25 research outputs found
Characterizing the metabolism of Dehalococcoides with a constraint-based model
Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of "incomplete" pathways, such as the TCA-cycle, CO 2 fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes
Organohalide respiration, mediated by Dehalococcoides mccartyi, is a useful bioremediation process that transforms ground
water pollutants and known human carcinogens such as trichloroethene and vinyl chloride into benign ethenes. Successful
application of this process depends on the fundamental understanding of the respiration and metabolism of D. mccartyi.
Reductive dehalogenases, encoded by rdhA genes of these anaerobic bacteria, exclusively catalyze organohalide respiration
and drive metabolism. To better elucidate D. mccartyi metabolism and physiology, we analyzed available transcriptomic
data for a pure isolate (Dehalococcoides mccartyi strain 195) and a mixed microbial consortium (KB-1) using the previously
developed pan-genome-scale reconstructed metabolic network of D. mccartyi. The transcriptomic data, together with
available proteomic data helped confirm transcription and expression of the majority genes in D. mccartyi genomes. A
composite genome of two highly similar D. mccartyi strains (KB-1 Dhc) from the KB-1 metagenome sequence was
constructed, and operon prediction was conducted for this composite genome and other single genomes. This operon
analysis, together with the quality threshold clustering analysis of transcriptomic data helped generate experimentally
testable hypotheses regarding the function of a number of hypothetical proteins and the poorly understood mechanism of
energy conservation in D. mccartyi. We also identified functionally enriched important clusters (13 for strain 195 and 11 for
KB-1 Dhc) of co-expressed metabolic genes using information from the reconstructed metabolic network. This analysis
highlighted some metabolic genes and processes, including lipid metabolism, energy metabolism, and transport that
potentially play important roles in organohalide respiration. Overall, this study shows the importance of an organism’s
metabolic reconstruction in analyzing various ‘‘omics’’ data to obtain improved understanding of the metabolism and
physiology of the organism
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
Gene sequences annotated as proteins of unknown or non-specific function and hypothetical proteins account for a large fraction of most genomes. In the strictly anaerobic and organohalide respiring Dehalococcoides mccartyi, this lack of annotation plagues almost half the genome. Using a combination of bioinformatics analyses and genome-wide metabolic modelling, new or more specific annotations were proposed for about 80 of these poorly annotated genes in previous investigations of D. mccartyi metabolism. Herein, we report the experimental validation of the proposed reannotations for two such genes (KB1_0495 and KB1_0553) from D. mccartyi strains in the KB-1 community. KB1_0495 or DmIDH was originally annotated as an NAD+-dependent isocitrate dehydrogenase, but biochemical assays revealed its activity primarily with NADP+ as a cofactor. KB1_0553, also denoted as DmPMI, was originally annotated as a hypothetical protein/sugar isomerase domain protein. We previously proposed that it was a bifunctional phosphoglucose isomerase/phosphomannose isomerase, but only phosphomannose isomerase activity was identified and confirmed experimentally. Further bioinformatics analyses of these two protein sequences suggest their affiliation to potentially novel enzyme families within their respective larger enzyme super families
Genome-scale in-silico metabolic modeling of Dehalococcoides sp. strain CBDB1
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New insights into Dehalococcoides metabolism from an Integrated metabolic transcriptomics study
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Bioremediation of chlorinated ethenes by a Dehalococcoides mccartyi-containing mixed enrichment culture cultivated in a medium containing no exogenous vitamins
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Metabolic network reconstruction of Dehalococcoides sp. strain CBDB1
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A systems-level study of the transcriptional changes of Dehalococcoides metabolism
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Analysis and Design of a Genetic Circuit for Dynamic Metabolic Engineering
Recent advances in synthetic biology
have equipped us with new
tools for bioprocess optimization at the genetic level. Previously,
we have presented an integrated <i>in silico</i> design
for the dynamic control of gene expression based on a density-sensing
unit and a genetic toggle switch. In the present paper, analysis of
a serine-producing <i>Escherichia coli</i> mutant shows
that an instantaneous ON-OFF switch leads to a maximum theoretical
productivity improvement of 29.6% compared to the mutant. To further
the design, global sensitivity analysis is applied here to a mathematical
model of serine production in <i>E. coli</i> coupled with
a genetic circuit. The model of the quorum sensing and the toggle
switch involves 13 parameters of which 3 are identified as having
a significant effect on serine concentration. Simulations conducted
in this reduced parameter space further identified the optimal ranges
for these 3 key parameters to achieve productivity values close to
the maximum theoretical values. This analysis can now be used to guide
the experimental implementation of a dynamic metabolic engineering
strategy and reduce the time required to design the genetic circuit
components