We thank all members of the Kerscher lab for their support. We thank Mark Hochstrasser for yeast strain MHY3765. This work was supported by NSF grant 1051970 (to OK) and a Howard Hughes Medical Institute Undergraduate Travel grant and Monroe Scholars Program Grant (to ES).

Purification of 6xHIS-tagged proteins expressed in budding yeast cells under native conditions
1. Growth of Yeast Cells and Induction of Protein Expression
(Modified from 2)
OPTIONAL: Use logarithmically growing yeast cultures expressing protein of interest instead of the galactose-induced cultures described below.
<ol>
	<li>Transform cells of a Gal+ yeast strain with a plasmid encoding a galactose-inducible 6xHIS-tagged protein of choice. For example, see reagents list.</li>
	<li>Inoculate transformants in 5 ml of appropriate selective media (e.g. SD-uracil) containing 2% sucrose. Incubate at 30 &#176;C O/N, rotating.</li>
	<li>Dilute O/N culture so that the optical density at 600 nm measures 0.3 (OD600 = 0.3) in 33 ml of selective media with 2% sucrose. Grow at 30 &#176;C, shaking (&#916;150 rpm).</li>
	<li>When the culture has reached OD600 = 0.8-1.5, induce expression of the desired protein by adding 17 ml of 3x YEP with 6% galactose (Recipe in Table 1), for a final concentration of 1x YEP with 2% galactose. Total culture volume is now 50 ml. Incubate, shaking, at 30 &#176;C for an additional 5-6 hr. 
	Note: the culture volume can be varied. In step 1.3, dilute into two-thirds of the desired final volume. In step 1.4, add one-third the final volume of 3x YEP/6% galactose.</li>
	<li>Measure the OD600 of the induced culture and centrifuge &#916;150-200 OD600 units of cells for 5 min at 5,000 rpm at 4 &#176;C.</li>
	<li>Resuspend cell pellet with 1 ml ice-cold 1x PBS with 1x protease inhibitor cocktail and transfer to a 2 ml screw cap tube.</li>
	<li>Centrifuge cells for 1 min at 15,000 rpm at 4 &#176;C. Decant supernatant.</li>
	<li>Snap freeze cell pellet in liquid nitrogen, followed by immediate cell lysis or storage at -80 &#176;C until further use.</li>
</ol>
2. Homogenization of Yeast Cells and Extraction of Proteins
<ol>
	<li>To the frozen cell pellet from the previous step, add 200 &#181;l of acid-washed glass beads and 500 &#181;l of ice-cold lysis buffer (Recipe in Table 1 or use cell lysis buffer of choice).</li>
	<li>Briefly pipette up and down. It is not required to fully resuspend the cell pellet. Keep tubes on ice at all times. 
	Note: The end of the pipette tip may be cut off before pipetting up and down.</li>
	<li>At 4 &#176;C, place the tube(s) with cells into the bead mill, balance, lock, and run the machine as per manufacturer&#39;s instructions.</li>
	<li>Run the bead beater containing the tube(s) for 20 sec at 5.5 m/sec, then place on slushy ice for 1 min. Repeat 6x&#160;in total.</li>
	<li>Clear the extracted proteins by centrifugation for 15 min at 15,000 rpm at 4 &#176;C. OPTIONAL: remove small particulates by centrifugation through a SpinX filter.</li>
	<li>Prepare a sample of the whole cell extract (WCE) to confirm presence of the protein of interest by Western Blot:
	<ol>
		<li>Add WCE corresponding with 2 OD600 units of cells (e.g.&#160;5 &#181;l of cleared extract if 200 OD600 units of cells were harvested) to 800 &#181;l 20% trichloroacetic acid (TCA). Vortex to mix.</li>
