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| Status |
Public on Dec 31, 2008 |
| Title |
Microarray-based Analysis of Polyamine Transport and Metabolism in the Model Marine Bacterium Silicibacter pomeroyi |
| Platform organism |
Ruegeria pomeroyi DSS-3 |
| Sample organism |
Ruegeria pomeroyi |
| Experiment type |
Expression profiling by array
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| Summary |
Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.
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| Overall design |
Silicibacter pomeroyi DSS-3 cells were grown in chemostat in a modified marine basal medium (MBM) containing spermidine as sole carbon and nitrogen source. Serine was used as a substrate to provide comparative data for an amino acid. After reach stable condition, total RNA were extracted, mRNA were purified and aa-aRNA were amplified and fluoresently labled before hybridize on array chips. The array design is described in Burgmann et al., 2007
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| Contributor(s) |
Mou X, Sun S, Moran MA |
| Citation missing |
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| Submission date |
Dec 01, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Xiaozhen Mou |
| E-mail(s) |
xmou@kent.edu
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| Phone |
330-672-3625
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| Fax |
330-672-3713
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| Organization name |
Kent State University
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| Department |
Biological Sciences
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| Street address |
41 cunningham Hall, P. O. box 5190
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| City |
Kent |
| State/province |
OH |
| ZIP/Postal code |
44242 |
| Country |
USA |
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| Platforms (1) |
| GPL4067 |
UGAmamlab_Silicibacter_pomeroyi_DSS-3_8k_v1.0 |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA110609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13781_RAW.tar |
9.5 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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