Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.

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Genome-wide characterization of NtHD-ZIP IV: different roles in abiotic stress response and glandular Trichome induction

BMC Plant Biology ◽

10.1186/s12870-019-2023-4 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Hongying Zhang ◽

Xudong Ma ◽

Wenjiao Li ◽

Dexin Niu ◽

Zhaojun Wang ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Stress Responses ◽

Leucine Zipper ◽

Regulatory Gene ◽

Glandular Trichomes ◽

Glandular Trichome ◽

Tissue Expression ◽

Abiotic Stress Response ◽

Epidermal Development

Abstract Background The plant-specific homeodomain-leucine zipper class IV (HD-ZIP IV) gene family has been involved in the regulation of epidermal development. Results Fifteen genes coding for HD-ZIP IV proteins were identified (NtHD-ZIP-IV-1 to NtHD-ZIP-IV-15) based on the genome of N. tabacum. Four major domains (HD, ZIP, SAD and START) were present in these proteins. Tissue expression pattern analysis indicated that NtHD-ZIP-IV-1, − 2, − 3, − 10, and − 12 may be associated with trichome development; NtHD-ZIP-IV-8 was expressed only in cotyledons; NtHD-ZIP-IV-9 only in the leaf and stem epidermis; NtHD-ZIP-IV-11 only in leaves; and NtHD-ZIP-IV-15 only in the root and stem epidermis. We found that jasmonates may induce the generation of glandular trichomes, and that NtHD-ZIP-IV-1, − 2, − 5, and − 7 were response to MeJA treatment. Dynamic expression under abiotic stress and after application of phytohormones indicated that most NtHD-ZIP IV genes were induced by heat, cold, salt and drought. Furthermore, most of these genes were induced by gibberellic acid, 6-benzylaminopurine, and salicylic acid, but were inhibited by abscisic acid. NtHD-ZIP IV genes were sensitive to heat, but insensitive to osmotic stress. Conclusion NtHD-ZIP IV genes are implicated in a complex regulatory gene network controlling epidermal development and abiotic stress responses. The present study provides evidence to elucidate the gene functions of NtHD-ZIP IVs during epidermal development and stress response.

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An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Communications Biology ◽

10.1038/s42003-020-0866-8 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Carina Steliana Carianopol ◽

Aaron Lorheed Chan ◽

Shaowei Dong ◽

Nicholas J. Provart ◽

Shelley Lumba ◽

...

Keyword(s):

Abscisic Acid ◽

Abiotic Stress ◽

Stress Response ◽

Stress Responses ◽

Energy Homeostasis ◽

Plant Stress ◽

Interaction Network ◽

Abiotic Stress Response ◽

Functional Studies ◽

Transcriptional Changes

AbstractYeast Snf1 (Sucrose non-fermenting1), mammalian AMPK (5′ AMP-activated protein kinase) and plant SnRK1 (Snf1-Related Kinase1) are conserved heterotrimeric kinase complexes that re-establish energy homeostasis following stress. The hormone abscisic acid (ABA) plays a crucial role in plant stress response. Activation of SnRK1 or ABA signaling results in overlapping transcriptional changes, suggesting these stress pathways share common targets. To investigate how SnRK1 and ABA interact during stress response in Arabidopsis thaliana, we screened the SnRK1 complex by yeast two-hybrid against a library of proteins encoded by 258 ABA-regulated genes. Here, we identify 125 SnRK1- interacting proteins (SnIPs). Network analysis indicates that a subset of SnIPs form signaling modules in response to abiotic stress. Functional studies show the involvement of SnRK1 and select SnIPs in abiotic stress responses. This targeted study uncovers the largest set of SnRK1 interactors, which can be used to further characterize SnRK1 role in plant survival under stress.

