NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato

Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops

We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of diverse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their individual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops.

An apple (Malus domestica) NAC transcription factor enhances drought tolerance in transgenic apple plants

Plant NAC proteins constitute one of the largest transcription factor families. They play pivotal functions during responses to various abiotic stresses. However, knowledge on roles of NAC proteins in abiotic stress tolerance as well as corresponding mechanisms has not been fully studied in perennial woody plants, including domesticated apple (Malus domestica). In the present study, we characterized the role of apple MdNAC1 transcription factor in response to drought stress. Apple plants overexpressing MdNAC1 gene exhibited promoted tolerance to drought stress, as evident by reduced water loss and electrolyte leakage in leaves, and maintenance of photosynthesis and photosynthetic pigments content under drought conditions. In addition, the levels of malondialdehyde (MDA) and reactive oxygen species (ROS) were significantly lower for transgenic apple lines than those for nontransgenic plants under drought conditions. This was accompanied by higher activities of several antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as increased expression of the associated genes in transgenic lines. Together, our results indicate that overexpression of the apple MdNAC1 gene enhances drought stress tolerance in apple plants by promoting higher photosynthesis and activities of ROS-scavenging enzymes.

Tomato fruit ripening factor NOR controls leaf senescence

NAC transcription factors (TFs) are important regulators of expressional reprogramming during plant development, stress responses, and leaf senescence. NAC TFs also play important roles in fruit ripening. In tomato (Solanum lycopersicum), one of the best characterized NACs involved in fruit ripening is NON-RIPENING (NOR), and the non-ripening (nor) mutation has been widely used to extend fruit shelf life in elite varieties. Here, we show that NOR additionally controls leaf senescence. Expression of NOR increases with leaf age, and developmental as well as dark-induced senescence are delayed in the nor mutant, while overexpression of NOR promotes leaf senescence. Genes associated with chlorophyll degradation as well as senescence-associated genes (SAGs) show reduced and elevated expression, respectively, in nor mutants and NOR overexpressors. Overexpression of NOR also stimulates leaf senescence in Arabidopsis thaliana. In tomato, NOR supports senescence by directly and positively regulating the expression of several senescence-associated genes including, besides others, SlSAG15 and SlSAG113, SlSGR1, and SlYLS4. Finally, we find that another senescence control NAC TF, namely SlNAP2, acts upstream of NOR to regulate its expression. Our data support a model whereby NAC TFs have often been recruited by higher plants for both the control of leaf senescence and fruit ripening.

Functional characterization of poplar NAC13 gene in salt tolerance

Transcription factor (TF) genes play a critical role in plant abiotic and biotic stress responses. In this study, we cloned a poplar TF NAC13 gene (Potri.001G404100.1), which is significantly up-regulated to salt stress. Then we developed gene overexpression and antisense suppression constructions driven by CaMV35S, and successfully transferred them to a poplar variety 84 K (Populus alba × P. glandulosa), respectively. Evidence from molecular assay indicated that NAC13 overexpression and antisense suppression fragments have been integrated into the poplar genome. The morphological and physiological characterization and salt treatment results indicated the NAC13-overexpressing transgenic plants enhance salt tolerance significantly, compared to wide type. In contrast, the NAC13-suppressing transgenic plants are significantly sensitive to salt stress, compared to wide type. Evidence from transgenic Arabidopsis expressing GUS gene indicated that the gene driven by NAC13 promoter is mainly expressed in the roots and leaves of young plants. These studies indicate that the NAC13 gene plays a vital role in salt stress response.

Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance

Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.

The NAC family transcription factor GmNAC42-1 regulates biosynthesis of the anticancer and neuroprotective glyceollins in soybean

BACKGROUND

Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean (Glycine max L. Merr) that have important roles in providing defense against pathogens. They also have impressive anticancer and neuroprotective activities in mammals. Despite their potential usefulness as therapeutics, glyceollins are not economical to synthesize and are biosynthesized only transiently and in low amounts in response to specific stresses. Engineering the regulation of glyceollin biosynthesis may be a promising approach to enhance their bioproduction, yet the transcription factors (TFs) that regulate their biosynthesis have remained elusive. To address this, we first aimed to identify novel abiotic stresses that enhance or suppress the elicitation of glyceollins and then used a comparative transcriptomics approach to search for TF gene candidates that may positively regulate glyceollin biosynthesis.

