Abstract
The transcriptomic datasets of the plant model organism Arabidopsis thaliana grown in the International Space Station provided by GeneLab have been mined to isolate the impact of spaceflight microgravity on gene expressions related to root growth. A set of computational tools is used to identify the hub genes that respond differently in spaceflight with controlled lighting compared to on the ground. These computational tools based on graph-theoretic approaches are used to infer gene regulatory networks from the transcriptomic datasets. The three main algorithms used for network analyses are Least Absolute Shrinkage and Selection Operator (LASSO), Pearson correlation, and the Hyperlink-Induced Topic Search (HITS) algorithm. Graph-based spectral analyses reveal distinct properties of the spaceflight microgravity networks for the Wassilewskija (WS), Columbia (Col)-0, and mutant phytochromeD (phyD) ecotypes. The set of hub genes that are significantly altered in spaceflight microgravity are mainly involved in cell wall synthesis, protein transport, response to auxin, stress responses, and catabolic processes. Network analysis highlights five important root growth-regulating hub genes that have the highest outdegree distribution in spaceflight microgravity networks. These concerned genes coding for proteins are identified from the Gene Regulatory Networks (GRNs) corresponding to spaceflight total light environment. Furthermore, network analysis uncovers genes that encode nucleotide-diphospho-sugar interconversion enzymes that have higher transcriptional regulation in spaceflight microgravity and are involved in cell wall biosynthesis.
Highlights
Gravity plays a key role in plant growth [1]
We show that the GRN generated for the GeneLab Arabidopsis datasets are sparse networks or graphs
Two columns of 20,000 samples of gene expression values of Arabidopsis ecotypes WS and Col-0 root growth in spaceflight from GLDS-7 and GLDS-120 datasets are plotted in Figure 2 (A) and (B), respectively
Summary
Gravity plays a key role in plant growth [1]. Arabidopsis thaliana (Arabidopsis) is a flowering plant that has been chosen by biologists as a model plant organism to study the effects of gravity and other environmental stressors, since it has a short life cycle and because of the existence of a multitude of mutants and transgenic plants. The current visibility of Arabidopsis research reflects the growing realization among biologists that this simple angiosperm can serve as a convenient model for plant biology and for addressing fundamental questions of biological structure and function common to all Eukaryotes [2]. The International Space Station (ISS) is currently equipped with all capabilities to collect data needed to address fundamental questions of plant physiology and development in spaceflight microgravity [3]. The effect of gravity and mechanical stimulation on the growth of the root apex of Arabidopsis has resulted in transient changes in gene expressions [5]. The effect of spaceflight microgravity on Arabidopsis root growth is presented in [6]. Cell wall modeling in the roots, shoots, and hypocotyls of plants is an important metabolic adaptation brought about by genes and proteins. Several of the cell wall proteome changes have been corroborated with transcriptomic changes in spaceflight [8]
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