Temporal microarray analysis of Dehalococcoides ethenogenes during the transition into the stationary phase

Dehalococcoides bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were applied to monitor dynamic changes in the transcriptome as Dehalococcoides ethenogenes strain 195 transitioned from exponential growth into the stationary phase. In total, 415 non-redundant genes were identified as differentially expressed. As expected, genes involved with translation and energy metabolism were down-regulated while genes involved with general stress response, transcription, and signal transduction were up-regulated. Unexpected, however, was the 8- to 10-fold up-regulation of four putative reductive dehalogenases (RDases) (DET0173, DET0180, DET1535, and DET1545). Another unexpected finding was the up-regulation of a large number of genes located within integrated elements, including a putative prophage and a muti-copy transposon. Finally, genes encoding the dominant hydrogenase-RDase respiratory chain of this strain (Hup and TceA) were expressed at stable levels throughout the experiment, providing molecular evidence that strain 195 can uncouple dechlorination from net growth. Keywords: time course, stationary phase Dehalococcoides ethenogens strain 195 was grown in batch-pure cultures with TCE as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Parallel biological cultures were sacrificed and RNA was extracted at different times after inoculation. These times corresponded to the early exponential, late exponential, transition, early stationary, and late stationary growth phases. Microarrays were then used to compare the transcriptome during these different growth phases. Genes were identified as differentially expressed if they were more than 2-fold up-regulated or down-regulated between any two time-points during the experiment. In addition, differentially expressed genes had to have a false discovery rate less than 1% and an absolute hybridization signal intensity greater than 300 during at least one time point. Genes that met these conditions were further characterized with hierarchical clustering and COG analysis.