Overexpression of Arabidopsis aspartic protease APA1 gene confers drought tolerance

Genetically correlated leaf tensile and morphological traits are driven by growing season length in a widespread perennial grass

PREMISE

Leaf tensile resistance, a leaf's ability to withstand pulling forces, is an important determinant of plant ecological strategies. One potential driver of leaf tensile resistance is growing season length. When growing seasons are long, strong leaves, which often require more time and resources to construct than weak leaves, may be more advantageous than when growing seasons are short. Growing season length and other ecological conditions may also impact the morphological traits that underlie leaf tensile resistance.

METHODS

To understand variation in leaf tensile resistance, we measured size-dependent leaf strength and size-independent leaf toughness in diverse genotypes of the widespread perennial grass Panicum virgatum (switchgrass) in a common garden. We then used quantitative genetic approaches to estimate the heritability of leaf tensile resistance and whether there were genetic correlations between leaf tensile resistance and other morphological traits.

RESULTS

Leaf tensile resistance was positively associated with aboveground biomass (a proxy for fitness). Moreover, both measures of leaf tensile resistance exhibited high heritability and were positively genetically correlated with leaf lamina thickness and leaf mass per area (LMA). Leaf tensile resistance also increased with the growing season length in the habitat of origin, and this effect was mediated by both LMA and leaf thickness.

CONCLUSIONS

Differences in growing season length may promote selection for different leaf lifespans and may explain existing variation in leaf tensile resistance in P. virgatum. In addition, the high heritability of leaf tensile resistance suggests that P. virgatum will be able to respond to climate change as growing seasons lengthen.

Aspartyl proteases identified as candidate genes of a fiber length QTL, qFLD05, that regulates fiber length in cotton (Gossypium hirsutum L.)

KEY MESSAGE

GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.

Multi-omics insights into the positive role of strigolactone perception in barley drought response

BACKGROUND

Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response.

RESULTS

We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley.

CONCLUSIONS

Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms.

The roles of plant proteases and protease inhibitors in drought response: a review

Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes' level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.

Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut

BACKGROUND

Drought stress has negative effects on plant growth and productivity. In this study, a comprehensive analysis of physiological responses and gene expression was performed. The responses and expressions were compared between drought-tolerant (DT) and drought-sensitive (DS) peanut varieties to investigate the regulatory mechanisms and hub genes involved in the impact of drought stress on culture.

RESULTS

The drought-tolerant variety had robust antioxidative capacities with higher total antioxidant capacity and flavonoid contents, and it enhanced osmotic adjustment substance accumulation to adapt to drought conditions. KEGG analysis of differentially expressed genes demonstrated that photosynthesis was strongly affected by drought stress, especially in the drought-sensitive variety, which was consistent with the more severe suppression of photosynthesis. The hub genes in the key modules related to the drought response, including genes encoding protein kinase, E3 ubiquitin-protein ligase, potassium transporter, pentatricopeptide repeat-containing protein, and aspartic proteinase, were identified through a comprehensive combined analysis of genes and physiological traits using weighted gene co-expression network analysis. There were notably differentially expressed genes between the two varieties, suggesting the positive roles of these genes in peanut drought tolerance.

CONCLUSION

A comprehensive analysis of physiological traits and relevant genes was conducted on peanuts with different drought tolerances. The findings revealed diverse drought-response mechanisms and identified candidate genes for further research.

PhePLATZ1, a PLATZ transcription factor in moso bamboo (Phyllostachys edulis), improves drought resistance of transgenic Arabidopsis thaliana

Drought is one of the most serious environmental stresses. Plant AT-rich sequence and zinc-binding (PLATZ) proteins perform indispensable functions to regulate plant growth and development and to respond to environmental stress. In this present study, we identified PhePLATZ1 in moso bamboo and found that its expression was up-regulated in response to 20% PEG-6000 and abscisic acid (ABA) treatments. Next, transgenic PhePLATZ1-overexpressing Arabidopsis lines were generated. Overexpression of PhePLATZ1 improved drought stress resistance of transgenic plants by mediating osmotic regulation, enhancing water retention capacity and reducing membrane and oxidative damage. These findings were corroborated by analysing physiological indicators including chlorophyll, relative water content, leaf water loss rate, electrolyte leakage, H₂O₂, proline, malondialdehyde content and the enzyme activities of peroxidase and catalase. Subsequent seed germination and seedling root length experiments that included exposure to exogenous ABA treatments showed that ABA sensitivity decreased in transgenic plants relative to wild-type plants. Moreover, transgenic PhePLATZ1-overexpressing plants promoted stomatal closure in response to ABA treatment, suggesting that PhePLATZ1 might play a positive regulatory role in the drought resistance of plants via the ABA signaling pathway. In addition, the transgenic PhePLATZ1-OE plants showed altered expression of some stress-related genes when grown under drought conditions. Taken together, these findings improve our understanding of the drought response of moso bamboo and provide a key candidate gene for the molecular breeding of this species for drought tolerance.

RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response

Heat stress is one of the significant constraints affecting wheat production worldwide. To ensure food security for ever-increasing world population, improving wheat for heat stress tolerance is needed in the presently drifting climatic conditions. At the molecular level, heat stress tolerance in wheat is governed by a complex interplay of various heat stress-associated genes. We used a comparative transcriptome sequencing approach to study the effect of heat stress (5°C above ambient threshold temperature of 20°C) during grain filling stages in wheat genotype K7903 (Halna). At 7 DPA (days post-anthesis), heat stress treatment was given at four stages: 0, 24, 48, and 120 h. In total, 115,656 wheat genes were identified, including 309 differentially expressed genes (DEGs) involved in many critical processes, such as signal transduction, starch synthetic pathway, antioxidant pathway, and heat stress-responsive conserved and uncharacterized putative genes that play an essential role in maintaining the grain filling rate at the high temperature. A total of 98,412 Simple Sequences Repeats (SSR) were identified from de novo transcriptome assembly of wheat and validated. The miRNA target prediction from differential expressed genes was performed by psRNATarget server against 119 mature miRNA. Further, 107,107 variants including 80,936 Single nucleotide polymorphism (SNPs) and 26,171 insertion/deletion (Indels) were also identified in de novo transcriptome assembly of wheat and wheat genome Ensembl version 31. The present study enriches our understanding of known heat response mechanisms during the grain filling stage supported by discovery of novel transcripts, microsatellite markers, putative miRNA targets, and genetic variant. This enhances gene functions and regulators, paving the way for improved heat tolerance in wheat varieties, making them more suitable for production in the current climate change scenario.

In-Depth Proteomic Analysis of the Secondary Dormancy Induction by Hypoxia or High Temperature in Barley Grains

In barley, incubation of primary dormant (D1) grains on water under conditions that do not allow germination, i.e. 30°C in air and 15°C or 30°C in 5% O2, induces a secondary dormancy (D2) expressed as a loss of the ability to germinate at 15°C in air. The aim of this study was to compare the proteome of barley embryos isolated from D1 grains and D2 ones after induction of D2 at 30°C or in hypoxia at 15°C or 30°C. Total soluble proteins were analyzed by 2DE gel-based proteomics, allowing the selection of 130 differentially accumulated proteins (DAPs) among 1,575 detected spots. According to the protein abundance profiles, the DAPs were grouped into six abundance-based similarity clusters. Induction of D2 is mainly characterized by a down-accumulation of proteins belonging to cluster 3 (storage proteins, proteases, alpha-amylase inhibitors and histone deacetylase HD2) and an up-accumulation of proteins belonging to cluster 4 (1-Cys peroxiredoxin, lipoxygenase2 and caleosin). The correlation-based network analysis for each cluster highlighted central protein hub. In addition, most of genes encoding DAPs display high co-expression degree with 19 transcription factors. Finally, this work points out that similar molecular events accompany the modulation of dormancy cycling by both temperature and oxygen, including post-translational, transcriptional and epigenetic regulation.

Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress

Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.

Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

The crop wild relative, Fragaria nilgerrensis, is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve useful to guide the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and the genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibited the highest genetic diversity. Redundancy analysis suggests that both environment and geographic variables shaped a significant proportion of genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweeps scans and genome-environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis.

Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms

Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.

Cell-to-Cell Connection in Plant Grafting-Molecular Insights into Symplasmic Reconstruction

Grafting is a means to connect tissues from two individual plants and grow a single chimeric plant through the establishment of both apoplasmic and symplasmic connections. Recent molecular studies using RNA-sequencing data have provided genetic information on the processes involved in tissue reunion, including wound response, cell division, cell-cell adhesion, cell differentiation and vascular formation. Thus, studies on grafting increase our understanding of various aspects of plant biology. Grafting has also been used to study systemic signaling and transport of micromolecules and macromolecules in the plant body. Given that graft viability and molecular transport across graft junctions largely depend on vascular formation, a major focus in grafting biology has been the mechanism of vascular development. In addition, it has been thought that symplasmic connections via plasmodesmata are fundamentally important to share cellular information among newly proliferated cells at the graft interface and to accomplish tissue differentiation correctly. Therefore, this review focuses on plasmodesmata formation during grafting. We take advantage of interfamily grafts for unambiguous identification of the graft interface and summarize morphological aspects of de novo formation of plasmodesmata. Important molecular events are addressed by re-examining the time-course transcriptome of interfamily grafts, from which we recently identified the cell-cell adhesion mechanism. Plasmodesmata-associated genes upregulated during graft healing that may provide a link to symplasm establishment are described. We also discuss future research directions.

Plant protease as regulator and signaling molecule for enhancing environmental stress-tolerance

Proteases are ubiquitous in prokaryotes and eukaryotes. Plant proteases are key regulators of various physiological processes, including protein homeostasis, organelle development, senescence, seed germination, protein processing, environmental stress response, and programmed cell death. Proteases are involved in the breakdown of peptide bonds resulting in irreversible posttranslational modification of the protein. Proteases act as signaling molecules that specifically regulate cellular function by cleaving and triggering receptor molecules. Peptides derived from proteolysis regulate ROS signaling under oxidative stress in the plant. It degrades misfolded and abnormal proteins into amino acids to repair the cell damage and regulates the biological process in response to environmental stress. Proteases modulate the biogenesis of phytohormones which control plant growth, development, and environmental stresses. Protein homeostasis, the overall balance between protein synthesis and proteolysis, is required for plant growth and development. Abiotic and biotic stresses are major factors that negatively impact cellular survivability, biomass production, and reduced crop yield potentials. Therefore, the identification of various stress-responsive proteases and their molecular functions may elucidate valuable information for the development of stress-resilient crops with higher yield potentials. However, the understanding of molecular mechanisms of plant protease remains unexplored. This review provides an overview of proteases related to development, signaling, and growth regulation to acclimatize environmental stress in plants.

Exploitation of Drought Tolerance-Related Genes for Crop Improvement

Drought has become a major threat to food security, because it affects crop growth and development. Drought tolerance is an important quantitative trait, which is regulated by hundreds of genes in crop plants. In recent decades, scientists have made considerable progress to uncover the genetic and molecular mechanisms of drought tolerance, especially in model plants. This review summarizes the evaluation criteria for drought tolerance, methods for gene mining, characterization of genes related to drought tolerance, and explores the approaches to enhance crop drought tolerance. Collectively, this review illustrates the application prospect of these genes in improving the drought tolerance breeding of crop plants.

Melatonin Enhances Seed Germination and Seedling Growth of Medicago sativa Under Salinity via a Putative Melatonin Receptor MsPMTR1

Alfalfa (Medicago sativa L.) is an important forage crop, and salt stress is a major limiting factor in its yield. Melatonin (MT) is a multi-regulatory molecule in plants. We showed that basal MT content was positively correlated with the salt tolerance degree of different alfalfa varieties. MT and its precursor 5-HT fully recovered seed germination while partially ameliorated seedling growth of salt-stressed alfalfa. The 5-HT showed some divergent effects from MT with regards to growth amelioration under salinity. Salt stress caused stunted plant growth in soil culture, while MT ameliorated it by elevating plant height, fresh weight, branching number, and chlorophyll content. Silencing of a putative MT receptor, MsPMTR1, which was shown to be membrane-localized, abolished the ameliorative effects of MT on salt-stressed alfalfa seedling growth, while overexpression of MsPMTR1 improved plant growth under salt stress. The RNA sequencing analysis showed that nine pathway genes were specifically induced by MT treatment compared with salt stress. These MT-responsive differentially expressed genes include basal metabolic pathway genes, such as "ribosome, elongation factor," "sugar and lipid metabolism," and "photosynthesis" and stress-related genes encoding "membrane integrity" related proteins, heat shock protein, peroxidase/oxidoreductase, and protease. Several abiotic stress response-related genes, such as DRE, ARF, HD-ZF, MYB, and REM were repressed by NaCl treatment while induced by MT treatment. In summary, we demonstrated the importance of MsPMTR1 in MT-mediated salt tolerance in alfalfa, and we also analyzed the regulatory mechanism of MT during alfalfa seed germination under salt stress.

