Functional analysis of the group 4 late embryogenesis abundant proteins reveals their relevance in the adaptive response during water deficit in Arabidopsis

Macromolecular crowding sensing during osmotic stress in plants

Osmotic stress conditions occur at multiple stages of plant life. Changes in water availability caused by osmotic stress induce alterations in the mechanical properties of the plasma membrane, its interaction with the cell wall, and the concentration of macromolecules in the cytoplasm. We summarize the reported players involved in the sensing mechanisms of osmotic stress in plants. We discuss how changes in macromolecular crowding are perceived intracellularly by intrinsically disordered regions (IDRs) in proteins. Finally, we review methods for dynamically monitoring macromolecular crowding in living cells and discuss why their implementation is required for the discovery of new plant osmosensors. Elucidating the osmosensing mechanisms will be essential for designing strategies to improve plant productivity in the face of climate change.

Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth

With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.

Genome-wide analysis and functional validation reveal the role of late embryogenesis abundant genes in strawberry (Fragaria × ananassa) fruit ripening

BACKGROUND

Late embryogenesis abundant (LEA) proteins play important roles in plant growth and development, as well as stresses responsiveness. Nowadays, it has been found that LEAs also have function in fruit ripening. However, the comprehensive analysis on a genome-wide basis of LEA family remains limited, and the role of LEA in fruit ripening has not been fully explored yet, especially in strawberry, an economic important plant and ideal material for studying fruit ripening.

RESULTS

In this study, a total of 266 putative LEA proteins were identified and characterized in strawberry genome. Subcellular localization prediction indicated that they were mostly localized in chloroplast, cytoplasm and nucleus. Duplication events detection revealed that whole genome duplication or segmental was the main driver for the expansion of LEA family in strawberry. The phylogenetic analysis suggested that FaLEAs were classified into eight groups, among which, LEA2 was the largest subgroup with 179 members, followed by LEA3, dehydrin (DHN), LEA4 and SMP (seed maturation protein). The LEA1 and DHN groups were speculated to play dominant roles in strawberry fruit development and ripening, according to their larger proportion of members detected as differentially expressed genes during such process. Notably, the expression of FaLEA167 belonging to LEA1 group was altered by strawberry maturation, and inhibited by overexpression of negative regulators of ripening (a cytosolic/plastid glyceraldehyde-3-phosphate dehydrogenase, FaGAPC2 and a cytosolic pyruvate kinase, FaPKc2.2). Subsequently, overexpression of FaLEA167 significantly increased the percentage of fruit at green stage, while reduced the full red fruit proportion. In consistent, the anthocyanins content and the fruit skin color variable reflecting a range from greenness to redness (a* value) were significantly reduced. Whereas, FaLEA167 overexpression apparently up-regulated citric acid, soluble protein and malondialdehyde content, but had no obvious effects on total soluble solids, sugar, flavonoids, phenolics content and antioxidant capacity.

CONCLUSIONS

These findings not only provided basic information of FaLEA family for further functional research, but also revealed the involvement of FaLEA167 in negatively regulating strawberry fruit ripening, giving new insights into understanding of FaLEA functions.

IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

Alternative conformations of a group 4 Late Embryogenesis Abundant protein associated to its in vitro protective activity

Late Embryogenesis Abundant (LEA) proteins are a group of intrinsically disordered proteins implicated in plant responses to water deficit. In vitro studies revealed that LEA proteins protect reporter enzymes from inactivation during low water availability. Group 4 LEA proteins constitute a conserved protein family, displaying in vitro protective capabilities. Under water deficiency or macromolecular crowding, the N-terminal of these proteins adopts an alpha-helix conformation. This region has been identified as responsible for the protein in vitro protective activity. This study investigates whether the attainment of alpha-helix conformation and/or particular amino acid residues are required for the in vitro protective activity. The LEA4-5 protein from Arabidopsis thaliana was used to generate mutant proteins. The mutations altered conserved residues, deleted specific conserved regions, or introduced prolines to hinder alpha-helix formation. The results indicate that conserved residues are not essential for LEA4-5 protective function. Interestingly, the C-terminal region was found to contribute to this function. Moreover, alpha-helix conformation is necessary for the protective activity only when the C-terminal region is deleted. Overall, LEA4-5 shows the ability to adopt alternative functional conformations under the tested conditions. These findings shed light on the in vitro mechanisms by which LEA proteins protect against water deficit stress.

Design of functional intrinsically disordered proteins

Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.

Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos

KEY MESSAGE

This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.

Identification and expression analysis of LEA gene family members in pepper (Capsicum annuum L.)

Pepper (Capsicum annuum L.) is an economically important crop containing capsaicinoids in the seed and placenta, which has various culinary, medical, and industrial applications. Late embryogenesis abundant (LEA) proteins are a large group of hydrophilic proteins participating in the plant stress response and seed development. However, to date there have been no genome-wide analyses of the LEA gene family in pepper. In the present study, 82 LEA genes were identified in the C. annuum genome and classified into nine subfamilies. Most CaLEA genes contain few introns (≤ 2) and are unevenly distributed across 10 chromosomes. Eight pairs of tandem duplication genes and two pairs of segmental duplication genes were identified in the LEA gene family; these duplicated genes were highly conserved and may have performed similar functions during evolution. Expression profile analysis indicated that CaLEA genes exhibited different tissue expression patterns, especially during embryonic development and stress response, particularly in cold stress. Three out of five CaLEA genes showed induced expression upon cold treatment. In summary, we have comprehensively reviewed the LEA gene family in pepper, offering a new perspective on the evolution of this family.

