Arginase activity is a useful marker of nitrogen limitation during alcoholic fermentations.

Nitrogen deficiency in musts is one of the causes of sluggish or stuck fermentations. In this work we propose that arginase activity determination can be useful for detecting nitrogen starvation early in vinification. CAR1 and YGP1 genes are not specifically induced under conditions of nitrogen starvation. However, a significant increase in the enzymatic activity of arginase, the product of the CAR1 gene, is detected in vinifications carried out with musts containing limiting amounts of nitrogen. Moreover, on adding ammonia to a nitrogen-deficient vinification, even at late stages, this enzymatic activity is repressed, and growth rate is restored simultaneously. We also investigate the role…

Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals

The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenyl­ation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and poly­adenyl­ation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as"words"). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of singl…

Exploring the potential of some yeast strains in the stereoselective synthesis of aldol reaction products and its reduced 1,3-dialcohol derivatives

Abstract The behavior of two yeast strains has been studied under different conditions. Both microorganims catalyzed the aldol reaction between activated aldehydes and acetone when a large amount of the latter was present in the reaction medium producing, with moderate stereoselectivity, the aldol product with the R configuration. No reduction of any of the products present in the medium was detected. On the other hand, the carbonyl group of the racemic aldol was reduced to produce chiral 1,3-dialcohol derivatives when water was employed as the only solvent. In this case, the resolution of the racemic starting material was also possible with one of the biocatalysts, and the aldol was recove…

Functional Genomics in Wine Yeast: DNA Arrays and Next Generation Sequencing

Since their very beginning, DNA array and next-generation sequencing technologies have been used with Saccharomyces cerevisiae cells. In the last 7 years, an increasing number of studies have focused on the study of wine strains and winemaking. The uncovering of the genomic features of these strains and expression profiles under the different stressful conditions that they have to deal with have contributed significantly to the knowledge of how this amazing microorganism can convert grape must into a drink that has enormously influenced mankind for 7000 years.This review presents a synopsis of DNA array and next-generation sequencing (NGS) technologies and focus mainly in their use in study…

Making your own gene library

Study of the First Hours of Microvinification by the Use of Osmotic Stress-response Genes as Probes

Summary When yeast cells are inoculated into grape must for vinification they find stress conditions because of osmolarity, which is due to very high sugar concentration, and pH lower than 4. In this work an analysis of the expression of three osmotic stress induced genes ( GPD1 , HSP12 and HSP104 ) under microvinification conditions is shown as a way to probe those stress situations and the regulatory mechanisms that control them. The results indicate that during the first hours of microvinification there is an increase in the GPD1 mRNA levels with a maximum about one hour after inoculation, and a decrease in the amount of HSP12 and HSP104 mRNAs, although with differences between them. The…

Dissection of the elements of osmotic stress response transcription factor Hot1 involved in the interaction with MAPK Hog1 and in the activation of transcription.

Abstract The response to hyperosmotic stress is mediated by the HOG pathway. The MAP kinase Hog1 activates several transcription factors, regulates chromatin-modifying enzymes and, through its interaction with RNA polymerase II, it directs this enzyme to osmotic stress-controlled genes. For such targeting, this kinase requires the interaction with transcription factors Hot1 and Sko1. However, phosphorylation of these proteins by Hog1 is not required for their functionality. In this study, we aim to identify the Hot1 elements involved in Hog1-binding and in the activation of transcription. Two-hybrid experiments demonstrated that the Hot1 sequence between amino acids 340 and 534 and the CD e…

Phylogenetic origin and transcriptional regulation at the post-diauxic phase of SPI1, in Saccharomyces cerevisiae

15 pages, 4 figures, supplementary material

Use of Saccharomyces cerevisiae as a whole cell system for aldol condensation in organic medium: Study of the factors affecting the biotransformation

Abstract Saccharomyces cerevisiae has been employed as a whole cell catalyst for a number of asymmetric transformations. This work explores the ability of this microorganism to carry out the asymmetric aldol condensation between 4-nitrobenzaldehyde and acetone. For this purpose, lyophilized cells of the FY86 laboratory strain from stationary phase cultures were employed. This reaction shows stereoselectivity, and its progress is affected by the water concentration in the medium, temperature and the growth stage of the yeast culture. Cell lysis experiments indicate that activity responsible for this biotransformation is located in the soluble fraction.

Expression profile of genes involved in hydrogen sulphide liberation by Saccharomyces cerevisiae grown under different nitrogen concentrations

AbstractThe present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in S. cerevisiae associated to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were downregulated when yeast stopped growing which could associate M…

The C-terminal region of the Hot1 transcription factor binds GGGACAAA-related sequences in the promoter of its target genes

Response to hyperosmotic stress in the yeast Saccharomyces cerevisiae involves the participation of the general stress response mediated by Msn2/4 transcription factors and the HOG pathway. One of the transcription factors activated through this pathway is Hot1, which contributes to the control of the expression of several genes involved in glycerol synthesis and flux, or in other functions related to adaptation to adverse conditions. This work provides new data about the interaction mechanism of this transcription factor with DNA. By means of one-hybrid and electrophoretic mobility assays, we demonstrate that the C-terminal region, which corresponds to amino acids 610-719, is the DNA-bindi…

The introduction of fluorine atoms or trifluoromethyl groups in short cationic peptides enhances their antimicrobial activity

The effect of introducing fluorine atoms or trifluoromethyl groups in either the peptidic chain or the C-terminal end of cationic pentapeptides is reported. Three series of amide and ester peptides were synthesised and their antimicrobial properties evaluated. An enhanced activity was found in those derivatives whose structure contained fluorine, suggesting an increase in their hydrophobicity.

A sequence element downstream of the yeast HTB1 gene contributes to mRNA 3' processing and cell cycle regulation.

Histone mRNAs accumulate in the S phase and are rapidly degraded as cells progress into the G(2) phase of the cell cycle. In Saccharomyces cerevisiae, fusion of the 3' untranslated region and downstream sequences of the yeast histone gene HTB1 to a neomycin phosphotransferase open reading frame is sufficient to confer cell cycle regulation on the resulting chimera gene (neo-HTB1). We have identified a sequence element, designated the distal downstream element (DDE), that influences both the 3'-end cleavage site selection and the cell cycle regulation of the neo-HTB1 mRNA. Mutations in the DDE, which is located approximately 110 nucleotides downstream of the HTB1 gene, lead to a delay in the…

Whole-Cell Biocatalysis in Seawater: New Halotolerant Yeast Strains for the Regio- and Stereoselectivity Reduction of 1-Phenylpropane-1,2-Dione in Saline-Rich Media.

The application of green chemistry concepts in catalysis has considerably increased in recent years, and the interest in using sustainable solvents in the chemical industry is growing. One of the recent proposals to fall in line with this is to employ seawater as a solvent in biocatalytic processes. This involves selecting halotolerant strains capable of carrying out chemical conversions in the presence of the salt concentrations found in this solution. Recent studies by our group have revealed the interest in using strains belonging to Debaryomyces and Schwanniomyces for catalytic processes run in this medium. In the present work, we select other yeasts based on their halotolerance to wide…

Chromatin structure of the yeast FBP1 gene: transcription-dependent changes in the regulatory and coding regions.

We have studied the chromatin structure of the Saccharomyces cerevisiae FBP1 gene, which codes for fructose-1,6-bisphosphatase. A strong, constitutive, DNase I, micrococcal nuclease and S1 nuclease hypersensitive site is present close to the 3′ end of the coding region. In the repressed state, positioned nucleosomes exist around this site, and subtle changes occur in this nucleosomal organization upon derepression. A DNase I hypersensitive region is located within the promoter between positions −540 and −400 and it extends towards the gene in the derepressed state, leading to an alteration of nucleosomal positioning. Psoralen crosslinking of chromatin, which is used for the first time to st…

The Saccharomyces cerevisiae flavodoxin-like proteins Ycp4 and Rfs1 play a role in stress response and in the regulation of genes related to metabolism

SPI1 is a gene whose expression responds to many environmental stimuli, including entry into stationary phase. We have performed a screening to identify genes that activate SPI1 promoter when overexpressed. The phosphatidylinositol- 4-phosphate 5-kinase gene MSS4 was identified as a positive activator of SPI1. Another SPI1 transcriptional regulator isolated was the flavodoxin-like gene YCP4. YCP4 and its homolog RFS1 regulate the expression of many genes during the late stages of growth. The double deletion mutant in YCP4 and its homolog RFS1 has an impact on gene expression related to metabolism by increasing the expression of genes involved in hexose transport and glycolysis, and decreasi…

Response of yeast cells to high glucose involves molecular and physiological differences when compared to other osmostress conditions.

Yeast cells can be affected by several causes of osmotic stress, such as high salt, sorbitol or glucose concentrations. The last condition is particularly interesting during natural processes where this microorganism participates. Response to osmostress requires the HOG (High Osmolarity Glycerol) pathway and several transcription factors, including Hot1, which plays a key role in high glucose concentrations. In this work, we describe how the yeast response to osmotic stress shows differences in accordance with the stress agent responsible for it. Compared with other conditions, under high glucose stress, delocalization of MAPK (Mitogen-Activated Protein Kinase) Hog1 is slower, induction of …

Transcriptomic and Proteomic Approach for Understanding the Molecular Basis of Adaptation of Saccharomyces cerevisiae to Wine Fermentation

ABSTRACT Throughout alcoholic fermentation, Saccharomyces cerevisiae cells have to cope with several stress conditions that could affect their growth and viability. In addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. Commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiological traits, but little is known about the molecular basis of the fermentative behavior of these strains. In this work, we present the first transcriptomic and proteomic comparison between …

Effect of addition of Lewis/Brönsted acids in the asymmetric aldol condensation catalyzed by trifluoroacetate salts of proline-based dipeptides

Abstract Proline-based dipeptides catalyze aldol condensations with good yield and stereoselectivity after addition of zinc or sodium acetate to the trifluoroacetate peptide. The chirality of the N-terminal proline in the catalyst determines the absolute configuration of the aldol product, but stereoselectivity depends on the configuration of both amino acids, and is higher for the enantiomeric pair R–S, S–R. Regarding the nature of the second component, optimal results in both yield and stereoselectivity are obtained when neutral unbranched primary amino acids are used.

A natural A/T-rich sequence from the yeast FBP1 gene exists as a cruciform in Escherichia coli cells.

Abstract Palindromic or semipalindromic sequences can adopt cruciform structures in DNA in vitro. It has been demonstrated in some cases that A/T-rich cruciforms exist also in vivo in Escherichia coli. The biological function of those structures is not understood although putative cruciforms have been found in interesting locations on replication origins, operators, or transcriptional termination regions. Here we show by means of the use of structure-dependent nucleases that the 3′ end of the yeast FBP1 gene contains a stable cruciform both in vitro and in E. coli cells and that in both cases, its extrusion depends on the DNA supercoiling state.

Addition of ammonia or amino acids to a nitrogen-depleted medium affects gene expression patterns in yeast cells during alcoholic fermentation

Yeast cells require nitrogen and are capable of selectively using good nitrogen sources in preference to poor ones by means of the regulatory mechanism known as nitrogen catabolite repression (NCR). Herein, the effect of ammonia or amino acid addition to nitrogen-depleted medium on global yeast expression patterns in yeast cells was studied using alcoholic fermentation as a system. The results indicate that there is a differential reprogramming of the gene expression depending on the nitrogen source added. Ammonia addition resulted in a higher expression of genes involved in amino acids biosynthesis while amino acid addition prepares the cells for protein biosynthesis. Therefore, a high per…

Analysis of the stress resistance of commercial wine yeast strains

Alcoholic fermentation is an essential step in wine production that is usually conducted by yeasts belonging to the species Saccharomyces cerevisiae. The ability to carry out vinification is largely influenced by the response of yeast cells to the stress conditions that affect them during this process. In this work, we present a systematic analysis of the resistance of 14 commercial S. cerevisiae wine yeast strains to heat shock, ethanol, oxidative, osmotic and glucose starvation stresses. Significant differences were found between these yeast strains under certain severe conditions, Vitilevure Pris Mouse and Lalvin T73 being the most resistant strains, while Fermiblanc arom SM102 and UCLM …

Saccharomyces Yeasts I

Publisher Summary This chapter discusses the microbiological aspects of saccharomyces yeasts in wine production. Yeasts, which play a central role in the winemaking process, are unicellular fungi that reproduce by budding. Most yeast belongs to the phylum Ascomycota on the basis of their sexual development. The selection of wine yeasts with specific genetic markers provides a system for the precise monitoring of the growth of particular strains during fermentation. Analyses of this type have shown that fermentation is driven mainly by inoculated yeasts, although these sometimes become only partially established. The growth of the natural flora is not completely suppressed during the initial…

Adaptive evolution of wine yeast.

Abstract Alcoholic fermentation is one of the main phases in wine production. It is usually conducted by yeasts belonging to the species Saccharomyces cerevisiae. Industrial S. cerevisiae strains are highly specialized organisms, which have evolved to utilize to their full potential the different environments or ecological niches. So, during the alcoholic fermentation, the yeast has been adapted to different kinds of stress conditions; this adaptation is call “domestication”. In this review, we describe the different mechanisms involved in the adaptive evolution of wine yeast strains.

A novel approach for the improvement of stress resistance in wine yeasts

During wine production yeast cells are affected by several stress conditions that could affect their viability and fermentation efficiency. In this work we describe a novel genetic manipulation strategy designed to improve stress resistance in wine yeasts. This strategy involves modifying the expression of the transcription factor MSN2, which plays an important role in yeast stress responses. The promoter in one of the genomic copies of this gene has been replaced by the promoter of the SPI1 gene, encoding for a cell wall protein of unknown function. SPI1 is expressed at late phases of growth and is regulated by Msn2p. This modification allows self-induction of MSN2 expression. MSN2 gene tr…

Improved Biocatalytic Activity of theDebaryomycesSpecies in Seawater

Quadern de pràctiques de Mètodes en Biologia Molecular i Enginyeria Genètica

El document inclou la descripció d'alguns experiments de laboratori sobre Enginyeria Genètica que són aplicables per a estudiants de graus de Bioquímica i Ciències Biomèdiques i de Biotecnologia El document forma part dels materials docents programats mitjançant l'ajut del Servei de Política Lingüística de la Universitat de València.