		<li>Centrifuge for 2.5 min at 15,000 rpm at 4 &#176;C. Decant the supernatant, but be careful to retain the pellet.</li>
		<li>Add 800 &#181;l of 2% TCA to the pellet and vortex the tube, followed by centrifugation for 2.5 min at 15,000 rpm at 4 &#176;C. Decant the supernatant, but be careful to retain the pellet.</li>
		<li>Add 100 &#181;l of TCA Sample Buffer (Recipe in Table 1), vortex to dissolve pellet. Note: If the sample buffer becomes acidic (turns yellow) after addition to the pellet, add aliquots of &#916;10 &#181;l Tris base [1M] until the sample is blue again.</li>
		<li>Incubate in a 100 &#176;C heat block for 2-5 min.</li>
		<li>Vortex again to fully dissolve if remnants of pellet are still present. Pellets prepared by this method are notoriously difficult to fully dissolve. It may take &#916;10 min of vortexing to completely dissolve pellets.</li>
		<li>Store sample at -80 &#176;C until further use.</li>
	</ol>
	</li>
	<li>Snap freeze aliquots of remaining cleared WCE in liquid nitrogen and store at -80 &#176;C until further use.</li>
</ol>
3. Batch Purification of Proteins from Yeast Cell Homogenates
Note: This purification method was optimized for purification of 6xHIS-tagged proteins on Co2+ metal affinity resin.
<ol>
	<li>Resin Equilibration
	<ol>
		<li>For a sample of cleared WCE prepared from &#916;20-40 OD600 units of cells, add 50-100 &#181;l of affinity resin to a microcentrifuge tube. Proteins extracted from cells that did not express the desired protein or a nonspecific resin, such as amylose, may be used as controls for nonspecific binding.</li>
		<li>Wash resin 5x with 1 ml of wash buffer: invert top-over-bottom until resin is resuspended, and then spin for 1 min at 5,000 rpm at 4 &#176;C. Aspirate the supernatant. 
		Note: if performing extraction and purification on the same day, resin equilibration can be performed prior to extraction.</li>
	</ol>
	</li>
	<li>Protein Binding for Affinity Purification
	<ol>
		<li>Add 100-200 &#181;l of cleared lysate (&#916;20-40 OD600 units) to 50-100 &#181;l washed beads, and bring the total volume to 1 ml with lysis buffer.</li>
		<li>Incubate with nutation or rocking at 4 &#176;C for 2-5 hr.</li>
		<li>Spin for 1 min at 5,000 rpm at 4 &#176;C.</li>
		<li>If desired, save a sample of the remaining supernatant for subsequent analysis of unbound proteins. TCA precipitate as detailed above for the WCE (step 2.6).</li>
		<li>Wash resin with bound proteins 5x with 1 ml of wash buffer, followed by a spin for 1 min at 5,000 rpm at 4 &#176;C. Keep samples cold during washes.</li>
	</ol>
	</li>
	<li>Elution of Bound Proteins
	<ol>
		<li>Add 150 &#181;l elution buffer to resin, nutate at 4 &#176;C for 5 min, spin for 1 min at 5,000 rpm at 4 &#176;C and save the supernatant in a new tube. OPTIONAL: Repeat 2x and pool elutions.</li>
		<li>Prepare eluted sample for Western blot: To 25 &#181;l of eluted proteins, add 25 &#181;l 2x lithium dodecyl sulfate (LDS) sample buffer with 2 &#181;l &#946;-mercaptoethanol (BME) and incubate in a 100 &#176;C heat block for 2 min. 
		Note: Standard 2X Laemmli sample buffer may also be used.</li>
		<li>Snap freeze excess eluted protein in liquid nitrogen. 
