Comparative genomics and transcriptomics of organohalide-respiring bacteria and regulation of rdh gene transcription

Comparison of the genomes of organohalide-respiring bacteria has improved our understanding of the genetic background of the organohalide respiration process. In this chapter the remarkable differences between obligate and facultative organohalide-respiring bacteria in the number of reductive dehalogenaseencoding genes and the numbers and types of accessory genes are discussed in relation to different lifestyles and evolutionary aspects. Furthermore, the putative function of accessory genes is discussed and a unifying nomenclature is proposed. The genomes also reflect distinct mechanisms for the synthesis or acquisition of the corrinoid cofactors of reductive dehalogenases, which are well in accord with the observed growth requirements of the respective organohalide-respiring bacteria. The value of microarray-based comparative genomics, transcriptomics, and quantitative transcription analyses for understanding the physiology and environmental significance of organohalide respiration is discussed. The reductive dehalogenase genes are in general associated with genes encoding transcriptional regulators, which are likely involved in sensing the halogenated electron acceptors. The role of two types of regulators in transcriptional regulation of organohalide respiration has been investigated. A multiple antibiotic resistance regulator (MarR)-type regulator was shown to regulate negatively the transcription of reductive dehalogenase genes in Dehalococcoides mccartyi. In Desulfitobacterium hafniense, the cAMP receptor protein/fumarate and nitrate reduction (CRP/FNR) regulator, CprK, activates transcription of reductive dehalogenase genes. The molecular mechanism of how ortho- chlorophenols act as effectors has been elucidated and how, through the induction of structural changes, they lead to DNA binding of the regulator.