Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress

Overexpression of soybean GmDHN9 gene enhances drought resistance of transgenic Arabidopsis

Soybean is one of the important oil crops and a major source of protein and lipids. Drought can cause severe soybean yields. Dehydrin protein (DHN) is a subfamily of LEA proteins that play an important role in plant responses to abiotic stresses. In this study, the soybean GmDHN9 gene was cloned and induced under a variety of abiotic stresses. Results showed that the GmDHN9 gene response was more pronounced under drought induction. Subcellular localization results indicated that the protein was localized in the cytoplasm. The role of transgenic Arabidopsis plants in drought stress response was further studied. Under drought stress, the germination rate, root length, chlorophyll, proline, relative water content, and antioxidant enzyme content of transgenic Arabidopsis thaliana transgenic genes were higher than those of wild-type plants, and transgenic plants contained less O2-, H2O2 and MDA contents. In short, the GmDHN9 gene can regulate the homeostasis of ROS and enhance the drought resistance of plants.

Isolation and functional characterization of cold-induced gene (AmCIP) promoter from Ammopiptanthus mongolicus

AmCIP is a dehydrin-like protein which involved in abiotic stress tolerance in xerophytes evergreen woody plant A. mongolicus. AmCIP could be induced in the cotyledon and radicle during cold acclimation. To further elucidate the regulation of the upstream region of the gene, we isolated and characterized the promoter of AmCIP. Herein, a 1115 bp 5'-flanking region of AmCIP genomic DNA was isolated and cloned by genome walking from A. mongolicus and the segment sequence was identified as "PrAmCIP" promoter. Analysis of the promoter sequence revealed the presences of some basic cis-acting elements, which were related to various environmental stresses and plant hormones. GUS histochemical staining of transgene tobacco showed that PrAmCIP was induced by 4℃, 55℃, NaCl, mannitol and ABA, whereas it could hardly drive GUS gene expression under normal conditions. Furthermore, we constructed three deletion fragments and genetically transformed them into Arabidopsis thaliana. GUS histochemical staining showed that the MYCATERD1 element of the CP7 fragment (-189 ∼ -1) may be a key element in response to drought. In conclusion, we provide an inducible promoter, PrAmCIP, which can be applied to the development of transgenic plants for abiotic stresse tolerance.

Growth and transcriptional response of wheat and rice to the tertiary amine BMVE

Introduction

Seed vigor is largely a product of sound seed development, maturation processes, genetics, and storage conditions. It is a crucial factor impacting plant growth and crop yield and is negatively affected by unfavorable environmental conditions, which can include drought and heat as well as cold wet conditions. The latter leads to slow germination and increased seedling susceptibility to pathogens. Prior research has shown that a class of plant growth regulators called substituted tertiary amines (STAs) can enhance seed germination, seedling growth, and crop productivity. However, inconsistent benefits have limited STA adoption on a commercial scale.

Methods

We developed a novel seed treatment protocol to evaluate the efficacy of 2-(N-methyl benzyl aminoethyl)-3-methyl butanoate (BMVE), which has shown promise as a crop seed treatment in field trials. Transcriptomic analysis of rice seedlings 24 h after BMVE treatment was done to identify the molecular basis for the improved seedling growth. The impact of BMVE on seed development was also evaluated by spraying rice panicles shortly after flower fertilization and subsequently monitoring the impact on seed traits.

Results

BMVE treatment of seeds 24 h after imbibition consistently improved wheat and rice seedling shoot and root growth in lab conditions. Treated wheat seedlings grown to maturity in a greenhouse also resulted in higher biomass than controls, though only under drought conditions. Treated seedlings had increased levels of transcripts involved in reactive oxygen species scavenging and auxin and gibberellic acid signaling. Conversely, several genes associated with increased reactive oxygen species/ROS load, abiotic stress responses, and germination hindering processes were reduced. BMVE spray increased both fresh and mature seed weights relative to the control for plants exposed to 96 h of heat stress. BMVE treatment during seed development also benefited germination and seedling growth in the next generation, under both ambient and heat stress conditions.

Discussion

The optimized experimental conditions we developed provide convincing evidence that BMVE does indeed have efficacy in plant growth enhancement. The results advance our understanding of how STAs work at the molecular level and provide insights for their practical application to improve crop growth.

