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Series GSE118890 Query DataSets for GSE118890
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
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.
 
Overall design mRNA reads of a temperature-shift timecourse were generated by sequencing, using Illumina HiSeq2000, PE-Reads, 2x100bp.
 
Contributor(s) Rossoni AW, Schoenknecht G, Lee HJ, Rupp RL, Flachbart S, Mettler-Altmann T, Weber AP, Eisenhut M
Citation(s) 30590832
Submission date Aug 22, 2018
Last update date May 29, 2019
Contact name Andreas PM Weber
E-mail(s) aweber@hhu.de
Organization name Heinrich-Heine-University
Department Institute for Plant Biochemistry
Street address Universitätsstr. 1
City Düsseldorf
ZIP/Postal code 40225
Country Germany
 
Platforms (1)
GPL22605 Illumina HiSeq 2000 (Galdieria sulphuraria)
Samples (25)
GSM3349826 Hot_T48_1_Rep B
GSM3349827 Hot_T48_1_Rep C
GSM3349828 Cold_T3_2_Rep A
Relations
BioProject PRJNA487158
SRA SRP158568

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE118890_GEO_Mothertable.xlsx 8.4 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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