|
| Status |
Public on Dec 09, 2007 |
| Title |
Global response of Silicibacter pomeroyi strain DSS3 to dimethyl sulfoniopropionate (DMSP) |
| Platform organism |
Ruegeria pomeroyi DSS-3 |
| Sample organisms |
Ruegeria pomeroyi; Ruegeria pomeroyi DSS-3 |
| Experiment type |
Expression profiling by array
|
| Summary |
Dimethylsufoniopropionate (DMSP) is an important and abundant organic sulfur compound and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alpha-proteobacteria, including Silicibacter pomeroyi strain DSS3, are known to be a key phylogenetic group involved in DMSP degradaton. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. S. pomeroyi is capable of performing two major pathways of DMSP degradation, making it an interesting model organism. Based on the full genome sequence of this strain we designed an oligonucleotide-based microarray for the detection of transcripts of nearly all genes. The array was used to study the transcriptional response of S. pomeroyi cultures to additions of DMSP or Acetate in a time series experiment. We identified a number of DMSP-upregulated genes that could be assigned to potential roles in the metabolization of DMSP. DMSP also affected the transcription of other groups of genes, including genes for transport and metabolization of peptides, amino-acids and polyamines. High DMSP concentrations may be a chemical signal indicating phytoplankton abundance and elicit a regulatory response aimed at making maximum use of the available nutrients under these conditions.
Keywords: Microarray, marine bacterium, messenger RNA, transcription, sulfur metabolism
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| Overall design |
The array design is based on the complete genome sequence of S. pomeroyi strain DSS 3 and available from Genbank (Accession numbers CP000031 and CP000032). Probes for all identified potential genes were designed by Combimatrix using proprietary software. A total of 4161 genes out of the 4348 identified potential genes on the S. pomeroyi genome are represented on the array. When possible, two probes per gene were designed.
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| Citation(s) |
17922758 |
| |
| Submission date |
Aug 09, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Shulei Sun |
| E-mail(s) |
shulei@uga.edu
|
| Phone |
(706)542-0341
|
| Organization name |
UGA
|
| Department |
Marine Science
|
| Street address |
Department of Marine Science
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
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| Platforms (1) |
| GPL4067 |
UGAmamlab_Silicibacter_pomeroyi_DSS-3_8k_v1.0 |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA95997 |
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