		OPTIONAL: strip remaining proteins from resin with an equal volume of 2x LDS sample buffer at 65 &#176;C for 5 min, remove the LDS-eluted proteins to a new tube, then add 2 &#181;l BME to the eluted proteins, not to the resin. This order is to prevent removal of any ions or antibodies that are conjugated to the beads.</li>
		<li>Store samples at -80 &#176;C until further use.</li>
	</ol>
	</li>
	<li>Western Blot and probe with appropriate antibodies to visualize proteins.
	<ol>
		<li>Load 10-20 &#181;l (&#916;1-3 OD600 units) of each sample and 3-10 &#181;l of a protein ladder in an SDS-PAGE gel of choice. Gels routinely used for this protocol include 4-12% Bis-Tris and 8% Tris-Glycine.</li>
		<li>Run gel at 200 V for 50 min.</li>
		<li>Transfer proteins from gel to a PVDF membrane by semi-dry transfer at 19 V for 20-30 min (recipe in Table 1).</li>
		<li>Block membrane in 4% milk/1x Tris buffered saline-TWEEN (TBST) for 1 hr at RT or O/N at 4 &#176;C (recipe in Table 1).</li>
		<li>Incubate membrane with primary antibody to the epitope-tagged protein of interest in 4% milk/1x TBST for 1-3 hr at RT or O/N at 4 &#176;C.</li>
		<li>Wash membrane 3x for 5 min each with 1x TBST.</li>
		<li>Incubate membrane with appropriate secondary horseradish peroxidase (HRP) -conjugated antibody for 1-3 hr at RT.</li>
		<li>Wash membrane 3x for 15 min each in a large volume of 1x TBST.</li>
		<li>Cover membrane with ECL substrate and wrap in saran wrap.</li>
		<li>Expose membrane to film and develop to visualize proteins.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Klis, F. M., Boorsma, A., De Groot, P. W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+wall+construction+inSaccharomyces+cerevisiae.">Cell wall construction inSaccharomyces cerevisiae.</a> Yeast. 23 (3), 185-202 (2006).</li><li>Gelperin, D. M., White, M. 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=Biochemical+and+genetic+analysis+of+the+yeast+proteome+with+a+movable+ORF+collection.">Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.</a> Genes Dev. 19 (23), 2816-2826 (2005).</li><li>Caserta, E., Haemig, H. A. H., 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=In+Vivo+and+In+Vitro+Analyses+of+Regulation+of+the+Pheromone-Responsive+prgQ+Promoter+by+the+PrgX+Pheromone+Receptor+Protein.">In Vivo and In Vitro Analyses of Regulation of the Pheromone-Responsive prgQ Promoter by the PrgX Pheromone Receptor Protein.</a> J. Bacteriol. 194 (13), 3386-3394 (2012).</li><li>Ghaemmaghami, S., Huh, W. -. 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=Global+analysis+of+protein+expression+in+yeast.">Global analysis of protein expression in yeast.</a> Nature. 425 (6959), 737-741 (2003).</li><li>Hannich, J. T., Lewis, 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=Defining+the+SUMO-modified+proteome+by+multiple+approaches+in+Saccharomyces+cerevisiae.">Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae.</a> J. Biol. Chem. 280 (6), 4102-4110 (2005).</li><li>Xie, Y., Rubenstein, E. M., Matt, T., Hochstrasser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO-independent+in+vivo+activity+of+a+SUMO-targeted+ubiquitin+ligase+toward+a+short-lived+transcription+factor.">SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor.</a> Genes Dev. 24 (9), 893-903 (2010).</li><li>Daum, G. G., B&#246;hni, P. C. P., Schatz, G. 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The authors have nothing to disclose.

