Submitted to: International Conference on Microbial Genomes
Publication Type: Abstract Only
Publication Acceptance Date: April 17, 2004
Publication Date: April 13, 2004
Citation: Liu, Z., Slininger, P.J. 2004. Global gene expression analysis of ethanologenic yeasts in adaptation to bioethanol fermentation inhibitory stress [abstract]. International Conference on Microbial Genomes. Genomes 2004. p. 61. Technical Abstract: Biomass pretreatment of lignocellulosic materials for degradation and saccharification generates inhibitory compounds, which interfere with subsequent bioethanol fermentation. We have demonstrated adaptation abilities of ethanologenic yeasts to furfural and 5-hydroxymethylfurfural under defined culture conditions. In this study, we explore global analysis of gene expression for the yeasts in response to fermentation inhibitory compounds using optimized 70-mer oligo microarray. We designed and synthesized several 70-mer amino modified nucleotides as quality controls using exogenous nucleic acids, which were incorporated into the microarray and each of the array experiments. Our oligo microarray consisted of 13,440 elements with replicated arrays representing 6,388 genes of Saccharomyces cerevisiae and quality control components including spiking controls, positive controls, and negative controls. A unique reference RNA was generated and applied to each microarray experiment. High-quality RNA with purity greater than 1.80 was used. Efficiency of cDNA synthesis and fluorescent probe labeling were evaluated using an in-house developed sGel electrophoresis and by NanoDrop spectrophotometry. Probes with matched labeling efficiency and proper length of cDNA populations were used to perform hybridization. Data acquisition was completed using Axon Instruments GenePix 4000B scanner and GenePix Pro 4.2. Raw data were treated with restricted high stringent and analyzed using GeneSpring 6.0. Saccharomyces Genome Database and Gene Ontology were used for gene annotation and standard nomenclature. Specific hypothetic functions of unknown genes as well as partially described genes were tentatively assigned. Our results provide insight to cell sensing and the adaptive response of yeasts to inhibitory stress, which will lead to a better understanding of the molecular mechanisms involved in the stress tolerance and strategies to engineer more efficient bioethanol fermentation.