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

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 condit...

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Autores principales: Manian, Vidya, Orozco-Sandoval, Jairo, Diaz-Martinez, Victor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234954/
https://www.ncbi.nlm.nih.gov/pubmed/34205326
http://dx.doi.org/10.3390/genes12060938
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author Manian, Vidya
Orozco-Sandoval, Jairo
Diaz-Martinez, Victor
author_facet Manian, Vidya
Orozco-Sandoval, Jairo
Diaz-Martinez, Victor
author_sort Manian, Vidya
collection PubMed
description 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.
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spelling pubmed-82349542021-06-27 Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight Manian, Vidya Orozco-Sandoval, Jairo Diaz-Martinez, Victor Genes (Basel) Article 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. MDPI 2021-06-19 /pmc/articles/PMC8234954/ /pubmed/34205326 http://dx.doi.org/10.3390/genes12060938 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Manian, Vidya
Orozco-Sandoval, Jairo
Diaz-Martinez, Victor
Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title_full Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title_fullStr Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title_full_unstemmed Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title_short Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
title_sort detection of genes in arabidopsis thaliana l. responding to dna damage from radiation and other stressors in spaceflight
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234954/
https://www.ncbi.nlm.nih.gov/pubmed/34205326
http://dx.doi.org/10.3390/genes12060938
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