Transcriptome Profiling and Physiological Studies Reveal a Major Role for Aromatic Amino Acids in Mercury Stress Tolerance in Rice Seedlings

Chen, Yun An; Chang, Wen Chang; Trịnh, Ngọc Nam; Huang, Li; Chen, Ying-Chih; Chen, Kai; Huang, Tsai Lien; Lin, Chung Yi; Huang, Hao

doi:10.1371/journal.pone.0095163

Cited by 57 publications

(52 citation statements)

References 56 publications

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“…Phenylalanine, tyrosine, and tryptophan are essential components of proteins and precursors for various secondary metabolites that influence plant growth (Tzin and Galili 2010). Chen et al (2014) found that aromatic amino acids play important roles in confronting mercury (Hg) stress in rice seedlings. The phosphatidylinositol signaling system and the inositol phosphate metabolism pathway are also known to be involved in stress resistance.…”

Section: Transcriptome Analysis Of the Cold-tolerant Varietymentioning

confidence: 99%

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

Han

Cui

et al. 2020

Rice

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In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered 'strong', indicating that weedy rice populations indeed have relatively strong coldtolerance capacity as a whole, and the robust cold-tolerant varieties WR29 and WR157 were identified. Regression analysis showed that the metrics including the nitrogen recovery index, superoxide dismutase (SOD) content and malondialdehyde (MDA) content correlated significantly (P < 0.05) with cold tolerance and could be used as indicators of cold tolerance. On the basis of a transcriptome analysis of WR157, a robust cold-tolerant variety identified in this study, a total of 4645 putative DEGs were identified in treated groups compared to the control groups, with 2123 upregulated DEGs and 2522 downregulated DEGs. All upregulated DEGs were enriched on 1388 terms, all downregulated DEGs were enriched on 1566 terms; 911 of the 2123 upregulated DEGs fell into 98 KEGG categories and 1103 of the 2522 downregulated DEGs were in 115 categories. Further analysis showed that GO: 0019740 and GO:0006808 are involved in nitrogen utilization; GO:0009269 and GO:0009414 are related to the stress response; and GO:0016491 and GO:0016614 are related to oxidoreductase activity. Background: Weedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; however, the comprehensive mechanism governing its cold tolerance is poorly understood. Conclusion: Our comprehensive evaluation based on five morphological indices and nine physiological indicators revealed outstanding levels of cold-tolerance capacity among weedy rice varieties from different regions and revealed some terms related to cold tolerance via transcriptome analysis. Our results underscored the reliable evaluation methods for additional cold tolerance studies and revealed several genes related to cold tolerance, which will help researchers breed cultivated rice varieties to increase their cold-tolerance capacity. These traits have the ability to increase seedling survival rate and growth, as well as future yields.

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Section: Transcriptome Analysis Of the Cold-tolerant Varietymentioning

confidence: 99%

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

Han

Cui

et al. 2020

Rice

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“…Activity of ACS increased in B. juncea plants exposed to Cd (Asgher et al, 2014 ), Ni or Zn (Khan and Khan, 2014 ), as well as in Cd-exposed T. aestivum plants (Khan et al, 2015 ). Transcript levels of ACS and ACO genes were rapidly enhanced in Cu-exposed B. oleracea (Jakubowicz et al, 2010 ), Al-exposed A. thaliana (Sun et al, 2010 ), chromium (Cr)-exposed Oryza sativa (Trinh et al, 2014 ), and Hg-treated O. sativa (Chen et al, 2014 ) and M. sativa plants (Montero-Palmero et al, 2014a ). In addition, Cd was shown to enhance ACS gene expression in G. max (Chmielowska-Bąk et al, 2013 ) and ACS and/or ACO transcription in H. vulgare (Cao et al, 2014 ), O. sativa (Trinh et al, 2014 ) and A. thaliana plants (Herbette et al, 2006 ; Weber et al, 2006 ; Schellingen et al, 2014 ; Table 1 ).…”

