Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight

Abstract

Ionizing radiation present in extraterrestrial environment is an important factor that affects plants grown in spaceflight. Pearson correlation-based gene regulatory network inferencing from transcriptional responses of the plant Arabidopsis thaliana L. grown in real and simulated spaceflight conditions acquired by GeneLab, followed by topological and spectral analysis of the networks is performed. Gene regulatory subnetworks are extracted for DNA damage response processes. Analysis of radiation-induced ATR/ATM protein–protein interactions in Arabidopsis reveals interaction profile similarities under low radiation doses suggesting novel mechanisms of DNA damage response involving non-radiation-induced genes regulating other stress responses in spaceflight. The Jaccard similarity index shows that the genes AT2G31320, AT4G21070, AT2G46610, and AT3G27060 perform similar functions under low doses of radiation. The incremental association Markov blanket method reveals non-radiation-induced genes linking DNA damage response to root growth and plant development. Eighteen radiation-induced genes and sixteen non-radiation-induced gene players have been identified from the ATR/ATM protein interaction complexes involved in heat, salt, water, osmotic stress responses, and plant organogenesis. Network analysis and logistic regression ranking detected AT3G27060, AT1G07500, AT5G66140, and AT3G21280 as key gene players involved in DNA repair processes. High atomic weight, high energy, and gamma photon radiation result in higher intensity of DNA damage response in the plant resulting in elevated values for several network measures such as spectral gap and girth. Nineteen flavonoid and carotenoid pigment activations involved in pigment biosynthesis processes are identified in low radiation dose total light spaceflight environment but are not found to have significant regulations under very high radiation dose environment.

Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis

“…The genes differentially expressed in response to spaceflight share similarities with many documented terrestrial responses. Hallmarks of spaceflight responses include differential expression of genes involved in pathways associated with cell wall remodeling, reactive oxygen species (ROS), pathogen attacks, wounding, salt stress, drought stress, and hormone signaling ( Hoson et al, 2002 ; Gao et al, 2008 ; Salmi and Roux, 2008 ; Blancaflor, 2013 ; Correll et al, 2013 ; Paul et al, 2013 ; Zupanska et al, 2013 ; Ferl et al, 2014 ; Inglis et al, 2014 ; Nakashima et al, 2014 ; Sugimoto et al, 2014 ; Kwon et al, 2015 ; Schüler et al, 2015 ; Zhang et al, 2015 ; Ferl and Paul, 2016 ; Herranz et al, 2019 ; Vandenbrink et al, 2019 ; Barker et al, 2020 ; Califar et al, 2020 ; Kruse et al, 2020 ; Angelos et al, 2021 ; Manian et al, 2021b ). Plants further respond to spaceflight with changes in DNA methylation, again similarly to the epigenetic effects that occur during terrestrial stresses.…”

Detection of Target Genes for Drug Repurposing to Treat Skeletal Muscle Atrophy in Mice Flown in Spaceflight

“…The datasets were combined, and the significantly regulated genes were extracted using the Pearson correlation and Incremental Association Markov Blanket (IAMB) methods. For details on the implementation of Pearson correlation and IAMB, please refer to [ 32 ]. Pearson identified the most correlated genes and IAMB identified causally related genes.…”

Regulatory Network of Serine/Arginine-Rich (SR) Proteins: The Molecular Mechanism and Physiological Function in Plants

“…Besides the effect on the growth and development, the SR proteins work in response to stresses and hormones [ 81 , 82 , 83 , 84 , 85 , 86 ]. The hypersensitivity of expression regulation in response to environmental stresses of SR genes has been well studied in Arabidopsis and rice [ 66 , 81 ].…”