A multi-level approach reveals key physiological and molecular traits in the response of two rice genotypes subjected to water deficit at the reproductive stage

Rice is more vulnerable to drought than maize, wheat, and sorghum because its water requirements remain high throughout the rice life cycle. The effects of drought vary depending on the timing, intensity, and duration of the events, as well as on the rice genotype and developmental stage. It can affect all levels of organization, from genes to the cells, tissues, and/or organs. In this study, a moderate water deficit was applied to two contrasting rice genotypes, IAC 25 and CIRAD 409, during their reproductive stage. Multi-level transcriptomic, metabolomic, physiological, and morphological analyses were performed to investigate the complex traits involved in their response to drought. Weighted gene network correlation analysis was used to identify the specific molecular mechanisms regulated by each genotype, and the correlations between gene networks and phenotypic traits. A holistic analysis of all the data provided a deeper understanding of the specific mechanisms regulated by each genotype, and enabled the identification of gene markers. Under non-limiting water conditions, CIRAD 409 had a denser shoot, but shoot growth was slower despite better photosynthetic performance. Under water deficit, CIRAD 409 was weakly affected regardless of the plant level analyzed. In contrast, IAC 25 had reduced growth and reproductive development. It regulated transcriptomic and metabolic activities at a high level, and activated a complex gene regulatory network involved in growth-limiting processes. By comparing two contrasting genotypes, the present study identified the regulation of some fundamental processes and gene markers, that drive rice development, and influence its response to water deficit, in particular, the importance of the biosynthetic and regulatory pathways for cell wall metabolism. These key processes determine the biological and mechanical properties of the cell wall and thus influence plant development, organ expansion, and turgor maintenance under water deficit. Our results also question the genericity of the antagonism between morphogenesis and organogenesis observed in the two genotypes.

Plant dehydrins and dehydrin-like proteins: characterization and participation in abiotic stress response

Abiotic stress has a significant impact on plant growth and development. It causes changes in the subcellular organelles, which, due to their stress sensitivity, can be affected. Cellular components involved in the abiotic stress response include dehydrins, widely distributed proteins forming a class II of late embryogenesis abundant protein family with characteristic properties including the presence of evolutionarily conserved sequence motifs (including lysine-rich K-segment, N-terminal Y-segment, and often phosphorylated S motif) and high hydrophilicity and disordered structure in the unbound state. Selected dehydrins and few poorly characterized dehydrin-like proteins participate in cellular stress acclimation and are also shown to interact with organelles. Through their functioning in stabilizing biological membranes and binding reactive oxygen species, dehydrins and dehydrin-like proteins contribute to the protection of fragile organellar structures under adverse conditions. Our review characterizes the participation of plant dehydrins and dehydrin-like proteins (including some organellar proteins) in plant acclimation to diverse abiotic stress conditions and summarizes recent updates on their structure (the identification of dehydrin less conserved motifs), classification (new proposed subclasses), tissue- and developmentally specific accumulation, and key cellular activities (including organellar protection under stress acclimation). Recent findings on the subcellular localization (with emphasis on the mitochondria and plastids) and prospective applications of dehydrins and dehydrin-like proteins in functional studies to alleviate the harmful stress consequences by means of plant genetic engineering and a genome editing strategy are also discussed.

Drought and recovery in barley: key gene networks and retrotransposon response

Introduction

During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses.

Methods

Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis.

Results

The varieties differed by their critical SWC (ϴ_crit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated.

Discussion

The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.

Bioinformatic and functional analysis of OsDHN2 under cadmium stress

As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.

Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities

The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N'-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.

Full-length transcriptional analysis reveals the complex relationship of leaves and roots in responses to cold-drought combined stress in common vetch

Plant responses to single or combined abiotic stresses between aboveground and underground parts are complex and require crosstalk signaling pathways. In this study, we explored the transcriptome data of common vetch (Vicia sativa L.) subjected to cold and drought stress between leaves and roots via meta-analysis to identify the hub abiotic stress-responsive genes. A total of 4,836 and 3,103 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Transcriptome analysis results showed that the set of stress-responsive DEGs to concurrent stress is distinct from single stress, indicating a specialized and unique response to combined stresses in common vetch. Gene Ontology (GO) enrichment analyses identified that "Photosystem II," "Defence response," and "Sucrose synthase/metabolic activity" were the most significantly enriched categories in leaves, roots, and both tissues, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that "ABC transporters" are the most enriched pathway and that all of the genes were upregulated in roots. Furthermore, 29 co-induced DEGs were identified as hub genes based on the consensus expression profile module of single and co-occurrence stress analysis. In transgenic yeast, the overexpression of three cross-stress tolerance candidate genes increased yeast tolerance to cold-drought combined stress. The elucidation of the combined stress-responsive network in common vetch to better parse the complex regulation of abiotic responses in plants facilitates more adequate legume forage breeding for combined stress tolerance.

Increased dehydrin level decreases leaf rolling grade by altering the reactive oxygen species homeostasis and abscisic acid content in maize subjected to osmotic stress

Dehydrins (DHNs) are stress proteins involved in the development of protective reactions in plants against dehydration. The relationship between DHNs and morphological responses such as leaf rolling in plants exposed to water deficit is not well known. In this study, we detected how variations in DHN levels affect the leaf rolling response in maize exposed to osmotic stress in relation to the antioxidant system and ABA level. In this context, we altered the DHN levels in maize seedlings by treatment with bio-regulators (salicylic acid and abscisic acid) under PEG6000-free and PEG6000-induced osmotic stress. When the DHN levels were increased by the bio-regulators (25 µM SA and 100 µM ABA), the relative expression level of the Zea mays dehydrin COR410 gene increased in the seedlings, while reactive oxygen species (ROS) and leaf rolling grade decreased. Moreover, induction of DHNs caused increases in the antioxidant enzyme activity and content of antioxidant substances, and very high amounts of endogenous abscisic acid. When DHN level was suppressed by a bio-regulator (200 µM SA) in the maize seedlings, dehydrin COR410 expression level decreased, while ROS and the leaf rolling grade increased. Moreover, the antioxidant enzyme activity and content of antioxidant substances decreased in the seedlings, while the amount of abscisic acid increased. Taken all together, an increase in DHN level by bio-regulator treatment can stimulate the antioxidant system, enable abscisic acid regulation, and thus reduce leaf rolling through decreased ROS levels. The results also indicated that DHNs may be involved in the signal pathways inducing expression of some genes related to leaf rolling response, possibly by modulating ROS levels, in maize seedlings exposed to osmotic stress.

Physiological and molecular signatures reveal differential response of rice genotypes to drought and drought combination with heat and salinity stress

Rice is the staple food for more than 3.5 billion people worldwide. The sensitivity of rice to heat, drought, and salinity is well documented. However, rice response to combinations of these stresses is not well understood. A contrasting set of rice genotypes for heat (N22, Gharib), drought (Moroberekan, Pusa 1121) and salinity (Pokkali, IR64) were selected to characterize their response under drought, and combination of drought with heat and salinity at the sensitive seedling stage. Sensitive genotypes (IR64, Pusa 1121, Gharib) recorded higher reactive oxygen species accumulation (20-40%), membrane damage (8-65%) and reduction in photosynthetic efficiency (10-23%) across the stress and stress combinations as compared to stress tolerant checks. On the contrary, N22 and Pokkali performed best under drought + heat, and drought + salinity combination, respectively. Moreover, gene expression pattern revealed the highest expression of catalase (CAT), ascorbate peroxidase (APX) and GATA28a in N22 under heat + drought, whereas the highest expression of CAT, APX, superoxide dismutase (SOD), DEHYDRIN, GATA28a and GATA28b in Pokkali under drought + salinity. Interestingly, the phenotypic variation and expression level of genes highlighted the role of different set of physiological traits and genes under drought and drought combination with heat and salinity stress. This study reveals that rice response to stress combinations was unique with rapid readjustment at physiological and molecular levels. Moreover, phenotypic changes under stress combinations showed substantial adaptive plasticity in rice, which warrant further investigations at molecular level.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01162-y.

Involvement of dehydrin proteins in mitigating the negative effects of drought stress in plants

Drought stress-induced crop loss has been considerably increased in recent years because of global warming and changing rainfall pattern. Natural drought-tolerant plants entail the recruitment of a variety of metabolites and low molecular weight proteins to negate the detrimental effects of drought stress. Dehydrin (DHN) proteins are one such class of proteins that accumulate in plants during drought and associated stress conditions. These proteins are highly hydrophilic and perform multifaceted roles in the protection of plant cells during drought stress conditions. Evidence gathered over the years suggests that DHN proteins impart drought stress tolerance by enhancing the water retention capacity, elevating chlorophyll content, maintaining photosynthetic machinery, activating ROS detoxification, and promoting the accumulation of compatible solutes, among others. Overexpression studies have indicated that these proteins can be effectively targeted to mitigate the negative effects of drought stress and for the development of drought stress-tolerant crops to feed the ever-growing population in the near future. In this review, we describe the mechanism of DHNs mediated drought stress tolerance in plants and their interaction with several phytohormones to provide an in-depth understanding of DHNs function.

The Disordered Dehydrin and Its Role in Plant Protection: A Biochemical Perspective

Dehydrins are intrinsically disordered proteins composed of several well conserved sequence motifs known as the Y-, S-, F-, and K-segments, the latter of which is a defining feature of all dehydrins. These segments are interspersed by regions of low sequence conservation and are organized modularly, which results in seven different architectures: Kn, SKn, YnSKn, YnKn, KnS, FnK and FnSKn. Dehydrins are expressed ubiquitously throughout the plant kingdom during periods of low intracellular water content, and are capable of improving desiccation tolerance in plants. In vitro evidence of dehydrins shows that they are involved in the protection of membranes, proteins and DNA from abiotic stresses. However, the molecular mechanisms by which these actions are achieved are as of yet somewhat unclear. With regards to macromolecule cryoprotection, there is evidence to suggest that a molecular shield-like protective effect is primarily influenced by the hydrodynamic radius of the dehydrin and to a lesser extent by the charge and hydrophobicity. The interaction between dehydrins and membranes is thought to be a surface-level, charge-based interaction that may help to lower the transition temperature, allowing membranes to maintain fluidity at low temperatures and preventing membrane fusion. In addition, dehydrins are able to protect DNA from damage, showing that these abiotic stress protection proteins have multiple roles.

Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses

BACKGROUND

Bread wheat (Triticum aestivum) is an important staple cereal grain worldwide. The ever-increasing environmental stress makes it very important to mine stress-resistant genes for wheat breeding programs. Therefore, dehydrin (DHN) genes can be considered primary candidates for such programs, since they respond to multiple stressors.

RESULTS

In this study, we performed a genome-wide analysis of the DHN gene family in the genomes of wheat and its three relatives. We found 55 DHN genes in T. aestivum, 31 in T. dicoccoides, 15 in T. urartu, and 16 in Aegilops tauschii. The phylogenetic, synteny, and sequence analyses showed we can divide the DHN genes into five groups. Genes in the same group shared similar conserved motifs and potential function. The tandem TaDHN genes responded strongly to drought, cold, and high salinity stresses, while the non-tandem genes respond poorly to all stress conditions. According to the interaction network analysis, the cooperation of multiple DHN proteins was vital for plants in combating abiotic stress.

CONCLUSIONS

Conserved, duplicated DHN genes may be important for wheat being adaptable to a different stress conditions, thus contributing to its worldwide distribution as a staple food. This study not only highlights the role of DHN genes help the Triticeae species against abiotic stresses, but also provides vital information for the future functional studies in these crops.

AnDHN, a Dehydrin Protein From Ammopiptanthus nanus, Mitigates the Negative Effects of Drought Stress in Plants

Dehydrins (DHNs) play crucial roles in a broad spectrum of abiotic stresses in model plants. However, the evolutionary role of DHNs has not been explored, and the function of DHN proteins is largely unknown in Ammopiptanthus nanus (A. nanus), an ancient and endangered legume species from the deserts of northwestern China. In this study, we isolated a drought-response gene (c195333_g1_i1) from a drought-induced RNA-seq library of A. nanus. Evolutionary bioinformatics showed that c195333_g1_i1 is an ortholog of Arabidopsis DHN, and we renamed it AnDHN. Moreover, DHN proteins may define a class of proteins that are evolutionarily conserved in all angiosperms that have experienced a contraction during the evolution of legumes. Arabidopsis plants overexpressing AnDHN exhibited morpho-physiological changes, such as an increased germination rate, higher relative water content (RWC), higher proline (PRO) content, increased peroxidase (POD) and catalase (CAT) activities, lower contents of malondialdehyde (MDA), H₂O₂ and O₂ ^-, and longer root length. Our results showed that the transgenic lines had improved drought resistance with deep root system architecture, excellent water retention, increased osmotic adjustment, and enhanced reactive oxygen species (ROS) scavenging. Furthermore, the transgenic lines also had enhanced salt and cold tolerance. Our findings demonstrate that AnDHN may be a good candidate gene for improving abiotic stress tolerance in crops. Key Message: Using transcriptome analysis in Ammopiptanthus nanus, we isolated a drought-responsive gene, AnDHN, that plays a key role in enhancing abiotic stress tolerance in plants, with strong functional diversification in legumes.

Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus' flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses.

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants' survival in adverse environments.

Transcriptomic and Proteomic Analysis of Drought Stress Response in Opium Poppy Plants during the First Week of Germination

Water deficiency is one of the most significant abiotic stresses that negatively affects growth and reduces crop yields worldwide. Most research is focused on model plants and/or crops which are most agriculturally important. In this research, drought stress was applied to two drought stress contrasting varieties of Papaver somniferum (the opium poppy), a non-model plant species, during the first week of its germination, which differ in responses to drought stress. After sowing, the poppy seedlings were immediately subjected to drought stress for 7 days. We conducted a large-scale transcriptomic and proteomic analysis for drought stress response. At first, we found that the transcriptomic and proteomic profiles significantly differ. However, the most significant findings are the identification of key genes and proteins with significantly different expressions relating to drought stress, e.g., the heat-shock protein family, dehydration responsive element-binding transcription factors, ubiquitin E3 ligase, and others. In addition, metabolic pathway analysis showed that these genes and proteins were part of several biosynthetic pathways most significantly related to photosynthetic processes, and oxidative stress responses. A future study will focus on a detailed analysis of key genes and the development of selection markers for the determination of drought-resistant varieties and the breeding of new resistant lineages.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L

The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.

Impact of high or low levels of phosphorus and high sodium in soils on productivity and stress tolerance of Arundo donax plants

The potential of Arundo donax to grow in degraded soils, characterized by excess of salinity (Na+), and phosphorus deficiency (-P) or excess (+P) also coupled with salinity (+NaP), was investigated by combining in vivo plant phenotyping, quantification of metabolites and ultrastructural imaging of leaves with a transcriptome-wide screening. Photosynthesis and growth were impaired by + Na, -P and + NaP. While + Na caused stomatal closure, enhanced biosynthesis of carotenoids, sucrose and isoprene and impaired anatomy of cell walls, +P negatively affected starch production and isoprene emission, and damaged chloroplasts. Finally, +NaP largely inhibited photosynthesis due to stomatal limitations, increased sugar content, induced/repressed a number of genes 10 time higher with respect to + P and + Na, and caused appearance of numerous and large plastoglobules and starch granules in chloroplasts. Our results show that A. donax is sensitive to unbalances of soil ion content, despite activation of defensive mechanisms that enhance plant resilience, growth and biomass production of A. donax under these conditions.

Evolution of the modular, disordered stress proteins known as dehydrins

Dehydrins, plant proteins that are upregulated during dehydration stress conditions, have modular sequences that can contain three conserved motifs (the Y-, S-, and K-segments). The presence and order of these motifs are used to classify dehydrins into one of five architectures: Kn, SKn, KnS, YnKn, and YnSKn, where the subscript n describes the number of copies of that motif. In this study, an architectural and phylogenetic analysis was performed on 426 dehydrin sequences that were identified in 53 angiosperm and 3 gymnosperm genomes. It was found that angiosperms contained all five architectures, while gymnosperms only contained Kn and SKn dehydrins. This suggests that the ancestral dehydrin in spermatophytes was either Kn or SKn, and the Y-segment containing dehydrins first arose in angiosperms. A high-level split between the YnSKn dehydrins from either the Kn or SKn dehydrins could not be confidently identified, however, two lower level architectural divisions appear to have occurred after different duplication events. The first likely occurred after a whole genome duplication, resulting in the duplication of a Y3SK2 dehydrin; the duplicate subsequently lost an S- and K- segment to become a Y3K1 dehydrin. The second split occurred after a tandem duplication of a Y1SK2 dehydrin, where the duplicate lost both the Y- and S- segment and gained four K-segments, resulting in a K6 dehydrin. We suggest that the newly arisen Y3K1 dehydrin is possibly on its way to pseudogenization, while the newly arisen K6 dehydrin developed a novel function in cold protection.

Rice (Oryza sativa L.) tau class glutathione S-transferase (OsGSTU30) overexpression in Arabidopsis thaliana modulates a regulatory network leading to heavy metal and drought stress tolerance

OsGSTU30 increases the abiotic stress tolerance in plants either by its catalytic activity or by modulating the expression of stress responsive genes.

Mining Late Embryogenesis Abundant (LEA) Family Genes in Cleistogenes songorica, a Xerophyte Perennial Desert Plant

Plant growth and development depends on its ability to maintain optimal cellular homeostasis during abiotic and biotic stresses. Cleistogenes songorica, a xerophyte desert plant, is known to have novel drought stress adaptation strategies and contains rich pools of stress tolerance genes. Proteins encoded by Late Embryogenesis Abundant (LEA) family genes promote cellular activities by functioning as disordered molecules, or by limiting collisions between enzymes during stresses. To date, functions of the LEA family genes have been heavily investigated in many plant species except perennial monocotyledonous species. In this study, 44 putative LEA genes were identified in the C. songorica genome and were grouped into eight subfamilies, based on their conserved protein domains and domain organizations. Phylogenetic analyses indicated that C. songorica Dehydrin and LEA_2 subfamily proteins shared high sequence homology with stress responsive Dehydrin proteins from Arabidopsis. Additionally, promoter regions of CsLEA_2 or CsDehydrin subfamily genes were rich in G-box, drought responsive (MBS), and/or Abscisic acid responsive (ABRE) cis-regulatory elements. In addition, gene expression analyses indicated that genes from these two subfamilies were highly responsive to heat stress and ABA treatment, in both leaves and roots. In summary, the results from this study provided a comprehensive view of C. songoricaLEA genes and the potential applications of these genes for the improvement of crop tolerance to abiotic stresses.

Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478, a salt tolerant rice genotype

The jumonji (JMJ)-C domain containing proteins belong to histone demethylases family with the ability to demethylate the tri-methylated histone residues. They act as chromatin regulators to regulate many physiological functions in plants. The present study deals with the characterization of JMJ-C gene family members in wild as well as cultivated rice species and their expression analysis in salt tolerant rice genotype, FL478. The genome wide study identified 151 members belonging to JMJ-C gene family in 11 different Oryza species. We also studied their structure, genomic location, gene duplication events, phylogenetic relationship, in silico expression analysis and identified cis elements in their promoters. We also found a few JMJ-C gene family members in rice which underwent duplication before the whole genome duplication event of the rice. The qRT-PCR based expression profiling revealed that out of the total 15 rice JMJ-C members, two were highly expressed in the flag leaf stage of FL478 under salt treatment. These two candidate JMJ-C members were also found to render salinity tolerance when over-expressed in yeast cells. Thus, the present study helps in further structural as well as functional characterization of JMJ-C genes under salinity stress in Oryza species.

Investigating the mechanisms underlying phytoprotection by plant growth-promoting rhizobacteria in Spartina densiflora under metal stress

Pollution of coasts by toxic metals and metalloids is a worldwide problem for which phytoremediation using halophytes and associated microbiomes is becoming relevant. Metal(loid) excess is a constraint for plant establishment and development, and plant growth promoting rhizobacteria (PGPR) mitigate plant stress under these conditions. However, mechanisms underlying this effect remain elusive. The effect of toxic metal(loid)s on activity and gene expression of ROS-scavenging enzymes in roots of the halophyte Spartina densiflora grown on real polluted sediments in a greenhouse experiment was investigated. Sediments of the metal-polluted joint estuary of Tinto and Odiel rivers and control, unpollutred samples from the Piedras estuary were collected and submitted to ICP-OES. Seeds of S. densiflora were collected from the polluted Odiel marshes and grown in polluted and unpolluted sediments. Rhizophere biofilm-forming bacteria were selected based on metal tolerance and inoculated to S. densiflora and grown for 4 months. Fresh or frozen harvested plants were used for enzyme assays and gene expression studies, respectively. Metal excess induced SOD (five-fold increase), whereas CAT and ascorbate peroxidase displayed minor induction (twofold). A twofold increase of TBARs indicated membrane damage. Our results showed that metal-resistant PGPR (P. agglomerans RSO6 and RSO7 and B. aryabhattai RSO25) contributed to alleviate metal stress, as deduced from lower levels of all antioxidant enzymes to levels below those of non-exposed plants. The oxidative stress index (OSI) decreased between 50 and 75% upon inoculation. The results also evidenced the important role of PAL, involved in secondary metabolism and/or lignin synthesis, as a pathway for metal stress management in this halophyte upon inoculation with appropriate PGPR, since the different inoculation treatments enhanced PAL expression between 3.75- and five-fold. Our data confirm, at the molecular level, the role of PGPR in alleviating metal stress in S. densiflora and evidence the difficulty of working with halophytes for which little genetic information is available.

Improved short-term drought response of transgenic rice over-expressing maize C4 phosphoenolpyruvate carboxylase via calcium signal cascade

To understand the link between long-term drought tolerance and short-term drought responses in plants, transgenic rice (Oryza sativa L.) plants over-expressing the maize C_4-pepc gene encoding phosphoenolpyruvate carboxylase (PC) and wild-type (WT) rice plants were subjected to PEG 6000 treatments to simulate drought stress. Compared with WT, PC had the higher survival rate and net photosynthetic rate after 16days of drought treatment, and had higher relative water content in leaves after 2h of drought treatment as well, conferring drought tolerance. WT accumulated higher amounts of malondialdehyde, superoxide radicals, and H₂O₂ than PC under the 2-h PEG 6000 treatment, indicating greater damages in WT. Results from pretreatments with a Ca²⁺ chelator and/or antagonist showed that the regulation of the early drought response in PC was Ca²⁺-dependent. The NO and H₂O₂ levels in PC lines were also up-regulated via Ca²⁺ signals, indicating that Ca²⁺ in PC lines also reacted upstream of NO and H₂O₂. 2-h drought treatment increased the transcripts of CPK9 and CPK4 in PC via positive up-regulation of Ca²⁺. The transcripts of NAC6 [NACs (NAM, ATAF1, ATAF2, and CUC2)] and bZIP60 (basic leucine zipper, bZIP) were up-regulated, but those of DREB2B (dehydration-responsive element-binding protein, DREB) were down-regulated, both via Ca²⁺ signals in PC. PEPC activity, expressions of C₄-pepc, and the antioxidant enzyme activities in PC lines were up-regulated via Ca²⁺. These results indicated that Ca²⁺ signals in PC lines can up-regulate the NAC6 and bZIP60 and the downstream targets for early drought responses, conferring drought tolerance for the long term.

Overexpression of CsLEA11, a Y3SK2-type dehydrin gene from cucumber (Cucumis sativus), enhances tolerance to heat and cold in Escherichia coli

As the group II LEA (late embryogenesis abundant) proteins, dehydrins (DHNs) play an important role in plant growth and development, as well as in response to abiotic or biotic stress challenges. In this study, a DHN gene named CsLEA11 was identified and characterized from Cucumis sativus. Sequence analysis of CsLEA11 showed that it is a Y₃SK₂-type DHN protein rich in hydrophilic amino acids. Expression analyses revealed that the transcription of CsLEA11 could be significantly induced by heat and cold stress. The recombinant plasmid was transformed into Escherichia coli BL21 and isopropy-β-D-thiogalactoside (IPTG) was used to induce recombinant E. coli to express CsLEA11 gene. Overexpression of CsLEA11 in E. coli enhanced cell viability and conferred tolerance to heat and cold stress. Furthermore, CsLEA11 protein could protect the activity of lactate dehydrogenase (LDH) under heat stress. Taken together, our data demonstrate that CsLEA11 might function in tolerance of cucumber to heat and cold stress.