Unknown,Transcriptomics,Genomics,Proteomics

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Whole Genome Analysis of the Heat Stress Response in Commercial Baker's Yeast (Saccharomyces cerevisiae) with Comparative Statistical Approaches

ABSTRACT: Environmental conditions are quite eﬀective during propagation and industrial application of Baker’s yeast (Saccharomyces cerevisiae). The change of temperature is one of the most important conditions which aﬀects the dough-leaving capacity of yeast cells. Accordingly, heat changes play an essential role in the commercial and economic impact of the yeast. Recent technologies in genomics have been used for analysis of global gene expression proﬁles such as microarray and RNA sequencing to solve the problems related with industrial application of yeast. Hereby, the aim of this study is to explore the eﬀects of heat stresses on global gene expression proﬁles and to identify the candidate genes for the heat stress response in commercial baker’s yeast by using microarray technology and comparative statistical data analyses. Data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis of this dataset, all required statistical methods are performed comparatively in each step and the best performed ones are used in further computations. Hence, as the ﬁrst step of the analyses, diﬀerent background normalization algorithms such as MAS5.0, RMA, MBEI and GC-RMA were applied and the algorithm which gives the most accurate ﬁndings was chosen for the normalization procedure. As a result, expression values, computed from CEL ﬁles, were processed by Robust Multiarray Analysis (RMA) which is the selected procedure for the normalization of the systematic diﬀerences between samples. In order to determine diﬀerentially expressed genes under heat stress treatments, two diﬀerent methods, namely, the fold-change and the hypothesis testing approaches are executed. In the fold-change method, various cut-oﬀ values are implemented while diﬀerent multiple testing procedures are performed for the hypothesis testing. Under the heat shock and temperature-shift stress conditions, up/down regulated diﬀerentially expressed probes were functionally categorized into the diﬀerent groups via the cluster analyses. Transcriptome changes under the heat shock and temperature-shift stress treatments show that the number of diﬀerentially up-regulated genes among the heat shock proteins (HSPs) and transcription factors (TFs) changed signiﬁcantly. Consequently, the identiﬁcation of thousands of genes related with heat stress treatments via microarray technology and comparative statistical analysis resulted in the creation of big picture which provides the understanding of the importance for the baker’s yeast industrial applications.

ORGANISM(S): Saccharomyces cerevisiae S288c

SUBMITTER: Duygu Varol

PROVIDER: E-MTAB-3459 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Second fermentation in a bottle supposes such specific conditions that undergo yeasts to a set of stress situations like high ethanol, low nitrogen, low pH or sub-optimal temperature. Also, yeast have to grow until 1 or 2 generations and ferment all sugar available while they resist increasing CO2 pressure produced along with fermentation. Because of this, yeast for second fermentation must be selected depending on different technological criteria such as resistance to ethanol, pressure, high flocculation capacity, and good autolytic and foaming properties. All of these stress factors appear sequentially or simultaneously, and their superposition could amplify their inhibitory effects over yeast growth. Considering all of the above, it has supposed interesting to characterize the adaptive response of commercial yeast strain EC1118 during second-fermentation experiments under oenological/industrial conditions by transcriptomic profiling. We have pointed ethanol as the most relevant environmental condition in the induction of genes involved in respiratory metabolism, oxidative stress, autophagy, vacuolar and peroxisomal function, after comparison between time-course transcriptomic analysis in alcoholic fermentation and transcriptomic profiling in second fermentation. Other examples of parallelism include overexpression of cellular homeostasis and sugar metabolism genes. Finally, this study brings out the role of low-temperature on yeast physiology during second-fermentation. S. cerevisiae EC1118 pre-adapted to ethanol cells and sucrose (20 g/L) were added to 20 L of base wine (Cavas Freixenet, Sant Sadurní D’Anoia, Spain). Complete volume was bottled with 350 mL each one. All were sealed and incubated in static conditions at 16ºC for approximately 40 days after tirage. Three samples were taken during the process for transcriptional study of the physiological adaptation of yeast cells to industrial second fermentation conditions. A sample corresponding to exponential-growth phase under unstressed conditions (in YPD at 28ºC) was used as an external reference. Three timepoints from second-fermentation were monitored and three biological replicates from each timepoint were analyzed.

Dataset Information

Whole Genome Analysis of the Heat Stress Response in Commercial Baker's Yeast (Saccharomyces cerevisiae) with Comparative Statistical Approaches

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