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| Status |
Public on Jun 14, 2017 |
| Title |
Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary? |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural and metabolic differences between plants grown in space compared to plants on the Earth. Genes that are important in setting up the spaceflight responses are being identified; their role in spaceflight physiological adaptation are increasingly understood, and the fact that different genotypes adapt differently is recognized. However, the basic question of whether these spaceflight responses are required for survival has yet to be posed, and the fundamental notion that spaceflight responses may be non-adaptive has yet to be explored. Therefore the experiments presented here were designed to ask if portions of the plant spaceflight response can be genetically removed without causing loss of spaceflight survival and without causing increased stress responses. The CARA experiment compared the spaceflight transcriptome responses of two Arabidopsis ecotypes, Col-0 and WS, as well as that of a PhyD mutant of Col-0. When grown with the ambient light of the ISS, phyD displayed a significantly reduced spaceflight transcriptome response compared to Col-0, suggesting that altering the activity of a single gene can actually improve spaceflight adaptation by reducing the transcriptome cost of physiological adaptation. The WS genotype showed and even simpler spaceflight transcriptome response in the ambient light of the ISS, more broadly indicating that the plant genotype can be manipulated to reduce the transcriptome cost of plant physiological adaptation to spaceflight and suggesting that genetic manipulation might further reduce, or perhaps eliminate the metabolic cost of spaceflight adaptation. When plants were germinated and then left in the dark on the ISS, the WS genotype actually mounted a larger transcriptome response than Col-0, suggesting that the in-space light environment affects physiological adaptation, which further implies that manipulating the local habitat can also substantially impact the metabolic cost of spaceflight adaptation.
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| Overall design |
CARA Seed Lines and Planting: Three seed lines Wild-Type Wassilewskija (Ws), Columbia-0 (Col-0) and Col-0 PhyD (phyD) Mutants were tested for viability, sterility and ability to maintain dormancy before the launch. Tested batches of seeds were planted on phytagel plates as one genotype per plate for gene expression analysis in replicates of three. One set was planted for the flight and one for ground control. The plates were wrapped such that every surface of the plate was covered by two layers of Duvetyn Black-Out cloth (Seattle Fabrics) (Sng et al, 2014). The plates were stored 4° C until launch, and was then launched in a cold-stow bag to maintain the plates at 4° C until integration and activation on the ISS. On Orbit Operations and harvest: The dormant plates were activated on station by removing the Black-Out cloth wrapping 12 days after launch. The plates were then placed on a fabric that was mounted in the US Laboratory module on the wall adjoining the MELFI freezer and secured using Velcro. The plants were allowed to grow on orbit for 11 days; some in the ambient light of ISS and some in the dark. The dark-grown plates were first activated by exposing the seeds to light for 4 hours, and then re-wrapped in Black-Out cloth for the duration of the growth period. A corresponding set of seedlings were grown as ground control in KSC. At 11 days, seedlings were photographed, harvested into KFT containing RNAlater solutions and returned for post-flight analysis. All plates were harvested into KFTs with their counterpart (e.g. Light 1 was harvested with Dark 1). Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI, the -32°C freezer. Following SpaceX-3 splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer on May 22, 2014. The PIs retrieved the plant samples from the KFTs on May 29, 2014 and transferred the samples back to the University of Florida. The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared among genotypes within a treatment (spaceflight or unit gravity) and between treatments (spaceflight versus ground control) for each genotype.
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| Web link |
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180186
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| Contributor(s) |
Paul A, Sng NJ, Zupanska AK, Krishnamurthy A, Ferl RJ |
| Citation(s) |
28662188 |
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| Submission date |
Feb 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J. Ferl |
| E-mail(s) |
ferllabuf@gmail.com
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| Phone |
352-273-8030
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| Organization name |
University of Florida
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| Department |
Horticultural Sciences
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| Lab |
Ferl's lab
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| Street address |
1301 Fifield Hall PO Box 110690
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| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (36)
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| GSM2493759 |
Light grown, Ground Control, Col-0 Rep1 |
| GSM2493760 |
Light grown, Ground Control, Col-0 Rep2 |
| GSM2493761 |
Light grown, Ground Control, Col-0 Rep3 |
| GSM2493762 |
Light grown, Ground Control, WS Rep1 |
| GSM2493763 |
Light grown, Ground Control, WS Rep2 |
| GSM2493764 |
Light grown, Ground Control, WS Rep3 |
| GSM2493765 |
Light grown, Ground Control, PhyD Rep1 |
| GSM2493766 |
Light grown, Ground Control, PhyD Rep2 |
| GSM2493767 |
Light grown, Ground Control, PhyD Rep3 |
| GSM2493768 |
Dark grown, Ground Control, Col-0 Rep1 |
| GSM2493769 |
Dark grown, Ground Control, Col-0 Rep2 |
| GSM2493770 |
Dark grown, Ground Control, Col-0 Rep3 |
| GSM2493771 |
Dark grown, Ground Control, WS Rep1 |
| GSM2493772 |
Dark grown, Ground Control, WS Rep2 |
| GSM2493773 |
Dark grown, Ground Control, WS Rep3 |
| GSM2493774 |
Dark grown, Ground Control, PhyD Rep1 |
| GSM2493775 |
Dark grown, Ground Control, PhyD Rep2 |
| GSM2493776 |
Dark grown, Ground Control, PhyD Rep3 |
| GSM2493777 |
Light grown, Spaceflight, Col-0 Rep1 |
| GSM2493778 |
Light grown, Spaceflight, Col-0 Rep2 |
| GSM2493779 |
Light grown, Spaceflight, Col-0 Rep3 |
| GSM2493780 |
Light grown, Spaceflight, WS Rep1 |
| GSM2493781 |
Light grown, Spaceflight, WS Rep2 |
| GSM2493782 |
Light grown, Spaceflight, WS Rep3 |
| GSM2493783 |
Light grown, Spaceflight, PhyD Rep1 |
| GSM2493784 |
Light grown, Spaceflight, PhyD Rep2 |
| GSM2493785 |
Light grown, Spaceflight, PhyD Rep3 |
| GSM2493786 |
Dark grown, Spaceflight, Col-0 Rep1 |
| GSM2493787 |
Dark grown, Spaceflight, Col-0 Rep2 |
| GSM2493788 |
Dark grown, Spaceflight, Col-0 Rep3 |
| GSM2493789 |
Dark grown, Spaceflight, WS Rep1 |
| GSM2493790 |
Dark grown, Spaceflight, WS Rep2 |
| GSM2493791 |
Dark grown, Spaceflight, WS Rep3 |
| GSM2493792 |
Dark grown, Spaceflight, PhyD Rep1 |
| GSM2493793 |
Dark grown, Spaceflight, PhyD Rep2 |
| GSM2493794 |
Dark grown, Spaceflight, PhyD Rep3 |
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| Relations |
| BioProject |
PRJNA375085 |
| SRA |
SRP100064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94983_1._LT_GC_Col-0_to_LT_GC_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_10._DK_FLT_WS_to_DK_GC_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_11._LT_FLT_Col-0_to_LT_GC_Col-0.xlsx.gz |
3.2 Mb |
(ftp)(http) |
XLSX |
| GSE94983_12._DK_FLT_Col-0_to_DK_GC_Col-0.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_13._LT_FLT_PhyD_to_LT_GC_PhyD.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_14._DK_FLT_PhyD_to_DK_GC_PhyD.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_15._DK_GC_WS_to_LT_GC_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_16._DK_FLT_WS_to_LT_FLT_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_17._DK_GC_Col-0_to_LT_GC_Col-0.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_18._DK_FLT_Col-0_to_LT_FLT_Col-0.xlsx.gz |
3.2 Mb |
(ftp)(http) |
XLSX |
| GSE94983_19._DK_GC_PhyD_to_LT_GC_PhyD.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_2._LT_FLT_Col-0_to_LT_FLT_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_20._DK_FLT_PhyD_to_LT_FLT_PhyD.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_3._DK_GC_Col-0_to_DK_GC_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_4._DK_FLT_Col-0_to_DK_FLT_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE94983_5._LT_GC_Col-0_to_LT_GC_PhyD.xlsx.gz |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSE94983_6._LT_FLT_Col-0_to_LT_FLT_PhyD.xlsx.gz |
2.3 Mb |
(ftp)(http) |
XLSX |
| GSE94983_7._DK_GC_Col-0_to_DK_GC_PhyD.xlsx.gz |
2.3 Mb |
(ftp)(http) |
XLSX |
| GSE94983_8._DK_FLT_Col-0_to_DK_FLT_PhyD.xlsx.gz |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSE94983_9._LT_FLT_WS_to_LT_GC_WS.xlsx.gz |
3.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
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| Processed data are available on Series record |
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