RESULTS

Acidity stress (pH 3.0 medium) and dehydration exerted prolonged (week-long) inductive or suppressive effects on glyceollin biosynthesis, respectively. RNA-seq found that all known biosynthetic genes were oppositely regulated by acidity stress and dehydration, but known isoflavonoid TFs were not. Systemic acquired resistance (SAR) genes were highly enriched in the geneset. We chose to functionally characterize the NAC (NAM/ATAF1/2/CUC2)-family TF GmNAC42-1 that was annotated as an SAR gene and a homolog of the Arabidopsis thaliana (Arabidopsis) indole alkaloid phytoalexin regulator ANAC042. Overexpressing and silencing GmNAC42-1 in elicited soybean hairy roots dramatically enhanced and suppressed the amounts of glyceollin metabolites and biosynthesis gene mRNAs, respectively. Yet, overexpressing GmNAC42-1 in non-elicited hairy roots failed to stimulate the expressions of all biosynthesis genes. Thus, GmNAC42-1 was necessary but not sufficient to activate all biosynthesis genes on its own, suggesting an important role in the glyceollin gene regulatory network (GRN). The GmNAC42-1 protein directly bound the promoters of biosynthesis genes IFS2 and G4DT in the yeast one-hybrid (Y1H) system.

CONCLUSIONS

Acidity stress is a novel elicitor and dehydration is a suppressor of glyceollin biosynthesis. The TF gene GmNAC42-1 is an essential positive regulator of glyceollin biosynthesis. Overexpressing GmNAC42-1 in hairy roots can be used to increase glyceollin yields > 10-fold upon elicitation. Thus, manipulating the expressions of glyceollin TFs is an effective strategy for enhancing the bioproduction of glyceollins in soybean.

Physiological and transcriptomic responses of reproductive stage soybean to drought stress

KEY MESSAGE

The dynamic alterations of the physiological and molecular processes in reproductive stage soybean indicated the dramatic impact caused by drought. Drought is a major abiotic stress that limits soybean (Glycine max) production. Most prior studies were focused on either model species or crops that are at their vegetative stages. It is known that the reproductive stage of soybean is more susceptible to drought. Therefore, an understanding on the responsive mechanisms during this stage will not only be important for basic plant physiology, but the knowledge can also be used for crop improvement via either genetic engineering or molecular breeding. In this study, physiological measurements and RNA-Seq analysis were used to dissect the metabolic alterations and molecular responses in the leaves of soybean grown at drought condition. Photosynthesis rate, stomata conductance, transpiration, and water potential were reduced. The activities of SOD and CAT were increased, while the activity of POD stayed unchanged. A total of 2771 annotated genes with at least twofold changes were found to be differentially expressed in the drought-stressed plants in which 1798 genes were upregulated and 973 were downregulated. Via KEGG analysis, these genes were assigned to multiple molecular pathways, including ABA biogenesis, compatible compound accumulation, secondary metabolite synthesis, fatty acid desaturation, plant transcription factors, etc. The large number of differentially expressed genes and the diverse pathways indicated that soybean employs complicated mechanisms to cope with drought. Some of the identified genes and pathways can be used as targets for genetic engineering or molecular breeding to improve drought resistance in soybean.

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

Milestones achieved in response to drought stress through reverse genetic approaches

Drought stress is the most important abiotic stress that constrains crop production and reduces yield drastically. The germplasm of most of the cultivated crops possesses numerous unknown drought stress tolerant genes. Moreover, there are many reports suggesting that the wild species of most of the modern cultivars have abiotic stress tolerant genes. Due to climate change and population booms, food security has become a global issue. To develop drought tolerant crop varieties knowledge of various genes involved in drought stress is required. Different reverse genetic approaches such as virus-induced gene silencing (VIGS), clustered regularly interspace short palindromic repeat (CRISPR), targeting induced local lesions in genomes (TILLING) and expressed sequence tags (ESTs) have been used extensively to study the functionality of different genes involved in response to drought stress. In this review, we described the contributions of different techniques of functional genomics in the study of drought tolerant genes.

