The ethanol tolerance in Saccharomyces cerevisiae under a phenomics perspective

Ethanol (EtOH) is a substantial stressor for Saccharomyces cerevisiae. Data integration from strains with different phenotypes, including EtOH stress-responsive lncRNAs, are still not available. We covered these issues seeking systems modifications that drive the divergences between higher (HT) and lower (LT) EtOH tolerant strains under their highest stress conditions. We showed that these phenotypes are neither related to high viability nor faster population rebound after stress relief. LncRNAs work on many stress-responsive systems in a strain-specific manner promoting the EtOH tolerance. Cells use membraneless RNA/protein storage and degradation systems to endure the stress harming, and lncRNAs jointly promote EtOH tolerance. CTA1 and longevity are primer systems promoting phenotype-specific gene expression. The lower cell viability and growth under stress is a by-product of sphingolipids and inositol phosphorylceramide dampening, acerbated in HTs by sphinganine, ERG9, and squalene overloads; LTs diminish this harm by accumulating inositol 1-phosphate. The diauxic shift drives an EtOH buffering by promoting an energy burst under stress, mainly in HTs. Analysis of mutants showed genes and lncRNAs in three strains critical for their EtOH tolerance. Finally, longevity, peroxisome, energy and lipid metabolisms, RNA/protein degradation and storage systems are the main pathways driving the EtOH tolerance phenotypes.

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Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity

Communications Biology ◽

10.1038/s42003-021-01684-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Marcin Luzarowski ◽

Rubén Vicente ◽

Andrei Kiselev ◽

Mateusz Wagner ◽

Dennis Schlossarek ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Small Molecules ◽

Phosphoglycerate Kinase ◽

Glycolytic Enzyme ◽

Diauxic Shift ◽

Cellular Processes ◽

Targeted Analysis ◽

Global Mapping ◽

Biochemical Approach ◽

User Friendly

AbstractProtein–metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein–small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/. By interpolating PROMIS with the list of predicted protein–metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.

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Oenological Potential of Autochthonous Saccharomyces cerevisiae Yeast Strains from the Greek Varieties of Agiorgitiko and Moschofilero

Beverages ◽

10.3390/beverages7020027 ◽

2021 ◽

Vol 7 (2) ◽

pp. 27

Author(s):

Dimitrios Kontogiannatos ◽

Vicky Troianou ◽

Maria Dimopoulou ◽

Polydefkis Hatzopoulos ◽

Yorgos Kotseridis

Keyword(s):

Saccharomyces Cerevisiae ◽

Alcoholic Fermentation ◽

Ethanol Tolerance ◽

Random Amplified Polymorphic Dna ◽

Yeast Strains ◽

Rapd Pcr ◽

Autochthonous Yeast ◽

Polymerase Chain ◽

Grape Varieties ◽

H2s Production

Nemea and Mantinia are famous wine regions in Greece known for two indigenous grape varieties, Agiorgitiko and Moschofilero, which produce high quality PDO wines. In the present study, indigenous Saccharomyces cerevisiae yeast strains were isolated and identified from spontaneous alcoholic fermentation of Agiorgitiko and Moschofilero musts in order to evaluate their oenological potential. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) recovered the presence of five distinct profiles from a total of 430 yeast isolates. The five obtained strains were evaluated at microvinifications trials and tested for basic oenological and biochemical parameters including sulphur dioxide and ethanol tolerance as well as H2S production in sterile grape must. The selected autochthonous yeast strains named, Soi2 (Agiorgitiko wine) and L2M (Moschofilero wine), were evaluated also in industrial (4000L) fermentations to assess their sensorial and oenological characteristics. The volatile compounds of the produced wines were determined by GC-FID. Our results demonstrated the feasibility of using Soi2 and L2M strains in industrial fermentations for Agiorgitiko and Moschofilero grape musts, respectively.

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Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Molecular and Cellular Biology ◽

10.1128/mcb.13.11.6866 ◽

1993 ◽

Vol 13 (11) ◽

pp. 6866-6875 ◽

Cited By ~ 20

Author(s):

D C Hagen ◽

L Bruhn ◽

C A Westby ◽

G F Sprague

Keyword(s):

Saccharomyces Cerevisiae ◽

Binding Site ◽

Dna Sequences ◽

Point Mutations ◽

Transcription Activation ◽

Specific Gene ◽

Binding Assays ◽

Weak Binding

Transcription activation of alpha-specific genes in Saccharomyces cerevisiae is regulated by two proteins, MCM1 and alpha 1, which bind to DNA sequences, called P'Q elements, found upstream of alpha-specific genes. Neither MCM1 nor alpha 1 alone binds efficiently to P'Q elements. Together, however, they bind cooperatively in a manner that requires both the P' sequence, which is a weak binding site for MCM1, and the Q sequence, which has been postulated to be the binding site for alpha 1. We analyzed a collection of point mutations in the P'Q element of the STE3 gene to determine the importance of individual base pairs for alpha-specific gene transcription. Within the 10-bp conserved Q sequence, mutations at only three positions strongly affected transcription activation in vivo. These same mutations did not affect the weak binding to P'Q displayed by MCM1 alone. In vitro DNA binding assays showed a direct correlation between the ability of the mutant sequences to form ternary P'Q-MCM1-alpha 1 complexes and the degree to which transcription was activated in vivo. Thus, the ability of alpha 1 and MCM1 to bind cooperatively to P'Q elements is critical for activation of alpha-specific genes. In all natural alpha-specific genes the Q sequence is adjacent to the degenerate side of P'. To test the significance of this geometry, we created several novel juxtapositions of P, P', and Q sequences. When the Q sequence was opposite the degenerate side, the composite QP' element was inactive as a promoter element in vivo and unable to form stable ternary QP'-MCM1-alpha 1 complexes in vitro. We also found that addition of a Q sequence to a strong MCM1 binding site allows the addition of alpha 1 to the complex. This finding, together with the observation that Q-element point mutations affected ternary complex formation but not the weak binding of MCM1 alone, supports the idea that the Q sequence serves as a binding site for alpha 1.

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High cAMP Levels Antagonize the Reprogramming of Gene Expression that Occurs at the Diauxic Shift in Saccharomyces Cerevisiae

Microbiology ◽

10.1099/13500872-142-3-459 ◽

1996 ◽

Vol 142 (3) ◽

pp. 459-467 ◽

Cited By ~ 51

Author(s):

E. Boy-Marcotte ◽

D. Tadi ◽

M. Perrot ◽

H. Boucherie ◽

M. Jacquet

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Diauxic Shift ◽

Camp Levels

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Effects of Lactobacillus plantarum on the ethanol tolerance of Saccharomyces cerevisiae

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11198-x ◽

2021 ◽

Vol 105 (6) ◽

pp. 2597-2611

Author(s):

Xianlin He ◽

Bo Liu ◽

Yali Xu ◽

Ze Chen ◽

Hao Li

Keyword(s):

Saccharomyces Cerevisiae ◽

Lactobacillus Plantarum ◽

Ethanol Tolerance

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SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5829-5842.1993 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5829-5842

Author(s):

P Zheng ◽

D S Fay ◽

J Burton ◽

H Xiao ◽

J L Pinkham ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Dna Damage ◽

Dna Synthesis ◽

Genomic Library ◽

Excision Repair ◽

Low Frequency ◽

S Phase ◽

Upstream Region ◽

Specific Gene

SPK1 was originally discovered in an immunoscreen for tyrosine-protein kinases in Saccharomyces cerevisiae. We have used biochemical and genetic techniques to investigate the function of this gene and its encoded protein. Hybridization of an SPK1 probe to an ordered genomic library showed that SPK1 is adjacent to PEP4 (chromosome XVI L). Sporulation of spk1/+ heterozygotes gave rise to spk1 spores that grew into microcolonies but could not be further propagated. These colonies were greatly enriched for budded cells, especially those with large buds. Similarly, eviction of CEN plasmids bearing SPK1 from cells with a chromosomal SPK1 disruption yielded viable cells with only low frequency. Spk1 protein was identified by immunoprecipitation and immunoblotting. It was associated with protein-Ser, Thr, and Tyr kinase activity in immune complex kinase assays. Spk1 was localized to the nucleus by immunofluorescence. The nucleotide sequence of the SPK1 5' noncoding region revealed that SPK1 contains two MluI cell cycle box elements. These elements confer S-phase-specific transcription to many genes involved in DNA synthesis. Northern (RNA) blotting of synchronized cells verified that the SPK1 transcript is coregulated with other MluI box-regulated genes. The SPK1 upstream region also includes a domain highly homologous to sequences involved in induction of RAD2 and other excision repair genes by agents that induce DNA damage. spk1 strains were hypersensitive to UV irradiation. Taken together, these findings indicate that SPK1 is a dual-specificity (Ser/Thr and Tyr) protein kinase that is essential for viability. The cell cycle-dependent transcription, presence of DNA damage-related sequences, requirement for UV resistance, and nuclear localization of Spk1 all link this gene to a crucial S-phase-specific role, probably as a positive regulator of DNA synthesis.

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Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance

Biotechnology for Biofuels ◽

10.1186/s13068-015-0216-0 ◽

2015 ◽

Vol 8 (1) ◽

pp. 32 ◽

Cited By ~ 63

Author(s):

Tim Snoek ◽

Martina Picca Nicolino ◽

Stefanie Van den Bremt ◽

Stijn Mertens ◽

Veerle Saels ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Large Scale ◽

Ethanol Tolerance ◽

Genome Shuffling ◽

Robot Assisted

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Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1.

Molecular and Cellular Biology ◽

10.1128/mcb.9.11.5228 ◽

1989 ◽

Vol 9 (11) ◽

pp. 5228-5230 ◽

Cited By ~ 54

Author(s):

C A Keleher ◽

S Passmore ◽

A D Johnson

Keyword(s):

Saccharomyces Cerevisiae ◽

Gene Product ◽

Strong Evidence ◽

Regulatory Proteins ◽

Yeast Cells ◽

Specific Gene ◽

Yeast Gene ◽

Yeast Protein ◽

Transcriptional Regulatory

To bring about repression of a family fo genes in Saccharomyces cerevisiae called the a-specific genes, two transcriptional regulatory proteins, alpha 2 and GRM (general regulator of matin type), bind cooperatively to an operator found upstream of each a-specific gene. To date, GRM has been defined only biochemically. In this communication we show that the product of a single yeast gene (MCM1) is sufficient to bind cooperatively with alpha 2 to the operator. We also show that antiserum raised against the MCM1 gene product recognizes GRM from yeast cells. These results, in combination with previous observations, provide strong evidence that MCM1 encodes the GRM activity.

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Identification of a DNA segment that is necessary and sufficient for alpha-specific gene control in Saccharomyces cerevisiae: implications for regulation of alpha-specific and a-specific genes.

Molecular and Cellular Biology ◽

10.1128/mcb.8.1.309 ◽

1988 ◽

Vol 8 (1) ◽

pp. 309-320 ◽

Cited By ~ 40

Author(s):

E E Jarvis ◽

D C Hagen ◽

G F Sprague

Keyword(s):

Saccharomyces Cerevisiae ◽

Binding Site ◽

Transcript Level ◽

Cell Types ◽

Specific Gene ◽

Alpha Cells ◽

Transcription Activator ◽

Noncoding Sequences ◽

Necessary And Sufficient ◽

Activation Sequence

STE3 mRNA is present only in Saccharomyces cerevisiae alpha cells, not in a or a/alpha cells, and the transcript level increases about fivefold when cells are treated with a-factor mating pheromone. Deletions in the 5' noncoding region of STE3 defined a 43-base-pair (bp) upstream activation sequence (UAS) that can impart both modes of regulation to a CYC1-lacZ fusion when substituted for the native CYC1 UAS. UAS activity required the alpha 1 product of MAT alpha, which is known to be required for transcription of alpha-specific genes. A chromosomal deletion that removed only 14 bp of the STE3 UAS reduced STE3 transcript levels 50- to 100-fold, indicating that the UAS is essential for expression. The STE3 UAS shares a 26-bp homology with the 5' noncoding sequences of the only other known alpha-specific genes, MF alpha 1 and MF alpha 2. We view the homology as having two components--a nearly palindromic 16-bp "P box" and an adjacent 10-bp "Q box." A synthetic STE3 P box was inactive as a UAS; a perfect palindrome P box was active in all three cell types. We propose that the P box is the binding site for a transcription activator, but that alpha 1 acting via the Q box is required for this activator to bind to the imperfect P boxes of alpha-specific genes. Versions of the P box are also found upstream of a-specific genes, within the binding sites of the repressor alpha 2 encoded by MAT alpha. Thus, the products of MAT alpha may render gene expression alpha or a-specific by controlling access of the same transcription activator to its binding site, the P box.

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Storage and Condition of Biomass Influence to Biosorption of Lead (II) and Zinc(II) by Saccharomyces cerevisiae Biomass

Indonesian Journal of Chemistry ◽

10.22146/ijc.21955 ◽

2010 ◽

Vol 1 (1) ◽

pp. 11-15

Author(s):

Jasmidi Jasmidi ◽

Eko Sugiharto ◽

Mudjiran Mudjiran

Keyword(s):

Saccharomyces Cerevisiae ◽

Atomic Absorption ◽

Room Temperature ◽

Final Concentration ◽

Biomass Storage ◽

Lead And Zinc ◽

The Difference ◽

Biomass Influence ◽

And Storage ◽

Zinc Storage

The influence of length and condition of Biomass Storage on the biosorption of lead and zinc that present together in a solution by Saccharomyces cerevisiae biomass were studied. In this experiment, variables of length and condition of biomass storage were examined. Concentration of lead and zinc were determined by atomic absorption spectrophotometric (AAS) using air-acetilene as atomizing flame. Loading of lead and zinc on the biomass were determined as the difference between the initial and the final concentration of lead and zinc in the solution. Biosorption of lead and zinc were influenced by condition and storage of the biomass. Storage of biomass in the room temperature for one week cause an increasing uptake. Storage for longer period result in decrease of lead and zinc uptake. Storage of biomass in a freezer up to 2 weeks increased the uptake of lead, but did not influence the uptake of zinc. Storage for longer period decreased the uptake of both of lead and zinc. For all condition the uptake of lead higher than the uptake of zinc by Saccharomyces cerevisiae.

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