DEHALOCOCCOIDES AND REDUCTIVE DECHLORINATION OF CHLORINATED SOLVENTS - Bioaugmentation for Groundwater Remediation - page 62

and the presence of five distinct hydrogenase complexes suggests that Dhc have fine-tuned
responses to environmental hydrogen concentrations. The small genome size, the presence of
multiple RDase and five hydrogenase gene operons (clusters of genes related to a specific
metabolic function or pathway), and the absence of genes predicted to encode utilization of
other substrates all support the extreme metabolic specialization of Dhc .
These findings suggest a model for Dhc evolution, in which all Dhc genomes contain a
highly conserved set of core housekeeping genes, with a few HPRs where most of the variability
resides. Dhc evolution is discussed further in Section 2.11 , but the emerging conceptual model is
that the ancestor of these organisms arose early in the history of life on Earth, and modern Dhc
represent an evolved and highly specialized bacterial group adapted to use a wide variety of
halogenated organics by exchange of RDase genes.

2.7.2 Dehalococcoides Reductive Dehalogenases Gene Operons

Dhc RDase genes were first identified through reverse genetics approaches and the appli-
cation of degenerate PCR primers designed using sequences of known RDase genes (H¨lscher
et al., 2004 ; Krajmalnik-Brown et al., 2004 ;M¨ller et al., 2004 ). Subsequently, the analysis of
Dhc genomes revealed a large diversity of RDase genes and the presence of multiple RDase
genes on individual genomes (Table 2.5 ). A generic Dhc RDase operon is depicted in Figure 2.5 .

Table 2.5. Features of Genomes from Dhc Isolates

Predicted
ORFs

# of putative
RDase genes Dhc strain Size [bp] Accession # Reference

195 1,469,720 1,591 17 CP000027 Seshadri et al.,

2005

CBDB1 1,395,502 1,458 32 AJ965256 Kube et al.,

2005

BAV1 1,341,892 1,371 11 CP000688 McMurdie et al.,

2009

VS 1,413,474 1,447 36 CP001827 McMurdie et al.,

2009

GT 1,360,154 1,417 20 CP001924 Unpublished

1,000 bp

rdhR, rdhC , rdhD
or phage-related gene

rdhG, rdhH , cprC
or phage-related gene

rdhA rdhB

Consensus sequence for twin
arginine translocation (Tat) system

Consensus sequences for
Iron-Sulfur Cluster binding sites

Figure 2.5. Organization of a typical RDase operon in Dhc. All Dhc RDase gene clusters consist of
rdhA (blue) encoding the catalytic subunit and rdhB (red) encoding a transmembrane anchor,
which is located downstream of rdhA. Most (putative) Dhc RDase gene clusters lack one or all of
the accessory genes rdhC, rdhD and rdhG, which can be located on the forward or reverse strands.
The functions of the accessory genes are unclear. Arrows indicate the direction of the open
reading frames (ORFs) in a typical rdh operon. rdh abbreviates reductive dehalogenase homolo-
gous genes.