TRANSCRIPTOMIC ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN ANTIOXIDANT ENZYME MUTANTS
Keywords:
Antioxidant Enzymes, Oxidative Stress, Reactive Oxygen Species, TranscriptomicAnalysis, Transcriptional RegulationAbstract
Reactive oxygen species (ROS) are key regulators of cellularsignallingand stress responses in plants.Antioxidant enzymes maintain redox homeostasis by controlling ROS accumulation. Mutationsaffecting antioxidant pathways can disrupt cellular balance and trigger extensive transcriptionalchanges. Understanding the transcriptional responses associated with antioxidant enzyme mutants isimportant for elucidating molecular mechanisms of oxidative stress regulation. The present studyaimed to identify differentially expressed genes and regulatory mechanisms associated withantioxidant enzyme mutants using transcriptomic data analysis. A secondary transcriptomic datasetobtained from a publicly available repository wasanalysedto evaluate gene expression changesacross antioxidant-related mutants,including vtc1, vtc2, cat2, aox1a, tapx, and sal1. Differentiallyexpressed genes were identified based on fold-change patterns, followed by functional annotation todetermine associated biological processes. Promoter analysis was conducted to identify ROS-responsive transcription factors and potential regulatory motifs controlling candidate geneexpression.The results showed that there are significant changes in the expression of genes inantioxidant enzyme mutants. The genes are related to oxidative stress response, metabolic regulation,signal transduction, and homeostasis. Both unique and common changes were found in the mutants.This implies that there are common oxidative stresssignallingpathways. The promoter analysisshowed that many ROS-responsive transcription factors are related to differentially expressed genes.The results showed that disruption of antioxidant enzyme pathways causes extensive transcriptionalreprogramming related to stress response genes. The results can be used to understand the regulationof genes depending on redox status and can be used to improve stress tolerance in plants.
References
Molina-Márquez A, Kelterborn S, Hegemann P, Pérez-Rodríguez M, Vigara J and León R,
(2026). Characterization of phytoene desaturase knockout carotenoid-deficient microalgalmutants generated by CAS9-ribonucleoproteincomplexes. Physiologia Plantarum. 178:e70811.DOI: 10.1111/ppl.70811.
Mekureyaw MF, Pandey C, Sorty AM, Hennessy RC, Nicolaisen MH, Liu F and others, (2026).
Biofilm formation byPseudomonas putidaKT2440 contributes to improve tomato drought stressresilience and priming for enhanced gene regulation. J. Plant Physiol. 317:154704. DOI:10.1016/j.jplph.2026.154704.
Jia C, Yang H, Yang T, Yu Q, Wang J and Wang B, (2025). Comprehensive metabolomic and
transcriptomic analyses reveal SlSnRK2.6/SlCHPP-SlbHLH95-SlPDS module regulating tomatofruit carotene biosynthesis. J. Agric. Food Chem. 73:28493-28510. DOI:10.1021/acs.jafc.5c04313.
Cao L, Zhang D, Fahim AM, Liu H, Zhang Z, Hu D and others, (2025). Comprehensive
transcriptome analysis provides molecular insights into the heterosis-associated drought toleranceand reveals ZmbHLH137 that promotes drought tolerance in maize seedlings. Front. Plant Sci.16:1565650. DOI: 10.3389/fpls.2025.1565650.
Liu J, Cui W, Zhang Y, Dong J, Sun Z and Mandlaa, (2025). Factors affecting ethanol tolerance
inKazachstania unisporaMkaz: membrane characteristics and antioxidative stress. FoodMicrobiol. 131:104801. DOI: 10.1016/j.fm.2025.104801.
Hu S, Luo K, Tang T, Ma G, Peng Y, Zhang Y and others, (2025). Characterization of a
topramezone-resistant rice mutant TZR1: insights into GST-mediated detoxification andantioxidant responses. Plants. 14:425. DOI: 10.3390/plants14030425.
Xu R, Li AP, Tan X, Tang X, He XP, Wang LX and others, (2024). Patchouli essential oil extends
the lifespanand healthspan ofCaenorhabditis elegansthrough JNK-1/DAF-16. Life Sci.360:123270. DOI: 10.1016/j.lfs.2024.123270.
Zhou Z, Zhi T, Zou J and Chen G, (2024). Transcriptome analysis to identify genes related to
programmed cell death resulted from manipulating of BnaFAH ortholog by CRISPR/Cas9 in
Brassica napus. Sci. Rep. 14:26389. DOI: 10.1038/s41598-024-77877-7.
Şen A, Gümüş T, Temel A, Öztürk İ and Çelik Ö, (2024). Biochemical and proteomic analyses in
drought-tolerant wheat mutants obtained by gamma irradiation. Plants. 13:2702. DOI:10.3390/plants13192702.
Zhang H, Zhang H, Wu Y, Zhang H, Zhang H, Sun N and others, (2024). AtMYB72 aggravates
photosynthetic inhibition and oxidative damage inArabidopsis thalianaleaves. Plant SignalBehav. DOI: 10.1080/15592324.2024.2371694.
