Work in the author&rsquo;s laboratory is funded by the Canadian Institutes of Health Research, the Canada Foundation for Innovation, the Natural Sciences and Engineering Research Council and Concordia University.

Construction of diploid strains 
Protocol for production of diploids by mating
<ol>
	<li>The initial strains should be struck out on YPD, or selective medium if necessary, to produce single colonies. The two haploid strains should be of opposite mating type (ie. MATa and MAT&#945;).</li>
	<li>Using a sterile inoculation loop pick a small portion of a colony from one of the two haploid strains. On a new YPD plate streak the loop once in a straight line across the plate. Mark the direction of the streak with an arrow on the bottom of the plate.</li>
	<li>Repeat this for the second strain on the same YPD plate. This time streak the colony perpendicular to the first, crossing the first streak with the second. Mark the direction of the second streak and note the area where the second streak crosses the first. This area will be where diploids will be produced.</li>
	<li>Incubate the YPD plate at 30&#176;C overnight.</li>
	<li>Replica plate the YPD plate onto selective media that will selectively permit growth of the newly-formed diploids.</li>
	<li>Pick a single colony if possible, or a small portion of the diploid streak and streak onto the same selective medium to generate single colonies.</li>
</ol>
Sporulation and digestion of asci 
Protocol
<ol>
	<li>Pick single colonies from the plate above and make small (1cm x 1cm) patches on sporulation (SPO) plates and incubate at 30&#176;C for 3-7 days to sporulate.</li>
	<li>Sporulation can be checked by looking at cells from each patch under a light microscope. Place cells on a microscope slide in 5-10 &#956;l of water, place a coverslip on top of the droplet, and look for the presence of asci. If asci are not easily found then put back in the incubator.</li>
	<li>If there is effective sporulation in one of the patches, prepare a sterile 15mL conical tube with 100&#956;L of tetrad juice.</li>
	<li>Pick cells up from this sporulation patch with a sterile 3mm inoculation loop (cells should cover &#188; of the loop) and place in the tetrad juice. Gently swirl the loop to allow the cells to fall off the loop and mix with the solution.</li>
	<li>Leave in tetrad juice (containing zymolyase) for 4-10mins (depending on the concentration and activity of zymolyase and the strain itself).This allows for digestion of the cell wall surrounding the ascospores.</li>
	<li>Mark the top and bottom of the inoculum region on a YPD plate.</li>
	<li>Optional. Reaction can be stopped by adding 1mL of ice cold sterile dH2O. Allow the cells to settle for 5mins. Remove 1mL from the supernatant then mix lightly by hand and keep on ice.</li>
	<li>Take 5&#956;L of digested cells from step 5 and gently place drops in a line in the inoculum region of the pre-marked YPD plate.</li>
	<li>Use a sterile 3mm inoculation loop to very gently spread the drops 1-3 times in a line while barely making contact with the agar.</li>
	<li>Allow the liquid to absorb into the agar (If step 7 is omitted, this is when the digestion of the outer cell wall will be reduced or stop). Proceed to the dissection microscope.</li>
</ol>
Dissection of Asci 
Protocol
Note that the following protocol is described for a Singer MSM System 200 micromanipulation microscope. This protocol can be followed with slight modifications if using a manual micromanipulator such as a Zeiss micromanipulator MR.
<ol>
	<li>Focus on a region of the plate where half of the field contains cells and half is empty. Slowly bring the needle into focus such that it touches the empty region of the field. This will ensure that the needle does not contain cells from a previous use. Contact between the needle and the agar is seen as a dark black circle that slowly comes into focus.</li>
	<li>Go to the matrix at position A1 and make a mark by piercing the agar again. This is to help determine the orientation of the plate if it is taken off the microscope before completion.</li>
	<li>Switch to the search mode. Locate an asci. Preferably choose asci which are in areas where the cells are well spread out. Avoid areas with cell clusters. The four ascospores from an asci should still be attached to each other. Two ascospores may be slightly larger than the other two. Avoid picking asci where one ascospore is loose and not connected to the rest of the ascospores.</li>
