Biomedical Engineering Reference
In-Depth Information
The historical basis for correlating transcript abundance with activity is that gene induction
and transcription (i.e., mRNA production) occurs specifically in response to the substrate (e.g.,
a chlorinated electron acceptor) and further, mRNA turnover is rapid and the transcripts are
quickly degraded after protein biosynthesis. This model applies to many model microorgan-
isms, such as
E. coli
, and is outlined in every microbiology textbook; however, the classical
model may not apply to slow-growing dechlorinating bacteria such as
Dhc
. For example, a
single chlorinated substrate can induce the expression of multiple RDase genes, suggesting that
the presence of specific mRNA transcripts may not be firmly linked with a specific dechlorina-
tion reaction (Johnson et al.,
2008
). Also, RDase gene transcript turnover in
Dhc
can be slow, so
that biomarker transcripts may persist after the chlorinated compound has been dechlorinated.
Further, the relative
tceA
transcript levels increase following oxygen exposure, suggesting that
RDase gene expression is also a stress response and therefore can be uncoupled from
dechlorination activity (Amos et al.,
2008a
). Although gene expression monitoring is promising,
procedural advances are needed and the regulation of
Dhc
transcription must be understood in
greater detail before transcript measurements will be useful to infer dechlorination activity and
rates.
Recent technological advances in proteomic workflows allow the identification of peptides
of biomarker proteins, though quantitative proteomic techniques remain elusive (Aebersold and
Mann,
2003
; Ram et al.,
2005
; Werner et al.,
2009
). The analysis of the catalysts (i.e., specific
RDases) is a direct measure of activity. Detection of peptides of
Dhc
biomarker proteins has
been accomplished with
Dhc
pure cultures and dechlorinating consortia (Werner et al.,
2009
);
however, the applicability of this approach to complex environmental samples with high
microbial diversity and low biomass has yet to be demonstrated. Independent of the technology
used, a prerequisite for obtaining defensible results is knowledge of process-specific biomar-
kers. Further, internal standards are needed to analytically measure biomarker loss during
sampling, shipment and storage and during sample processing in the analytical laboratory.
2.11
DEHALOCOCCOIDES
EVOLUTION AND
DISSEMINATION OF REDUCTIVE
DEHALOGENASE GENES
Dhc
are unique bacteria because of their streamlined genomes and extreme specialization
with regard to substrate utilization (i.e., strictly hydrogenotrophic organohalide respirers).
Many argue that the evolution of reductive dechlorination of chlorinated ethenes started at
the beginning of the twentieth century after the introduction of anthropogenic compounds,
which are also called xenobiotics, into the environment. Although humans have introduced
large quantities of diverse halogenated compounds into the environment, the assertion that
these chemicals have no natural counterparts has been proven wrong. Literally thousands of
haloorganics are produced by natural processes (e.g., combustion and geogenic processes,
volcanic emissions) dating back to before life originated on Earth (Gribble,
2003
,
2005
;
H¨ggblom and Bossert,
2003
). Furthermore, numerous biological processes, sometimes in
concert with abiotic reactions, generate a variety of halogenated compounds, including PCE,
TCE and other CAHs (Weissflog et al.,
2005
). Processes generating haloorganic compounds
may have been operational for billions of years, possibly before life originated on Earth. Hence,
it is likely that reductive dechlorination evolved early in life's history on Earth and that the
capability to perform organohalide respiration arose long before humans released chlorinated
compounds into the environment. The small, streamlined genomes and the minimalist, highly
specialized lifestyle of
Dhc
(i.e., strictly hydrogenotrophic organohalide respirers) likely reflect
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