DGBY

2014/10/20

WebSite: http://www.naro.affrc.go.jp/org/nfri/english/Useful/yeast/index.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/dgby

This database compiles the transcriptomics and phenomics data about the stress tolerance of baker's yeast.

README Content

1. Database Component
2. Data Description
3. License
4. Update History
5. Literature
6. Contact address

1. Database Component

1. README
2. Experiments List
3. Transcriptome data - Initial stage of dough fermentation
4. Transcriptome data - High-sugar stressL
5. Transcriptome data - Air-drying stress
6. Phenome data - High-sugar stress
7. Phenome data - Freeze-thaw stress
8. Phenome data - Air-drying stresss

2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "DGBY" data.
File	README_e.html(English)

2.2 Experiments list

Data name	Experiments list
Description of data contents	Published experimental data
File	dgby_main_en.zip (1KB)

Data items are the following:

Data item	Description
Data file (Excel)	Name of data file in Excel format
Simple search	Table in the simple search site
Reference (PubMed)	PubMed ID of reference

2.3 Transcriptome data - Initial stage of dough fermentation

Data name	Transcriptome data - Initial stage of dough fermentation
Description of data contents	Gene expression profiles of baker's yeast during initial dough-fermentation were investigated using liquid fermentation (LF) media to obtain insights at the molecular level into rapid adaptation mechanisms of baker's yeast. Results showed the onset of fermentation caused drastic changes in gene expression profiles within 15 min. Genes involved in the tricarboxylic acid (TCA) cycle were downregulated and genes involved in glycolysis were upregulated, indicating a metabolic shift from respiration to fermentation. Genes involved in ethanol production (PDC genes and ADH1), in glycerol synthesis (GPD1 and HOR2), and in low-affinity hexose transporters (HXT1 and HXT3) were upregulated at the beginning of model dough-fermentation. Among genes upregulated at 15 min, several genes classified as transcription were downregulated within 30 min. These down-regulated genes are involved in messenger RNA splicing and ribosomal protein biogenesis and in transcriptional regulator (SRB8, MIG1). In contrast, genes involved in amino acid metabolism and in vitamin metabolism, such as arginine biosynthesis, riboflavin biosynthesis, and thiamin biosynthesis, were subsequently upregulated after 30 min. Interestingly, the genes involved in the unfolded protein response (UPR) pathway were also subsequently upregulated. Our study presents the first overall description of the transcriptional response of baker's yeast during dough-fermentation, and will thus help clarify genomic responses to various stresses during commercial fermentation processes.
File	GEO Accession No: GSE3043

2.4 Transcriptome data - High-sugar stress

Data name	Transcriptome data - Initial stage of dough fermentation
Description of data contents	In the modern baking industry, high-sucrose-tolerant (HS) and maltose-utilizing (LS) yeast were developed using breeding techniques and are now used commercially. Sugar utilization and high-sucrose tolerance differ significantly between HS and LS yeasts. We analyzed the gene expression profiles of HS and LS yeasts under different sucrose conditions in order to determine their basic physiology. Two-way hierarchical clustering was performed to obtain the overall patterns of gene expression. The clustering clearly showed that the gene expression patterns of LS yeast differed from those of HS yeast. Quality threshold clustering was used to identify the gene clusters containing upregulated genes (cluster 1) and downregulated genes (cluster 2) under high-sucrose conditions. Clusters 1 and 2 contained numerous genes involved in carbon and nitrogen metabolism, respectively. The expression level of the genes involved in the metabolism of glycerol and trehalose, which are known to be osmoprotectants, in LS yeast was higher than that in HS yeast under sucrose concentrations of 5-40%. No clear correlation was found between the expression level of the genes involved in the biosynthesis of the osmoprotectants and the intracellular contents of the osmoprotectants. The current gene expression data were compared with data previously reported in a comprehensive analysis of a gene deletion strain collection. Welch's t-test for this comparison showed that the relative growth rates of the deletion strains whose deletion occurred in genes belonging to cluster 1 were significantly higher than the average growth rates of all deletion strains.
File	GEO Accession No: GSE4295 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4295)

