This work was supported by a Joseph P. Healey grant from the University of Massachusetts Boston (L.S.H.) and R15 GM86805 from the NIH (L.S.H.). S.M.P. is supported in part by a Sanofi-Genzyme Fellowship at the University of Massachusetts Boston.

1. Preparing for Sporulation
Note: The media described in this protocol are made using standard recipes and methods13,17. Table 1 gives the formulation for 1 L of the various media used in this protocol.
<table border="1" cellpadding="0" cellspacing="0" height="180" width="469">
	<colgroup>
		<col />
		<col />
		<col span="3" />
		<col />
		<col span="2" />
	</colgroup>
	<tbody>
		<tr height="15">
			<td height="15" style="height:20px;"></td>
			<td style="width: 55px;">Bacto Peptone</td>
			<td style="width: 50px;">Yeast Extract</td>
			<td style="width: 50px;">Bacto Agar</td>
			<td style="width: 60px;">Dextrose</td>
			<td style="width: 70px;">Potassium Acetate</td>
			<td style="width: 60px;">Glycerol</td>
			<td style="width: 60px;">ddH2O</td>
		</tr>
		<tr height="15">
			<td height="15" style="height:20px;">YPG plates</td>
			<td>20 g</td>
			<td>10 g</td>
			<td>20 g</td>
			<td>-</td>
			<td>-</td>
			<td>30 ml</td>
			<td>970 ml</td>
		</tr>
		<tr height="15">
			<td height="15" style="height:20px;">YPD plates</td>
			<td>20 g</td>
			<td>10 g</td>
			<td>20 g</td>
			<td>20 g</td>
			<td>-</td>
			<td>-</td>
			<td>1,000 ml</td>
		</tr>
		<tr height="15">
			<td height="15" style="height:20px;">YPD liquid</td>
			<td>20 g</td>
			<td>10 g</td>
			<td>-</td>
			<td>20 g</td>
			<td>-</td>
			<td>-</td>
			<td>1,000 ml</td>
		</tr>
		<tr height="15">
			<td height="15" style="height:20px;">YPA liquid</td>
			<td>20 g</td>
			<td>10 g</td>
			<td>-</td>
			<td>-</td>
			<td>20 g</td>
			<td>-</td>
			<td>1,000 ml</td>
		</tr>
		<tr height="15">
			<td style="height: 20px; width: 80px;">Sporulation media</td>
			<td>-</td>
			<td>-</td>
			<td>-</td>
			<td>-</td>
			<td>10 g</td>
			<td>-</td>
			<td>1,000 ml</td>
		</tr>
	</tbody>
</table>
Table 1: Media formulations. Amounts are given for 1 L of media. Specifics about media ingredients can be found in the Materials Table.
<ol>
	<li>If All Sporulating Cells will be the Same Genotype, Follow This Procedure:
	<ol>
		<li>Thaw yeast strain to be used onto a YPG (YPGlycerol) plate. Grow yeast for 12-16 hr at 30 &#176;C. Importantly, SK1 cells are also poised to sporulate, so SK1 strains should not be left too long on YPG plates, or they may sporulate on the plate. 
		Note: A freshly thawed strain grown on YPG is preferred, as utilization of glycerol as a carbon source requires oxidative phosphorylation, and thus selects for cells that have functional mitochondrial DNA. SK1 cells have a tendency to lose functional mitochondrial DNA and become petites. Functional mitochondrial DNA is needed for sporulation.</li>
		<li>Streak yeast from the YPG plate onto a YPD (YPDextrose) plate for single colonies. Grow yeast on YPD plate 24-28 hr at 30 &#176;C.</li>
		<li>After about 36-48 hr of growth on YPD solid media, start a 25 ml YPD culture using a single colony from the YPD plate. Grow this culture until cells are about OD600 = 4.0 to 7.0. Perform this step at 30 &#176;C overnight in a shaking incubator, shaking at 220 rpm.</li>
		<li>From the YPD culture, use an appropriate amount of cells to start 1,000 ml of YPA (YPAcetate) culture that is OD600 = 0.1 for each 96 well plate need in Section 2. Grow yeast in a 30 &#176;C shaking incubator (shaking at 220 rpm) until the culture OD600 is between 1.3 to 1.5. 
		Note: Inoculate 100 ml of YPA culture for each 96 multiwell plate to be screened in Section 2. For example, if screening four 96 multiwell plates, 400 ml of YPA culture will be needed. Starting with 10% extra volume in the YPA culture is necessary to protect against evaporative volume loss. Typically, it will take between 12-16 hr for cells to reach the appropriate OD600; the amount of time may vary depending on the genotype of the yeast strain. YPA is the presporulation media. Pregrowth in acetate helps induce expression of genes (such as IME1) needed for efficient and synchronous sporulation6.</li>
		<li>Spin at 1,800 x g in a table top centrifuge for 5 min to pellet cells grown in YPA. Wash cells 1x with 0.5 volume of sterile autoclaved deionized water. Spin again, and discard wash. Resuspend cells in 1x volume sporulation media. Continue to Section 2.</li>
	</ol>
	</li>
	<li>If using cells for sporulation that are of different genotypes, (i.e., transformed with different plasmids or containing different mutations, typically obtained and stored as frozen stocks), array cells of the different genotypes into a 96 multiwell format. Then, follow this procedure:
	<ol>
		<li>Use a sterile 96 prong frogger to transfer cells from thawed frozen stocks in 96 multiwell plate(s) onto YPG solid media. Grow yeast overnight at 30 &#176;C.</li>
		<li>Using a sterile 96 prong frogger, transfer cells from YPG solid media onto YPD solid media or selective solid media (i.e., synthetic minimal media lacking amino acids, if the cells contain plasmids that require selection). Grow yeast at 30 &#176;C until colonies are formed for each strain, typically 1 day on YPD and 2 days if selective media is necessary.</li>
		<li>Aliquot 1.2 ml of YPD liquid media or selective liquid media into each well of a 96 deep 2 ml multiwell plate. Transfer cells from solid media into liquid media using a frogger, cover with a plastic lid held in place by tape, and grow overnight in 30 &#176;C shaker, shaking at 220 rpm. 
		Note: To minimize contamination, cover plates using the plastic lids from a rectangular petri plate. Hold lids in place using a piece of tape, so that air circulation is minimally restricted.</li>
		<li>Centrifuge plates at 1,800 x g for 5 min, using a swinging bucket centrifuge with adaptors to accommodate 96 well plates. Pour off media from cells; add 500 &#181;l YPA to each well and resuspend pelleted cells in the YPA. Cover with plastic lid held in place by tape.</li>
		<li>Grow cells for 15 hr at 30 &#176;C in a shaking incubator, shaking at 220 rpm. Continue to Section 2.</li>
	</ol>
	</li>
</ol>
2. Sporulating Cells in a 96 Multiwell Format
<ol>
	<li>Add either one 3 mm sterile solid glass bead or a sterile 5 mm x 2 mm magnetic stir bar into each well of a 96 well plate with 1.3 ml wells. (See Representative Results below for a discussion on whether to use a bead or a stir bar.)</li>
	<li>If all cells to be screened are of the same genotype, go to 2.2.1. If cells to be screened are of different genotypes, go to 2.2.2.
	<ol>
		<li>Take cells from step 1.1.5 and aliquot 500 &#181;l of cells plus media into each well of the 96 multiwell plate. Cover with plastic lid held in place by tape. Proceed to 2.3.</li>
		<li>Spin cells that are in YPA from 1.2.4 at 1,800 x g for 5 min, using a swinging bucket centrifuge with adaptors to accommodate 96 well plates. Pour off media from cells. Add 500 &#181;l of sporulation media to each well and resuspend pelleted cells in the sporulation media. Cover with plastic lid held in place by tape. Proceed to 2.3.</li>
	</ol>
	</li>
	<li>If using a glass bead, place samples in a shaking incubator at 30&#176; C and shake at 220 rpm for sporulation. If using a magnetic stir bar, place samples on a stir plate inside of a 30 &#176;C incubator for sporulation. 
	Note: The exact stir speed for the magnetic stir bars is not very important, as long as all bars are moving energetically and the culture is aerated.</li>
	<li>To monitor progression through sporulation, withdraw samples from the sporulating culture for visualization, Add 6 &#181;l of cells from the sporulating cultures to 24 &#181;l of sporulation media in a 96 well coverslip plate (1:5 dilution). Leave cells to settle for 5 min before examining cells using an inverted microscope. 
	Note: In wild type SK1 cells, compact mature spores will form by 36 hours after transfer to sporulation media. Progression through sporulation can be monitored by microscopy using fluorescent markers, such as a nuclear marker (i.e., Htb2-mCherry18) to examine the meiotic division or a prospore membrane marker (i.e., G2019) to examine spore morphogenesis. Alternatively, the formation of refractile spores can be seen using Nomarski DIC microscopy starting about 12 hr after transfer to sporulation media.</li>
</ol>

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The authors have no competing financial interests.

Here we present a protocol for sporulating SK1 yeast in a 96 multiwell format. Aeration is key for efficient sporulation, which requires the use of either a stir bar or a glass bead in each well. When cells are sporulated in a 96 multiwell plate in a shaking incubator without either a bead or a stir bar, cells do not sporulate efficiently. Only a small increase in sporulation efficiency is seen when cells are sporulated without either a bead or a stir bar in a shaking incubator, compared to being at 30 &#176;C without ag...

Sporulation in the budding yeast has been studied to provide insights into many aspects of biology, including the control of chromosome segregation during meiosis1, mechanisms of genetic recombination2, the control of development by cell signaling3, nutritional control of development4, the transcriptional regulation of development5, and the examination of spore formation6. Spore formation includes a novel cell division event involving the formation of new membrane compartments within the mother cell followed by the deposition of a protective spore wall6. These studies that examine sporulating cells often take advantage of the rapidly sporulating yeast strain SK1, which can undergo the process of sporulation in about 24 hr in a relatively efficient fashion7,8. Although optimization of sporulation conditions for budding yeast have been described9-13, these experiments examined sporulation on solid media or in larger scale liquid cultures where sporulation is carried out using culture tubes or flasks.
Here we describe a method for sporulating yeast in a 96 multiwell plate format. We find that for this method, aeration is critical for synchronous and efficient sporulation, and have devised techniques to ensure sufficient sporulation a small-volume multiwell format. Sporulating in a 96 multiwell plate format allows for cells to be screened using high-throughput techniques and reagents optimized for a multiwell plate format, such screening for high copy suppressors using a tiled library14-16.

<table><tbody><tr><td>Nunc 1.3 ml DeepWell Plates</td><td>ThermoScientific</td><td>260251</td><td>Used for sporulation</td></tr><tr><td>Nunc 2.0 ml DeepWell plates</td><td>ThermoScientific</td><td>278743</td><td>Used for presporulation growth, step 1.2.3</td></tr><tr><td>3 mm glass bead</td><td>Fisher</td><td>11-312A</td><td>Used for sporulation</td></tr><tr><td>5 mm x 2 mm stir bar, pack of 12</td><td>Fisher</td><td>14-511-82</td><td>Used for sporulation</td></tr><tr><td>96 well frogger</td><td>V&amp;amp;P Scientific</td><td>VP407</td><td>needed for step 1.2</td></tr><tr><td>library copier</td><td>V&amp;amp;P Scientific</td><td>VP381</td><td>needed for step 1.2; to be used with the frogger</td></tr><tr><td>rectangular Petri dish</td><td>ThermoScientific</td><td>264728</td><td>needed for step 1.2</td></tr><tr><td>Bacto Peptone</td><td>BD</td><td>211677</td><td>needed for media</td></tr><tr><td>Yeast Extract</td><td>BD</td><td>212750</td><td>needed for media</td></tr><tr><td>Bacto Agar</td><td>BD</td><td>212750</td><td>needed for media</td></tr><tr><td>Dextrose</td><td>Fisher</td><td>D16-3</td><td>needed for media</td></tr><tr><td>Potassium Acetate</td><td>Fisher</td><td>P171-500</td><td>needed for media</td></tr><tr><td>Glycerol</td><td>Fisher</td><td>G33-500</td><td>needed for media</td></tr><tr><td>Black 96 well glass bottom plate</td><td>MatTek</td><td>PBK96G-1.5.5-F</td><td>needed for step 2.4</td></tr></tbody></table>

efficient sporulation of saccharomyces cerevisiae in a 96 multiwell format

During times of nutritional stress, Saccharomyces cerevisiae undergoes gametogenesis, known as sporulation. Diploid yeast cells that are starved for nitrogen and carbon will initiate the sporulation process. The process of sporulation includes meiosis followed by spore formation, where the haploid nuclei are packaged into environmentally resistant spores. We have developed methods for the efficient sporulation of budding yeast in 96 multiwell plates, to increase the throughput of screening yeast cells for sporulation phenotypes. These methods are compatible with screening with yeast containing plasmids requiring nutritional selection, when appropriate minimal media is used, or with screening yeast with genomic alterations, when a rich presporulation regimen is used. We find that for this method, aeration during sporulation is critical for spore formation, and have devised techniques to ensure sufficient aeration that are compatible with the 96 multiwell plate format. Although these methods do not achieve the typical ~80% level of sporulation that can be achieved in large-volume flask based experiments, these methods will reliably achieve about 50-60% level of sporulation in small-volume multiwell plates.

To assess this protocol, sporulation efficiencies obtained from sporulating cells in multiwell plates (as described above) were compared to cells sporulated using larger volumes in flasks (Table 2). The use of multiwell plates did not achieve the high efficiency seen when sporulating in flasks, where ~80% efficiency can be routinely seen. Sporulating in multiwell plates with proper aeration (provided by glass beads or stir bars) can achieve sufficient sporulation efficien...

Watch this Scientific Journal Video about Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format at JoVE.com

Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format

Here, sporulation of Saccharomyces cerevisiae is carried out in a 96 multiwell format.

Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format

During times of nutritional stress, Saccharomyces cerevisiae undergoes gametogenesis, known as sporulation. Diploid yeast cells that are starved for ...

efficient-sporulation-saccharomyces-cerevisiae-96-multiwell

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10.1K Views.  University of Massachusetts Boston. Here, sporulation of Saccharomyces cerevisiae is carried out in a 96 multiwell format.

Video: Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format

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.

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.

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

A high-throughput method to globally study the organelle morphology in S. cerevisiae

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help achieve an comprehensive understanding of molecular pathways. In Saccharomyces cerevisiae, with the development of the non-essential gene deletion array, we can globally study the morphology of different organelles like the endoplasmic reticulum (ER) and the mitochondria using GFP (or variant)-markers in different gene backgrounds. However, incorporating GFP markers in each single mutant individually is a labor-intensive process. Here, we describe a procedure that is routinely used in our laboratory. By using a robotic system to handle high-density yeast arrays and drug selection techniques, we can significantly shorten the time required and improve reproducibility. In brief, we cross a GFP-tagged mitochondrial marker (Apc1-GFP) to a high-density array of 4,672 nonessential gene deletion mutants by robotic replica pinning.  Through diploid selection, sporulation, germination and dual marker selection, we recover both alleles. As a result, each haploid single mutant contains Apc1-GFP incorporated at its genomic locus. Now, we can study the morphology of mitochondria in all non-essential mutant background. Using this high-throughput approach, we can conveniently study and delineate the pathways and genes involved in the inheritance and the formation of organelles in a genome-wide setting.

GFP-fusion proteins are widely used to visualize organelles by confocal microscopy. However, screening for mutations that affect the morphology of organelles generally requires individual mutagenesis and is time consuming. Here, we demonstrate a method to simultaneously incorporate organelle-GFP markers in almost 5,000 non-essential genes in yeast.

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help ...

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

Mutations introduced in the spliceosome or its substrate have significantly contributed to our understanding of the intricacies of spliceosomal function. Whether disease-related or functionally selected, many of these mutations have been studied using growth assays in the model organism Saccharomyces cerevisiae (yeast). The splicing-specific copper growth assay, or ACT1-CUP1 assay, provides a comprehensive analysis of mutation at the phenotypic level. The ACT1-CUP1 assay utilizes reporters that confer copper tolerance when correctly spliced. Thus, in the presence of copper, changes in yeast viability correlate to changes in mRNA production through splicing. In a typical experiment, the yeast spliceosome is challenged with different non-consensus splicing reporters and the splicing factor mutation of interest to detect any synergetic or antithetical impact on splicing. Here a full description of copper plate preparation, plating of yeast cells, and data evaluation are given. A selection of complimentary experiments is described, highlighting the versatility of the ACT1-CUP1 reporters. The ACT1-CUP1 assay is a handy tool in the splicing toolbox thanks to the direct read-out of mutational effect(s) and the comparative possibilities from the continuing use in the field.

The ACT1-CUP1 assay, a copper growth assay, provides a quick readout of precursor messenger RNA (pre-mRNA) splicing and the impact mutant splicing factors have on spliceosomal function. This study provides a protocol and highlights the customization possible to address the splicing question of interest.

Mutations introduced in the spliceosome or its substrate have significantly contributed to our understanding of the intricacies of spliceosomal function. ...

Genetics

Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography

Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in situ. Owing to the strong interaction of an electron with the matter, high-resolution cryo-ET studies are limited to specimens with a thickness of less than 200 nm, which restricts the applicability of cryo-ET only to the peripheral regions of a cell. A complex workflow that comprises the preparation of thin cellular cross-sections by cryo-focused ion beam micromachining (cryo-FIBM) was introduced during the last decade to enable the acquisition of cryo-ET data from the interior of larger cells. We present a protocol for the preparation of cellular lamellae from a sample vitrified by plunge freezing utilizing Saccharomyces cerevisiae as a prototypical example of a eukaryotic cell with wide utilization in cellular and molecular biology research. We describe protocols for vitrification of S. cerevisiae into isolated patches of a few cells or a continuous monolayer of the cells on a TEM grid and provide a protocol for lamella preparation by cryo-FIB for these two samples.

Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography

We present a protocol for lamella preparation of plunge frozen biological specimens by cryo-focused ion beam micromachining for high-resolution structural studies of macromolecules in situ with cryo-electron tomography. The presented protocol provides guidelines for the preparation of high-quality lamellae with high reproducibility for structural characterization of macromolecules inside the&#160;Saccharomyces cerevisiae.

Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in ...

Biochemistry

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 ...

Competitive Genomic Screens of Barcoded Yeast Libraries

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for fast, parallel methods to define gene function becomes ever more important. Collections of genome-wide deletion mutants in yeasts and E. coli have served as workhorses for functional characterization of gene function, but this approach is not scalable, current gene-deletion approaches require each of the thousands of genes that comprise a genome to be deleted and verified. Only after this work is complete can we pursue high-throughput phenotyping. Over the past decade, our laboratory has refined a portfolio of competitive, miniaturized, high-throughput genome-wide assays that can be performed in parallel. This parallelization is possible because of the inclusion of DNA 'tags', or 'barcodes,' into each mutant, with the barcode serving as a proxy for the mutation and one can measure the barcode abundance to assess mutant fitness. In this study, we seek to fill the gap between DNA sequence and barcoded mutant collections. To accomplish this we introduce a combined transposon disruption-barcoding approach that opens up parallel barcode assays to newly sequenced, but poorly characterized microbes. To illustrate this approach we present a new Candida albicans barcoded disruption collection and describe how both microarray-based and next generation sequencing-based platforms can be used to collect 10,000 - 1,000,000 gene-gene and drug-gene interactions in a single experiment.

We have developed comprehensive, unbiased genome-wide screens to understand gene-drug and gene-environment interactions. Methods for screening these mutant collections are presented.

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily.  The tempo of these advances is ...

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 ...

High-throughput Screening for Protein-based Inheritance in S. cerevisiae

The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived inheritance encoded in protein conformation (rather than sequence) has long been viewed as paradigm-shifting but rare. The best characterized examples of such epigenetic elements are prions, which possess a self-assembling behavior that can drive the heritable manifestation of new phenotypes. Many archetypal prions display a striking N/Q-rich sequence bias and assemble into an amyloid fold. These unusual features have informed most screening efforts to identify new prion proteins. However, at least three known prions (including the founding prion, PrPSc) do not harbor these biochemical characteristics. We therefore developed an alternative method to probe the scope of protein-based inheritance based on a property of mass action: the transient overexpression of prion proteins increases the frequency at which they acquire a self-templating conformation. This paper describes a method for analyzing the capacity of the yeast ORFeome to elicit protein-based inheritance. Using this strategy, we previously found that &gt;1% of yeast proteins could fuel the emergence of biological traits that were long-lived, stable, and arose more frequently than genetic mutation. This approach can be employed in high throughput across entire ORFeomes or as a targeted screening paradigm for specific genetic networks or environmental stimuli. Just as forward genetic screens define numerous developmental and signaling pathways, these techniques provide a methodology to investigate the influence of protein-based inheritance in biological processes.

High-throughput Screening for Protein-based Inheritance in S. cerevisiae

This protocol describes a high-throughput methodology to functionally screen for protein-based inheritance in S. cerevisiae.

The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived ...

Saccharomyces cerevisiae Exponential Growth Kinetics in Batch Culture to Analyze Respiratory and Fermentative Metabolism

Saccharomyces cerevisiae cells in the exponential phase sustain their growth by producing ATP through fermentation and/or mitochondrial respiration. The fermentable carbon concentration mainly governs how the yeast cells generate ATP; thus, the variation in fermentable carbohydrate levels drives the energetic metabolism of S. cerevisiae. This paper describes a high-throughput method based on exponential yeast growth to estimate the effects of concentration changes and nature of the carbon source on respiratory and fermentative metabolism. The growth of S. cerevisiae is measured in a microplate or shaken conical flask by determining the optical density (OD) at 600 nm. Then, a growth curve is built by plotting OD versus time, which allows identification and selection of the exponential phase, and is fitted with the exponential growth equation to obtain kinetic parameters. Low specific growth rates with higher doubling times generally represent a respiratory growth. Conversely, higher specific growth rates with lower doubling times indicate fermentative growth. Threshold values of doubling time and specific growth rate are estimated using well-known respiratory or fermentative conditions, such as non-fermentable carbon sources or higher concentrations of fermentable sugars. This is obtained for each specific strain. Finally, the calculated kinetic parameters are compared with the threshold values to establish whether the yeast shows fermentative and/or respiratory growth. The advantage of this method is its relative simplicity for understanding the effects of a substance/compound on fermentative or respiratory metabolism. It is important to highlight that growth is an intricate and complex biological process; therefore, preliminary data from this method must be corroborated by the quantification of oxygen consumption and accumulation of fermentation byproducts. Thereby, this technique can be used as a preliminary screening of compounds/substances that may disturb or enhance fermentative or respiratory metabolism.

Saccharomyces cerevisiae Exponential Growth Kinetics in Batch Culture to Analyze Respiratory and Fermentative Metabolism

Here we present a protocol to estimate the respiratory and fermentative metabolism by fitting the exponential growth of Saccharomyces cerevisiae to the exponential growth equation. Calculation of the kinetic parameters allows for the screening of influences of substances/compounds on fermentation or mitochondrial respiration.

Saccharomyces cerevisiae cells in the exponential phase sustain their growth by producing ATP through fermentation and/or mitochondrial respiration. The ...

Examination of Mitotic and Meiotic Fission Yeast Nuclear Dynamics by Fluorescence Live-cell Microscopy

Live-cell imaging is a microscopy technique used to examine cell and protein dynamics in living cells. This imaging method is not toxic, generally does not interfere with cell physiology, and requires minimal experimental handling. The low levels of technical interference enable researchers to study cells across multiple cycles of mitosis and to observe meiosis from beginning to end. Using fluorescent tags such as Green Fluorescent Protein (GFP) and Red Fluorescent Protein (RFP), researchers can analyze different factors whose functions are important for processes like transcription, DNA replication, cohesion, and segregation. Coupled with data analysis using Fiji (a free, optimized ImageJ version), live-cell imaging offers various ways of assessing protein movement, localization, stability, and timing, as well as nuclear dynamics and chromosome segregation. However, as is the case with other microscopy methods, live-cell imaging is limited by the intrinsic properties of light, which put a limit to the resolution power at high magnifications, and is also sensitive to photobleaching or phototoxicity at high wavelength frequencies. However, with some care, investigators can bypass these physical limitations by carefully choosing the right conditions, strains, and fluorescent markers to allow for the appropriate visualization of mitotic and meiotic events.

Here, we present live-cell imaging which is a non-toxic microscopy method that allows researchers to study protein behavior and nuclear dynamics in living fission yeast cells during mitosis and meiosis.

Live-cell imaging is a microscopy technique used to examine cell and protein dynamics in living cells. This imaging method is not toxic, generally does ...

Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format

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