Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress

Khan, Sardar-Ali; Li, Mengzhan; Wang, Suo-Min; Yin, Hengfu

doi:10.3390/ijms19061634

Cited by 202 publications

(136 citation statements)

References 234 publications

(276 reference statements)

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“…Unlike animals, plants are sessile in nature and responses to abiotic stress are associated with activation of gene regulatory networks and pathways involved in stress response (Shinozaki et al ., 2007; Zeller et al ., 2009). The role of transcription factors and signal transduction components in adaptive stress responses has been revealed (Xiong et al ., 2001; Mizoi et al ., Zhu et al ., 2016; Khan et al ., 2018). Epigenetic modifications associated with chromatin re-organization can also play significant role in stress responses (Bruce et al ., 2007; Probst et al ., 2015; Garg et al ., 2015; Neto et al ., 2017).…”

Section: Introductionmentioning

confidence: 99%

Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars

Rajkumar

Shankar

Garg

et al. 2019

Preprint

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Word count: 5338 25 26Highlight: Bisulphite sequencing revealed single base resolution DNA methylation, and 27 cultivar-specific differential methylation patterns and correlation with gene expression that 28 control desiccation and salinity stress response in the rice cultivars. 29 30 2 Abstract 31 DNA methylation is an epigenetic mark that controls gene expression in response to internal and 32 environmental cues. In this study, we sought to understand the role of DNA methylation in 33 response to desiccation and salinity stresses in three rice cultivars (IR64, stress-sensitive; 34Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) via bisulphite sequencing. We 35 identified DNA methylation patterns in different genomic/genic regions and analysed their 36 correlation with gene expression. Methylation in CG context within gene body and methylation 37 in CHH context in distal promoter regions were positively correlated with gene expression. 38However, methylation in other sequence contexts and genic regions was negatively correlated 39 with gene expression. DNA methylation was found to be most dynamic in CHH context under 40 stress condition(s) in the rice cultivars. The expression profiles of genes involved in de-novo 41 methylation were correlated with methylation dynamics. Hypomethylation in Nagina 22 and 42 hypermethylation in Pokkali in response to desiccation and salinity stress, respectively, were 43 correlated with higher expression of abiotic stress response related genes. Our results suggest an 44 important role of DNA methylation in abiotic stress responses in rice in cultivar-specific 45 manner. This study provides useful resource of DNA methylomes that can be integrated with 46 other data to understand abiotic stress response in rice. 47 48 49

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Section: Introductionmentioning

confidence: 99%

Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars

Rajkumar

Shankar

Garg

et al. 2019

Preprint

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“…The population in our planet is projected to rise to 9 billion by the year 2050 (Hussain., 2006), together with the rapid changes in climate there is an urgent need to speed up the productivity of major crops. Understanding molecular mechanisms and mining stress-responsive genes that control plant responses to different abiotic stresses is a major prerequisite in the development of stress-resistant and high yielding crop varieties (Khan et al, 2018). To safeguard the global food production, crops (like maize) that are well adapted to adverse environmental conditions should be established (Vinocur and Altman, 2005).…”

Section: Resultsmentioning

confidence: 99%

“…A diagrammatic representation of gene expression and abiotic stress signal perception in plants via ABA-independent and ABA-dependent pathways (Modified fromGahlaut et al, 2016;Khan et al, 2018).Abbreviations: Abscisic acid (ABA), Reactive oxygen species (ROS), myeloblastosis oncogene (MYB), myelocytomatosis oncogene (MYC), Zincfinger homeodomain (ZF-HD) regulon, ABA-responsive element binding protein (AREB), ABAindependent regulons include; the NAC (CUC, NAM and ATAF), The cis-acting element (DRE), ABA-binding factor (ABF), The cis-acting element (CRE), Dehydration responsive element binding proteins (DREBs), C-repeat (CRT), (ZFR) zinc finger RNA binding protein, (NARC) NAC recognition site, (MYBRS) MYB recognition site, (MYCRS) MYC recognition site, Nuclear transcription factor Y (NF-Y), Heat Shock Factors (HSFs), Inducer of CBF Expression (ICE).…”

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confidence: 99%

Peer Review #1 of "Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era (v0.1)"

Mohamed¹

2019

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Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in various regions around the world, and recently, this has become a constant threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activities of transcription factors, which are families of genes coding for specific transcription factor proteins. Transcription factor target genes form a regulon that is involved in the repression/activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each transcription factor family, the downstream target genes they regulate, and the specific transcription factor genes involved in multiple abiotic stress responses in maize and other staple crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons that are involved in abiotic stress regulation will be briefly discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from different plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize that take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq. Conclusion: In conclusion, it is expected that all the information provided in this review will in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

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“…Plants utilize receptors, membrane channels, various types of kinases and phosphatases, ion fluxes, calcium/calmodulin interactive proteins, reactive oxygen species (ROS) and phytohormones for sensing and signaling different types of stresses [1]. Transcription factors (TFs) participate in the signaling cascades, and are a key component in regulating gene expression in response to biotic and abiotic stresses and in growth and development [2,3]. While there are about 60 different transcription factor families in plants [4], several families are more frequently associated with biotic and abiotic stress responses in plants, such as MYB (v-myb avian myeloblastosis viral oncogene homolog) [5], bHLH [6], AP2/ERF [7,8], WRKY [9], NAC [10], and bZIP transcription factors [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor

2020

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Background: Biotic and abiotic stresses are the major cause of reduced growth, persistence, and yield in agriculture. Over the past decade, RNA-Sequencing and the use of transgenics with altered expression of stress related genes have been utilized to gain a better understanding of the molecular mechanisms leading to salt tolerance in a variety of species. Identification of transcription factors that, when overexpressed in plants, improve multiple stress tolerance may be valuable for crop improvement, but sometimes overexpression leads to deleterious effects during normal plant growth. Results: Brachypodium constitutively expressing the BdbZIP26:GFP gene showed reduced stature compared to wild type plants (WT). RNA-Seq analysis comparing WT and bZIP26 transgenic plants revealed 7772 differentially expressed genes (DEGs). Of these DEGs, 987 of the DEGs were differentially expressed in all three transgenic lines. Many of these DEGs are similar to those often observed in response to abiotic and biotic stress, including signaling proteins such as kinases/phosphatases, calcium/calmodulin related proteins, oxidases/reductases, hormone production and signaling, transcription factors, as well as disease responsive proteins. Interestingly, there were many DEGs associated with protein turnover including ubiquitin-related proteins, F-Box and U-box related proteins, membrane proteins, and ribosomal synthesis proteins. Transgenic and control plants were exposed to salinity stress. Many of the DEGs between the WT and transgenic lines under control conditions were also found to be differentially expressed in WT in response to salinity stress. This suggests that the over-expression of the transcription factor is placing the plant in a state of stress, which may contribute to the plants diminished stature. Conclusion: The constitutive expression of BdbZIP26:GFP had an overall negative effect on plant growth and resulted in stunted plants compared to WT plants under control conditions, and a similar response to WT plants under salt stress conditions. The results of gene expression analysis suggest that the transgenic plants are in a constant state of stress, and that they are trying to allocate resources to survive.

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Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress

Cited by 202 publications

References 234 publications

Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars

Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars

Peer Review #1 of "Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era (v0.1)"

Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor

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