Section: Metal Stress Affects Ethylene Biosynthesis and Signaling At mentioning

confidence: 99%

“…Recently, a whole-genome transcriptional profile from M. sativa seedlings exposed to 3 μM Hg for 3, 6 and 24 h demonstrated significant upregulation of several ethylene-responsive genes such as ERF1 , mostly during the earliest hours of exposure (Montero-Palmero et al, 2014a ). Similarly, Hg exposure affected genes related to ethylene signaling in M. truncatula (Zhou et al, 2013 ), O. sativa (Chen et al, 2014 ), H. vulgare plants (Lopes et al, 2013 ). Furthermore, roots of O. sativa plants exposed to 200 μM Cr for up to 3 h showed an increased expression of the EIN3;4 gene (Trinh et al, 2014 ), while the EIN2 gene was induced in Pb-exposed A. thaliana plants (Cao et al, 2009 ; Table 1 ).…”

Section: Metal Stress Affects Ethylene Biosynthesis and Signaling At mentioning

confidence: 99%

Ethylene and Metal Stress: Small Molecule, Big Impact

et al. 2016

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The phytohormone ethylene is known to mediate a diverse array of signaling processes during abiotic stress in plants. Whereas many reports have demonstrated enhanced ethylene production in metal-exposed plants, the underlying molecular mechanisms are only recently investigated. Increasing evidence supports a role for ethylene in the regulation of plant metal stress responses. Moreover, crosstalk appears to exist between ethylene and the cellular redox balance, nutrients and other phytohormones. This review highlights our current understanding of the key role ethylene plays during responses to metal exposure. Moreover, particular attention is paid to the integration of ethylene within the broad network of plant responses to metal stress.

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“…A total of eight previously published rice microarray data sets were downloaded from Gene Expression Omnibus database [(GSE IDs: GSE33375, GSE63152, GSE41719, GSE41733, GSE34899, GSE27413, and GSE34895) 1 ] ( Chi et al, 2011 , 2013 ; Huang et al, 2012 , 2014 ; Lin et al, 2013a , b ; Chen et al, 2014 ). Each data set was composed of three biological replicates.…”

Section: Methodsmentioning

confidence: 99%

“…Our previous works have revealed early molecular responses (1 and 3 h) of rice to individual rhizotoxins ( Chi et al, 2011 , 2013 ; Huang et al, 2012 , 2014 ; Lin et al, 2013a , b ; Chen et al, 2014 ). In the present study, we focused on the early GSR of rice by integrating previously published data.…”

Section: Introductionmentioning

confidence: 99%

Integrating Early Transcriptomic Responses to Rhizotoxins in Rice (Oryza sativa. L.) Reveals Key Regulators and a Potential Early Biomarker of Cadmium Toxicity

et al. 2017

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As sessile organisms, plants were constantly challenged with biotic and abiotic stresses. Transcriptional activation of stress-responsive genes is a crucial part of the plant adaptation to environmental changes. Here, early response of rice root to eight rhizotoxic stressors: arsenate, copper, cadmium, mercury, chromate, vanadate, ferulic acid and juglone, was analyzed using published microarray data. There were 539 general stress response (GSR) genes up-regulated under all eight treatments, including genes related to carbohydrate metabolism, phytohormone balance, and cell wall structure. Genes related to transcriptional coactivation showed higher Ka/Ks ratio compared to the other GSR genes. Network analysis discovered complicated interaction within GSR genes and the most connected signaling hubs were WRKY53, WRKY71, and MAPK5. Promoter analysis discovers enriched SCGCGCS cis-element in GSR genes. Moreover, GSR genes tend to be intronless and genes with shorter total intron length were induced in a higher level. Among genes uniquely up-regulated by a single stress, a phosphoenolpyruvate carboxylase kinase (PPCK) was identified as a candidate biomarker for detecting cadmium contamination. Our findings provide insights into the transcriptome dynamics of molecular response of rice to different rhizotoxic stress and also demonstrate potential use of comparative transcriptome analysis in identifying a novel potential early biomarker.

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Transcriptome Profiling and Physiological Studies Reveal a Major Role for Aromatic Amino Acids in Mercury Stress Tolerance in Rice Seedlings

Cited by 57 publications

References 56 publications

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

Ethylene and Metal Stress: Small Molecule, Big Impact

Integrating Early Transcriptomic Responses to Rhizotoxins in Rice (Oryza sativa. L.) Reveals Key Regulators and a Potential Early Biomarker of Cadmium Toxicity

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