Defense and Offense Strategies: The Role of Aspartic Proteases in Plant-Pathogen Interactions

Plant aspartic proteases (APs; E.C.3.4.23) are a group of proteolytic enzymes widely distributed among different species characterized by the conserved sequence Asp-Gly-Thr at the active site. With a broad spectrum of biological roles, plant APs are suggested to undergo functional specialization and to be crucial in developmental processes, such as in both biotic and abiotic stress responses. Over the last decade, an increasing number of publications highlighted the APs' involvement in plant defense responses against a diversity of stresses. In contrast, few studies regarding pathogen-secreted APs and AP inhibitors have been published so far. In this review, we provide a comprehensive picture of aspartic proteases from plant and pathogenic origins, focusing on their relevance and participation in defense and offense strategies in plant-pathogen interactions.

Investigation of an Antioxidative System for Salinity Tolerance in Oenanthe javanica

Abiotic stress, such as drought and salinity, severely affect the growth and yield of many plants. Oenanthe javanica (commonly known as water dropwort) is an important vegetable that is grown in the saline-alkali soils of East Asia, where salinity is the limiting environmental factor. To study the defense mechanism of salt stress responses in water dropwort, we studied two water dropwort cultivars, V11E0022 and V11E0135, based on phenotypic and physiological indexes. We found that V11E0022 were tolerant to salt stress, as a result of good antioxidant defense system in the form of osmolyte (proline), antioxidants (polyphenols and flavonoids), and antioxidant enzymes (APX and CAT), which provided novel insights for salt-tolerant mechanisms. Then, a comparative transcriptomic analysis was conducted, and Gene Ontology (GO) analysis revealed that differentially expressed genes (DEGs) involved in the carbohydrate metabolic process could reduce oxidative stress and enhance energy production that can help in adaptation against salt stress. Similarly, lipid metabolic processes can also enhance tolerance against salt stress by reducing the transpiration rate, H₂O₂, and oxidative stress. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs involved in hormone signals transduction pathway promoted the activities of antioxidant enzymes and reduced oxidative stress; likewise, arginine and proline metabolism, and flavonoid pathways also stimulated the biosynthesis of proline and flavonoids, respectively, in response to salt stress. Moreover, transcription factors (TFs) were also identified, which play an important role in salt stress tolerance of water dropwort. The finding of this study will be helpful for crop improvement under salt stress.

The Role of Proteases in Determining Stomatal Development and Tuning Pore Aperture: A Review

Plant proteases, the proteolytic enzymes that catalyze protein breakdown and recycling, play an essential role in a variety of biological processes including stomatal development and distribution, as well as, systemic stress responses. In this review, we summarize what is known about the participation of proteases in both stomatal organogenesis and on the stomatal pore aperture tuning, with particular emphasis on their involvement in numerous signaling pathways triggered by abiotic and biotic stressors. There is a compelling body of evidence demonstrating that several proteases are directly or indirectly implicated in the process of stomatal development, affecting stomatal index, density, spacing, as well as, size. In addition, proteases are reported to be involved in a transient adjustment of stomatal aperture, thus orchestrating gas exchange. Consequently, the proteases-mediated regulation of stomatal movements considerably affects plants' ability to cope not only with abiotic stressors, but also to perceive and respond to biotic stimuli. Even though the determining role of proteases on stomatal development and functioning is just beginning to unfold, our understanding of the underlying processes and cellular mechanisms still remains far from being completed.