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Series GSE27611 Query DataSets for GSE27611
Status Public on Mar 01, 2013
Title Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis
Platform organisms Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195; Dehalococcoides mccartyi CBDB1; Dehalococcoides mccartyi VS
Sample organism Dehalococcoides
Experiment type Genome variation profiling by array
Summary 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.
 
Overall design The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from the two newly isolated Dehalococcoides strains 11a and 11a5 were analyzed.
 
Contributor(s) Lee PK, Cheng D, West KA, Alvarez-Cohen L, He J
Citation(s) 23480482
Submission date Mar 01, 2011
Last update date Jun 03, 2013
Contact name Patrick Lee
E-mail(s) leep@berkeley.edu
Organization name University of California, Berkeley
Department Civil and Environmental Engineering
Street address 209 O'Brien Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL10838 [4dehalosa520666F] Affymetrix Dehalococcoides genus 4.8K array
Samples (6)
GSM684503 gDNA_Strain 11a_rep1
GSM684504 gDNA_Strain 11a_rep2
GSM684505 gDNA_Strain 11a_rep3
Relations
BioProject PRJNA138259

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27611_RAW.tar 13.0 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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