RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions

ABSTRACT The response of Saccharomyces cerevisiae to cocultivation with Lachancea thermotolerans during alcoholic fermentations has been investigated using tandem mass tag (TMT)-based proteomics. At two key time-points, S. cerevisiae was sorted from single S. cerevisiae fermentations and from mixed fermentations using flow cytometry sorting. Results showed that the purity of sorted S. cerevisiae was above 96% throughout the whole mixed-culture fermentation, thereby validating our sorting methodology. By comparing protein expression of S. cerevisiae with and without L. thermotolerans, 26 proteins were identified as significantly regulated proteins at the early death phase (T1), and 32 significantly regulated proteins were identified at the late death phase (T2) of L. thermotolerans in mixed cultures. At T1, proteins involved in endocytosis, increasing nutrient availability, cell rescue and resistance to stresses were upregulated, and proteins involved in proline synthesis and apoptosis were downregulated. At T2, proteins involved in protein synthesis and stress responses were up- and downregulated, respectively. These data indicate that S. cerevisiae was stressed by the presence of L. thermotolerans at T1, using both defensive and fighting strategies to keep itself in a dominant position, and that it at T2 was relieved from stress, perhaps increasing its enzymatic machinery to ensure better survival.

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Genome-Wide Transcriptional Analysis of Aerobic and Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

Journal of Bacteriology ◽

10.1128/jb.181.24.7409-7413.1999 ◽

1999 ◽

Vol 181 (24) ◽

pp. 7409-7413 ◽

Cited By ~ 189

Author(s):

J. J. M. ter Linde ◽

H. Liang ◽

R. W. Davis ◽

H. Y. Steensma ◽

J. P. van Dijken ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Microarrays ◽

Growth Parameter ◽

Open Reading Frames ◽

Transcriptional Analysis ◽

Anaerobic Conditions ◽

Chemostat Cultivation ◽

Transcript Levels ◽

Genome Wide ◽

Transcriptional Adaptation

ABSTRACT The yeast Saccharomyces cerevisiae is unique among eukaryotes in exhibiting fast growth in both the presence and the complete absence of oxygen. Genome-wide transcriptional adaptation to aerobiosis and anaerobiosis was studied in assays using DNA microarrays. This technique was combined with chemostat cultivation, which allows controlled variation of a single growth parameter under defined conditions and at a fixed specific growth rate. Of the 6,171 open reading frames investigated, 5,738 (93%) yielded detectable transcript levels under either aerobic or anaerobic conditions; 140 genes showed a >3-fold-higher transcription level under anaerobic conditions. Under aerobic conditions, transcript levels of 219 genes were >3-fold higher than under anaerobic conditions.

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Transcriptome Analysis of Responses to Dengue Virus 2 Infection in Aedes albopictus (Skuse) C6/36 Cells

Viruses ◽

10.3390/v13020343 ◽

2021 ◽

Vol 13 (2) ◽

pp. 343

Author(s):

Manjin Li ◽

Dan Xing ◽

Duo Su ◽

Di Wang ◽

Heting Gao ◽

...

Keyword(s):

Dengue Virus ◽

Aedes Albopictus ◽

Bioinformatics Analysis ◽

Interaction Mechanism ◽

Transcriptional Analysis ◽

Functional Verification ◽

Mosquito Vector ◽

Rna Seq ◽

Sequencing Data ◽

Qrt Pcr

Dengue virus (DENV), a member of the Flavivirus genus of the Flaviviridae family, can cause dengue fever (DF) and more serious diseases and thus imposes a heavy burden worldwide. As the main vector of DENV, mosquitoes are a serious hazard. After infection, they induce a complex host–pathogen interaction mechanism. Our goal is to further study the interaction mechanism of viruses in homologous, sensitive, and repeatable C6/36 cell vectors. Transcriptome sequencing (RNA-Seq) technology was applied to the host transcript profiles of C6/36 cells infected with DENV2. Then, bioinformatics analysis was used to identify significant differentially expressed genes and the associated biological processes. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to verify the sequencing data. A total of 1239 DEGs were found by transcriptional analysis of Aedes albopictus C6/36 cells that were infected and uninfected with dengue virus, among which 1133 were upregulated and 106 were downregulated. Further bioinformatics analysis showed that the upregulated DEGs were significantly enriched in signaling pathways such as the MAPK, Hippo, FoxO, Wnt, mTOR, and Notch; metabolic pathways and cellular physiological processes such as autophagy, endocytosis, and apoptosis. Downregulated DEGs were mainly enriched in DNA replication, pyrimidine metabolism, and repair pathways, including BER, NER, and MMR. The qRT-PCR results showed that the concordance between the RNA-Seq and RT-qPCR data was very high (92.3%). The results of this study provide more information about DENV2 infection of C6/36 cells at the transcriptome level, laying a foundation for further research on mosquito vector–virus interactions. These data provide candidate antiviral genes that can be used for further functional verification in the future.

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Improving Ethyl Acetate Production in Baijiu Manufacture by Wickerhamomyces anomalus and Saccharomyces cerevisiae Mixed Culture Fermentations

BioMed Research International ◽

10.1155/2019/1470543 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Guangsen Fan ◽

Chao Teng ◽

Dai Xu ◽

Zhilei Fu ◽

Pengxiao Liu ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Ethyl Acetate ◽

Mixed Culture ◽

Nutrient Competition ◽

Acetate Production ◽

Mixed Fermentation ◽

Wickerhamomyces Anomalus ◽

Flavor Perception ◽

Positive Effect

Ethyl acetate content has strong influence on the style and quality of Baijiu. Therefore, this study investigated the effect of Saccharomyces cerevisiae Y3401 on the production of ethyl acetate by Wickerhamomyces anomalus Y3604. Analysis of cell growth showed that Y3401 influences Y3604 by nutrient competition and inhibition by metabolites, while the effect of Y3604 on Y3401 was mainly competition for nutrients. Mixed fermentation with two yeasts was found to produce more ethyl acetate than a single fermentation. The highest yield of ethyl acetate was 2.99 g/L when the inoculation ratio of Y3401:Y3604 was 1:2. Synergistic fermentation of both yeasts improved ethyl acetate production and increased the content of other flavor compounds in liquid and simulated solid-state fermentation for Baijiu. Saccharomyces cerevisiae had a positive effect on ethyl acetate production in mixed culture and provides opportunities to alter the aroma and flavor perception of Baijiu.

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Effects of mediums on fermentation behavior and aroma composition in pure and mixed culture of Saccharomyces cerevisiae with Torulaspora delbrueckii

International Journal of Food Science & Technology ◽

10.1111/ijfs.15081 ◽

2021 ◽

Author(s):

Boqin Zhang ◽

Changqing Duan ◽

Guoliang Yan

Keyword(s):

Saccharomyces Cerevisiae ◽

Mixed Culture ◽

Torulaspora Delbrueckii

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Studies on Mixed Culture Saccharomyces cerevisiae and Micrococcus sp. Part III

Nippon Nōgeikagaku Kaishi ◽

10.1271/nogeikagaku1924.44.99 ◽

1970 ◽

Vol 44 (2) ◽

pp. 99-101

Author(s):

Zenya SHOJI

Keyword(s):

Saccharomyces Cerevisiae ◽

Mixed Culture

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Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.654177 ◽

2021 ◽

Vol 9 ◽

Author(s):

Minhye Shin ◽

Heeyoung Park ◽

Sooah Kim ◽

Eun Joong Oh ◽

Deokyeol Jeong ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Xylose Fermentation ◽

Sugar Metabolism ◽

Pentose Phosphate ◽

Biofuel Production ◽

Rna Seq ◽

Loss Of Function ◽

Lignocellulosic Biofuel ◽

Pentose Sugar ◽

Transcriptomic Changes

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

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