Transcriptome analysis of Comamonas testosteroni R2 cultivated in phenol-degrading chemostat reactor

A collapsing process of phenol-degrading Comamonas testosteroni strain R2 was investigated by physiological and transcriptome approaches. Strain R2 grew aerobically under batch conditions with phenol as sole carbon source. whereas a sudden accumulation of phenol was observed under chemostat conditions. Proportion of living cells to dead cells increased and phenol- and catechol-degrading activities decreased gradually, suggesting that some metabolites produced from strain R2 accumulated in the culture and caused a negative feedback. The crude extract of supernatant collected from the collapsed culture exhibited the competitive inhibition to the phenol hydroxylase and the catechol dioxygenase. Transcriptomic analyses showed that genes encoding ammonium transporter AmtB was up-regulated to approximately 190-folds at the collapsing status, suggesting the increase of ammonium concentration in the cells. Transcriptional levels of almost of genes encoding enzymes in gluconeogenesis, glycolysis, TCA cycle, glyoxylate shunt, pentose phosphate pathway, urea cycle, amino acids and nucleotide syntheses decreased relatively in 40% to 70% levels of stable conditions, whereas the activities of glutamine synthetase, glutamate synthase, and metabolic pathways from citrate to 2-oxoglutarate in TCA cycle increased relatively and was maintained, respectively, suggesting that the supply of carbon skeleton was limited. These results suggested that the negative feedback caused an imbalance between carbon and nitrogen metabolisms, resulted in the collapse.