Genome-wide identification of late embryogenesis abundant protein family and their key regulatory network in Pinus tabuliformis cold acclimation

Cold acclimation is a crucial biological process that enables conifers to overwinter safely. The late embryogenesis abundant (LEA) protein family plays a pivotal role in enhancing freezing tolerance during this process. Despite its importance, the identification, molecular functions and regulatory networks of the LEA protein family have not been extensively studied in conifers or gymnosperms. Pinus tabuliformis, a conifer with high ecological and economic values and with high-quality genome sequence, is an ideal candidate for such studies. Here, a total of 104 LEA genes were identified from P. tabuliformis, and we renamed them according to their subfamily group: PtLEA1-PtLEA92 (group LEA1-LEA6), PtSMP1-PtSMP6 (group seed maturation protein) and PtDHN1-PtDHN6 (group Dehydrin). While the sequence structure of P. tabuliformis  LEA genes are conserved, their physicochemical properties exhibit unique characteristics within different subfamily groupings. Notably, the abundance of low-temperature responsive elements in PtLEA genes was observed. Using annual rhythm and temperature gradient transcriptome data, PtLEA22 was identified as a key gene that responds to low-temperature induction while conforming to the annual cycle of cold acclimation. Overexpression of PtLEA22 enhanced Arabidopsis freezing tolerance. Furthermore, several transcription factors potentially co-expressed with PtLEA22 were validated using yeast one-hybrid and dual-luciferase assays, revealing that PtDREB1 could directly bind PtLEA22 promoter to positively regulate its expression. These findings reveal the genome-wide characterization of P. tabuliformis  LEA genes and their importance in the cold acclimation, while providing a theoretical basis for studying the molecular mechanisms of cold acclimation in conifers.

Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches

Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.

An intrinsically disordered region-containing protein mitigates the drought-growth trade-off to boost yields

Drought stress poses a serious threat to global agricultural productivity and food security. Plant resistance to drought is typically accompanied by a growth deficit and yield penalty. Herein, we report a previously uncharacterized, dicotyledon-specific gene, Stress and Growth Interconnector (SGI), that promotes growth during drought in the oil crop rapeseed (Brassica napus) and the model plant Arabidopsis (Arabidopsis thaliana). Overexpression of SGI conferred enhanced biomass and yield under water-deficient conditions, whereas corresponding CRISPR SGI mutants exhibited the opposite effects. These attributes were achieved by mediating reactive oxygen species (ROS) homeostasis while maintaining photosynthetic efficiency to increase plant fitness under water-limiting environments. Further spatial-temporal transcriptome profiling revealed dynamic reprogramming of pathways for photosynthesis and stress responses during drought and the subsequent recovery. Mechanistically, SGI represents an intrinsically disordered region-containing protein that interacts with itself, catalase isoforms, dehydrins, and other drought-responsive positive factors, restraining ROS generation. These multifaceted interactions stabilize catalases in response to drought and facilitate their ROS-scavenging activities. Taken altogether, these findings provide insights into currently underexplored mechanisms to circumvent trade-offs between plant growth and stress tolerance that will inform strategies to breed climate-resilient, higher yielding crops for sustainable agriculture.

CiXTH29 and CiLEA4 Role in Water Stress Tolerance in Cichorium intybus Varieties

Drought causes massive crop quality and yield losses. Limiting the adverse effects of water deficits on crop yield is an urgent goal for a more sustainable agriculture. With this aim, six chicory varieties were subjected to drought conditions during seed germination and at the six week-old plant growth stage, in order to identify some morphological and/or molecular markers of drought resistance. Selvatica, Zuccherina di Trieste and Galatina varieties, with a high vegetative development, showed a major germination index, greater seedling development (6 days of growth) and a greater dehydration resistance (6 weeks of growth plus 10 days without water) than the other ones (Brindisina, Esportazione and Rossa Italiana). Due to the reported involvement, in the abiotic stress response, of xyloglucan endotransglucosylase/hydrolases (XTHs) and late embryogenesis abundant (LEA) multigene families, XTH29 and LEA4 expression profiles were investigated under stress conditions for all analyzed chicory varieties. We showed evidence that chicory varieties with high CiXTH29 and CiLEA4 basal expression and vegetative development levels better tolerate drought stress conditions than varieties that show overexpression of the two genes only in response to drought. Other specific morphological traits characterized almost all chicory varieties during dehydration, i.e., the appearance of lysigen cavities and a general increase of the amount of xyloglucans in the cell walls of bundle xylem vessels. Our results highlighted that high CiXTH29 and CiLEA4 basal expression, associated with a high level of vegetative growth, is a potential marker for drought stress tolerance.

Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM and IPD3 in Arabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress

Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.

Identification of the BcLEA Gene Family and Functional Analysis of the BcLEA73 Gene in Wucai (Brassica campestris L.)