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S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Frontiers in Plant Science ◽

10.3389/fpls.2021.802802 ◽

2022 ◽

Vol 12 ◽

Author(s):

Hong Wang ◽

Yunting Zhang ◽

Ayla Norris ◽

Cai-Zhong Jiang

Keyword(s):

Stress Response ◽

Plant Growth ◽

Fruit Quality ◽

Stress Responses ◽

Growth And Development ◽

Leucine Zipper ◽

Sugar Metabolism ◽

Bzip Transcription Factor ◽

Biological Functions ◽

Plant Growth And Development

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5′ leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

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Mediator Complex: A Pivotal Regulator of ABA Signaling Pathway and Abiotic Stress Response in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms21207755 ◽

2020 ◽

Vol 21 (20) ◽

pp. 7755

Author(s):

Leelyn Chong ◽

Pengcheng Guo ◽

Yingfang Zhu

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Rna Polymerase Ii ◽

Signaling Pathway ◽

Stress Responses ◽

Abiotic Stresses ◽

Current Knowledge ◽

Mediator Complex ◽

Aba Signaling ◽

Abiotic Stress Response

As an evolutionarily conserved multi-protein complex, the Mediator complex modulates the association between transcription factors and RNA polymerase II to precisely regulate gene transcription. Although numerous studies have shown the diverse functions of Mediator complex in plant development, flowering, hormone signaling, and biotic stress response, its roles in the Abscisic acid (ABA) signaling pathway and abiotic stress response remain largely unclear. It has been recognized that the phytohormone, ABA, plays a predominant role in regulating plant adaption to various abiotic stresses as ABA can trigger extensive changes in the transcriptome to help the plants respond to environmental stimuli. Over the past decade, the Mediator complex has been revealed to play key roles in not only regulating the ABA signaling transduction but also in the abiotic stress responses. In this review, we will summarize current knowledge of the Mediator complex in regulating the plants’ response to ABA as well as to the abiotic stresses of cold, drought and high salinity. We will particularly emphasize the involvement of multi-functional subunits of MED25, MED18, MED16, and CDK8 in response to ABA and environmental perturbation. Additionally, we will discuss potential research directions available for further deciphering the role of Mediator complex in regulating ABA and other abiotic stress responses.

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Plant Non-Coding RNAs: Origin, Biogenesis, Mode of Action and Their Roles in Abiotic Stress

International Journal of Molecular Sciences ◽

10.3390/ijms21218401 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8401

Author(s):

Joram Kiriga Waititu ◽

Chunyi Zhang ◽

Jun Liu ◽

Huan Wang

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Stress Responses ◽

Current Knowledge ◽

Fine Tuning ◽

Abiotic Stress Response ◽

Underlying Basis ◽

Substantial Progress ◽

Non Coding Rnas ◽

Sequencing And Expression

As sessile species, plants have to deal with the rapidly changing environment. In response to these environmental conditions, plants employ a plethora of response mechanisms that provide broad phenotypic plasticity to allow the fine-tuning of the external cues related reactions. Molecular biology has been transformed by the major breakthroughs in high-throughput transcriptome sequencing and expression analysis using next-generation sequencing (NGS) technologies. These innovations have provided substantial progress in the identification of genomic regions as well as underlying basis influencing transcriptional and post-transcriptional regulation of abiotic stress response. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as essential regulators of plants abiotic stress response. However, shared traits in the biogenesis of ncRNAs and the coordinated cross-talk among ncRNAs mechanisms contribute to the complexity of these molecules and might play an essential part in regulating stress responses. Herein, we highlight the current knowledge of plant microRNAs, siRNAs, and lncRNAs, focusing on their origin, biogenesis, modes of action, and fundamental roles in plant response to abiotic stresses.

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Genome- and Transcriptome-Wide Characterization of bZIP Gene Family Identifies Potential Members Involved in Abiotic Stress Response and Anthocyanin Biosynthesis in Radish (Raphanus sativus L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20246334 ◽

2019 ◽

Vol 20 (24) ◽

pp. 6334 ◽

Cited By ~ 3

Author(s):

Lianxue Fan ◽

Liang Xu ◽

Yan Wang ◽

Mingjia Tang ◽

Liwang Liu

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Leucine Zipper ◽

Anthocyanin Biosynthesis ◽

Functional Characterization ◽

Abiotic Stress Response ◽

Basic Leucine Zipper ◽

Promoter Sequences ◽

Encoding Genes

Basic leucine zipper (bZIP) transcription factors play crucial roles in various abiotic stress responses as well as anthocyanin accumulation. Anthocyanins are most abundant in colorful skin radish, which exhibit strong antioxidant activity that offers benefits for human health. Here, a total of 135 bZIP-encoding genes were identified from radish genome. Synteny analysis showed that 104 radish and 63 Arabidopsis bZIP genes were orthologous. Transcriptome analysis revealed that 10 RsbZIP genes exhibited high-expression levels in radish taproot (RPKM>10). Specifically, RsbZIP010 exhibited down-regulated expression under Cd, Cr and Pb stresses, whereas RsbZIP031 and RsbZIP059 showed significant down-regulation under heat and salt stresses, respectively. RT-qPCR analysis indicated that RsbZIP011 and RsbZIP102 were significantly up-regulated in the tissues of radish with high anthocyanin contents. Furthermore, the promoter sequences of 39 anthocyanin-related genes were found to contain G-box or ACE-box elements that could be recognized by bZIP family members. Taken together, several RsbZIPs might be served as critical regulators in radish taproot under Cd, Cr, Pb, heat and salt stresses. RsbZIP011 and RsbZIP102 were the potential participants in anthocyanin biosynthesis pathway of radish. These results facilitate further investigation on functional characterization of bZIP genes in response to abiotic stress and anthocyanin biosynthesis in radish.

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The bZIP Transcription Factor GmbZIP15 Negatively Regulates Salt- and Drought-Stress Responses in Soybean

International Journal of Molecular Sciences ◽

10.3390/ijms21207778 ◽

2020 ◽

Vol 21 (20) ◽

pp. 7778

Author(s):

Man Zhang ◽

Yanhui Liu ◽

Hanyang Cai ◽

Mingliang Guo ◽

Mengnan Chai ◽

...

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Drought Stress ◽

Stress Responses ◽

Negative Regulator ◽

Bzip Transcription Factor ◽

Antioxidant Enzyme Activities ◽

Oilseed Crop ◽

Abiotic Stress Response ◽

Salt And Drought Stress

Soybean (Glycine max), as an important oilseed crop, is constantly threatened by abiotic stress, including that caused by salinity and drought. bZIP transcription factors (TFs) are one of the largest TF families and have been shown to be associated with various environmental-stress tolerances among species; however, their function in abiotic-stress response in soybean remains poorly understood. Here, we characterized the roles of soybean transcription factor GmbZIP15 in response to abiotic stresses. The transcript level of GmbZIP15 was suppressed under salt- and drought-stress conditions. Overexpression of GmbZIP15 in soybean resulted in hypersensitivity to abiotic stress compared with wild-type (WT) plants, which was associated with lower transcript levels of stress-responsive genes involved in both abscisic acid (ABA)-dependent and ABA-independent pathways, defective stomatal aperture regulation, and reduced antioxidant enzyme activities. Furthermore, plants expressing a functional repressor form of GmbZIP15 exhibited drought-stress resistance similar to WT. RNA-seq and qRT-PCR analyses revealed that GmbZIP15 positively regulates GmSAHH1 expression and negatively regulates GmWRKY12 and GmABF1 expression in response to abiotic stress. Overall, these data indicate that GmbZIP15 functions as a negative regulator in response to salt and drought stresses.

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BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes

International Journal of Molecular Sciences ◽

10.3390/ijms22126437 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6437

Author(s):

