Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Neto, Joao Braga de Abreu; Frei, Michael

doi:10.3389/fpls.2015.01260

Cited by 23 publications

(11 citation statements)

References 89 publications

(123 reference statements)

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“…Based on previous studies, antioxidant activity plays an important role in abiotic and even biotic stresses tolerance, but despite its important role in plant defense against osmotic stress, amount of up-regulated DEGs in this group was low in each tissue and in each stress, so that amount of this group was 1.4 and 0.94 percent in leaf and 0.85 and 1.1 percent in root respectively under drought and salt stresses. This kind of results has also been reported in earlier studies [25]. Genes encoded antioxidant activity are one of the most important genes in response to abiotic stresses.…”

Section: Resultssupporting

confidence: 88%

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Ghorbani

Alemzadeh

Razi

2019

Heliyon

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Microarray expression profile analysis is a useful approach to increase our knowledge about genes involved in regulatory networks and signal transduction pathways related to abiotic stress tolerance. Salt and drought, as two important abiotic stresses, adversely affect plant productivity in the world every year. To understand stress response mechanisms and identify genes and proteins which play critical roles in these mechanisms, the study of individual genes and proteins cannot be considered as an effective approach. On the other hand, the availability of new global data provides us an effective way to shed some light on the central role of molecules involved in stress response mechanisms in the plant. A meta-analysis of salt and drought stress responses was carried out using 38 samples of different experiments from leaves and roots of Arabidopsis plants exposed to drought and salt stresses. We figured out the number of differentially expressed genes (DEGs) was higher in roots under both stresses. Also, we found that the number of common DEGs under both stresses was more in roots and also the number of common DEGs in both tissues under salt stress was more than drought stress. The highest percent of DEGs was related to cell and cell part (about 87%). Around 9% and 7% of DEGs in roots and leaves encoded transcription factors, respectively. Network analysis revealed that three transcription factor families HSF, AP2/ERF and C2H2, may have critical roles in salt and drought stress response mechanisms in Arabidopsis and some proteins like STZ may be introduced as a new candidate gene for enhancing salt and drought tolerance in crop plants.

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Section: Resultssupporting

confidence: 88%

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Ghorbani

Alemzadeh

Razi

2019

Heliyon

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“…Sixty genes associated with drought stress in rice were identified through a structured literature survey from meta-analysis data [ 44 – 46 ]. Then the genes were divided based on their expression levels under drought condition into three categories: high-, intermediate- and low-expression genes.…”

Section: Methodsmentioning

confidence: 99%

“…For validation of discriminating power and accuracy of the ARSCU, 60 other rice genes were randomly selected from 43233 genes studied for their response to drought stress [44] and their ARSCU were calculated by the program (S2 Table). The results were correlated with the expression datafrom the published meta-analysis [44]. ARSCU calculator was able to predict genes with different expression level under drought stress in rice with an accuracy of 88.3%) Fig 4B).…”

Section: Validation Of Discriminating Power Of Arscumentioning

confidence: 99%

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

et al. 2020

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We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.

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“…It was striking that the aforementioned metallochaperone ZmHIPP27 is one common stress-responsive gene (Table 3 ), and this is reminiscent of its rice ortholog OsHIPP42, which was one of the HIPPs associated with the response to a wide range of abiotic stresses including heavy metal (As, Cd, Cr, and Pb) toxicity [ 74 ]. HIPPs are unique to vascular plants and function in heavy metal homeostasis and regulating the transcriptional response to abiotic stresses and pathogens [ 41 , 75 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

Cheng

Ming

et al. 2018

BMC Genomics

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BackgroundMetal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress.ResultsTo unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress.Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize.Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves.ConclusionsThese novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5109-8) contains supplementary material, which is available to authorized users.

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Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Cited by 23 publications

References 89 publications

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

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