Late embryogenesis abundant (LEA) proteins are important developmental proteins in the response of plants to abiotic stress. In our previous study, BcLEA73 was differentially expressed under low-temperature stress. Herein, we combined bioinformatics analysis, subcellular localization, expression assays, and stress experiments (including salt, drought, and osmotic stress) to identify and analyze the BcLEA gene family. Gene cloning and functional analysis of BcLEA73 were performed in tobacco and Arabidopsis. Based on the sequence homology and the available conservative motif, 82 BrLEA gene family members were identified and were divided into eight subfamilies in the genome-wide database of Chinese cabbage. The analysis showed that the BrLEA73 gene was located on chromosome A09 and belonged to the LEA_6 subfamily. Quantitative real-time PCR analysis indicated that the BcLEA genes were differentially expressed to varying degrees in the roots, stems, leaves, and petioles of Wucai. The overexpressed BcLEA73 transgenic plants exhibited no significant differences in root length and seed germination rates compared to the wild-type (WT) plants under control conditions. Under salt and osmotic stress treatment, the root length and seed germination rates of the BcLEA73-OE strain were significantly greater than those of WT plants. Under salt stress, the total antioxidant capacity (T-AOC) of the BcLEA73-OE lines increased significantly, and the relative conductivity, (REL), hydrogen peroxide (H2O2) content, and superoxide anion (O2-) production rate decreased significantly. Under drought treatment, the survival rate of the BcLEA73-OE lines was significantly higher than that of WT plants. These results showed that the BcLEA73 gene of Wucai functions in enhancing the tolerance of plants to salt, drought, and osmotic stress. This study provides a theoretical basis to explore the relevant functions of the BcLEA gene family members of Wucai.

Overexpression of maize GOLDEN2 in rice and maize calli improves regeneration by activating chloroplast development

Golden2 (G2), a member of the GARP transcription factor superfamily, regulates several biological processes and phytohormone signaling pathways in plants. In this study, we used a rice codon-optimized maize G2 gene (rZmG2) to improve the regeneration efficiency of rice and maize calli for genetic transformation. We isolated a promoter driving strong and callus-specific expression from rice to drive rZmG2 transcription from a transgene after transformation of two indica and two japonica rice cultivars. The resulting rZmG2 transgenic calli turned green in advance at the differentiation stage, thus significantly raising the regeneration rates of the transgenic indica and japonica rice plants relative to control transformations. Similar effect of this gene on improving maize transformation was also observed. Transcriptome sequencing and RT-qPCR analyses showed that many rice genes related to chloroplast development and phytohormones are upregulated in rZmG2-transgenic calli. These results demonstrate that rZmG2 can promote embryogenic callus differentiation and improve regeneration efficiency by activating chloroplast development and phytohormone pathways. We also established a heat-inducible Cre/loxP-based gene-excision system to remove rZmG2 and the antibiotic selectable gene after obtaining the transgenic plants. This study provides a useful tool for functional genomics work and biotechnology in plants.

Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development

Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins imperatively associated with plant growth and development, as well as cell protection from abiotic stress. However, the genome-wide characterization of LEA gene family remains limited, especially in aquatic species such as lotus (Nelumbo spp.). Here, 57 putative LEA genes, including 28 NnLEAs and 29 NlLEAs were identified in the N.nucifera and N.lutea genomes, respectively. A total of 27 homologous LEA gene pairs were identified, indicating high degree of sequence homologies between the two Nelumbo species. Secondary structure prediction indicated high prevalence of alpha (α) helix structure among LEA proteins in the LEA_1, LEA_4, and SMP groups. Screening of putative promoter cis-elements revealed that NnLEA genes were involved in diverse biological processes. Most NnLEA genes were predominantly expressed in the late cotyledons and plumules development stages, suggesting their potential vital roles in lotus seed maturation. In addition, genes co-expressed with NnLEAs were involved in ABA signaling, seed maturation, and development processes. Overall, this study provides new insights for the in-depth understanding of the functions of NnLEA proteins in lotus seed development, and could act as a useful reference for the molecular breeding of seeds with prolonged lifespan.

OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response

The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca²⁺-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.

LEAfing through literature: late embryogenesis abundant proteins coming of age-achievements and perspectives

To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review, we summarize current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, post-translational modifications, or water deprivation, we provide a detailed summary of current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil to helix transitions, self-assembly, and their recently discovered ability to undergo liquid-liquid phase separation. We point out the promising potential of LEA proteins in biotechnological and agronomic applications, and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity.

Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum)

Switchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought-responsive diterpenoids as oxygenated furanoditerpenoids. Drought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.

Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions

Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.

Genome-wide identification and expression analyses of late embryogenesis abundant (LEA) gene family in tobacco (Nicotiana tabacum L.) reveal their function in abiotic stress responses

Late embryogenesis abundant (LEA) proteins play an important role in plant growth and response to abiotic stresses. However the late embryogenesis abundant (LEA) gene family in Nicotiana tabacum has not been systematically studied. In this study, 123 NtLEA genes were identified in Nicotiana tabacum, and divided into 8 groups, including LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, LEA_6, DHN (dehydratin) and SMP (Seed Maturation Protein). The LEA_2 group is the most abundant of the NtLEA family. The gene structure, conserved motifs, subcellular localization and physicochemical properties of the NtLEA genes were analyzed. RNA-seq and qPCR analyses showed that the NtLEA genes were significantly induced under two different abiotic stresses and showed different expression patterns. The expression patterns of 35 NtLEA genes responding to ABA and 3 NtLEA genes responding to NaCl abiotic stress, respectively, were characterized. The protein-protein interaction network revealed that most NtLEA proteins (>78%) had the potential function to enhance tobacco resistance to abiotic stress. The transcriptional regulatory network showed that 21 transcription factor families were involved in regulating the expression of the NtLEA genes. These results are beneficial for future studies of the function of the NtLEA genes.

