Differential quantitative regulation of specific gene groups and pathways under drought stress in rice

Sharma, Eshan; Jain, Mukesh; Khurana, Jitendra P.

doi:10.1016/j.ygeno.2018.11.024

Cited by 16 publications

(10 citation statements)

References 61 publications

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“…In wheat species, there was a remarkable correlation of the drought tolerance at the gene-transcript level and the properties of the antioxidant enzymes, such as ascorbate peroxidase, superoxide dismutase, and glutathione peroxidase, of the same species [90]. The regulatory mechanism of differentially expressed genes (DEGs) was identified in rice under drought stress conditions [91].…”

Section: Expression Of Group II Lea Genes Under Drought Stressmentioning

confidence: 99%

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

et al. 2021

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In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants’ survival in adverse environments.

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Section: Expression Of Group II Lea Genes Under Drought Stressmentioning

confidence: 99%

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Thorough knowledge of stress tolerance mechanism can help in crop improvement and management. Divergent genes and pathways associated with desiccation stress are reported (Li et al ., 2016; Parvathi and Nataraja, 2017; Priya et al ., 2019; Sharma et al ., 2019; Azzouz-Olden et al ., 2020). In transgenic plants, stress-inducible genes such as LEA, HSPs, AREB/ABFs, bZIPs contributed to enhanced stress tolerance (Ali et al ., 2017).…”

Section: Introductionmentioning

confidence: 99%

Assessment of DNA methylation pattern under drought stress using methylation-sensitive randomly amplified polymorphism analysis in rice

Sapna¹,

Ashwini²,

Ramesh³

et al. 2020

Plant Genet. Resour.

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DNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

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“…Earlier, our approach was tested by a third-party group of researchers on the study of drought stress response in rice [6]. Authors detected differential quantitative regulation of some gene groups under drought stress conditions.…”

Section: Discussionmentioning

confidence: 99%

“…For example, auxin most strongly upregulates its signaling pathway but it is not the only positive response, as many processes were upregulated moderately (e.g., "histone modifications") and weakly (e.g., "translation" and "gene expression" in general). Sharma and co-authors found many GO terms that fold-change-specifically differ between drought-tolerant and drought-sensitive rice varieties [6]. Fold-change-specific GO terms were occasionally detected in animal transcriptomes as well, e.g., very weak but significant activation of immunity-related processes have been shown in [7].…”

Section: Introductionmentioning

confidence: 99%

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups

Wiebe

Omelyanchuk

Mukhin

et al. 2020

Genes

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Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.

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Differential quantitative regulation of specific gene groups and pathways under drought stress in rice

Cited by 16 publications

References 61 publications

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

Assessment of DNA methylation pattern under drought stress using methylation-sensitive randomly amplified polymorphism analysis in rice

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups

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