Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae

Abstract Background The brewer’s yeast Saccharomyces cerevisiae is exploited in several industrial processes, ranging from food and beverage fermentation to the production of biofuels, pharmaceuticals and complex chemicals. The large genetic and phenotypic diversity within this species offers a formidable natural resource to obtain superior strains, hybrids, and variants. However, most industrially relevant traits in S. cerevisiae strains are controlled by multiple genetic loci. Over the past years, several studies have identified some of these QTLs. However, because these studies only focus on a limited set of traits and often use different techniques and starting strains, a global view of industrially relevant QTLs is still missing. Results Here, we combined the power of 1125 fully sequenced inbred segregants with high-throughput phenotyping methods to identify as many as 678 QTLs across 18 different traits relevant to industrial fermentation processes, including production of ethanol, glycerol, isobutanol, acetic acid, sulfur dioxide, flavor-active esters, as well as resistance to ethanol, acetic acid, sulfite and high osmolarity. We identified and confirmed several variants that are associated with multiple different traits, indicating that many QTLs are pleiotropic. Moreover, we show that both rare and common variants, as well as variants located in coding and non-coding regions all contribute to the phenotypic variation. Conclusions Our findings represent an important step in our understanding of the genetic underpinnings of industrially relevant yeast traits and open new routes to study complex genetics and genetic interactions as well as to engineer novel, superior industrial yeasts. Moreover, the major role of rare variants suggests that there is a plethora of different combinations of mutations that can be explored in genome editing.

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Saccharomyces cerevisiae Fermentation of 28 Barley and 12 Oat Cultivars

Fermentation ◽

10.3390/fermentation7020059 ◽

2021 ◽

Vol 7 (2) ◽

pp. 59

Author(s):

Timothy J. Tse ◽

Daniel J. Wiens ◽

Jianheng Shen ◽

Aaron D. Beattie ◽

Martin J. T. Reaney

Keyword(s):

Saccharomyces Cerevisiae ◽

Acetic Acid ◽

Lactic Acid ◽

Succinic Acid ◽

Alcoholic Fermentation ◽

Ethanol Yield ◽

Cereal Crops ◽

Fermentation Products ◽

Barley Cultivars ◽

Oat Cultivars

As barley and oat production have recently increased in Canada, it has become prudent to investigate these cereal crops as potential feedstocks for alcoholic fermentation. Ethanol and other coproduct yields can vary substantially among fermented feedstocks, which currently consist primarily of wheat and corn. In this study, the liquified mash of milled grains from 28 barley (hulled and hull-less) and 12 oat cultivars were fermented with Saccharomyces cerevisiae to determine concentrations of fermentation products (ethanol, isopropanol, acetic acid, lactic acid, succinic acid, α-glycerylphosphorylcholine (α-GPC), and glycerol). On average, the fermentation of barley produced significantly higher amounts of ethanol, isopropanol, acetic acid, succinic acid, α-GPC, and glycerol than that of oats. The best performing barley cultivars were able to produce up to 78.48 g/L (CDC Clear) ethanol and 1.81 g/L α-GPC (CDC Cowboy). Furthermore, the presence of milled hulls did not impact ethanol yield amongst barley cultivars. Due to its superior ethanol yield compared to oats, barley is a suitable feedstock for ethanol production. In addition, the accumulation of α-GPC could add considerable value to the fermentation of these cereal crops.

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Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae

Cell Death Discovery ◽

10.1038/s41420-020-00392-x ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Francesco Monticolo ◽

Emanuela Palomba ◽

Maria Luisa Chiusano

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Death ◽

Acetic Acid ◽

Programmed Cell Death ◽

Differential Expression ◽

Ribosomal Proteins ◽

Relative Proportion ◽

Duplication Event ◽

Genome Duplication Event ◽

Cell Death Pathway

AbstractProgrammed cell death involves complex molecular pathways in both eukaryotes and prokaryotes. In Escherichia coli, the toxin–antitoxin system (TA-system) has been described as a programmed cell death pathway in which mRNA and ribosome organizations are modified, favoring the production of specific death-related proteins, but also of a minor portion of survival proteins, determining the destiny of the cell population. In the eukaryote Saccharomyces cerevisiae, the ribosome was shown to change its stoichiometry in terms of ribosomal protein content during stress response, affecting the relative proportion between ohnologs, i.e., the couple of paralogs derived by a whole genome duplication event. Here, we confirm the differential expression of ribosomal proteins in yeast also during programmed cell death induced by acetic acid, and we highlight that also in this case pairs of ohnologs are involved. We also show that there are different trends in cytosolic and mitochondrial ribosomal proteins gene expression during the process. Moreover, we show that the exposure to acetic acid induces the differential expression of further genes coding for products related to translation processes and to rRNA post-transcriptional maturation, involving mRNA decapping, affecting translation accuracy, and snoRNA synthesis. Our results suggest that the reprogramming of the overall translation apparatus, including the cytosolic ribosome reorganization, are relevant events in yeast programmed cell death induced by acetic acid.

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Eukaryotic translation factor eIF5A contributes to acetic acid tolerance in Saccharomyces cerevisiae via transcriptional factor Ume6p

Biotechnology for Biofuels ◽

10.1186/s13068-021-01885-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yanfei Cheng ◽

Hui Zhu ◽

Zhengda Du ◽

Xuena Guo ◽

Chenyao Zhou ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Acetic Acid ◽

Adaptive Response ◽

Acid Tolerance ◽

Peptide Bond ◽

Transcriptional Factor ◽

Yeast Cells ◽

Acetic Acid Tolerance ◽

Translation Factor ◽

Industrial Strains

Abstract Background Saccharomyces cerevisiae is well-known as an ideal model system for basic research and important industrial microorganism for biotechnological applications. Acetic acid is an important growth inhibitor that has deleterious effects on both the growth and fermentation performance of yeast cells. Comprehensive understanding of the mechanisms underlying S. cerevisiae adaptive response to acetic acid is always a focus and indispensable for development of robust industrial strains. eIF5A is a specific translation factor that is especially required for the formation of peptide bond between certain residues including proline regarded as poor substrates for slow peptide bond formation. Decrease of eIF5A activity resulted in temperature-sensitive phenotype of yeast, while up-regulation of eIF5A protected transgenic Arabidopsis against high temperature, oxidative or osmotic stress. However, the exact roles and functional mechanisms of eIF5A in stress response are as yet largely unknown. Results In this research, we compared cell growth between the eIF5A overexpressing and the control S. cerevisiae strains under various stressed conditions. Improvement of acetic acid tolerance by enhanced eIF5A activity was observed all in spot assay, growth profiles and survival assay. eIF5A prompts the synthesis of Ume6p, a pleiotropic transcriptional factor containing polyproline motifs, mainly in a translational related way. As a consequence, BEM4, BUD21 and IME4, the direct targets of Ume6p, were up-regulated in eIF5A overexpressing strain, especially under acetic acid stress. Overexpression of UME6 results in similar profiles of cell growth and target genes transcription to eIF5A overexpression, confirming the role of Ume6p and its association between eIF5A and acetic acid tolerance. Conclusion Translation factor eIF5A protects yeast cells against acetic acid challenge by the eIF5A-Ume6p-Bud21p/Ime4p/Bem4p axles, which provides new insights into the molecular mechanisms underlying the adaptive response and tolerance to acetic acid in S. cerevisiae and novel targets for construction of robust industrial strains.

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Examining the effect of mitochondrial DNA variants on blood pressure in two Finnish cohorts

Scientific Reports ◽

10.1038/s41598-020-79931-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jaakko Laaksonen ◽

Pashupati P. Mishra ◽

Ilkka Seppälä ◽

Leo-Pekka Lyytikäinen ◽

Emma Raitoharju ◽

...

Keyword(s):

Blood Pressure ◽

Mitochondrial Dna ◽

Genome Wide Association Study ◽

Rare Variants ◽

Meta Analysis ◽

Noncommunicable Diseases ◽

Nucleotide Polymorphisms ◽

Genetic Determinants ◽

Genome Wide ◽

Mitochondrial Dna Variants

AbstractHigh blood pressure (BP) is a major risk factor for many noncommunicable diseases. The effect of mitochondrial DNA single-nucleotide polymorphisms (mtSNPs) on BP is less known than that of nuclear SNPs. We investigated the mitochondrial genetic determinants of systolic, diastolic, and mean arterial BP. MtSNPs were determined from peripheral blood by sequencing or with genome-wide association study SNP arrays in two independent Finnish cohorts, the Young Finns Study and the Finnish Cardiovascular Study, respectively. In total, over 4200 individuals were included. The effects of individual common mtSNPs, with an additional focus on sex-specificity, and aggregates of rare mtSNPs grouped by mitochondrial genes were evaluated by meta-analysis of linear regression and a sequence kernel association test, respectively. We accounted for the predicted pathogenicity of the rare variants within protein-encoding and the tRNA regions. In the meta-analysis of 87 common mtSNPs, we did not observe significant associations with any of the BP traits. Sex-specific and rare-variant analyses did not pinpoint any significant associations either. Our results are in agreement with several previous studies suggesting that mtDNA variation does not have a significant role in the regulation of BP. Future studies might need to reconsider the mechanisms thought to link mtDNA with hypertension.

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Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.1.6.535-543.1981 ◽

1981 ◽

Vol 1 (6) ◽

pp. 535-543

Author(s):

G B Kiss ◽

A A Amin ◽

R E Pearlman

Keyword(s):

Saccharomyces Cerevisiae ◽

High Frequency ◽

Deoxyribonucleic Acid ◽

Tetrahymena Thermophila ◽

The Other ◽

Yeast Cells ◽

Origin Of Replication ◽

Autonomous Replication ◽

Coding Regions ◽

Dna Fragment

Plasmids containing the nontranscribed central and terminal, but not the coding, regions of the extrachromosomal ribosomal deoxyribonucleic acid (rDNA) of Tetrahymena thermophila are capable of autonomous replication in Saccharomyces cerevisiae. These plasmids transform S. cerevisiae at high frequency; transformants are unstable in the absence of selection, and plasmids identical to those used for transformation were isolated from the transformed yeast cells. One plasmid contains a 1.85-kilobase Tetrahymena DNA fragment which includes the origin of bidirectional replication of the extrachromosomal rDNA. The other region of Tetrahymena rDNA allowing autonomous replication of plasmids in S. cerevisiae is a 650-base pair, adenine plus thymine-rich segment from the rDNA terminus. Neither of these Tetrahymena fragments shares obvious sequence homology with the origin of replication of the S. cerevisiae 2-microns circle plasmid or with ars1, an S. cerevisiae chromosomal replicator.

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Isolation and transcriptional characterization of three genes which function at start, the controlling event of the Saccharomyces cerevisiae cell division cycle: CDC36, CDC37, and CDC39

Molecular and Cellular Biology ◽

10.1128/mcb.3.5.881-891.1983 ◽

1983 ◽

Vol 3 (5) ◽

pp. 881-891

Author(s):

H J Breter ◽

J Ferguson ◽

T A Peterson ◽

S I Reed

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Division ◽

Dna Sequences ◽

Shuttle Vector ◽

Control Process ◽

Haploid Cell ◽

Loop Analysis ◽

Mrna Species ◽

Coding Regions ◽

Plasmid Library

The genes CDC36, CDC37, and CDC39, thought to function in the cell division control process in Saccharomyces cerevisiae, were isolated from a recombinant plasmid library prepared by partial digestion of S. cerevisiae genomic DNA with Sau3A and insertion into the S. cerevisiae-Escherichia coli shuttle vector YRp7. In each case, S. cerevisiae DNA sequences were identified which could complement mutant alleles of the gene in question and which could direct integration of a plasmid at the chromosomal location known to correspond to that gene. Complementing DNA segments were subcloned to remove extraneous coding regions. The coding regions corresponding to CDC36, CDC37, and CDC39 were then identified and localized by R-loop analysis. The estimated sizes of the three coding regions were 615, 1,400, and 2,700 base pairs, respectively. Transcriptional orientation of the coding regions was established by using M13 vectors to prepare strand-specific probes followed by hybridization to blots of electrophoresed S. cerevisiae mRNA. The intracellular steady-state abundance of the mRNA species corresponding to the genes was estimated by comparing hybridization signals on RNA blots to that of a previously determined standard, the cell cycle start gene CDC28. The quantities calculated for the three mRNA species were low, ranging from 1.5 +/- 1 copies per haploid cell for the CDC36 mRNA to 3.1 +/- 1.5 and 4.6 +/- 2 copies per haploid cell for the CDC37 and CDC39 mRNAs, respectively. The CDC28 mRNA had been previously estimated at 7.0 +/- 2 copies per cell.

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Fabrication of TiO2/Carbon Photocatalyst using Submerged DC Arc Discharged in Ethanol/Acetic Acid Medium

IOP Conference Series Materials Science and Engineering ◽

10.1088/1757-899x/202/1/012058 ◽

2017 ◽

Vol 202 ◽

pp. 012058 ◽

Cited By ~ 1

Author(s):

T E Saraswati ◽

A O Nandika ◽

I F Andhika ◽

Patiha ◽

C Purnawan ◽

...

Keyword(s):

Acetic Acid ◽

Acid Medium ◽

Acetic Acid Medium ◽

Ethanol Acetic Acid ◽

Dc Arc

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Cytochrome c Trp65Ser substitution results in inhibition of acetic acid-induced programmed cell death in Saccharomyces cerevisiae

Mitochondrion ◽

10.1016/j.mito.2011.08.007 ◽

2011 ◽

Vol 11 (6) ◽

pp. 987-991 ◽

Cited By ~ 5

Author(s):

Nicoletta Guaragnella ◽

Salvatore Passarella ◽

Ersilia Marra ◽

Sergio Giannattasio

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Death ◽

Acetic Acid ◽

Cytochrome C ◽

Programmed Cell Death

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Characteristics of Piperine Solubility in Multiple Solvent

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.236-238.2495 ◽

2011 ◽

Vol 236-238 ◽

pp. 2495-2498 ◽

Cited By ~ 2

Author(s):

Xue Song Huang ◽

Xian Zhe Lin ◽

Mo Ting Guo ◽

Ya Zou

Keyword(s):

Experimental Data ◽

High Performance Liquid Chromatography ◽

Acetic Acid ◽

High Performance ◽

Authentic Sample ◽

Allometric Model ◽

Experiment Data ◽

Reverse Phase ◽

Ethanol Acetic Acid ◽

Acetic Acid Water

The solution of piperine in multiple solvent including ethanol, acetic acid, water and HCl were investigated to extract more piperine from piper fruit. Piperine was determined by reverse phase high-performance liquid chromatography with Diamonsil column (C18,5 μm ,250 mm×4. 6 mm) at 343 nm. Experiment data were simulated by Allometric model and the formula is Z=0.9+ 4.54×10-10×x5.675+1.8029×y2.12848+2.37×10-10×x5.675×y2.12848(Z:sample solution,mol/mL,x: the percentage of ethanol’s volume, ml/100mL,y: the acetic acid in the authentic sample solution, g/100mL), the adj·R2=0.997, the comparative deviation less than 2%. These results are good in agreement with experimental data. It reveals that the model can meet the requirements of the selection and design in extracting piperine from piper fruit.

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