This protocol focuses on the preparation of intact, native, and post-translationally modified proteins from budding yeast cells for down-stream applications. Before attempting this protocol, it is critical to determine if the protein of interest can be readily detected in protein extracts prepared under denaturing conditions12. If polyclonal antibodies are not available it may be advantageous to epitope tag the protein of interest so that the fusion protein can be detected on Western blots. In the present prot...

The awesome power of yeast genetics is legendary, but the preparation and analysis of native proteins from budding yeast, Saccharomyces cerevisiae, is often fraught with problems. The latter is due to the considerable mechanical strength and elasticity of the yeast cell wall1. Different means have been described for the enzymatic, chemical, mechanical, and pressure-based disruption of yeast cells to obtain whole-cell protein extract 2-6. These techniques vary widely in their efficacy to yield cell-representative, native protein extracts that can be used for subsequent analyses or purification steps. For example, the yeast cell wall can be removed with lytic enzymes (e.g. zymolyase) and resulting spheroblasts can be disrupted by shearing, detergents, or osmotic lysis to release proteins. This approach has been successfully employed as the starting point for many subcellular fractionations but it requires lengthy incubations that are not compatible with the stability of some proteins7.
Proprietary yeast lysis reagents (such as detergents) for the chemical extraction of proteins of yeast cells are commercially available but the efficacy of these reagents in protein extraction and their effect on subsequent biochemical characterization of proteins is not always clear8. High pressure homogenizers, often referred to as French presses, effectively break yeast cells by first subjecting them to high pressure and then extruding them through a small opening in a pressure cell. This technique produces high quality extracts but the equipment is very expensive and may not be suitable for small quantities of cells or multiple samples9. Therefore, mechanical disruption of yeast cells in a bead mill is often the method of choice for native yeast protein preparations10. This technique involves mechanical disruption of the yeast cell wall with acid-washed glass beads, which can be conducted with a variety of shakers, vortexers or bead mills. Notably, this method can be used to simultaneously process multiple smaller samples (1 ml of cells or less). Many different beads or bead mill disruption matrices are now commercially available to disrupt almost any kind of cell type in 2 ml tubes. Considering the other techniques and equipment, a bead mill has the added advantage that the disruption of yeast cells occurs very fast, which helps to preserve post-translational modifications such as sumoylation, especially when the appropriate buffers with protease and/or proteasome inhibitors are utilized and the temperature of extracts is controlled.
This protocol focuses on the fast, effective, and reliable extraction of endogenous and over-expressed proteins under gentle conditions with the ultimate goal to preserve protein function, interactions, and post-translational modifications. Growth media, cell lysis buffer compositions, and bead mill settings are optimized to maintain protein interactions and post-translational modifications such as sumoylation and ubiquitylation.

<table border="0" cellpadding="0" cellspacing="0" width="1039">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Omni Bead Ruptor 24</td>
			<td style="width:124px;">Omni International</td>
			<td style="width:119px;">19-010</td>
			<td style="width:580px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Yeast ORF strain in BG1805</td>
			<td>ThermoScientific</td>
			<td>YSC3869</td>
			<td>GAL+ yeast strain that can be used for induction and extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">pYES2.1 TOPO vector</td>
			<td>Life Technologies</td>
			<td>K4150-01</td>
			<td>GAL+ yeast strain that can be used for induction and extraction; contains a V5/6xHIS tag</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Halt Protease Inhibitor Single-Use Cocktail (100x)</td>
			<td>Thermo Scientific</td>
			<td style="width:119px;">1860932</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">2.0 ml Skirted Tube with Tethered Screw Cap</td>
			<td>BioExpress</td>
			<td style="width:119px;">C-3369-3</td>
			<td>Make sure that the tube properly fits in the bead ruptor</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Glass beads, acid-washed, 425-600 &#181;m (30-40 US sieve)</td>
			<td>Sigma-Aldrich</td>
			<td>G8772</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Corning Costar Spin-X centrifuge tube filters</td>
			<td>Sigma-Aldrich</td>
			<td style="width:119px;">CLS8161</td>
			<td>Use for additional filtering of clarified lysate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TALON Metal Affinity Resin</td>
			<td style="width:124px;">Clontech</td>
			<td>635502</td>
			<td>For the purification of 6xHIS tagged proteins</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NuPAGE LDS Sample Buffer (4x)</td>
			<td style="width:124px;">Life Technologies</td>
			<td>NP0007</td>
			<td>To prepare and/or elute samples prior to SDS-PAGE and Western Blotting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NuPAGE 4-12% Bis-Tris Gel</td>
			<td style="width:124px;">Life Technologies</td>
			<td style="width:119px;">NP0321BOX</td>
			<td>Precast gels often used for SDS-PAGE prior to Western Blotting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Simply Blue</td>
			<td style="width:124px;">Life Technologies</td>
			<td style="width:119px;">#LC6060</td>
			<td>Protein gel stain</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Mammalian Lysis Buffer</td>
			<td>Promega</td>
			<td style="width:119px;">G9381</td>
			<td>Alternative commercial lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Anti-V5 agarose</td>
			<td>Sigma</td>
			<td style="width:119px;">A7345</td>
			<td>Method of immunoprecipitation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ECL</td>
			<td style="width:124px;">Millipore</td>
			<td style="width:119px;">WBKL S0 050</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PVDF membrane</td>
			<td style="width:124px;">Millipore</td>
			<td>IPVH00010</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">BIS-TRIS gels</td>
			<td style="width:124px;">Life Technologies</td>
			<td>NP0321BOX</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">anti-myc antibody</td>
			<td style="width:124px;">Covance</td>
			<td style="width:119px;">mms-150R</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">secondary antibody</td>
			<td style="width:124px;">Abcam</td>
			<td style="width:119px;">ab97040</td>
			<td>Goat pAb to mouse IgG (HRP)</td>
		</tr>
	</tbody>
</table>