SK, Sheoran S, K. UB, K. BN, Kumar S, Singh AN, Singh HV. Seed Longevity in Legumes: Deeper Insights Into Mechanisms and Molecular Perspectives

Sustainable agricultural production largely depends upon the viability and longevity of high-quality seeds during storage. Legumes are considered as rich source of dietary protein that helps to ensure nutritional security, but associated with poor seed longevity that hinders their performance and productivity in farmer's fields. Seed longevity is the key determinant to assure proper seed plant value and crop yield. Thus, maintenance of seed longevity during storage is of prime concern and a pre-requisite for enhancing crop productivity of legumes. Seed longevity is significantly correlated with other seed quality parameters such as germination, vigor, viability and seed coat permeability that affect crop growth and development, consequently distressing crop yield. Therefore, information on genetic basis and regulatory networks associated with seed longevity, as well as molecular dissection of traits linked to longevity could help in developing crop varieties with good storability. Keeping this in view, the present review focuses towards highlighting the molecular basis of seed longevity, with special emphasis on candidate genes and proteins associated with seed longevity and their interplay with other quality parameters. Further, an attempt was made to provide information on 3D structures of various genetic loci (genes/proteins) associated to seed longevity that could facilitate in understanding the interactions taking place within the seed at molecular level. This review compiles and provides information on genetic and genomic approaches for the identification of molecular pathways and key players involved in the maintenance of seed longevity in legumes, in a holistic manner. Finally, a hypothetical fast-forward breeding pipeline has been provided, that could assist the breeders to successfully develop varieties with improved seed longevity in legumes.

Desiccation Tolerance in Ramonda serbica Panc.: An Integrative Transcriptomic, Proteomic, Metabolite and Photosynthetic Study

The resurrection plant Ramonda serbica Panc. survives long desiccation periods and fully recovers metabolic functions within one day upon watering. This study aimed to identify key candidates and pathways involved in desiccation tolerance in R. serbica. We combined differential transcriptomics and proteomics, phenolic and sugar analysis, FTIR analysis of the cell wall polymers, and detailed analysis of the photosynthetic electron transport (PET) chain. The proteomic analysis allowed the relative quantification of 1192 different protein groups, of which 408 were differentially abundant between hydrated (HL) and desiccated leaves (DL). Almost all differentially abundant proteins related to photosynthetic processes were less abundant, while chlorophyll fluorescence measurements implied shifting from linear PET to cyclic electron transport (CET). The levels of H2O2 scavenging enzymes, ascorbate-glutathione cycle components, catalases, peroxiredoxins, Fe-, and Mn superoxide dismutase (SOD) were reduced in DL. However, six germin-like proteins (GLPs), four Cu/ZnSOD isoforms, three polyphenol oxidases, and 22 late embryogenesis abundant proteins (LEAPs; mainly LEA4 and dehydrins), were desiccation-inducible. Desiccation provoked cell wall remodeling related to GLP-derived H2O2/HO● activity and pectin demethylesterification. This comprehensive study contributes to understanding the role and regulation of the main metabolic pathways during desiccation aiming at crop drought tolerance improvement.

Glyphosate-induced GhAG2 is involved in resistance to salt stress in cotton

KEY MESSAGE

The transcription of GhAG2 was strongly enhanced by glyphosate treatment. Overexpression of GhAG2 could improve plant tolerance to salt and salicylic acid stress. Although glyphosate has been widely used as an herbicide over the past decade owing to its high efficacy on weed controls and worldwide commercialization of glyphosate-resistant crops, little is known about the glyphosate-induced responses and transcriptional changes in cotton plants. Here, we report the identification of 26 differentially expressed genes after glyphosate treatment, among which, six highly up-regulated sequences share homology to cotton expressed sequence tags (ESTs) responsive to abiotic stresses. In addition, we cloned GhAG2, a gene whose transcription was strongly enhanced by glyphosate treatment and other abiotic stresses. Transgenic GhAG2 plants showed improved tolerance to salt, and salicylic acid (SA) stress. The results could open the door to exploring the function of the GhAG2 proteins, the glyphosate-induced transcriptional profiles, and the physiological biochemical responses in cotton and other crops. GhAG2 could also be used to improve salt stress tolerance through breeding and biotechnology in crops. Furthermore, these results could provide guidelines to develop a glyphosate-inducible system for controlled expression of targeted genes in plants.

In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc

Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hallmark. To propose their role in R. serbica desiccation tolerance, we structurally characterised LEAPs and evaluated LEA gene expression levels in hydrated and desiccated leaves. By integrating de novo transcriptomics and homologues LEAP domains, 318 R. serbica LEAPs were identified and classified according to their conserved motifs and phylogeny. The in silico analysis revealed that hydrophilic LEA4 proteins exhibited an exceptionally high tendency to form amphipathic α-helices. The most abundant, atypical LEA2 group contained more hydrophobic proteins predicted to fold into the defined globular domains. Within the desiccation-upregulated LEA genes, the majority encoded highly disordered DEH1, LEA1, LEA4.2, and LEA4.3 proteins, while the greatest portion of downregulated genes encoded LEA2.3 and LEA2.5 proteins. While dehydrins might chelate metals and bind DNA under water deficit, other intrinsically disordered LEAPs might participate in forming intracellular proteinaceous condensates or adopt amphipathic α-helical conformation, enabling them to stabilise desiccation-sensitive proteins and membranes. This comprehensive LEAPs structural characterisation is essential to understanding their function and regulation during desiccation aiming at crop drought tolerance improvement.

Molecular Aspects of Seed Development Controlled by Gibberellins and Abscisic Acids

Plants have evolved seeds to permit the survival and dispersion of their lineages by providing nutrition for embryo growth and resistance to unfavorable environmental conditions. Seed formation is a complicated process that can be roughly divided into embryogenesis and the maturation phase, characterized by accumulation of storage compound, acquisition of desiccation tolerance, arrest of growth, and acquisition of dormancy. Concerted regulation of several signaling pathways, including hormonal and metabolic signals and gene networks, is required to accomplish seed formation. Recent studies have identified the major network of genes and hormonal signals in seed development, mainly in maturation. Gibberellin (GA) and abscisic acids (ABA) are recognized as the main hormones that antagonistically regulate seed development and germination. Especially, knowledge of the molecular mechanism of ABA regulation of seed maturation, including regulation of dormancy, accumulation of storage compounds, and desiccation tolerance, has been accumulated. However, the function of ABA and GA during embryogenesis still remains elusive. In this review, we summarize the current understanding of the sophisticated molecular networks of genes and signaling of GA and ABA in the regulation of seed development from embryogenesis to maturation.

Accumulation of Glycogen and Upregulation of LEA-1 in C. elegans daf-2(e1370) Support Stress Resistance, Not Longevity

DAF-16-dependent activation of a dauer-associated genetic program in the C. elegans insulin/IGF-1 daf-2(e1370) mutant leads to accumulation of large amounts of glycogen with concomitant upregulation of glycogen synthase, GSY-1. Glycogen is a major storage sugar in C. elegans that can be used as a short-term energy source for survival, and possibly as a reservoir for synthesis of a chemical chaperone trehalose. Its role in mitigating anoxia, osmotic and oxidative stress has been demonstrated previously. Furthermore, daf-2 mutants show increased abundance of the group 3 late embryogenesis abundant protein LEA-1, which has been found to act in synergy with trehalose to exert its protective role against desiccation and heat stress in vitro, and to be essential for desiccation tolerance in C. elegans dauer larvae. Here we demonstrate that accumulated glycogen is not required for daf-2 longevity, but specifically protects against hyperosmotic stress, and serves as an important energy source during starvation. Similarly, lea-1 does not act to support daf-2 longevity. Instead, it contributes to increased resistance of daf-2 mutants to heat, osmotic, and UV stress. In summary, our experimental results suggest that longevity and stress resistance can be uncoupled in IIS longevity mutants.

Internal and External Regulatory Elements Controlling Somatic Embryogenesis in Catharanthus: A Model Medicinal Plant

Somatic or in vitro embryogenesis is a unique embryo producing process from vegetative cells observed in plants since 1958. Even over 60 years of research, the transition of somatic cells into embryonic fate is still not elucidated fully. Various networks and signaling elements have been noted to play important role in this "vegetative to reproductive" transition process. The networks include genotypes, explant types, the sugar/carbohydrate sources, cultural/environmental conditions like light quality and intensity, dissolved oxygen (DO) level, cell density, plant growth regulator (PGR) (auxin and cytokinin) signaling, PGR-gene interplay, stresses are important and cause new cellular reprogramming during embryonic acquisition. A wide array of genes, specific to zygotic embryogenesis, also express during somatic embryogenesis. A few embryogenesis-specific genes such as SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE, LEAFY COTYLEDON, AGAMOUS-LIKE 15, and BABY BOOM are crucial and have been discussed. The chapter focuses the importance of these gene products, e.g., proteins, enzymes, and transcription factors in regulating embryogenesis. Many of these encoded proteins act as potential somatic embryogenesis markers. Besides, important elements such as genotype, herbaceous/woody plants' response in culture in inducing embryos have been discussed. All these elements are connected and form network in complex fashion thus difficult to unfold fully; some of the current progress and developments have been presented in this chapter.

Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis

Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.

Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers

LEA proteins are involved in plant stress tolerance. In Arabidopsis, the LEA_4 Pfam group is the biggest group with the majority of its members being expressed in dry seeds. To assess subcellular localization in vivo, we investigated 11 seed-expressed LEA_4 proteins in embryos dissected from dry seeds expressing LEA_4 fusion proteins under its native promoters with the Venus fluorescent protein (proLEA_4::LEA_4:Venus). LEA_4 proteins were shown to be localized in the endoplasmic reticulum, nucleus, mitochondria, and plastids. LEA9, in addition to the nucleus, was also found in cytoplasmic condensates in dry seeds dependent on cellular hydration level. Most investigated LEA_4 proteins were detected in 4-d-old seedlings. In addition, we assessed bioinformatic tools for predicting subcellular localization and promoter motifs of 11 seed-expressed LEA_4 proteins. Ratiometric bimolecular fluorescence complementation assays showed that LEA7, LEA29, and LEA48 form homodimers while heterodimers were formed between LEA7-LEA29 and LEA42-LEA48 in tobacco leaves. Interestingly, LEA48 homodimers and LEA42-LEA48 heterodimers formed droplets structures with liquid-like behavior. These structures, along with LEA9 cytoplasmic condensates, may have been formed through liquid-liquid phase separation. These findings suggest possible important roles of LLPS for LEA protein functions.

Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L

Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding line subjected to acute drought stress followed by recovery (rewatering), at three stages of plant development. Among them, two NAC transcription factor (TF) genes, i.e., CaNAC072 and CaNAC104, were always upregulated after drought stress and downregulated after recovery. The two TF proteins were observed to be localized in the nucleus following their transient expression in Nicotiana benthamiana leaves. The expression of the two NACs was also induced by NaCl, polyethylene glycol (PEG) and abscisic acid (ABA) treatments, suggesting that CaNAC072 is an early, while CaNAC104 is a late abiotic stress-responsive gene. Virus-induced gene silencing (VIGS) of CaNAC104 did not affect the pepper plantlet’s tolerance to drought stress, while VIGS of CaNAC072 increased drought tolerance. Heterologous expression of CaNAC072 in Arabidopsis thaliana as well as in plants mutated for its homolog ANAC072 did not increase drought stress tolerance. This highlights a different role of the two NAC homologs in the two species. Here, we discuss the complex role of NACs as transcriptional switches in the response to drought stress in bell pepper.

BASIC PENTACYSTEINE2 negatively regulates osmotic stress tolerance by modulating LEA4-5 expression in Arabidopsis thaliana

Osmotic stress substantially affects plant growth and development. Study of plant transcription factors involved in osmotic stress can enhance our understanding of the mechanisms of plant osmotic stress tolerance and how the tolerance of plants to osmotic stress can be improved. Here, we identified the specific function of Arabidopsis thaliana BARLEY B RECOMBINANT/BASIC PENTACYSTEINE transcription factor, BPC2, in the osmotic stress response. Phenotypic analysis showed that loss-of-function of BPC2 led to an increase in osmotic stress tolerance in the seedling growth stage. Physiological analysis showed that mutation of BPC2 in Arabidopsis alleviated osmotic-induced increases in H₂O₂ accumulation, the malondialdehyde (MDA) content, and percent electrolyte leakage. BPC2 was localized in the nucleus. RNA-seq and qRT-PCR analysis showed that BPC2 could negatively regulate the expression of late embryogenesis abundant (LEA) genes (LEA3, LEA4-2, and LEA4-5). Further analysis showed that BPC2 could directly bind to the promoter of LEA4-5 in vitro and in vivo. Overexpression of BPC2 enhanced hypersensitivity to osmotic stress in the seedling growth stage. Overexpression of BPC2 led to decreases in LEA4-5 expression and aggravated osmotic-induced increases in H₂O₂ accumulation, the MDA content, and percent electrolyte leakage. Overall, our results indicate that BPC2 negatively regulates LEA4-5 expression to modulate osmotic-induced H₂O₂ accumulation, the MDA content, and percent electrolyte leakage, all of which affect the osmotic stress response in Arabidopsis thaliana.

Systems biology of resurrection plants

Plant species that exhibit vegetative desiccation tolerance can survive extreme desiccation for months and resume normal physiological activities upon re-watering. Here we survey the recent knowledge gathered from the sequenced genomes of angiosperm and non-angiosperm desiccation-tolerant plants (resurrection plants) and highlight some distinct genes and gene families that are central to the desiccation response. Furthermore, we review the vast amount of data accumulated from analyses of transcriptomes and metabolomes of resurrection species exposed to desiccation and subsequent rehydration, which allows us to build a systems biology view on the molecular and genetic mechanisms of desiccation tolerance in plants.

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.

Overexpression of ZmDHN11 could enhance transgenic yeast and tobacco tolerance to osmotic stress

KEY MESSAGE

Maize group II LEA protein ZmDHN11 could protect protein activity and confer resistance to osmotic stress on transgenic yeast and tobacco. Late embryogenesis abundant (LEA) proteins are widely assumed to play crucial roles in environmental stress tolerance, but their function has remained obscure. Dehydrins are group II LEA proteins, which are highly hydrophilic plant stress proteins. In the present study, a novel group II LEA protein, ZmDHN11, was cloned and identified from maize. The expression of ZmDHN11 was induced by high osmotic stress, low temperature, salinity, and ABA (abscisic acid). The ZmDHN11 protein specifically accumulated in the nuclei and cytosol. Further study indicated that ZmDHN11 is phosphorylated by the casein kinase CKII. ZmDHN11 protected the activity of LDH under water-deficit stress. The overexpression of ZmDHN11 endows transgenic yeast and tobacco with tolerance to osmotic stress.

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)

The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.

Overexpression of AtBBD1, Arabidopsis Bifunctional Nuclease, Confers Drought Tolerance by Enhancing the Expression of Regulatory Genes in ABA-Mediated Drought Stress Signaling

Drought is the most serious abiotic stress, which significantly reduces crop productivity. The phytohormone ABA plays a pivotal role in regulating stomatal closing upon drought stress. Here, we characterized the physiological function of AtBBD1, which has bifunctional nuclease activity, on drought stress. We found that AtBBD1 localized to the nucleus and cytoplasm, and was expressed strongly in trichomes and stomatal guard cells of leaves, based on promoter:GUS constructs. Expression analyses revealed that AtBBD1 and AtBBD2 are induced early and strongly by ABA and drought, and that AtBBD1 is also strongly responsive to JA. We then compared phenotypes of two AtBBD1-overexpression lines (AtBBD1-OX), single knockout atbbd1, and double knockout atbbd1/atbbd2 plants under drought conditions. We did not observe any phenotypic difference among them under normal growth conditions, while OX lines had greatly enhanced drought tolerance, lower transpirational water loss, and higher proline content than the WT and KOs. Moreover, by measuring seed germination rate and the stomatal aperture after ABA treatment, we found that AtBBD1-OX and atbbd1 plants showed significantly higher and lower ABA-sensitivity, respectively, than the WT. RNA sequencing analysis of AtBBD1-OX and atbbd1 plants under PEG-induced drought stress showed that overexpression of AtBBD1 enhances the expression of key regulatory genes in the ABA-mediated drought signaling cascade, particularly by inducing genes related to ABA biosynthesis, downstream transcription factors, and other regulatory proteins, conferring AtBBD1-OXs with drought tolerance. Taken together, we suggest that AtBBD1 functions as a novel positive regulator of drought responses by enhancing the expression of ABA- and drought stress-responsive genes as well as by increasing proline content.

The in vitro structure and functions of the disordered late embryogenesis abundant three proteins

Late embryogenesis abundant (LEA) proteins are produced during seed embryogenesis and in vegetative tissue in response to various abiotic stressors. A correlation has been established between LEA expression and stress tolerance, yet their precise biochemical mechanism remains elusive. LEA proteins are very rich in hydrophilic amino acids, and they have been found to be intrinsically disordered proteins (IDPs) in vitro. Here, we perform biochemical and structural analyses of the four LEA3 proteins from Arabidopsis thaliana (AtLEA3). We show that the LEA3 proteins are disordered in solution but have regions with propensity for order. All LEA3 proteins were effective cryoprotectants of LDH in the freeze/thaw assays, while only one member, AtLEA3-4, was shown to bind Cu²⁺ and Fe³⁺ ions with micromolar affinity. As well, only AtLEA3-4 showed binding and a gain in α-helicity in the presence of the membrane mimic dodecylphosphocholine (DPC). We explored this interaction in greater detail using ¹⁵ N-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance, and demonstrate that two sets of conserved motifs present in AtLEA3-4 are involved in the interaction with the DPC micelles, which themselves gain α-helical structure.

DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana

Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.

The canonical RdDM pathway mediates the control of seed germination timing under salinity

Plants respond to adverse environmental cues by adjusting a wide variety of processes through highly regulated mechanisms to maintain plant homeostasis for survival. As a result of the sessile nature of plants, their response, adjustment and adaptation to the changing environment is intimately coordinated with their developmental programs through the crosstalk of regulatory networks. Germination is a critical process in the plant life cycle, and thus plants have evolved various strategies to control the timing of germination according to their local environment. The mechanisms involved in these adjustment responses are largely unknown, however. Here, we report that mutations in core elements of canonical RNA-directed DNA methylation (RdDM) affect the germination and post-germination growth of Arabidopsis seeds grown under salinity stress. Transcriptomic and whole-genome bisulfite sequencing (WGBS) analyses support the involvement of this pathway in the control of germination timing and post-germination growth under salinity stress by preventing the transcriptional activation of genes implicated in these processes. Subsequent transcriptional effects on genes that function in relation to these developmental events support this conclusion.

Temperature and Soil Moisture Stress Modulate the Host Defense Response in Chickpea During Dry Root Rot Incidence

Dry root rot caused by the necrotrophic phytopathogenic fungus Rhizoctonia bataticola is an emerging threat to chickpea production in India. In the near future, the expected increase in average temperature and inconsistent rainfall patterns resultant of changing climatic scenarios are strongly believed to exacerbate the disease to epidemic proportions. The present study aims to quantify the collective role of temperature and soil moisture content (SMC) on disease progression in chickpea under controlled environmental conditions. In our study, we could find that both temperature and soil moisture played a decisive role in influencing the dry root rot disease scenario. As per the disease susceptibility index (DSI), a combination of high temperature (35°C) and low SMC (60%) was found to elicit the highest disease susceptibility in chickpea. High pathogen colonization was realized in chickpea root tissue at all time-points irrespective of genotype, temperature, and SMC. Interestingly, this was in contrast to the DSI where no visible symptoms were recorded in the roots or foliage during the initial time-points. For each time-point, the colonization was slightly higher at 35°C than 25°C, while the same did not vary significantly with respect to SMC. Furthermore, the differential expression study revealed the involvement of host defense-related genes like endochitinase and PR-3-type chitinase (CHI III) genes in delaying the dry root rot (DRR) disease progression in chickpea. Such genes were found to be highly active during the early stages of infection especially under low SMC.

Overexpression of OsC3H10, a CCCH-Zinc Finger, Improves Drought Tolerance in Rice by Regulating Stress-Related Genes

CCCH zinc finger proteins are members of the zinc finger protein family, and are known to participate in the regulation of development and stress responses via the posttranscriptional regulation of messenger RNA in animals and yeast. However, the molecular mechanism of CCCHZF-mediated drought tolerance is not well understood. We analyzed the functions of OsC3H10, a member of the rice CCCHZF family. OsC3H10 is predominantly expressed in seeds, and its expression levels rapidly declined during seed imbibition. The expression of OsC3H10 was induced by drought, high salinity and abscisic acid (ABA). Subcellular localization analysis revealed that OsC3H10 localized not only in the nucleus but also to the processing bodies and stress granules upon stress treatment. Root-specific overexpression of OsC3H10 was insufficient to induce drought tolerance, while the overexpression of OsC3H10 throughout the entire plant enhanced the drought tolerance of rice plants. Transcriptome analysis revealed that OsC3H10 overexpression elevated the expression levels of genes involved in stress responses, including LATE EMBRYOGENESIS ABUNDANT PROTEINs (LEAs), PATHOGENESIS RELATED GENEs (PRs) and GERMIN-LIKE PROTEINs (GLPs). Our results demonstrated that OsC3H10 is involved in the regulation of the drought tolerance pathway by modulating the expression of stress-related genes.

Functional characterization and regulatory mechanism of wheat CPK34 kinase in response to drought stress

BACKGROUND

Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known to be involved in plant growth, development, and environmental stresses. However, biological functions and regulatory mechanisms of many plant CPKs have not been explored. In our previous study, abundance of the wheat CPK34 (TaCPK34) protein was remarkably upregulated in wheat plants suffering from drought stress, inferring that it could be involved in this stress. Therefore, here we further detected its function and mechanism in response to drought stress.

