scholarly journals Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ke Mao ◽  
Jie Yang ◽  
Min Wang ◽  
Huayu Liu ◽  
Xin Guo ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Plant Species ◽  
Stress Responses ◽  
Calcium Transport ◽  
Sequence Similarity ◽  
Structural Basis ◽  
Functional Study ◽  
Transport Capacity ◽  
Abiotic Stress Response

Abstract Background Calcium (Ca2+) plays an important role in plant growth and development, and the maintenance of calcium homeostasis is necessary for the survival of all plant species. Ca2+/H+ exchangers (CAXs) are a subgroup of the CaCA (Ca2+/cation antiporter) superfamily. In general, CAX proteins mediate cytosolic Ca2+ entry into vacuoles to prevent excessive accumulation of Ca2+ in the cytosol. The CaCA superfamily has been identified and characterised in many plant species; however, characterisation of the CaCA superfamily and functional study of apple CAX proteins have yet to be conducted in apple (Malus × domestica Borkh.). Results Here, we identified 21 CaCA family proteins in apple for the first time. Phylogenetic and gene structure analysis, as well as prediction of conserved motifs, suggested that these proteins could be classified into four groups: CAX, CCX, NCL, and MHX. Expression analysis showed that the 10 MdCAX genes we cloned strongly responded to calcium and abiotic stress treatments. Collinearity analysis and characterisation of calcium transport capacity resulted in the identification of a pair of segmental duplication genes: MdCAX3L-1 and MdCAX3L-2; MdCAX3L-2 showed strong calcium transport capacity, whereas MdCAX3L-1 showed no calcium transport capacity. Yeast two-hybrid (Y2H) assays showed that these two proteins could interact with each other. The high sequence similarity (94.6%) makes them a good model for studying the crucial residues and structural basis of the calcium transport of CAX proteins. Prediction of the protein interaction network revealed several proteins that may interact with CAX proteins and play important roles in plant stress responses, such as SOS2, CXIP1, MHX, NRAMP3, and MTP8. Conclusions Our analysis indicated that MdCAX proteins have strong calcium transport capacity and are involved in the abiotic stress response in apple. These findings provide new insight and rich resources for future studies of MdCAX proteins in apple.

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

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.

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

2020 ◽  
Vol 3 (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.

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

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10785
Author(s):  
Xue Yong ◽  
Tangchun Zheng ◽  
Xiaokang Zhuo ◽  
Sagheer Ahmad ◽  
Lulu Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Ornamental Plants ◽  
Evolutionary Relationship ◽  
Bzip Transcription Factor ◽  
Abiotic Stress Response ◽  
Flower Bud ◽  
Rosaceae Species

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.

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

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.

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

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.

scholarly journals Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuanda Lv ◽  
Fengqin Hu ◽  
Yongfeng Zhou ◽  
Feilong Wu ◽  
Brandon S. Gaut
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Transposable Elements ◽  
Rna Sequencing ◽  
Sequence Similarity ◽  
Long Terminal Repeat Retrotransposons ◽  
Differentially Expressed ◽  
Abiotic Stress Response ◽  
Total Rna ◽  
Non Coding Rnas

Abstract Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

scholarly journals 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

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.

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

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.

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

2019 ◽  
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.

scholarly journals Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops

2021 ◽  
Vol 12 ◽  
Author(s):  
Fredilson Veiga Melo ◽  
M. Margarida Oliveira ◽  
Nelson J. M. Saibo ◽  
Tiago Filipe Lourenço
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Stress Responses ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Post Translational Modification ◽  
Abiotic Stress Response ◽  
Physiological Mechanisms ◽  
Recent Developments ◽  
Mechanism Specificity

Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.

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