technique is generalizable to other processes in cell biology that directly or indirectly involve changes in membrane shape.

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during ...

Novel Production Protocol for Small-scale Manufacture of Probiotic Fermented Foods

A novel dried bacterial consortium of Lactobacillus rhamnosus yoba 2012 and Streptococcus thermophilus C106 is cultured in 1 L of milk. This fresh starter can be used for the production of fermented milk and other fermented foods either at home or at small-scale in rural settings. For the fresh starter, 1 L of milk is pasteurized in a pan that fits into a larger pan containing water, placed on a source of heat. In this water bath, the milk is heated and incubated at 85 &#176;C for 30 min. Thereafter, the milk is cooled down to 45 &#176;C, transferred to a vacuum flask, inoculated with the dried bacteria and left for at least 16 hr between 30 &#176;C and 45 &#176;C. For the purpose of frequent home production, the fresh starter is frozen into ice cubes, which can be used for the production of small volumes of up to 2 L of fermented milk. For the purpose of small-scale production in resource-poor countries, pasteurization of up to 100 L of milk is conducted in milk cans that are placed in a large sauce pan filled with water and heated on a fire at 85 &#176;C for 30 min, and subsequently cooled to 45 &#176;C. Next, the 100 L batch is inoculated with the 1 L freshly prepared starter mentioned before. To assure an effective fermentation at a temperature between 30 and 45 &#176;C, the milk can is covered with a blanket for 12 hr. For the production of non-dairy fermented foods, the fresh starter is left in a cheese cloth for 12 hr, and the drained-off whey can be subsequently used for the inoculation of a wide range of food raw materials, including vegetables and cereal-based foods.

A production protocol is described for the small-scale production of probiotic fermented dairy drink with the aid of a novel bacterial starter culture.

A novel dried bacterial consortium of Lactobacillus rhamnosus yoba 2012 and Streptococcus thermophilus C106 is cultured in 1 L of milk. This fresh starter ...

Sample Preparation for Mass Cytometry Analysis

Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities for deep analysis well beyond what is possible with conventional fluorescence-based flow cytometry. As with any new technology, there are critical steps that help ensure the reliable generation of high-quality data. Presented here is an optimized protocol that incorporates multiple techniques for the processing of cell samples for mass cytometry analysis. The methods described here will help the user avoid common pitfalls and achieve consistent results by minimizing variability, which can lead to inaccurate data. To inform experimental design, the rationale behind optional or alternative steps in the protocol and their efficacy in uncovering new findings in the biology of the system being investigated is covered. Lastly, representative data is presented to illustrate expected results from the techniques presented here.

This article describes the collection and processing of samples for mass cytometry analysis.

Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities ...

Determination of Plasma Membrane Partitioning for Peripherally-associated Proteins

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein using the profiles of fluorescence intensity across the plasma membrane. Measured fluorescence profiles are fitted by a model for membrane and cytoplasm fluorescence distribution along a line applied perpendicularly to the cell periphery. This model is constructed from the fluorescence intensity values in reference cells expressing a fluorescently-tagged marker for cytoplasm and with FM 4-64-labeled plasma membrane. The method can be applied to various cell types and organisms; however, only plasma membranes of non-neighboring cells can be evaluated. This fast microscopy-based method is suitable for experiments, where subtle and dynamic changes of plasma membrane-associated markers are expected and need to be quantified, e.g., in the analysis of mutant versions of proteins, inhibitor treatments, and signal transduction observations. The method is implemented in a multi-platform R package that is coupled with an ImageJ macro that serves as a user-friendly interface.

Here, we present a protocol to perform a quantitative analysis of the level of plasma-membrane association for fluorescently-tagged peripherally-associated protein. The method is based on the computational decomposition of membrane and cytoplasmic component of signal observed in cells labeled with plasma membrane fluorescent marker.

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein ...

Characterization of MLKL-mediated Plasma Membrane Rupture in Necroptosis

Necroptosis is a programmed cell death pathway triggered by activation of receptor interacting protein kinase 3 (RIPK3), which phosphorylates and activates the mixed lineage kinase-like domain pseudokinase, MLKL, to rupture or permeabilize the plasma membrane. Necroptosis is an inflammatory pathway associated with multiple pathologies including autoimmunity, infectious and cardiovascular diseases, stroke, neurodegeneration, and cancer. Here, we describe protocols that can be used to characterize MLKL as the executioner of plasma membrane rupture in necroptosis. We visualize the process of necroptosis in cells using live-cell imaging with conventional and confocal fluorescence&#160;microscopy, and in fixed cells using electron microscopy, which together revealed the redistribution of MLKL from the cytosol to the plasma membrane prior to induction of large holes in the plasma membrane. We present in vitro nuclear magnetic resonance (NMR) analysis using lipids to identify putative modulators of MLKL-mediated necroptosis. Based on this method, we identified quantitative lipid-binding preferences and phosphatidyl-inositol phosphates (PIPs) as critical binders of MLKL that are required for plasma membrane targeting and permeabilization in necroptosis.

We report methods for characterization of MLKL-mediated plasma membrane rupture in necroptosis including conventional and confocal live-cell microscopy imaging, scanning electron microscopy, and NMR-based lipid binding.

Necroptosis is a programmed cell death pathway triggered by activation of receptor interacting protein kinase 3 (RIPK3), which phosphorylates and ...

Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&amp;RUN Method and Data Analysis Workflow

Regulatory transcription factors control many important biological processes, including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage under targets and release using nuclease (CUT&amp;RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&amp;RUN is amenable to a higher-throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs than ChIP-seq. Here, a comprehensive CUT&amp;RUN protocol and accompanying data analysis workflow tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans are described. This detailed protocol includes all necessary experimental procedures, from epitope tagging of transcription factor-coding genes to library preparation for sequencing; additionally, it includes a customized computational workflow for CUT&amp;RUN data analysis.

Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow

This protocol describes an experimental method and data analysis workflow for cleavage under targets and release using nuclease (CUT&amp;RUN) in the human fungal pathogen Candida albicans.

Regulatory transcription factors control many important biological processes, including cellular differentiation, responses to environmental perturbations ...

Small-Scale Extraction of Caenorhabditis elegans Genomic DNA

Genomic DNA extraction from single or a few Caenorhabditis elegans has many downstream applications, including PCR for genotyping lines, cloning, and sequencing. The traditional proteinase K-based methods for genomic DNA extraction from C. elegans take several hours. Commercial extraction kits that effectively break open the C. elegans cuticle and extract genomic DNA are limited. An easy, faster (~15 min), and cost-efficient method of extracting C. elegans genomic DNA that works well for classroom and research applications is reported here. This DNA extraction method is optimized to use single or a few late-larval (L4) or adult nematodes as starting material for obtaining a reliable template to perform PCR. The results indicate that the DNA quality is suitable for amplifying gene targets of different sizes by PCR, permitting genotyping of single or a few animals even at dilutions to one-fiftieth of the genomic DNA from a single adult per reaction. The reported protocols can be reliably used to quickly produce DNA template from a single or a small sample of C. elegans for PCR-based applications.

Small-Scale Extraction of Caenorhabditis elegans Genomic DNA

Presented here is a description of the straightforward and relatively rapid isolation of Caenorhabditis elegans genomic DNA from one or a few animals using a commercially available tissue kit. The resulting gDNA preparation is a suitable template for PCR.

Genomic DNA extraction from single or a few Caenorhabditis elegans has many downstream applications, including PCR for genotyping lines, cloning, and ...