Funkner K, Poehlein A, Jehmlich N, Egelkamp R, Daniel R, Von Bergen M and others, (2024).
Proteomic and transcriptomic analysis of selenium utilization inMethanococcus maripaludis.mSystems. 9:e0133823. DOI: 10.1128/msystems.01338-23.
Hu Y, Zhao H, Xue L, Nie N, Zhang H, Zhao N and others, (2024). IBMYC2 contributes to salt
and drought stress tolerance via modulating anthocyanin accumulation and ROS-scavengingsystem in sweet potato. Int. J. Mol. Sci. 25:2096. DOI: 10.3390/ijms25042096.
Liu Y, Li Y, Wang A, Xu Z, Li C, Wang Z and others, (2024). Enhancing cold resistance in banana
(Musa spp.) through EMS-induced mutagenesis and L-Hyp pressure selection: phenotypicalterations, biomass composition and transcriptomic insights. BMC Plant Biol. 24:101. DOI:10.1186/s12870-024-04775-5.
Qiao Q, Wu C, Cheng TT, Yan Y, Zhang L, Wan YL and others, (2022). Comparative analysis of
the metabolome and transcriptome between the green and yellow-green regions of variegatedleaves in a mutant variety ofthe tree speciesPteroceltis tatarinowii. Int. J. Mol. Sci. 23:4950.DOI: 10.3390/ijms23094950.
Poli Y, Nallamothu V, Hao A, Goud MD, Wang X, Desiraju S and others, (2021). NH787 EMS
mutant of rice variety Nagina22 exhibits higher phosphate use efficiency.Sci. Rep. 11:9156. DOI:10.1038/s41598-021-88419-w.
Mishra S, Ganapathi TR and Srivastava A, (2022). Abiotic stress induced common-alarm signals
in plants. Mendeley Data. DOI: 10.17632/pb9xfsp4tw.2.
Xiong E, Dong G, Chen F, Zhang C, Li S, Zhang Y and others, (2020). Formyl tetrahydrofolate
deformylase affects hydrogen peroxide accumulation and leaf senescence by regulating folatestatus and redox homeostasis in rice. Sci. China Life Sci. 64:720-738. DOI: 10.1007/s11427-020-1773-7.
Wang D, Ren K, Tong S, Ying S and Feng M, (2020). Pleiotropic effects of Ubi4, a polyubiquitin
precursor required for ubiquitin accumulation, conidiation and pathogenicity of a fungal insectpathogen. Environ. Microbiol. 22:2564-2580. DOI: 10.1111/1462-2920.14940.
Keleku-Lukwete N, Suzuki M, Panda H, Otsuki A, Katsuoka F, Saito R and others, (2019). Nrf2
activation in myeloid cells and endothelial cells differentially mitigates sickle cell diseasepathology in mice. Blood Adv. 3:1285-1297. DOI: 10.1182/bloodadvances.2018017574.
LiZ, Pan X, Guo X, Fan K and Lin W, (2019). Physiological and transcriptome analyses of early
leaf senescence for ospls1 mutant rice (Oryza sativa L.) during the grain-filling stage. Int. J. Mol.Sci. 20:1098. DOI: 10.3390/ijms20051098.
Gil JV, Fuentes C, Verde MÁ, Miralles A, De Las Heras S, Fernández JM and others, (2026).
Phenocopies in acute lymphoblastic leukemia: redefining leukemia subtypes in the transcriptomicera. Blood Rev. DOI: 10.1016/j.blre.2026.101383.
Badiale G, Cervellera CF, Tonnini G, Pellati A, Romanelli MG, Corsi A and others, (2026). Hsa-
microRNA-34a-5p inhibits virus-negative Merkel cell carcinoma cell proliferation and migrationby regulating cell cycle-and EMT-related pathways and suppresses tumor spheroid formation. J.Dermatol. Sci.DOI: 10.1016/j.jdermsci.2026.02.002.
Xue Q, Xiao P, Yuan H, Zhao J, Liu B, He H and others, (2026). Quercetagetin phospholipid
complex self-microemulsifying delivery system for enhanced oral delivery and alcoholic liverinjury protection. Food Res. Int. 231:118773. DOI: 10.1016/j.foodres.2026.118773.
Authors unknown, (2026). Comparative phytotoxicity of phenanthrene and pyrene toLeymus
chinensis: insights from physiological and transcriptomic responses. Ecotoxicol. Environ. Saf.DOI: 10.1016/j.ecoenv.2026.120013.
Wang S, Li J, Chen Y, Gao T, Yong T, Zeng T and others, (2026). Oridonin derivative DLC13
targeting proliferating cell nuclear antigen to overcome oxaliplatin resistance in colorectal cancer.Drug Resist. Updates. DOI: 10.1016/j.drup.2026.101390.
