NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE15334 Query DataSets for GSE15334
Status Public on Jan 13, 2010
Title MR-1 gene expression profiles of iron response
Organism Shewanella oneidensis MR-1
Experiment type Expression profiling by array
Summary Time-series transcriptional profiles of Shewanella oneidensis type strain MR-1 under iron depletion and repletion conditions. Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, temporal gene expression profiles were examined for iron depletion and repletion to delineate the iron response of S. oneidensis and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. In conclusion, we identified major biological pathways that were differentially expressed during iron depletion and repletion.
 
Overall design Four biological replicates of S. oneidensis MR-1 cells were grown to the midlog phase (OD600 = 0.6). Samples were collected at time 0, and then at 1, 5, 10, 20, 40, and 60 min after adding 2,2'-dipyridyl to attain a final concentration of 160 uM. Thereafter, ferrous sulfate was added to final concentration of 200 uM, and cells were collected at 1, 5, 10, 20, 40, and 60 min.
 
Contributor(s) Yang Y
Citation(s) 19321007
Submission date Mar 23, 2009
Last update date Mar 21, 2012
Contact name Yunfeng Yang
E-mail(s) yangy@ornl.gov
Phone 865-576-3998
Fax 865-576-8646
Organization name Oak Ridge National Lab
Department Biosciences Division
Street address 1 Bethel Valley Road
City Oak Ridge
ZIP/Postal code 37830
Country USA
 
Platforms (1)
GPL3253 ORNL Shewanella oneidensis 11.5k array
Samples (52)
GSM496728 Time series time 0 before iron depletion, Replicate 1
GSM496729 Time series time 0 before iron depletion, Replicate 2
GSM496730 Time series time 0 before iron depletion, Replicate 3
Relations
BioProject PRJNA116563

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
GSE15334_RAW.tar 116.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap