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| Status |
Public on Jun 07, 2014 |
| Title |
RNA-seq analysis of polyhydroxyalkanoate-producing Ralstonia eutropha H16 |
| Organism |
Cupriavidus necator H16 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Ralstonia eutropha H16 is well-known to produce poly(3-hydroxybutyrate) [P(3HB)], a kind of polyhydroxyalkanoates attracted as bio-based biodegradable plastics, efficiently as an energy storage material under unbalanced growth conditions. To obtain further extended knowledge of PHA biosynthesis, this study employed quantitative transcriptome analysis based on deep sequencing of complementary DNA generated from RNA (RNA-seq) for R. eutropha H16.
Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined by using Illumina high-throughput sequencer.
The RNA-seq results supported induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in growth phase, and repression trends for genes involved in central metabolisms in PHA production phase. Interestingly, transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several selected genes for β-oxidation were significantly induced in PHA production phase even when the cells were grown on fructose.
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| Overall design |
mRNA profiles of R. eutropha H16 grown on fructose at different phases were generated by deep sequencing, in duplicate, using Illumina GAIIx.
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| Contributor(s) |
Fukui T |
| Citation(s) |
23879744 |
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| Submission date |
Jun 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiaki Fukui |
| E-mail(s) |
[email protected]
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| Organization name |
Tokyo Institute of Technology
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| Department |
Department of Bioengineering
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| Street address |
Nagatsuta 4259
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| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
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| Platforms (1) |
| GPL17263 |
Illumina Genome Analyzer IIx (Ralstonia eutropha H16) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA207670 |
| SRA |
SRP024299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47759_RAW.tar |
130.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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