	<li>Pick up an ascus with the needle. Slowly bring the needle up to the plate. When the shadow of the microneedle is seen, line this up with the ascus to be picked. Again approach the needle until the black outline of a circle (the tip of the needle) is seen. Touch the tetrad with this circle and then quickly pull the needle away. Make sure all four ascospores from an ascus have adhered to the needle and that no additional cells were gathered on the microneedle that are not part of this ascus.</li>
	<li>Pull the microneedle far away from the plate and go to the matrix (for the first ascus, go to position A1). Take note of each position where an ascus is relocated. Place the ascus down by touching the plate with the microneedle and pulling away until all four ascospores come off the microneedle. Gentle tapping of the needle arm or the platform holding the YPD plate is often useful at this step.</li>
	<li>Repeat steps 3-5 and place asci down at consecutive positions on the matrix until the desired number of asci have been picked.</li>
	<li>Go back to each ascus and break the four cells apart by teasing with the needle, tapping the platform gently or a combination of both. Pick up the cells leaving one behind at a new position in the matrix until each ascospore in each ascus is separated in rows of four.</li>
	<li>Place the YPD plate in an incubator at 30&#176;C for several days to observe the growth pattern.</li>
	<li>Replica plate the dissected cells to selective medium if necessary.</li>
</ol>
Relocation of Zygotes 
Protocol
<ol>
	<li>Streak out two haploid strains with opposite mating types on the appropriate medium to obtain single colonies.</li>
	<li>Mate these two strains as described above and allow to grow from 4 to 6 hours (or overnight if necessary).</li>
	<li>Check for zygotes under a light microscope. Zygotes will appear as dumbbell-shaped cells either with or without a bud.</li>
	<li>Pick cells up with a 3mm inoculation loop (cells should cover &#188; of the loop) and place gently in 100&#956;L of sterile dH2O.</li>
	<li>Mark the top and bottom of the inoculum region on a YPD plate.</li>
	<li>Take 5&#956;L and gently place drops in a line in the inoculum region of the pre-marked YPD plate.</li>
	<li>Use a 3mm inoculation loop to spread the drops in a line very gently while barely making contact with the agar.</li>
	<li>Allow the liquid to absorb into the agar. Proceed to the dissection microscope.</li>
	<li>Focus on a region of the plate where half of the field contains cells and half is empty. Slowly bring the needle into focus such that it touches the empty region of the field. This will ensure that the needle does not contain cells from a previous use. Contact between the needle and the agar is seen as a dark black circle that slowly comes into focus.</li>
	<li>Go to the matrix at position A1 and make a mark by piercing the agar again. This is to help determine the orientation of the plate if it is taken off the microscope before completion.</li>
	<li>Switch to the search mode. Locate a zygote.</li>
	<li>Pick up a zygote with the needle.</li>
	<li>Place zygotes individually on the matrix.</li>
	<li>Allow zygotes to grow for several days.</li>
	<li>Replica plate the zygotes onto the appropriate selective medium.</li>
</ol>
Representative Results
<img alt="" src="/files/ftp_upload/1146/1146fig1.jpg" /> 
Figure 1: The mating of two haploid strains of opposite mating types generates a diploid strain.
<img alt="" src="/files/ftp_upload/1146/1146fig2.jpg" /> 
Figure 2: (A) A YPD plate with thre results of a mating between a temperature sensitive strain (with a leu2 auxotrophy) and a wild type strain (LEU2). Digested cells are spread in the inoculum region on the left where thick growth between the two black lines is seen. Asci that have been dissected grow evenly spaced in the matrix on the right. (B) The plate in (A) was replicated onto an SD -Leucine drop-out plate. Note the 2:2 growth for the LEU2 marker indicating a validated ascospore was dissected. (C) The plate in (A) was replicated onto a YPD plate and incubated at 37&#176;C. Note the 2:2 growth that further validates that an ascospore was dissected.

<ol>
	<li>Sherman, F., Hicks, J., Guthrie, C., Fink, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micromanipulation+and+Dissection+of+Asci.">Micromanipulation and Dissection of Asci.</a> Guide to Yeast Genetics and Molecular Biology. , 21-37 (1991).</li></ol>

The authors have nothing to disclose.

Yeast dissection is a useful tool to select new strains with desired markers. When determining the theoretical growth pattern of four ascospores it is important to look at the genotype of the vegetative cell. If a plasmid is present, one must know if it is single, low or high copy as this will affect which ascospore(s) receive the plasmid and will affect predictions and conclusions regarding the strains being manipulated.
Certain strains can sporulate better than others producing many ascospor...

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Singer MSM System 200</td>
<td>Microscope</td>
<td>Singer Instruments</td>
<td>NA</td>
<td>&nbsp;</td>
<tr>
<td>D-sorbitol</td>
<td>Reagent</td>
<td>BioShop</td>
<td>SOR508</td>
<td>&nbsp;</td>
<tr>
<td>Tris</td>
<td>Reagent</td>
<td>BioShop</td>
<td>TRS001</td>
<td>&nbsp;</td>
<tr>
<td>Zymolyase 100T</td>
<td>Reagent</td>
<td>Seikagaku Corporation</td>
<td>120493</td>
<td>&nbsp;</td>
<tr>
<td>Yeast extract</td>
<td>Reagent</td>
<td>BioShop</td>
<td>YEX401</td>
<td>&nbsp;</td>
<tr>
<td>Peptone</td>
<td>Reagent</td>
<td>BioShop</td>
<td>PEP 403</td>
<td>&nbsp;</td>
<tr>
<td>D-glucose</td>
<td>Reagent</td>
<td>BioShop</td>
<td>GLU501</td>
<td>&nbsp;</td>
<tr>
<td>Yeast nitrogen base</td>
<td>Reagent</td>
<td>BioShop</td>
<td>YNB406</td>
<td>&nbsp;</td>
<tr>
<td>Bio-tryptone</td>
<td>Reagent</td>
<td>BioShop</td>
<td>TRP402</td>
<td>&nbsp;</td>
<tr>
<td>Sodium chloride</td>
<td>Reagent</td>
<td>BioShop</td>
<td>SOD002</td>
<td>&nbsp;</td>
<tr>
<td>Potassium acetate</td>
<td>Reagent</td>
<td>BioShop</td>
<td>POA 301</td>
<td>&nbsp;</td>
<tr>
<td>Agar</td>
<td>Reagent</td>
<td>BioShop</td>
<td>AGR003</td>
<td>&nbsp;</td>
<tr>
<td>Adenine sulfate</td>
<td>Reagent</td>
<td>BioShop</td>
<td>ADS201</td>
<td>&nbsp;</td>
<tr>
<td>L-uracil</td>
<td>Reagent</td>
<td>BioShop</td>
<td>URA 241</td>
<td>&nbsp;</td>
<tr>
<td>L-tryptophan</td>
<td>Reagent</td>
<td>BioShop</td>
<td>TRP 100</td>
<td>&nbsp;</td>
<tr>
<td>L-histidine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>HIS 200</td>
<td>&nbsp;</td>
<tr>
<td>L-arginine</td>
<td>Reagent</td>
<td>Amresco</td>
<td>0877-100G</td>
<td>&nbsp;</td>
<tr>
<td>L-methionine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>MET 222</td>
<td>&nbsp;</td>
<tr>
<td>L-tyrosine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>TYR 333</td>
<td>&nbsp;</td>
<tr>
<td>L-isoleucine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>ISO 910</td>
<td>&nbsp;</td>
<tr>
<td>L-valine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>VAL 201</td>
<td>&nbsp;</td>
<tr>
<td>L-lysine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>LYS 101</td>
<td>&nbsp;</td>
<tr>
<td>L-phenylalanine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>PHA 302</td>
<td>&nbsp;</td>
<tr>
<td>L-glutamic acid</td>
<td>Reagent</td>
<td>BioShop</td>
<td>GLU 202</td>
<td>&nbsp;</td>
<tr>
<td>L-threonine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>THR002</td>
<td>&nbsp;</td>
<tr>
<td>L-leucine</td>
<td>Reagent</td>
<td>BioShop</td>
<td>LEU 222</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

dissection of saccharomyces cerevisiae asci

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae exists in either a haploid or diploid state. The ability to combine alleles from two haploids and the ability to introduce modifications to the genome requires the production and dissection of asci. Asci production from haploid cells begins with the mating of two yeast haploid strains with compatible mating types to produce a diploid strain. This can be accomplished in a number of ways either on solid medium or in liquid. It is advantageous to select for the diploids in medium that selectively promotes their growth compared to either of the haploid strains. The diploids are then allowed to sporulate on nutrient-poor medium to form asci, a bundle of four haploid daughter cells resulting from meiotic reproduction of the diploid. A mixture of vegetative cells and asci is then treated with the enzyme zymolyase to digest away the membrane sac surrounding the ascospores of the asci. Using micromanipulation with a microneedle under a dissection microscope one can pick up individual asci and separate and relocate the four ascopores. Dissected asci are grown for several days and tested for the markers or alleles of interest by replica plating onto appropriate selective media.

Watch this Scientific Journal Video about Dissection of Saccharomyces Cerevisiae Asci at JoVE.com

Dissection of Saccharomyces Cerevisiae Asci

Micromanipulation of yeast cells is needed for meiotic genetic analysis or to select diploid zygotes. These micromanipulations are carried out using the microneedle of a dissection microscope. The microneedle is used to relocate cells and is controlled by a micromanipulator which are available with various degrees of automation.

Dissection of Saccharomyces Cerevisiae Asci

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae ...

dissection-of-saccharomyces-cerevisiae-asci

Research

JoVE Journal

Biology

18.5K Views.  Concordia University. Micromanipulation of yeast cells is needed for meiotic genetic analysis or to select diploid zygotes. These micromanipulations are carried out using the microneedle of a dissection microscope. The microneedle is used to relocate cells and is controlled by a micromanipulator which are available with various degrees of automation.

Video: Dissection of Saccharomyces Cerevisiae Asci

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground using a cryolysis procedure in a ball mill grinder and the resulting grindate brought into solution by urea solubilization. This procedure allows for the lysis of the cells in a metabolically inactive state, preserving phosphorylation and preventing reorientation of the phosphoproteome during cell lysis.  Following reduction, alkylation, trypsin digestion of the proteins, the samples are desalted on C18 columns and the sample complexity reduced by fractionation using hydrophilic interaction chromatography (HILIC). HILIC columns preferentially retain hydrophilic molecules which is well suited for phosphoproteomics.  Phosphorylated peptides tend to elute later in the chromatographic profile than the non phosphorylated counterparts. After fractionation, phosphopeptides are enriched using immobilized metal chromatography, which relies on charge-based affinities for phosphopeptide enrichment. At the end of this procedure the samples are ready to be quantitatively analyzed by mass spectrometry.

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Description of a quantitative phosphorylation procedure using cryolysis, urea solubilziation, HILIC fractionation and IMAC enrichment of phosphorylated peptides.

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground ...

Microarray Analysis for Saccharomyces cerevisiae

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen peroxide (H2O2), an oxidizing agent. In the experiment, yeast is grown for 48 hours in 1/2X YPD broth containing 3X glucose. The culture is split into a control and treated group. The experiment culture is treated with 0.5 mM H2O2 in Hanks Buffered Saline (HBSS) for 1 hour. The control culture is treated with HBSS only. Total RNA is extracted from both cultures and is converted to a biotin-labeled cRNA product through a multistep process. The final synthesis product is taken back to the UVM Microarray Core Facility and hybridized to the Affymetrix yeast GeneChips. The resulting gene expression data are uploaded into bioinformatics data analysis software.

Microarray Analysis for Saccharomyces cerevisiae

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen peroxide (H2O2), an oxidizing agent.

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen ...

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a quality control mechanism that can target and selectively degrade cellular material including organelles1-4. For example, damaged or redundant mitochondria (Fig. 1), not disposed of by autophagy, can represent a threat to cellular homeostasis and cell survival. In the yeast, Saccharomyces cerevisiae, nutrient deprivation (e.g., nitrogen starvation) or damage can promote selective turnover of mitochondria by autophagy in a process termed mitophagy 5-9.
We describe a simple fluorescence microscopy approach to assess autophagy. For clarity we restrict our description here to show how the approach can be used to monitor mitophagy in yeast cells. The assay makes use of a fluorescent reporter, Rosella, which is a dual-emission biosensor comprising a relatively pH-stable red fluorescent protein linked to a pH-sensitive green fluorescent protein. The operation of this reporter relies on differences in pH between the vacuole (pH ~ 5.0-5.5) and mitochondria (pH ~ 8.2) in living cells. Under growing conditions, wild type cells exhibit both red and green fluorescence distributed in a manner characteristic of the mitochondria. Fluorescence emission is not associated with the vacuole. When subjected to nitrogen starvation, a condition which induces mitophagy, in addition to red and green fluorescence labeling the mitochondria, cells exhibit the accumulation of red, but not green fluorescence, in the acidic vacuolar lumen representing the delivery of mitochondria to the vacuole. Scoring cells with red, but not green fluorescent vacuoles can be used as a measure of mitophagic activity in cells5,10-12.

