Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1011528 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25907666_1.fastq.gz | Fastqsanger.gz | |||
| SRR25907666_2.fastq.gz | Fastqsanger.gz | |||
| SRR25907667_1.fastq.gz | Fastqsanger.gz | |||
| SRR25907667_2.fastq.gz | Fastqsanger.gz | |||
| SRR25907668_1.fastq.gz | Fastqsanger.gz |
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Project description:Bacteria of the group “Dehalococcoides” display the ability to respire recalcitrant chlorinated organic compounds in laboratory and field site applications. Though reductive dehalogenases (RDases) have been shown to directly catalyze dechlorination reactions, the respiratory pathways and function of most genome-encoded RDases in Dehalococcoides strains remain incompletely described. In order to broaden the understanding of the biological organization of “Dehalococcoides”, this study monitored the trancriptomic response of “Dehalococcoides ethenogenes” stain 195 through microarray technology. Batch versus continuously fed cultures were examined and compared. When similarly respiring (~120 μeeq PCE/(L-hr)) batch and pseudo steady-state cultures were contrasted, the reductive dehalogenases (RDases) DET1545 and DET0180 were up-regulated in the PSS system indicating their activity at lower overall electron acceptor concentration.
2018-10-13 | GSE25499 | GEO
Project description:Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.
2013-03-01 | GSE27611 | GEO
Project description:The genomes of three newly isolated Dehalococcoides strains (11a, 11a5 and MB) were compared against known genomes in the Dehalococcoides genus via a microarray targeting four sequenced Dehalococcoides strains (195, CBDB1, BAV1, and VS). All three strains exhibit different dechlorination patterns, with strains 11a dechlorinating TCE to ethene, 11a5 dechlorinating TCE to VC and MB dechlorinating PCE only to isomers of DCE. Hybridization of their respective genomic DNA to the microarrays showed that the genomes of strains 11a and 11a5 show great similarity to each other and to strains CBDB1 and BAV1 of the Pinellas subgroup, while strain MB shows strong genome similarity to members of the Cornell subgroup. All genes within the respective subgroups that were not detected by microarray are within the respective high plasticity regions or integrated elements of the sequenced strains. A large number of reductive dehalogenase (RDase)-encoding genes are present within each genome, and the presence of the vcrA and tceA genes in strains 11a and 11a5 respectively, and the absence of any of the four functionally-characterized chlorinated ethene RDases (pceA, tceA, vcrA, bvcA) within strain MB appear to dictate chlorinated ethene usages regardless of the respective core genome phylogeny of the three strains. Considering the current data set together with previous comparative genomics results from application of the Dehalococcoides genus microarray to two other un-sequenced strains, the observed incongruence between the core genome phylogeny and chlorinated ethene usage of Dehalococcoides strains is likely driven by horizontal gene transfer of functional RDases. The other genomic features that are repeatedly observed in the microarray analyses of all five un-sequenced Dehalococcoides strains as well as the environmental implications on this work are presented in this study. The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from the two newly isolated Dehalococcoides strains 11a and 11a5 were analyzed.
2013-03-01 | E-GEOD-27611 | biostudies-arrayexpress
Project description:Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride and (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08.
2020-06-10 | PXD018558 | Pride
Project description:Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride and (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08.
2020-06-25 | PXD018595 | Pride
Project description:Biodegrades polychlorinated biphenyls
| PRJNA254 | ENA
Project description:Genome sequencing of Dehalococcoides mccartyi strains that metabolically dechlorinate polychlorinated biphenyls
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Project description:Genome sequencing of Dehalococcoides mccartyi strains that metabolically dechlorinate polychlorinated biphenyls
| PRJNA230430 | ENA
Project description:Genome sequencing of Dehalococcoides mccartyi strains that metabolically dechlorinate polychlorinated biphenyls
| PRJNA230429 | ENA