Influence of protocatechuic acid on gene expression in Blastobotrys raffinosifermentans LS3

Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to protocatechuic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine. In the study presented here, gene expression profiling was performed using a microarray produced by Agilent Technologies in 8 x 60 k format. The microarray was based on 6,025 annotated chromosomal sequences and 36 putative mitochondrial gene oligos, resulting in a total of 56,312 Blastobotrys raffinosifermentans LS3 specific oligos. Blastobotrys raffinosifermentans LS3 cells were cultivated overnight in YMM-glucose-NaNO3 and shifted to YMM-NaNO3 containing a mixture of either 0.5 % protocatechuic acid plus 1 % glucose or 1 % glucose only. After 15 min, 30 min, 2 h and 5 h of cultivation at 30 °C and 180 rpm, cells were harvested, total RNA was isolated, samples were labelled, and the microarray was hybridized according to the Agilent Technologies “One-Color Microarray-Based Gene Expression Analysis (v6.5)” instructions. R package limma was used for microarray data analysis. Background of raw expression data was corrected by “normexp” and normalized between arrays using “quantile”.