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

A robust approach to monitor the delivery of organelles to the acidic lumen of the yeast vacuole for degradation and recycling is described. The method relies on the specific labeling of target organelles with a genetically encoded dual-emission fluorescence pH-biosensor, and visualization of individual cells using fluorescence microscopy.

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must be maintained to avoid deleterious consequences 1. External or internal factors that disrupt this balance can lead to protein aggregation, toxicity and cell death. In humans this is a major contributing factor to the symptoms associated with neurodegenerative disorders such as Huntington's, Parkinson's, and Alzheimer's diseases 10. It is therefore essential that the proteins involved in maintenance of proteostasis be identified in order to develop treatments for these debilitating diseases. This article describes techniques for monitoring in vivo protein folding at near-real time resolution using the model protein firefly luciferase fused to green fluorescent protein (FFL-GFP). FFL-GFP is a unique model chimeric protein as the FFL moiety is extremely sensitive to stress-induced misfolding and aggregation, which inactivates the enzyme 12. Luciferase activity is monitored using an enzymatic assay, and the GFP moiety provides a method of visualizing soluble or aggregated FFL using automated microscopy. These coupled methods incorporate two parallel and technically independent approaches to analyze both refolding and functional reactivation of an enzyme after stress. Activity recovery can be directly correlated with kinetics of disaggregation and re-solubilization to better understand how protein quality control factors such as protein chaperones collaborate to perform these functions. In addition, gene deletions or mutations can be used to test contributions of specific proteins or protein subunits to this process. In this article we examine the contributions of the protein disaggregase Hsp104 13, known to partner with the Hsp40/70/nucleotide exchange factor (NEF) refolding system 5, to protein refolding to validate this approach.

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

This article describes the use of a firefly luciferase-GFP fusion protein to investigate in vivo protein folding in Saccharomyces cerevisiae. Using this reagent, refolding of a model heat-denatured protein can be monitored simultaneously by fluorescence microscopy and an enzymatic assay to probe the roles of proteostasis network components in protein quality control.

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must ...

Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein Expressed in Saccharomyces cerevisiae

Defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein cause cystic fibrosis (CF), an autosomal recessive disease that currently limits the average life expectancy of sufferers to &#60;40 years of age. The development of novel drug molecules to restore the activity of CFTR is an important goal in the treatment CF, and the isolation of functionally active CFTR is a useful step towards achieving this goal.
We describe two methods for the purification of CFTR from a eukaryotic heterologous expression system, S. cerevisiae. Like prokaryotic systems, S. cerevisiae can be rapidly grown in the lab at low cost, but can also traffic and posttranslationally modify large membrane proteins. The selection of detergents for solubilization and purification is a critical step in the purification of any membrane protein. Having screened for the solubility of CFTR in several detergents, we have chosen two contrasting detergents for use in the purification that allow the final CFTR preparation to be tailored to the subsequently planned experiments.
In this method, we provide comparison of the purification of CFTR in dodecyl-&#946;-D-maltoside (DDM) and 1-tetradecanoyl-sn-glycero-3-phospho-(1&#39;-rac-glycerol) (LPG-14). Protein purified in DDM by this method shows ATPase activity in functional assays. Protein purified in LPG-14 shows high purity and yield, can be employed to study post-translational modifications, and can be used for structural methods such as small-angle X-ray scattering and electron microscopy. However it displays significantly lower ATPase activity.

Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein Expressed in Saccharomyces cerevisiae

Heterologous expression and purification of the cystic fibrosis transmembrane conductance regulator (CFTR) are significant challenges and limiting factors in the development of drug therapies for cystic fibrosis. This protocol describes two methods for the isolation of milligram quantities of CFTR suitable for functional and structural studies.&#160;

Defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein cause cystic fibrosis (CF), an autosomal recessive disease that ...

EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1

Electron Paramagnetic Resonance (EPR) monitored redox titrations are a powerful method to determine the midpoint potential of cofactors in proteins and to identify and quantify the cofactors in their detectable redox state.
The technique is complementary to direct electrochemistry (voltammetry) approaches, as it does not offer information on electron transfer rates, but does establish the identity and redox state of the cofactors in the protein under study. The technique is widely applicable to any protein containing an electron paramagnetic resonance (EPR) detectable cofactor.
A typical titration requires 2 ml protein with a cofactor concentration in the range of 1-100 &#181;M. The protein is titrated with a chemical reductant (sodium dithionite) or oxidant (potassium ferricyanide) in order to poise the sample at a certain potential. A platinum wire and a Ag/AgCl reference electrode are connected to a voltmeter to measure the potential of the protein solution. A set of 13 different redox mediators is used to equilibrate between the redox cofactors of the protein and the electrodes. Samples are drawn at different potentials and the Electron Paramagnetic Resonance spectra, characteristic for the different redox cofactors in the protein, are measured. The plot of the signal intensity versus the sample potential is analyzed using the Nernst equation in order to determine the midpoint potential of the cofactor.

EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1

The goal of this protocol is to use electron paramagnetic resonance (EPR) monitored redox titrations to identify different cofactors of Saccharomyces cerevisiae Nar1. Redox titrations offer a very robust way to obtain midpoint potentials of different redox active cofactors in enzymes and proteins.

Electron Paramagnetic Resonance (EPR) monitored redox titrations are a powerful method to determine the midpoint potential of cofactors in proteins and to ...

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

mRNA steady state levels vary depending on environmental conditions. Regulation of the steady state accumulation levels of an mRNA ensures that the correct amount of protein is synthesized for the cell&#8217;s specific growth conditions. One approach for measuring mRNA decay rates is inhibiting transcription and subsequently monitoring the disappearance of the already present mRNA. The rate of mRNA decay can then be quantified, and an accurate half-life can be determined utilizing several techniques. In S. cerevisiae, protocols that measure mRNA half-lives have been developed and include inhibiting transcription of mRNA using strains that harbor a temperature sensitive allele of RNA polymerase II, rpb1-1. Other techniques for measuring mRNA half-lives include inhibiting transcription with transcriptional inhibitors such as thiolutin or 1,10-phenanthroline, or alternatively, by utilizing mRNAs that are under the control of a regulatable promoter such as the galactose inducible promoter and the TET-off system. Here, we describe measurement of S. cerevisiae mRNA decay rates using the temperature sensitive allele of RNA polymerase II. This technique can be used to measure mRNA decay rates of individual mRNAs or genome-wide.

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

The steady state level of specific mRNAs is determined by the rate of synthesis and decay of the mRNA. Genome-wide mRNA degradation rates or the decay rates of specific mRNAs can be measured by determining mRNA half-lives. This protocol focuses on measurement of mRNA decay rates in Saccharomyces cerevisiae.

mRNA steady state levels vary depending on environmental conditions. Regulation of the steady state accumulation levels of an mRNA ensures that the ...

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Here we present a cost-effective method for defining chemical-genetic interactions in budding yeast. The approach is built on fundamental techniques in yeast molecular biology and is well suited for the mechanistic interrogation of small to medium collections of chemicals and other media environments.

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. ...

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that involves the construction, cloning and expression of mutant libraries, coupled to high frequency homologous DNA recombination in vivo. Here, we present a protocol to create and screen mutant libraries in yeast based on the example of a fungal aryl-alcohol oxidase (AAO) to enhance its total activity. Two protein segments were subjected to focused-directed evolution by random mutagenesis and in vivo DNA recombination. Overhangs of ~50 bp flanking each segment allowed the correct reassembly of the AAO-fusion gene in a linearized vector giving rise to a full autonomously replicating plasmid. Mutant libraries enriched with functional AAO variants were screened in S. cerevisiae supernatants with a sensitive high-throughput assay based on the Fenton reaction. The general process of library construction in S. cerevisiae described here can be readily applied to evolve many other eukaryotic genes, avoiding extra PCR reactions, in vitro DNA recombination and ligation steps.

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

We present a detailed protocol to construct and screen mutant libraries for directed evolution campaigns in Saccharomyces cerevisiae.

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that ...