budding yeast protein extraction and purification for the study of function, interactions, and post-translational modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously hard to disrupt. Here we describe the use of a bead mill homogenizer for the extraction of proteins into buffers optimized to maintain the functions, interactions and post-translational modifications of proteins. Logarithmically growing cells expressing the protein of interest are grown in a liquid growth media of choice. The growth media may be supplemented with reagents to induce protein expression from inducible promoters (e.g. galactose), synchronize cell cycle stage (e.g. nocodazole), or inhibit proteasome function (e.g. MG132). Cells are then pelleted and resuspended in a suitable buffer containing protease and/or phosphatase inhibitors and are either processed immediately or frozen in liquid nitrogen for later use. Homogenization is accomplished by six cycles of 20 sec&#160;bead-beating (5.5 m/sec), each followed by one minute incubation on ice. The resulting homogenate is cleared by centrifugation and small particulates can be removed by filtration. The resulting cleared whole cell extract (WCE) is precipitated using 20% TCA for direct analysis of total proteins by SDS-PAGE followed by Western blotting. Extracts are also suitable for affinity purification of specific proteins, the detection of post-translational modifications, or the analysis of co-purifying proteins. As is the case for most protein purification protocols, some enzymes and proteins may require unique conditions or buffer compositions for their purification and others may be unstable or insoluble under the conditions stated. In the latter case, the protocol presented may provide a useful starting point to empirically determine the best bead-beating strategy for protein extraction and purification. We show the extraction and purification of an epitope-tagged SUMO E3 ligase, Siz1, a cell cycle regulated protein that becomes both sumoylated and phosphorylated, as well as a SUMO-targeted ubiquitin ligase subunit, Slx5.

Our representative results reveal that the described bead-beating and protein extraction protocol is useful for the reproducible preparation of proteins for a variety of downstream applications (summarized in Table 2). SDS-PAGE followed by Coomassie staining of WCEs show that a wide range of proteins (~12 to &#62;250 kDa) can be reproducibly extracted from yeast cells (Figure 1A). Discrete bands over a range of molecular weights are indicative of high quality protein extracts. The qualit...

Watch this Scientific Journal Video about Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications at JoVE.com

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

The preparation of high quality yeast cell extracts is a necessary first step in the analysis of individual proteins or entire proteomes. Here we describe a fast, efficient, and reliable homogenization protocol for budding yeast cells that has been optimized to preserve protein functions, interactions, and post-translational modifications.

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

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24.8K Views.  The College of William & Mary. The preparation of high quality yeast cell extracts is a necessary first step in the analysis of individual proteins or entire proteomes. Here we describe a fast, efficient, and reliable homogenization protocol for budding yeast cells that has been optimized to preserve protein functions, interactions, and post-translational modifications.

Video: Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Measuring Replicative Life Span in the Budding Yeast

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The budding yeast Saccharomyces cerevisiae has been used extensively to study the biology of aging, and several determinants of yeast longevity have been shown to be conserved in multicellular eukaryotes, including worms, flies, and mice 1. Due to the lack of easily quantified age-associated phenotypes, aging in yeast has been assayed almost exclusively by measuring the life span of cells in different contexts, with two different life span paradigms in common usage 2. Chronological life span refers to the length of time that a mother cell can survive in a non-dividing, quiescence-like state, and is proposed to serve as a model for aging of post-mitotic cells in multicellular eukaryotes. Replicative life span, in contrast, refers the number of daughter cells produced by a mother cell prior to senescence, and is thought to provide a model of aging in mitotically active cells. Here we present a generalized protocol for measuring the replicative life span of budding yeast mother cells. The goal of the replicative life span assay is to determine how many times each mother cell buds. The mother and daughter cells can be easily differentiated by an experienced researcher using a standard light microscope (total magnification 160X), such as the Zeiss Axioscope 40 or another comparable model. Physical separation of daughter cells from mother cells is achieved using a manual micromanipulator equipped with a fiber-optic needle. Typical laboratory yeast strains produce 20-30 daughter cells per mother and one life span experiment requires 2-3 weeks.