RESULTS

Transcripts of the TaCPK34 gene were significantly induced after PEG-stimulated water deficiency (20% PEG6000) or 100 μM abscisic acid (ABA) treatments. The TaCPK34 gene was transiently silenced in wheat genome by using barley stripe mosaic virus-induced silencing (BSMV-VIGS) method. After 14 days of drought stress, the transiently TaCPK34-silenced wheat seedlings showed more sensitivity compared with control, and the plant biomasses and relative water contents significantly decreased, whereas soluble sugar and MDA contents increased. The iTRAQ-based quantitative proteomics was employed to measure the protein expression profiles in leaves of the transiently TaCPK34-silenced wheat plants after drought stress. There were 6103 proteins identified, of these, 51 proteins exhibited significantly altered abundance, they were involved in diverse function. And sequence analysis on the promoters of genes, which encoded the above identified proteins, indicated that some promoters harbored some ABA-responsive elements. We determined the interactions between TaCPK34 and three identified proteins by using bimolecular fluorescent complementation (BiFC) method and our data indicated that TaCPK34directly interacted with the glutathione S-transferase 1 and prx113, respectively.

CONCLUSIONS

Our study suggested that the TaCPK34 gene played positive roles in wheat response to drought stress through directly or indirectly regulating the expression of ABA-dependent manner genes, which were encoding identified proteins from iTRAQ-based quantitative proteomics. And it could be used as one potential gene to develop crop cultivars with improved drought tolerance.

Conserved sequence motifs in the abiotic stress response protein late embryogenesis abundant 3

LEA3 proteins, a family of abiotic stress proteins, are defined by the presence of a tryptophan-containing motif, which we name the W-motif. We use Pfam LEA3 sequences to search the Phytozome database to create a W-motif definition and a LEA3 sequence dataset. A comprehensive analysis of these sequences revealed four N-terminal motifs, as well as two previously undiscovered C-terminal motifs that contain conserved acidic and hydrophobic residues. The general architecture of the LEA3 sequences consisted of an N-terminal motif with a potential mitochondrial transport signal and the twin-arginine motif cut-site, followed by a W-motif and often a C-terminal motif. Analysis of species distribution of the motifs showed that one architecture was found exclusively in Commelinids, while two were distributed fairly evenly over all species. The physiochemical properties of the different architectures showed clustering in a relatively narrow range compared to the previously studied dehydrins. The evolutionary analysis revealed that the different sequences grouped into clades based on architecture, and that there appear to be at least two distinct groups of LEA3 proteins based on their architectures and physiochemical properties. The presence of LEA3 proteins in non-vascular plants but their absence in algae suggests that LEA3 may have arisen in the evolution of land plants.

The N-Terminal Region of Soybean PM1 Protein Protects Liposomes during Freeze-Thaw

Late embryogenesis abundant (LEA) group 1 (LEA_1) proteins are intrinsically disordered proteins (IDPs) that play important roles in protecting plants from abiotic stress. Their protective function, at a molecular level, has not yet been fully elucidated, but several studies suggest their involvement in membrane stabilization under stress conditions. In this paper, the soybean LEA_1 protein PM1 and its truncated forms (PM1-N: N-terminal half; PM1-C: C-terminal half) were tested for the ability to protect liposomes against damage induced by freeze-thaw stress. Turbidity measurement and light microscopy showed that full-length PM1 and PM1-N, but not PM1-C, can prevent freeze-thaw-induced aggregation of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) liposomes and native thylakoid membranes, isolated from spinach leaves (Spinacia oleracea). Particle size distribution analysis by dynamic light scattering (DLS) further confirmed that PM1 and PM1-N can prevent liposome aggregation during freeze-thaw. Furthermore, PM1 or PM1-N could significantly inhibit membrane fusion of liposomes, but not reduce the leakage of their contents following freezing stress. The results of proteolytic digestion and circular dichroism experiments suggest that PM1 and PM1-N proteins bind mainly on the surface of the POPC liposome. We propose that, through its N-terminal region, PM1 functions as a membrane-stabilizing protein during abiotic stress, and might inhibit membrane fusion and aggregation of vesicles or other endomembrane structures within the plant cell.

Genes, proteins and other networks regulating somatic embryogenesis in plants

Background

Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network.

Main text (observation)

This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation.

Conclusions

The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.

Late Embryogenesis Abundant Protein-Client Protein Interactions

The intrinsically disordered proteins belonging to the LATE EMBRYOGENESIS ABUNDANT protein (LEAP) family have been ascribed a protective function over an array of intracellular components. We focus on how LEAPs may protect a stress-susceptible proteome. These examples include instances of LEAPs providing a shield molecule function, possibly by instigating liquid-liquid phase separations. Some LEAPs bind directly to their client proteins, exerting a holdase-type chaperonin function. Finally, instances of LEAP-client protein interactions have been documented, where the LEAP modulates (interferes with) the function of the client protein, acting as a surreptitious rheostat of cellular homeostasis. From the examples identified to date, it is apparent that client protein modulation also serves to mitigate stress. While some LEAPs can physically bind and protect client proteins, some apparently bind to assist the degradation of the client proteins with which they associate. Documented instances of LEAP-client protein binding, even in the absence of stress, brings to the fore the necessity of identifying how the LEAPs are degraded post-stress to render them innocuous, a first step in understanding how the cell regulates their abundance.