Exploring a role for ROS-equilibrating enzymes in plant stress tolerance and SARS-CoV-2-infected human cells - an interdisciplinary approach that targets resilience prediction

Abstract

This thesis is organized into three chapters comprising comprehensive in silico studies on public experimental data from diverse species to strengthen our insights into alternative oxidase AOX ) and its complementary candidate genes as functional markers involved in reprogramming and host cell resilience prediction. The first chapter elucidates the un ique expression pattern and organization of the AOX family from Vitis vinifera , which has been declared a model plant to validate the AOX family as a functional marker. We explored the expression of the AOX gene family across developmental stages and in re sponse to several biotic and abiotic stress conditions associated with the hidden regulatory potential of large introns. Transcriptomic expression of AOX2 was constitutively or developmentally regulated throughout the experiments. However, we identified AO X2 alternative splicing (intron 1 dependent) that changes exon1 of normal AOX2 and is effectively linked to increasing temperature. AOX1a and 1d are associated with biotic and abiotic stress. In addition, the AOX intronic sequence assessment identified 16 microRNA (miRNA) candidates only in the AOX2 introns, including the master regulator of plant development and stress responses mir 398. Among them, nine were conserved and validated in other plant species, whereas seven were considered potential novel miRN A candidates from V. vinifera . Enrichment analysis of the miRNA targets revealed the hierarchical functions of miRNAs in gene regulatory networks. The target genes mainly encode transcription factors, enzymes, and DNA binding proteins and have a potential role in biological and metabolic pathways, including plant growth and developmental processes, pathogen defense mechanisms, and stress responsive processes.Chapter two begins with validating the defined sets of genes complemented by AOX , called `ReprogVir us,` potentially involved in early cell reprogramming and host cell resilience prediction. To investigate the role of cell reprogramming initiation in the defined sets of genes, we performed transcript level expression analyses of the most critical genes i n the transcriptomic data of the two rice cultivars with contrasting responses to salt stress (Pokkali tolerant and IR29 susceptible) over a short period of 24 h. Our data support the involvement of alternative pathways and glycolysis/fermentation in the m ore efficient stress response observed in a salt stress tolerant rice genotype. This response is primarily associated with adaptive ROS balancing by AOX (via AOX1a expression), effective tuning of the antioxidant system, and rapid energy production (via fe rmentation). Both contribute to sustaining and optimizing respiration. Chapter three proceeds with validating the transcriptome level profiles of the most critical marker candidates from the 'ReprogVirus' gene sets identifying the major complex trait for complex trait for early de novo programming early de novo programming ‘oV‘CoV--MACMAC--TED’ in cultured human nasal TED’ in cultured human nasal epithelial cells infected by two SARSepithelial cells infected by two SARS--CoVCoV--2 variants differing in disease severity2 variants differing in disease severity. Significant . Significant upregulation of the upregulation of the candidatecandidate genes revealed virusgenes revealed virus--induced ROS/RNS deinduced ROS/RNS de--balancing, balancing, differential gldifferential glycolysis, fermentation, and cell cycle regulation, essential for cell survival and ycolysis, fermentation, and cell cycle regulation, essential for cell survival and escape from stress.escape from stress. In shortIn short, this thesis elucidates the diverse potential of , this thesis elucidates the diverse potential of AOXAOX as a functional as a functional marker gene for predicting cell resilience and mediating cell reprogrammingmarker gene for predicting cell resilience and mediating cell reprogramming under stress. In under stress. In parallel, this study justified the function of genes potentially substituting the role of plant parallel, this study justified the function of genes potentially substituting the role of plant AOXAOX in virusin virus--infected human nasal epithelial cells (NECs) with pinfected human nasal epithelial cells (NECs) with promisingromising therapeutic therapeutic strategies.strategies.