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Comparative Genomics and Transcriptomics of Organohalide-Respiring Bacteria and Regulation of rdh Gene Transcription

  • Thomas Kruse
  • Hauke Smidt
  • Ute LechnerEmail author
Chapter

Abstract

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 dehalogenase-encoding 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.

Keywords

Twin Arginine Translocation Reductive Dehalogenases Desulfitobacterium Hafniense Strain CBDB1 Organohalide Respiration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgement

This work was funded by the German Research Foundation (DFG research unit FOR 1530). Work of HS and TK was financially supported by the EcoLinc Project of the Netherlands Genomics Initiative, the BE-BASIC foundation through projects F07.001.05 and F08.004.01, as well as the European Community program FP7 (grants KBBE-211684; BACSIN, and KBBE-222625; METAEXPLORE). We are grateful to Gary Sawers for comments on the manuscript.

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© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
  2. 2.Institute of Biology/MicrobiologyMartin Luther University Halle-WittenbergHalleGermany

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