Muthusamy Muthusamy ◽

Jonghee Kim ◽

Sukhee Kim ◽

Soyoung Park ◽

Sooin Lee

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

Stress Response ◽

Heat Shock ◽

Brassica Rapa ◽

Stress Responses ◽

Abiotic Stress Response ◽

Glucosinolate Biosynthesis ◽

Stress Response Genes ◽

Transgenic Lines

Plant phosphoprotein phosphatases are ubiquitous and multifarious enzymes that respond to developmental requirements and stress signals through reversible dephosphorylation of target proteins. In this study, we investigated the hitherto unknown functions of Brassica rapa protein phosphatase 5.2 (BrPP5.2) by transgenic overexpression of B. rapa lines. The overexpression of BrPP5.2 in transgenic lines conferred heat shock tolerance in 65–89% of the young transgenic seedlings exposed to 46 °C for 25 min. The examination of purified recombinant BrPP5.2 at different molar ratios efficiently prevented the thermal aggregation of malate dehydrogenase at 42 °C, thus suggesting that BrPP5.2 has inherent chaperone activities. The transcriptomic dynamics of transgenic lines, as determined using RNA-seq, revealed that 997 and 1206 (FDR < 0.05, logFC ≥ 2) genes were up- and down-regulated, as compared to non-transgenic controls. Statistical enrichment analyses revealed abiotic stress response genes, including heat stress response (HSR), showed reduced expression in transgenic lines under optimal growth conditions. However, most of the HSR DEGs were upregulated under high temperature stress (37 °C/1 h) conditions. In addition, the glucosinolate biosynthesis gene expression and total glucosinolate content increased in the transgenic lines. These findings provide a new avenue related to BrPP5.2 downstream genes and their crucial metabolic and heat stress responses in plants.

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NDR1 and the Arabidopsis Plasma Membrane ATPase AHA5 are Required for Processes that Converge on Drought Tolerance and Immunity

10.1101/2021.06.10.445978 ◽

2021 ◽

Author(s):

Yi-Ju Lu ◽

Huan Chen ◽

Alex Corrion ◽

Pai Li ◽

Ilker Buyuk ◽

...

Keyword(s):

Plasma Membrane ◽

Abiotic Stress ◽

Stress Response ◽

Pseudomonas Syringae ◽

Stress Responses ◽

Cell Biology ◽

Dependent Manner ◽

Abiotic Stress Response ◽

Biotic And Abiotic Stress ◽

Plasma Membrane Atpase

NON-RACE-SPECIFIC DISEASE RISISTANCE1 (NDR1) is a key component of plant immune signaling, required for defense against the bacterial pathogen Pseudomonas syringae. Plant stress responses have overlapping molecular, physiological, and cell biology signatures, and given the central role of NDR1 during biotic stress perception and signaling, we hypothesized that NDR1 also functions in abiotic stress responses, including in a role that mediates signaling at the plasma membrane (PM) - cell wall (CW) continuum. Here, we demonstrate that NDR1 is required for the induction of drought stress responses in plants, a role that couples stress signaling in an abscisic acid-dependent manner. We show that NDR1 physically associates with the PM-localized H+-ATPases AHA1, AHA2 , and AHA5 and is required for proper regulation of H+-ATPase activity and stomatal guard cell dynamics, providing a mechanistic function of NDR1 during drought responses. In the current study, we demonstrate that NDR1 functions in signaling processes associated with both biotic and abiotic stress response pathways, a function we hypothesize represents NDR1's role in the maintenance of cellular homeostasis during stress. We propose a role for NDR1 as a core transducer of signaling between cell membrane processes and intercellular stress response activation.

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

10.1101/558064 ◽

2019 ◽

Cited By ~ 2

Author(s):

Mohan Singh Rajkumar ◽

Rama Shankar ◽

Rohini Garg ◽

Mukesh Jain

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Abiotic Stress ◽

Stress Response ◽

Salinity Stress ◽

Stress Responses ◽

Rice Cultivars ◽

Abiotic Stress Response ◽

Methylation Patterns

AbstractDNA methylation is an epigenetic mark that controls gene expression in response to internal and environmental cues. In this study, we sought to understand the role of DNA methylation in response to desiccation and salinity stresses in three rice cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) via bisulphite sequencing. We identified DNA methylation patterns in different genomic/genic regions and analysed their correlation with gene expression. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. However, methylation in other sequence contexts and genic regions was negatively correlated with gene expression. DNA methylation was found to be most dynamic in CHH context under stress condition(s) in the rice cultivars. The expression profiles of genes involved in de-novo methylation were correlated with methylation dynamics. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stress, respectively, were correlated with higher expression of abiotic stress response related genes. Our results suggest an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. This study provides useful resource of DNA methylomes that can be integrated with other data to understand abiotic stress response in rice.HighlightBisulphite sequencing revealed single base resolution DNA methylation, and cultivar-specific differential methylation patterns and correlation with gene expression that control desiccation and salinity stress response in the rice cultivars.

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