Omics · dataset · 2021
Transcriptome analysis of Pedobacter lusitanus NL19 grown in TSB and PC culture media
Listed in Teesside University Research Data Repository
We report the application of RNA-seq metodology to analyze the differentially expressed genes (DEGs) of Pedobacter lusitanus NL19 grown in two different culture media, TSB and PC, characterized to contain high and low concentration of peptone from casein (PC), respectively.
Description
Broth with higher concentrations of PC has been previously associated with the abolishment of antibiotic production by P. lusitanus NL19. RNA-seq results showed that P. lusitanus NL19 grown in TSB and in PC generated 22 783 626 and 43 625 972 sequence reads, respectively.
For gene expression analysis, 96,67% and 96,53% of the total fragments obtained for TSB and PC, respectively, were successfully mapped against P. lusitanus NL19 reference genome which allowed the identification of a total of 261 DEGs. More specifically, 108 genes were upregulated when NL19 was grown in TSB compared with its growth in PC, whereas 153 were downregulated. The biological function of most of these DEGs (53,7%) could not be predicted.
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For the others, genes involved in molecular functions and encoding cellular components were mostly upregulated and genes encoding biological processes were mostly downregulated. In general this study provided some insights on the main cellular pathways that are shaped in the presence of different concentrations of PC in P. lusitanus NL19, showing that high concentrations of PC strongly downregulates the de novo biosynthesis of biotin and the transcription of genes required for pedopeptin’s production, including a L-Dap biosynthetic operon.
On the other hand, it increases the transcription of MFS efflux pumps and iron-uptake systems.
Links
Where it is published
- DOI doi.org/10.17632/t5ryx5mk2k.3 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Earth & Environmental Science · RNA sequencing
Provenance · 1 source records, 7 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/t5ryx5mk2k.3 | 8 h ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[modality].local:modality:rna-seq | mapping · researchdata tees ac uk | vocabulary-mapper@1.0.0 | keywords['RNA Sequencing'] |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |