Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation      
dateReleased:
04-25-2012
description:
Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL). As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly up-regulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally down regulated in response to FNL and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition while others were associated with general stress responses. A number of genes related to the biological functions of nucleotide synthesis, replication, transcription, translation, and post-translational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate cellular nitrogen status in the environment. Dehalococcoides ethenogenes strain 195 was grown with or without ammonium in batch cultures with trichloroethene as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor. Microarrays were used to compare the transcriptome during fixed nitrogen limitation and triplicate biological samples were prepared for each condition. Differentially expressed genes between the two growth conditions were identified using a two-tailed Student's t-test, a false discovery rate of less than 1%, an absolute hybridization signal intensity of 300 or greater in one of the two conditions, and an expression ratio of two-fold or greater.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-28855
refinement:
raw
alternateIdentifiers:
28855
keywords:
functional genomics
dateModified:
05-10-2012
availability:
available
types:
gene expression
name:
Dehalococcoides ethenogenes 195
ID:
A-GEOD-6336
name:
Dehalococcoides ethenogenes strain 195 1.6K
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28855/E-GEOD-28855.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28855/E-GEOD-28855.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28855
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.