Computational Analysis of the Glycolytic Gene Expression Patterns in Different Saccharomyces cerevisiae Strains Grown in Solid State Fermentation Conditions


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Servili B., Turgut Genç T. , Türkel S.

28. ICYGMB (International conference on yeast genetics and molecular biology), Praha, Czech Republic, 27 August - 01 September 2017, vol.1, no.1, pp.1

  • Publication Type: Conference Paper / Full Text
  • Volume: 1
  • City: Praha
  • Country: Czech Republic
  • Page Numbers: pp.1

Abstract

Glycolytic enzyme genes are the highly expressed and subjected to transcriptional regulation by various regulators. Expression profiles of glycolytic genes may vary depending on the growth conditions and yeast strains. In this study, the expression profiles of glycolytic genes in three different Saccharomyces cerevisiae strains that are grown under solid state fermentation (SSF medium) conditions, were analyzed using bioinformatics tools. The row data on the transcriptome analysis were downloaded from EMBL-EBI (study ID: PRJNA212389). Transcript levels of each glycolytic genes were analyzed using Trimmomatic, Tophat2 and Featurecounts programs. Analysis of RNA seq data indicates that certain glycolytic genes were subjected to rapid reprogramming for transcription in response to SSF. It appears that transcription of HXK1, GLK1 and genes that encodes the key factors for the trehalose (TPS1, TPS2 and NTH1) and glycogen metabolism (PGM2, UGP1, GSY1, GSY2 and GPH1) is down regulated rapidly when the yeast strains inoculated into SSF medium. At the same time, genes that involves in glycerol metabolism (GPD1, GPP1/RHR2 and GPP2/HOR2) is activated. At the second stage (60 min after inoculation), while the transcription of GPD1 and GPP2/HOR2 decreases, transcription of TPI is activated. Transcription of genes involves in trehalose and glycogen metabolism remains at basal level during this stage. At the third stage (180 min after inoculation), transcription of HXK1, GLK1 and genes involves in trehalose and glycogen metabolism elevate to their initial level. Moreover, transcription of TDH1, PDC1, ADH1 and FBA1 is highly activated after second and third stage of SSF. Activation of genes that has a significant function in the lower glycolytic pathways suggest that yeasts grown under SSF conditions activates NADH biosynthesis for redox balance too. TDH1 encodes a multi-functional peptide that also present in the yeast cell wall and also secreted to growth medium. The transcription of GCR1, a major activator of glycolytic genes, activated by 2-fold in SSF medium and remains at activated level. In addition, we identified a remarkable changes in the expression of glucose transporter genes too. In conclusion, it appears that growth in SSF medium results with rapid changes in the transcription of glycolytic genes in S. cerevisiae. It seems that NADH production via glycerol and ethanol synthesis are the essential processes for growth in SSF medium for S. cerevisiae.

 

Key words: Glycolytic Genes, RNA seq, Saccharomyces cerevisiae