2.5 Transcriptome data - Air-drying stress

Data name	Transcriptome data - Air-drying stress
Description of data contents	Changes in the gene expression of commercial baker’s yeast during an air-drying process, which simulated dried yeast production, were analyzed. K-means clustering suggested that the genes involved in protein folding were transiently upregulated at early stages, and that the genes involved in fatty acid metabolism were continuously upregulated.
File	GEO Accession No: GSE6454

2.6 Phenome data - High-sugar stress

Data name	Phenome data - High-sugar stress
Description of data contents	Yeasts used in bread making are exposed to high concentrations of sucrose during sweet dough fermentation. Despite its importance, tolerance to high-sucrose stress is poorly understood at the gene level. To clarify the genes required for tolerance to high-sucrose stress, genome-wide screening was undertaken using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 273 deletions that yielded high sucrose sensitivity, approximately 20 of which were previously uncharacterized. These 273 deleted genes were classified based on their cellular function and localization of their gene products. Cross-sensitivity of the high-sucrose-sensitive mutants to high concentrations of NaCl and sorbitol was studied. Among the 273 sucrose-sensitive deletion mutants, 269 showed cross-sensitivities to sorbitol or NaCl, and four (i.e. ade5,7, ade6, ade8, and pde2) were specifically sensitive to high sucrose. The general stress response pathways via high-osmolarity glycerol and stress response element pathways and the function of the invertase in the ade mutants were similar to those in the wild-type strain. In the presence of high-sucrose stress, intracellular contents of ATP in ade mutants were at least twofold lower than that of the wild-type cells, suggesting that depletion of ATP is a factor in sensitivity to high-sucrose stress. The genes identified in this study might be important for tolerance to high-sucrose stress, and therefore should be target genes in future research into molecular modification for breeding of yeast tolerant to high-sucrose stress.
File	CSV: dbgy_high_sugar_stress.zip (90KB) Original File(Excel): High-sugar stress.xls (674KB)

Data items are the following:

Data item	Description
ORF	Systematic Name in SGD（Saccharomyces Genome Database；http://www.yeastgenome.org/)
GENE	Standard Gene Name in SGD
Growth rate YM/YW	Rate of growth in YPD medium (Mutant/Wild-type）
Growth rate SM/SW	Rate of growth in YPD medium containing 30% sucrose (Mutant/Wild-type）
DESCRIPTION (MIPS)	Description in MIPS（Munich Information Center for Protein Sequences）

2.7 Phenome data - Freeze-thaw stress

Data name	Phenome data - Freeze-thaw stress
Description of data contents	Yeasts used in bread making are exposed to freeze-thaw stress during frozen-dough baking. To clarify the genes required for freeze-thaw tolerance, genome-wide screening was performed using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 58 gene deletions that conferred freeze-thaw sensitivity. These genes were then classified based on their cellular function and on the localization of their products. The results showed that the genes required for freeze-thaw tolerance were frequently involved in vacuole functions and cell wall biogenesis. The highest numbers of gene products were components of vacuolar H+-ATPase. Next, the cross-sensitivity of the freeze-thaw-sensitive mutants to oxidative stress and to cell wall stress was studied; both of these are environmental stresses closely related to freeze-thaw stress. The results showed that defects in the functions of vacuolar H+-ATPase conferred sensitivity to oxidative stress and to cell wall stress. In contrast, defects in gene products involved in cell wall assembly conferred sensitivity to cell wall stress but not to oxidative stress. Our results suggest the presence of at least two different mechanisms of freeze-thaw injury: oxidative stress generated during the freeze-thaw process, and defects in cell wall assembly.
File	CSV: dgby_freeze_thaw_stress.zip (88KB) Original File(Excel): Freeze-thaw stress.xls (676KB)

Data items are the following:

Data item	Description
ORF	Systematic Name in SGD（Saccharomyces Genome Database；http://www.yeastgenome.org/）
GENE	Standard Gene Name in SGD
Growth rate BM/BW	Rate of growth in non-strees condition （Mutant/Wild-type）
Growth rate (AM/AW)/(BM/BW)	AM/AW represents rate of growth after exposure to freeze-thaw strees (Mutant/Wild-type), (AM/AW)/(BM/BW) represents rate of AM/AW to BM/BW
DESCRIPTION (MIPS)	Description in MIPS（Munich Information Center for Protein Sequences）

2.8 Phenome data - Air-drying stress

Data name	Phenome data - Air-drying stress
Description of data contents	Yeasts used in bread making are exposed to air-drying stress during dried yeast production processes. To clarify the genes required for air-drying tolerance, we performed genome-wide screening using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 278 gene deletions responsible for air-drying sensitivity. These genes were classified based on their cellular function and on the localization of their gene products. The results showed that the genes required for air-drying tolerance were frequently involved in mitochondrial functions and in connection with vacuolar H+-ATPase, which plays a role in vacuolar acidification. To determine the role of vacuolar acidification in air-drying stress tolerance, we monitored intracellular pH. The results showed that intracellular acidification was induced during air-drying and that this acidification was amplified in a deletion mutant of the VMA2 gene encoding a component of vacuolar H+-ATPase, suggesting that vacuolar H+-ATPase helps maintain intracellular pH homeostasis, which is affected by air-drying stress. To determine the effects of air-drying stress on mitochondria, we analyzed the mitochondrial membrane potential under air-drying stress conditions using MitoTracker. The results showed that mitochondria were extremely sensitive to air-drying stress, suggesting that a mitochondrial function is required for tolerance to air-drying stress. We also analyzed the correlation between oxidative-stress sensitivity and air-drying-stress sensitivity. The results suggested that oxidative stress is a critical determinant of sensitivity to air-drying stress, although ROS-scavenging systems are not necessary for air-drying stress tolerance.
File	CSV: dgby_air_drying_stress.zip (89KB) Original File(Excel): Air-drying stress.xls (676KB)

Data items are the following:

Data item	Description
ORF	Systematic Name in SGD (Saccharomyces Genome Database；http://www.yeastgenome.org/)
GENE	Standard Gene Name in SGD
Growth rate BM/BW	Rate of growth in non-stress condition (Mutant/Wild-type)
Growth rate (DM/DW)/(BM/BW)	DM/DW represents rate of growth after exposure to air-drying stress (Mutant/Wild-type). (DM/DW)/(BM/BW) represents rate of DM/DW to BM/BW.
DESCRIPTION (MIPS)	Description in MIPS（Munich Information Center for Protein Sequences)

3. License

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

4. Update History

Date	Update contents
2014/10/20	The URL of the portal site is changed.
2012/05/09	"Database maintenance site" and "URL of the original website" are updated.
2012/04/17	Expression of attribution in License is updated.
2012/03/08	DGBY english archive site is opened.
2006/10/02	DGBY(Database for Gene function and expression of Baker's Yeast) (http://nfri.naro.affrc.go.jp/yakudachi/yeast/index.html) is opened.

5. Literature

Tanaka F, Ando A, Nakamura T, Takagi H, Shima J.
Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation.
Food Microbiol. 2006 Dec;23(8):717-28. Epub 2006 Apr 4.
PMID: 16943074

Tanaka-Tsuno F, Mizukami-Murata S, Murata Y, Nakamura T, Ando A, Takagi H, Shima J.
Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions.
Yeast. 2007 Oct;24(10):901-11.
PMID: 17724779

Nakamura T, Mizukami-Murata S, Ando A, Murata Y, Takagi H, Shima J.
Changes in gene expression of commercial baker's yeast during an air-drying process that simulates dried yeast production.
J Biosci Bioeng. 2008 Oct;106(4):405-8.
PMID: 19000619

Ando A, Tanaka F, Murata Y, Takagi H, Shima J.
Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae.
FEMS Yeast Res. 2006 Mar;6(2):249-67.
PMID: 16487347

Ando A, Nakamura T, Murata Y, Takagi H, Shima J.
Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.
FEMS Yeast Res. 2007 Mar;7(2):244-53. Epub 2006 Sep 21.
PMID: 16989656

Shima J, Ando A, Takagi H.
Possible roles of vacuolar H+-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.
Yeast. 2008 Mar;25(3):179-90.
PMID: 18224659

6. Contact address

When you have any question about "DGBY", contact the following:

National Food Research Institute, National Agriculture and Food Research Organization (NARO)
2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan
Akira Ando
TEL: +81-29-838-8066
E-mail: aando[at]affrc[dot]go[dot]jp