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Temporal Transcriptomic Microarray Analysis of "Dehalococcoides ethenogenes" Strain 195 during the Transition into Stationary Phase ^,

David R. Johnson,^1, Eoin L. Brodie,² Alan E. Hubbard,³ Gary L. Andersen,² Stephen H. Zinder,⁴ and Lisa Alvarez-Cohen^1,2*

Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710,¹ Earth Sciences Division, Lawrence Berkeley National Laboratory,² School of Public Health, University of California, Berkeley, California 94720,³ Department of Microbiology, Cornell University, Ithaca, New York 14853⁴

Received 27 September 2007/ Accepted 15 February 2008

"Dehalococcoides" bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were used to monitor dynamic changes in the transcriptome as "Dehalococcoides ethenogenes" strain 195 transitioned from exponential growth into stationary phase. In total, 415 nonredundant 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 multicopy 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.

Published ahead of print on 29 February 2008.

Supplemental material for this article may be found at http://aem.asm.org/.

Present address: Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland.