Integrative transcriptomics and proteomics profiling of Arabidopsis thaliana elucidates novel mechanisms underlying spaceflight adaptation

Gbolaga O Olanrewaju; Natasha J Haveman; Michael J Naldrett; Anna-Lisa Paul; Robert J Ferl; Sarah E Wyatt

doi:10.3389/fpls.2023.1260429

Integrative transcriptomics and proteomics profiling of Arabidopsis thaliana elucidates novel mechanisms underlying spaceflight adaptation

Front Plant Sci. 2023 Nov 27:14:1260429. doi: 10.3389/fpls.2023.1260429. eCollection 2023.

Authors

Gbolaga O Olanrewaju^{1

2}, Natasha J Haveman³, Michael J Naldrett⁴, Anna-Lisa Paul^{5

6}, Robert J Ferl^{5

7}, Sarah E Wyatt^{1

2}

Affiliations

¹ Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States.
² Department of Environmental and Plant Biology, Ohio University Athens, OH, United States.
³ NASA Utilization & Life Sciences Office (UB-A), Kennedy Space Center, Merritt Island, FL, United States.
⁴ Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, United States.
⁵ Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States.
⁶ Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States.
⁷ Office of Research, University of Florida, Gainesville, FL, United States.

Abstract

Spaceflight presents a unique environment with complex stressors, including microgravity and radiation, that can influence plant physiology at molecular levels. Combining transcriptomics and proteomics approaches, this research gives insights into the coordination of transcriptome and proteome in Arabidopsis' molecular and physiological responses to Spaceflight environmental stress. Arabidopsis seedlings were germinated and grown in microgravity (µg) aboard the International Space Station (ISS) in NASA Biological Research in Canisters - Light Emitting Diode (BRIC LED) hardware, with the ground control established on Earth. At 10 days old, seedlings were frozen in RNA-later and returned to Earth. RNA-seq transcriptomics and TMT-labeled LC-MS/MS proteomic analysis of cellular fractionates from the plant tissues suggest the alteration of the photosynthetic machinery (PSII and PSI) in spaceflight, with the plant shifting photosystem core-regulatory proteins in an organ-specific manner to adapt to the microgravity environment. An overview of the ribosome, spliceosome, and proteasome activities in spaceflight revealed a significant abundance of transcripts and proteins involved in protease binding, nuclease activities, and mRNA binding in spaceflight, while those involved in tRNA binding, exoribonuclease activity, and RNA helicase activity were less abundant in spaceflight. CELLULOSE SYNTHASES (CESA1, CESA3, CESA5, CESA7) and CELLULOSE-LIKE PROTEINS (CSLE1, CSLG3), involved in cellulose deposition and TUBULIN COFACTOR B (TFCB) had reduced abundance in spaceflight. This contrasts with the increased expression of UDP-ARABINOPYRANOSE MUTASEs, involved in the biosynthesis of cell wall non-cellulosic polysaccharides, in spaceflight. Both transcripts and proteome suggested an altered polar auxin redistribution, lipid, and ionic intracellular transportation in spaceflight. Analyses also suggest an increased metabolic energy requirement for plants in Space than on Earth, hence, the activation of several shunt metabolic pathways. This study provides novel insights, based on integrated RNA and protein data, on how plants adapt to the spaceflight environment and it is a step further at achieving sustainable crop production in Space.

Keywords: Arabidopsis; BRIC LED; International Space Station; RNAseq; TMT; gravitropism; proteomics; spaceflight.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was partially funded by the National Aeronautics and Space Administration (NASA) Science Mission Directorate grants NASA#80NSSC19K1481 to SW, and NASA#80NSSC19K0130 to A-LP and RF. NASA employees had a key role in payload management, delivery, and processing but otherwise had no direct involvement in sample processing or downstream analysis.