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Status |
Public on Dec 31, 2018 |
Title |
Cold acclimation of the thermoacidophilic red alga Galdieria sulphuraria - changes in gene expression and involvement of horizontally acquired genes |
Organism |
Galdieria sulphuraria |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease. Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C and successive recovery at 46°C were targeted for sampling. Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.
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Overall design |
mRNA reads of a temperature-shift timecourse were generated by sequencing, using Illumina HiSeq2000, PE-Reads, 2x100bp.
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Contributor(s) |
Rossoni AW, Schoenknecht G, Lee HJ, Rupp RL, Flachbart S, Mettler-Altmann T, Weber AP, Eisenhut M |
Citation(s) |
30590832 |
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Submission date |
Aug 22, 2018 |
Last update date |
May 29, 2019 |
Contact name |
Andreas PM Weber |
E-mail(s) |
aweber@hhu.de
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Organization name |
Heinrich-Heine-University
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Department |
Institute for Plant Biochemistry
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Street address |
Universitätsstr. 1
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City |
Düsseldorf |
ZIP/Postal code |
40225 |
Country |
Germany |
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Platforms (1) |
GPL22605 |
Illumina HiSeq 2000 (Galdieria sulphuraria) |
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Samples (25)
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Relations |
BioProject |
PRJNA487158 |
SRA |
SRP158568 |
Supplementary file |
Size |
Download |
File type/resource |
GSE118890_GEO_Mothertable.xlsx |
8.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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