title: Involvement of glycolysis/gluconeogenesis and signaling regulatory pathways in Saccharomyces cerevisiae biofilms during fermentation.
abstract: Compared to free (free-living) cells, biofilm cells show increased resistance and stability to high-pressure fermentation conditions, although the reasons underlying these phenomena remain unclear. Here, we investigated biofilm formation with immobilized Saccharomyces cerevisiae cells grown on fiber surfaces during the process of ethanol fermentation. The development of biofilm colonies was visualized by fluorescent labeling and confocal microscopy. RNA from yeast cells at three different biofilm development periods was extracted and sequenced by high-throughput sequencing. We quantitated gene expression differences between biofilm cells and free cells and found that 2098, 1556, and 927 genes were significantly differentially expressed, respectively. We also validated the expression of previously reported genes and identified novel genes and pathways under the control of this system. Statistical analysis revealed that biofilm genes show significant gene expression changes principally in the initial period of biofilm formation compared to later periods. Carbohydrate metabolism, amino acid metabolism, signal transduction, and oxidoreductase activity were needed for biofilm formation. In contrast to previous findings, we observed some differential expression performances of FLO family genes, indicating that cell aggregation in our immobilized fermentation system was possibly independent of flocculation. Cyclic AMP-protein kinase A and mitogen-activated protein kinase pathways regulated signal transduction pathways during yeast biofilm formation. We found that carbohydrate metabolism, especially glycolysis/gluconeogenesis, played a key role in the development of S. cerevisiae biofilms. This work provides an important dataset for future studies aimed at gaining insight into the regulatory mechanisms of immobilized cells in biofilms, as well as for optimizing bioprocessing applications with S. cerevisiae.
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China ; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Zhenjian
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Liu
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhao
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Cheng
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Hengfei
authors.initials: H
authors.lastname: Ren
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Guo
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Huanqing
authors.initials: H
authors.lastname: Niu
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhuang
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Jinglan
authors.initials: J
authors.lastname: Wu
authors.affiliation: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China ; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing, China.
authors.forename: Hanjie
authors.initials: H
authors.lastname: Ying
keywords: FLO family genes; Saccharomyces cerevisiae; biochemical pathways; biofilms; glycolysis/gluconeogenesis; signaling pathways; transcriptional profiles