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Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes

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Abstract

The transcriptome of seedlings was analyzed from experiments performed on the International Space Station to study the interacting effects of light and gravity on plant tropisms (project named TROPI-2; Kiss et al. 2012). Seeds of Arabidopsis were germinated in space, and seedlings were then grown in the European Modular Cultivation System for 4 days at ~1g followed by exposure to a range of gravitational accelerations (from microgravity to 1g) and two light treatments (blue light with or without a 1 h pretreatment with red). At the end of the experiments, the cassettes containing the seedlings were frozen in the minus eighty laboratory freezer and returned to Earth on space shuttle mission STS-131. The RNA was extracted from whole seedlings and used for the transcriptome analyses. A comparison of 1g spaceflight samples with 1g ground controls identified 230 genes that were differentially regulated at least twofold, emphasizing the need for “in situ” tissue fixation on a 1g centrifuge as an important control for spaceflight experiments. A further comparison of all spaceflight samples with ground controls identified approximately 280 genes that were differentially regulated at least twofold. Of these genes, several were involved in regulating cell polarity (i.e., auxin, calcium, lipid metabolism), cell-wall development, oxygen status, and cell defense or stress. However, when the transcriptome of the all g-treated spaceflight samples was compared with microgravity samples, only ~130 genes were identified as being differently regulated (P ≤ 0.01). Of this subset, only 27 genes were at least twofold differently regulated between microgravity and 1g space samples and included putative/pseudo/undefined genes (14), transposable elements (5), an expansin (ATEXP24; At1g21240), a cell-wall kinase (WAK3; At1g21240), a laccase-like flavonoid oxidase (TT10; At5g48100), among others.

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Abbreviations

1g :

1× gravity Earth’s gravitational force

EMCS:

European Modular Cultivation System

GLACIER:

General laboratory active cryogenic ISS experiment refrigerator

ISS:

International Space Station

MELFI:

Minus eighty laboratory freezer

RT-qPCR:

Quantitative real time polymerase chain reaction

μg :

Microgravity

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Acknowledgments

This work was supported by the National Aeronautics and Space Administration (NNX10AF44G to J.Z.K). The authors gratefully acknowledge the support of NASA’s Ames Research Center (Mountain View, CA, USA), especially Marianne Steele, Kenny Vassigh, Ken Souza, Sid Sun, Bob Bowman, Kris Vogelsong, and Dave Heathcote. They also thank the Norwegian User Support and Operations Center (especially Carina Helle Berg, Gjert Aanes, and Knut Olav Helleseng), the European Space Agency, and the EADS team (especially Thomas Niedermaier, Anna Grinberg, and Reinhard Born) for their excellent technical support during spaceflight operations. In addition, Caitlin Bregitzer, Maggie Brown, Jessie Hall, and Katie Huntoon aided in the data collection at Miami University. Special thanks to Astronauts Williams and Creamer as well as other crew members for performing their experiments on board the ISS. The authors also thank Sharon Norton, Dejerianne T. Ostrow, and Yanping Zhang of the University of Florida ICBR, as well as Frédéric Souret, and Veronica Campbell from University of Florida.

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Authors and Affiliations

  1. Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA

    Melanie J. Correll & Tyler P. Pyle

  2. Department of Biology, University of Mississippi, University, MS, 38677, USA

    Katherine D. L. Millar & John Z. Kiss

  3. Department of Microbiology and Immunology, The State University of New York, Buffalo, NY, 14203, USA

    Yijun Sun

  4. New York State Center of Excellence in Bioinformatics and Life Sciences, The State University of New York, Buffalo, NY, 14203, USA

    Yijun Sun

  5. Electrical and Computer Engineering Department, University of Florida, Gainesville, FL, 32611, USA

    Jin Yao

  6. Department of Botany, Miami University, Oxford, OH, 45056, USA

    Richard E. Edelmann

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  1. Melanie J. Correll
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  2. Tyler P. Pyle
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  3. Katherine D. L. Millar
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  4. Yijun Sun
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  6. Richard E. Edelmann
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  7. John Z. Kiss
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Correspondence to Melanie J. Correll.

Electronic supplementary material

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425_2013_1909_MOESM1_ESM.docx

Suppl. Fig. S1 The mean RT-qPCR expression levels of JAZ7, CORI3, and MIPS2 from three spaceflight samples relative to two ground controls. The microarray data expression represent the mean from all spaceflight samples (n=16 arrays) and all ground controls (n=6 arrays). For qPCR, the expression ratio was performed using the \(2^{{ - \Updelta \Updelta C_{\text{T}} }}\) method (Livak Method; Livak and Schmittigen 2001) using UBC10 as the reference and ground controls as the calibrators. For arrays, the expression levels represent the fold change (log2) of spaceflight to ground controls (DOCX 71 kb)

425_2013_1909_MOESM2_ESM.docx

Suppl. Fig. S2 RT-qPCR (white bars) and microarray expression levels (dark bars) of DIR7 (At3g13650) from microgravity and incremental g-treatments in spaceflight with two samples from each treatment. The expression ratio was performed using the \(2^{{ - \Updelta \Updelta C_{\text{T}} }}\) method (Livak Method; Livak and Schmittigen 2001). The qPCR analysis used UBC10 as the reference and microgravity as the calibrator. For arrays, the expression levels represent log2 value to baseline divided by the relative to expression from microgravity to baseline. The arrows point to corresponding axis label (DOCX 46 kb)

Suppl. Table S1 (XLSX 11 kb)

Suppl. Table S2 (XLSX 26 kb)

Suppl. Table S3 (XLSX 35 kb)

Suppl. Table S4 (XLSX 31 kb)

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Correll, M.J., Pyle, T.P., Millar, K.D.L. et al. Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes. Planta 238, 519–533 (2013). https://doi.org/10.1007/s00425-013-1909-x

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  • DOI: https://doi.org/10.1007/s00425-013-1909-x

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