In this article we present a general protocol for measuring the replicative life span of yeast mother cells.

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The budding ...

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents (Methanol, Ethanol or 2-Propanol) and acetic acid are used for fixation, staining and destaining of proteins in a gel after SDS-PAGE. To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used. This usually results in evaporation of toxic or hazardous Methanol, Ethanol or 2-Propanol and a strong smell of acetic acid in the lab which should be avoided due to safety considerations. In a protocol originally published in two patent applications by E.M. Wondrak (US2001046709 (A1), US6319720 (B1)), an alternative composition of the staining solution is described in which no organic solvent or acid is used. The CBB is dissolved in bidistilled water (60-80mg of CBB G-250 per liter) and 35 mM HCl is added as the only other compound in the staining solution. The CBB staning of the gel is done after SDS-PAGE and thorough washing of the gel in bidistilled water. By heating the gel during the washing and staining steps, the process can be finished faster and no toxic or hazardous compunds are evaporating. The staining of proteins occurs already within 1 minute after heating the gel in staining solution and is fully developed after 15-30 min with a slightly blue background that is destained completely by prolonged washing of the stained gel in bidistilled water, without affecting the stained protein bands.

A short protocol for protein staining with Coomassie Brilliant Blue (CBB) G-250 in polyacrylamide gels is described without using organic solvents or acetic acid as in the classical staining procedures with CBB.

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents ...

Analysis of the Development of a Morphological Phenotype as a Function of Protein Concentration in Budding Yeast

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae. Although this protocol is based on the overexpression of a protein, it can easily be adapted for morphological phenotypes dependent on suppression of protein expression. Our lab is interested in studying the signaling properties of the endocytic adaptor protein epsin. To that purpose we used a dominant negative approach in which we over-expressed the conserved Epsin N-Terminal Homology (ENTH) domain in order to interfere with the functions of endogenous epsin-2 (Ent2 or YLR206W). We observed that overexpression of the ENTH domain of Ent2 (ENTH2) in wild type cells led to a cell division defect that is dependent on the mislocalization of a family of scaffolding proteins, septins.

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae.

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of ...

Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 base pairs of DNA associated with two each of histones H2A, H2B, H3, and H41. The N-terminal tails of histones are rich in lysine and arginine and are modified post-transcriptionally by acetylation, methylation, and other post-translational modifications (PTMs). The PTM configuration of nucleosomes can affect the transcriptional activity of associated DNA, thus providing a mode of gene regulation that is epigenetic in nature 2,3. We developed a method called nucleosome ELISA (NU-ELISA) to quantitatively determine global PTM signatures of nucleosomes extracted from cells. NU-ELISA is more sensitive and quantitative than western blotting, and is useful to interrogate the epiproteomic state of specific cell types. This video journal article shows detailed procedures to perform NU-ELISA analysis.

Nucleosome ELISA (NU-ELISA) is a sensitive and quantitative method to detect global patterns of post-translational modifications in preparations of native, intact nucleosomes. These modifications include methylations, acetylations, and phosphorylations at specific histone amino acid residues, and hence NU-ELISA provides a global proteomic assay of the overall chromatin modification states of specific cell types.

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 ...

Identification of Post-translational Modifications of Plant Protein Complexes

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to infection via the recruitment and activation of immune complexes. Activation of immune complexes is associated with post-translational modifications (PTMs) of proteins, such as phosphorylation, glycosylation, or ubiquitination. Understanding how these PTMs are choreographed will lead to a better understanding of how resistance is achieved.
Here we describe a protein purification method for nucleotide-binding leucine-rich repeat (NB-LRR)-interacting proteins and the subsequent identification of their post-translational modifications (PTMs). With small modifications, the protocol can be applied for the purification of other plant protein complexes. The method is based on the expression of an epitope-tagged version of the protein of interest, which is subsequently partially purified by immunoprecipitation and subjected to mass spectrometry for identification of interacting proteins and PTMs.
This protocol demonstrates that: i). Dynamic changes in PTMs such as phosphorylation can be detected by mass spectrometry; ii). It is important to have sufficient quantities of the protein of interest, and this can compensate for the lack of purity of the immunoprecipitate; iii). In order to detect PTMs of a protein of interest, this protein has to be immunoprecipitated to get a sufficient quantity of protein.

We describe here a protocol for the purification and characterization of plant protein complexes. We demonstrate that by immunoprecipitating a single protein within a complex, so we can identify its post-translational modifications and its interacting partners.

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method offers the opportunity of investigating interactions occurring in solution (thus avoiding problems due to closeby surfaces as in other single molecule methods), controlling the DNA extension and tracking interaction dynamics as a function of both mechanical parameters and DNA sequence. The methods for establishing successful optical trapping and nanometer localization of single molecules are illustrated. We illustrate the experimental conditions allowing the study of interaction of lactose repressor (lacI), labeled with Atto532, with a DNA molecule containing specific target sequences (operators) for LacI binding. The method allows the observation of specific interactions at the operators, as well as one-dimensional diffusion of the protein during the process of target search. The method is broadly applicable to the study of protein-DNA interactions but also to molecular motors, where control of the tension applied to the partner track polymer (for example actin or microtubules) is desirable.

Here we describe the instrumentation and methods for detecting single fluorescently-labeled protein molecules interacting with a single DNA molecule suspended between two optically trapped microspheres.

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Discovering Protein Interactions and Characterizing Protein Function Using HaloTag Technology

Research in proteomics has exploded in recent years with advances in mass spectrometry capabilities that have led to the characterization of numerous proteomes, including those from viruses, bacteria, and yeast.&#160; In comparison, analysis of the human proteome lags behind, partially due to the sheer number of proteins which must be studied, but also the complexity of networks and interactions these present. To specifically address the challenges of understanding the human proteome, we have developed HaloTag technology for protein isolation, particularly strong for isolation of multiprotein complexes and allowing more efficient capture of weak or transient interactions and/or proteins in low abundance. &#160;HaloTag is a genetically encoded protein fusion tag, designed for covalent, specific, and rapid immobilization or labelling of proteins with various ligands. Leveraging these properties, numerous applications for mammalian cells were developed to characterize protein function and here we present methodologies including: protein pull-downs used for discovery of novel interactions or functional assays, and cellular localization. We find significant advantages in the speed, specificity, and covalent capture of fusion proteins to surfaces for proteomic analysis as compared to other traditional non-covalent approaches. We demonstrate these and the broad utility of the technology using two important epigenetic proteins as examples, the human bromodomain protein BRD4, and histone deacetylase HDAC1.&#160; These examples demonstrate the power of this technology in enabling &#160;the discovery of novel interactions and characterizing cellular localization in eukaryotes, which will together further understanding of human functional proteomics. &#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;

HaloTag technology is a multifunctional technology which has shown significant success in isolation of both small and large protein complexes from mammalian cells.&#160; Here we highlight the advantages of this technology compared to existing alternatives and demonstrate its utility to study numerous aspects of protein function inside eukaryotic cells.

Research in proteomics has exploded in recent years with advances in mass spectrometry capabilities that have led to the characterization of numerous ...

Protein Purification Technique that Allows Detection of Sumoylation and Ubiquitination of Budding Yeast Kinetochore Proteins Ndc10 and Ndc80

Post-translational Modifications (PTMs), such as phosphorylation, methylation, acetylation, ubiquitination, and sumoylation, regulate the cellular function of many proteins. PTMs of kinetochore proteins that associate with centromeric DNA mediate faithful chromosome segregation to maintain genome stability. Biochemical approaches such as mass spectrometry and western blot analysis are most commonly used for identification of PTMs. Here, a protein purification method is described that allows the detection of both sumoylation and ubiquitination of the kinetochore proteins, Ndc10 and Ndc80, in Saccharomyces cerevisiae. A strain that expresses polyhistidine-Flag-tagged Smt3 (HF-Smt3) and Myc-tagged Ndc10 or Ndc80 was constructed and used for our studies. For detection of sumoylation, we devised a protocol to affinity purify His-tagged sumoylated proteins by using nickel beads and used western blot analysis with anti-Myc antibody to detect sumoylated Ndc10 and Ndc80. For detection of ubiquitination, we devised a protocol for immunoprecipitation of Myc-tagged proteins and used western blot analysis with anti-Ub antibody to show that Ndc10 and Ndc80 are ubiquitinated. Our results show that epitope tagged-protein of interest in the His-Flag tagged Smt3 strain facilitates the detection of multiple PTMs. Future studies should allow exploitation of this technique to identify and characterize protein interactions that are dependent on a specific PTM.

This manuscript describes the detection of sumoylation and ubiquitination of kinetochore proteins, Ndc10 and Ndc80, in the budding yeast Saccharomyces cerevisiae.

Post-translational Modifications (PTMs), such as phosphorylation, methylation, acetylation, ubiquitination, and sumoylation, regulate the cellular ...

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone function is mediated by extensive post-translational modification by a myriad of nuclear proteins. These modifications are critical for nuclear integrity as they regulate chromatin structure and recruit enzymes involved in gene regulation, DNA repair and chromosome condensation. Even though a large part of the scientific community adopts antibody-based techniques to characterize histone PTM abundance, these approaches are low throughput and biased against hypermodified proteins, as the epitope might be obstructed by nearby modifications. This protocol describes the use of nano liquid chromatography (nLC) and mass spectrometry (MS) for accurate quantification of histone modifications. This method is designed to characterize a large variety of histone PTMs and the relative abundance of several histone variants within single analyses. In this protocol, histones are derivatized with propionic anhydride followed by digestion with trypsin to generate peptides of 5 - 20 aa in length. After digestion, the newly exposed N-termini of the histone peptides are derivatized to improve chromatographic retention during nLC-MS. This method allows for the relative quantification of histone PTMs spanning four orders of magnitude.

This protocol outlines a fully integrated workflow for characterizing histone post-translational modifications using mass spectrometry (MS). The workflow includes histone purification from cell cultures or tissues, histone derivatization and digestion, MS analysis using nano-flow liquid chromatography and instructions for data analysis. The protocol is designed for completion within 2 - 3 days.

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone ...

Applications of pHluorin for Quantitative, Kinetic and High-throughput Analysis of Endocytosis in Budding Yeast

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal remodeling and vesicular trafficking in living cells. Quantitative methodologies using chimeric GFP fusions have been developed for many applications; however, GFP is somewhat resistant to proteolysis, thus its fluorescence persists in the lysosome/vacuole, which can impede quantification of cargo trafficking in the endocytic pathway. An alternative method for quantifying endocytosis and post-endocytic trafficking events makes use of superecliptic pHluorin, a pH-sensitive variant of GFP that is quenched in acidic environments. Chimeric fusion of pHluorin to the cytoplasmic tail of transmembrane cargo proteins results in a dampening of fluorescence upon incorporation of the cargo into multivesicular bodies (MVBs) and delivery to the lysosome/vacuole lumen. Thus, quenching of vacuolar fluorescence facilitates quantification of endocytosis and early events in the endocytic pathway. This paper describes methods using pHluorin-tagged cargos for quantification of endocytosis via fluorescence microscopy, as well as population-based assays using flow cytometry.

Accurate quantification of vesicular trafficking events often provides key insights into roles for specific proteins and the effects of mutations. This paper presents methods for using superecliptic pHluorin, a pH-sensitive GFP variant, as a tool for quantification of endocytic events in living cells using quantitative fluorescence microscopy and flow cytometry.

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal ...