Small‐scale hypoxic cultures for monitoring the spatial reorganization of glycolytic enzymes in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Yuki Yoshimura ◽  
Reina Hirayama ◽  
Natsuko Miura ◽  
Ryotaro Utsumi ◽  
Kouichi Kuroda ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Glycolytic Enzymes ◽  
Small Scale ◽  
Spatial Reorganization

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Influence of media composition and temperature on volatile aroma production by various wine yeast strains

2008 ◽  
Vol 26 (No. 5) ◽  
pp. 376-382 ◽  
Author(s):  
V. Petravić Tominac ◽  
K. Kovačević Ganić ◽  
D. Komes ◽  
L. Gracin ◽  
M. Banović ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Synthetic Medium ◽  
Aroma Compounds ◽  
Small Scale ◽  
Wine Yeasts ◽  
Wine Production ◽  
Yeast Strains ◽  
Aroma Production ◽  
Volatile Aroma ◽  
Volatile Aroma Compounds

Volatile aroma compounds production by two autochthonous <I>Saccharomyces cerevisiae</I> strains, isolated from Istria region, and three other yeast strains (<I>Saccharomyces bayanus</I> and two commercial <I>Saccharomyces cerevisiae</I> wine yeasts) was investigated on a small scale using synthetic VP4 medium and Graševina must at 12 and 20°C. The results obtained by gas chromatography analyses were compared with the aroma production properties of the native microflora, remaining after Graševina must sulphiting. In both media and at both temperatures, the wine yeasts investigated showed different metabolic profiles regarding the tested volatile aroma compounds, which should be taken in consideration for autochthonous wine production. Although the synthetic medium proved to be appropriate for the investigation of the fermentative properties, the determination of secondary aroma production by wine yeasts has to be conducted by must fermentation or possibly by fermentation of another synthetic medium whose composition would be more similar to must.

scholarly journals The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

PLoS Genetics ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. e1003176 ◽  
Author(s):  
Mario A. Fares ◽  
Orla M. Keane ◽  
Christina Toft ◽  
Lorenzo Carretero-Paulet ◽  
Gary W. Jones
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Small Scale ◽  
Functional Specialization ◽  
Whole Genome

scholarly journals The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae

2021 ◽  
Vol 22 (22) ◽  
pp. 12293
Author(s):  
Florian Mattenberger ◽  
Mario A. Fares ◽  
Christina Toft ◽  
Beatriz Sabater-Muñoz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Molecular Mechanisms ◽  
Functional Divergence ◽  
Small Scale ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Acidic Stress ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transcriptomic Response

The cell central metabolism has been shaped throughout evolutionary times when facing challenges from the availability of resources. In the budding yeast, Saccharomyces cerevisiae, a set of duplicated genes originating from an ancestral whole-genome and several coetaneous small-scale duplication events drive energy transfer through glucose metabolism as the main carbon source either by fermentation or respiration. These duplicates (~a third of the genome) have been dated back to approximately 100 MY, allowing for enough evolutionary time to diverge in both sequence and function. Gene duplication has been proposed as a molecular mechanism of biological innovation, maintaining balance between mutational robustness and evolvability of the system. However, some questions concerning the molecular mechanisms behind duplicated genes transcriptional plasticity and functional divergence remain unresolved. In this work we challenged S. cerevisiae to the use of lactic acid/lactate as the sole carbon source and performed a small adaptive laboratory evolution to this non-fermentative carbon source, determining phenotypic and transcriptomic changes. We observed growth adaptation to acidic stress, by reduction of growth rate and increase in biomass production, while the transcriptomic response was mainly driven by repression of the whole-genome duplicates, those implied in glycolysis and overexpression of ROS response. The contribution of several duplicated pairs to this carbon source switch and acidic stress is also discussed.

scholarly journals A novel AST2 mutation generated upon whole-genome transformation of Saccharomyces cerevisiae confers high tolerance to 5-Hydroxymethylfurfural (HMF) and other inhibitors

PLoS Genetics ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. e1009826
Author(s):  
Gert Vanmarcke ◽  
Quinten Deparis ◽  
Ward Vanthienen ◽  
Arne Peetermans ◽  
Maria R. Foulquié-Moreno ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lignocellulosic Biomass ◽  
Causative Mutation ◽  
Small Scale ◽  
Whole Genome ◽  
Biomass Hydrolysis ◽  
Inhibitor Tolerance ◽  
Cell Factories ◽  
Biomass Hydrolysates

Development of cell factories for conversion of lignocellulosic biomass hydrolysates into biofuels or bio-based chemicals faces major challenges, including the presence of inhibitory chemicals derived from biomass hydrolysis or pretreatment. Extensive screening of 2526 Saccharomyces cerevisiae strains and 17 non-conventional yeast species identified a Candida glabrata strain as the most 5-hydroxymethylfurfural (HMF) tolerant. Whole-genome (WG) transformation of the second-generation industrial S. cerevisiae strain MD4 with genomic DNA from C. glabrata, but not from non-tolerant strains, allowed selection of stable transformants in the presence of HMF. Transformant GVM0 showed the highest HMF tolerance for growth on plates and in small-scale fermentations. Comparison of the WG sequence of MD4 and GVM1, a diploid segregant of GVM0 with similarly high HMF tolerance, surprisingly revealed only nine non-synonymous SNPs, of which none were present in the C. glabrata genome. Reciprocal hemizygosity analysis in diploid strain GVM1 revealed AST2N406I as the only causative mutation. This novel SNP improved tolerance to HMF, furfural and other inhibitors, when introduced in different yeast genetic backgrounds and both in synthetic media and lignocellulose hydrolysates. It stimulated disappearance of HMF and furfural from the medium and enhanced in vitro furfural NADH-dependent reducing activity. The corresponding mutation present in AST1 (i.e. AST1D405I) the paralog gene of AST2, also improved inhibitor tolerance but only in combination with AST2N406I and in presence of high inhibitor concentrations. Our work provides a powerful genetic tool to improve yeast inhibitor tolerance in lignocellulosic biomass hydrolysates and other inhibitor-rich industrial media, and it has revealed for the first time a clear function for Ast2 and Ast1 in inhibitor tolerance.

scholarly journals Gcn5p and Ubp8p Affect Protein Ubiquitylation and Cell Proliferation by Altering the Fermentative/Respiratory Flux Balance in Saccharomyces cerevisiae

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Antonella De Palma ◽  
Giulia Fanelli ◽  
Elisabetta Cretella ◽  
Veronica De Luca ◽  
Raffaele Antonio Palladino ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Glucose Consumption ◽  
Redox Balance ◽  
Glycolytic Enzymes ◽  
Glycolytic Flux ◽  
Direct Role ◽  
Content Type ◽  
Proteomic Approach ◽  
Altered Glucose

ABSTRACT Protein ubiquitylation regulates not only endocellular trafficking and proteasomal degradation but also the catalytic activity of enzymes. In Saccharomyces cerevisiae, we analyzed the composition of the ubiquitylated proteomes in strains lacking acetyltransferase Gcn5p, Ub-protease Ubp8p, or both to understand their involvement in the regulation of protein ubiquitylation. We analyzed His6Ub proteins with a proteomic approach coupling micro-liquid chromatography and tandem mass spectrometry (μLC-MS/MS) in gcn5Δ, ubp8Δ and ubp8Δ gcn5Δ strains. The Ub-proteome altered in the absence of Gcn5p, Ubp8p, or both was characterized, showing that 43% of the proteins was shared in all strains, suggesting their functional relationship. Remarkably, all major glycolytic enzymes showed increased ubiquitylation. Phosphofructokinase 1, the key enzyme of glycolytic flux, showed a higher and altered pattern of ubiquitylation in gcn5Δ and ubp8Δ strains. Severe defects of growth in poor sugar and altered glucose consumption confirmed a direct role of Gcn5p and Ubp8p in affecting the REDOX balance of the cell. IMPORTANCE We propose a study showing a novel role of Gcn5p and Ubp8p in the process of ubiquitylation of the yeast proteome which includes main glycolytic enzymes. Interestingly, in the absence of Gcn5p and Ubp8p glucose consumption and redox balance were altered in yeast. We believe that these results and the role of Gcn5p and Ubp8p in sugar metabolism might open new perspectives of research leading to novel protocols for counteracting the enhanced glycolysis in tumors.

scholarly journals A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism

2015 ◽  
Vol 14 (8) ◽  
pp. 804-816 ◽  
Author(s):  
Daniel Solis-Escalante ◽  
Niels G. A. Kuijpers ◽  
Nuria Barrajon-Simancas ◽  
Marcel van den Broek ◽  
Jack T. Pronk ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Systems Approach ◽  
Gene Dosage ◽  
Physiological Role ◽  
Industrial Applications ◽  
Yeast Genome ◽  
Small Scale ◽  
Genetic Redundancy ◽  
Minimal Set ◽  
Content Type

ABSTRACTAs a result of ancestral whole-genome and small-scale duplication events, the genomes ofSaccharomyces cerevisiaeand many eukaryotes still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In ancestors of theSaccharomyceslineage, the duplication of glycolytic genes is purported to have played an important role leading toS. cerevisiae's current lifestyle favoring fermentative metabolism even in the presence of oxygen and characterized by a high glycolytic capacity. In modernS. cerevisiaestrains, the 12 glycolytic reactions leading to the biochemical conversion from glucose to ethanol are encoded by 27 paralogs. In order to experimentally explore the physiological role of this genetic redundancy, a yeast strain with a minimal set of 14 paralogs was constructed (the “minimal glycolysis” [MG] strain). Remarkably, a combination of a quantitative systems approach and semiquantitative analysis in a wide array of growth environments revealed the absence of a phenotypic response to the cumulative deletion of 13 glycolytic paralogs. This observation indicates that duplication of glycolytic genes is not a prerequisite for achieving the high glycolytic fluxes and fermentative capacities that are characteristic ofS. cerevisiaeand essential for many of its industrial applications and argues against gene dosage effects as a means of fixing minor glycolytic paralogs in the yeast genome. The MG strain was carefully designed and constructed to provide a robust prototrophic platform for quantitative studies and has been made available to the scientific community.

scholarly journals Saccharomyces Cerevisiae Glycolytic Enzymes are Stabilized by Association with Actin

2011 ◽  
Vol 100 (3) ◽  
pp. 301a
Author(s):  
Daniela Araiza ◽  
Olivera Toro ◽  
Armando Zepeda Bastida ◽  
Adela Mújica Miranda ◽  
Salvador Uribe Carvajal
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Glycolytic Enzymes

scholarly journals Evaluating and engineering Saccharomyces cerevisiae promoters for increased amylase expression and bioethanol production from raw starch

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
Marthinus W Myburgh ◽  
Shaunita H Rose ◽  
Marinda Viljoen-Bloom
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Corn Starch ◽  
Consolidated Bioprocessing ◽  
Ethanol Yield ◽  
Small Scale ◽  
Bioethanol Production ◽  
Raw Starch ◽  
Broken Rice ◽  
Available Carbon ◽  
Theoretical Ethanol Yield

ABSTRACT Bioethanol production from starchy biomass via consolidated bioprocessing (CBP) will benefit from amylolytic Saccharomyces cerevisiae strains that produce high levels of recombinant amylases. This could be achieved by using strong promoters and modification thereof to improve gene expression under industrial conditions. This study evaluated eight endogenous S. cerevisiae promoters for the expression of a starch-hydrolysing α-amylase gene. A total of six of the native promoters were modified to contain a promoter-proximal intron directly downstream of the full-length promoter. Varying results were obtained; four native promoters outperformed the ENO1P benchmark under aerobic conditions and two promoters showed better expression under simulated CBP conditions. The addition of the RPS25A intron significantly improved the expression from most promoters, displaying increased transcript levels, protein concentrations and amylase activities. Raw starch-utilising strains were constructed through co-expression of selected α-amylase cassettes and a glucoamylase gene. The amylolytic strains displayed improved fermentation vigour on raw corn starch and broken rice, reaching 97% of the theoretical ethanol yield and converting 100% of the available carbon to products within 120 h in small-scale CBP fermentations on broken rice. This study showed that enhanced amylolytic strains for the conversion of raw starch to ethanol can be achieved through turnkey promoter selection and/or engineering.

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