Engineering synthetic regulatory circuits in plants

Plant synthetic biology is a rapidly emerging field that aims to engineer genetic circuits to function in plants with the same reliability and precision as electronic circuits. These circuits can be used to program predictable plant behavior, producing novel traits to improve crop plant productivity, enable biosensors, and serve as platforms to synthesize chemicals and complex biomolecules. Herein we introduce the importance of developing orthogonal plant parts and the need for quantitative part characterization for mathematical modeling of complex circuits. In particular, transfer functions are important when designing electronic-like genetic controls such as toggle switches, positive/negative feedback loops, and Boolean logic gates. We then discuss potential constraints and challenges in synthetic regulatory circuit design and integration when using plants. Finally, we highlight current and potential plant synthetic regulatory circuit applications.

Molecular and functional characterization of ShNAC1, an NAC transcription factor from Solanum habrochaites

NAC transcription factors (TFs) are important regulators of plant adaptation to abiotic stress. In this study, we functionally characterized an NAC TF, ShNAC1, from Solanum habrochaites. ShNAC1 was up-regulated by drought, cold, and salt stresses, and it displayed lower expression at the late stage of stress treatments than its orthologous gene in S. lycopersicum. Overexpression of ShNAC1 in tomato resulted in reduced cold, drought, and salt tolerance. Additionally, ShNAC1 displayed the highest expression in senescent leaf, and overexpressing ShNAC1 accelerated salt- and dark-induced leaf senescence. ShNAC1 was located in the nucleus without transactivation activity. RNA-seq analysis revealed that 81% (190 out of 234) differentially-expressed genes (DEGs) showed down-regulation in the transgenic line L2 compared with wild-type, suggesting that ShNAC1 may function as a transcriptional repressor. Among these down-regulated DEGs, many were involved in stress responses, such as SlHKT1;1, SlMAPKKK59, SlJA2, SlTIL, SlALDH2B1, etc. Noticeably, one ACS gene and three ACO genes involved in ethylene biosynthesis were up-regulated, while seven ERF genes in the ethylene signal transduction pathway were down-regulated in the transgenic lines, respectively. Our results suggested that ShNAC1 negatively regulates tolerance to abiotic stress in tomato probably by modulating the ethylene biosynthesis and signal transduction pathways.

Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress

Owing to diverse abiotic stresses and global climate deterioration, the agricultural production worldwide is suffering serious losses. Breeding stress-resilient crops with higher quality and yield against multiple environmental stresses via application of transgenic technologies is currently the most promising approach. Deciphering molecular principles and mining stress-associate genes that govern plant responses against abiotic stresses is one of the prerequisites to develop stress-resistant crop varieties. As molecular switches in controlling stress-responsive genes expression, transcription factors (TFs) play crucial roles in regulating various abiotic stress responses. Hence, functional analysis of TFs and their interaction partners during abiotic stresses is crucial to perceive their role in diverse signaling cascades that many researchers have continued to undertake. Here, we review current developments in understanding TFs, with particular emphasis on their functions in orchestrating plant abiotic stress responses. Further, we discuss novel molecular mechanisms of their action under abiotic stress conditions. This will provide valuable information for understanding regulatory mechanisms to engineer stress-tolerant crops.

Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

Overexpression of a predominantly root-expressed NAC transcription factor in wheat roots enhances root length, biomass and drought tolerance

TaRNAC1 is a constitutively and predominantly root-expressed NAC transcription factor. TaRNAC1 overexpression in wheat roots confers increased root length, biomass and drought tolerance and improved grain yield under water limitation. A large and deep root system is an important trait for yield sustainability of dryland cereal crops in drought-prone environments. This study investigated the role of a predominantly root-expressed NAC transcription factor from wheat (TaRNAC1) in the root growth. Expression analysis showed that TaRNAC1 was a constitutively expressed gene with high level expression in the roots and was not drought-upregulated. Overexpression of TaRNAC1 in wheat using a predominantly root-expressed promoter resulted in increased root length and biomass observed at the early growth stage and a marked increase in the maturity root biomass with dry root weight of > 70% higher than that of the wild type plants. Analysis of some root growth-related genes revealed that the expression level of GA3-ox2, which encodes GIBBERELLIN 3-OXIDASE catalysing the conversion of inactive gibberellin (GA) to active GA, was elevated in the roots of transgenic wheat. TaRNAC1 overexpressing transgenic wheat showed more dehydration tolerance under polyethylene glycol (PEG) treatment and produced more aboveground biomass and grain under water-limited conditions than the wild type plants. These data suggest that TaRNAC1 may play a role in root growth and be used as a molecular tool for potential enlargement of root system in wheat.

Revisiting the Soybean GmNAC Superfamily

The NAC (NAM, ATAF, and CUC) genes encode transcription factors involved with the control of plant morph-physiology and stress responses. The release of the last soybean (Glycine max) genome assembly (Wm82.a2.v1) raised the possibility that new NAC genes would be present in the soybean genome. Here, we interrogated the last version of the soybean genome against a conserved NAC domain structure. Our analysis identified 32 putative novel NAC genes, updating the superfamily to 180 gene members. We also organized the genes in 15 phylogenetic subfamilies, which showed a perfect correlation among sequence conservation, expression profile, and function of orthologous Arabidopsis thaliana genes and NAC soybean genes. To validate our in silico analyses, we monitored the stress-mediated gene expression profiles of eight new NAC-genes by qRT-PCR and monitored the GmNAC senescence-associated genes by RNA-seq. Among ER stress, osmotic stress and salicylic acid treatment, all the novel tested GmNAC genes responded to at least one type of stress, displaying a complex expression profile under different kinetics and extension of the response. Furthermore, we showed that 40% of the GmNACs were differentially regulated by natural leaf senescence, including eight (8) newly identified GmNACs. The developmental and stress-responsive expression profiles of the novel NAC genes fitted perfectly with their phylogenetic subfamily. Finally, we examined two uncharacterized senescence-associated proteins, GmNAC065 and GmNAC085, and a novel, previously unidentified, NAC protein, GmNAC177, and showed that they are nuclear localized, and except for GmNAC065, they display transactivation activity in yeast. Consistent with a role in leaf senescence, transient expression of GmNAC065 and GmNAC085 induces the appearance of hallmarks of leaf senescence, including chlorophyll loss, leaf yellowing, lipid peroxidation and accumulation of H₂O₂. GmNAC177 was clustered to an uncharacterized subfamily but in close proximity to the TIP subfamily. Accordingly, it was rapidly induced by ER stress and by salicylic acid under late kinetic response and promoted cell death in planta. Collectively, our data further substantiated the notion that the GmNAC genes display functional and expression profiles consistent with their phylogenetic relatedness and established a complete framework of the soybean NAC superfamily as a foundation for future analyses.

JUNGBRUNNEN1 Confers Drought Tolerance Downstream of the HD-Zip I Transcription Factor AtHB13

Low water availability is the major environmental factor limiting growth and productivity of plants and crops and is therefore considered of high importance for agriculture affected by climate change. Identifying regulatory components controlling the response and tolerance to drought stress is thus of major importance. The NAC transcription factor (TF) JUNGBRUNNEN1 (JUB1) from Arabidopsis thaliana extends leaf longevity under non-stress growth conditions, lowers cellular hydrogen peroxide (H₂O₂) level, and enhances tolerance against heat stress and salinity. Here, we additionally find that JUB1 strongly increases tolerance to drought stress in Arabidopsis when expressed from both, a constitutive (CaMV 35S) and an abiotic stress-induced (RD29A) promoter. Employing a yeast one-hybrid screen we identified HD-Zip class I TF AtHB13 as an upstream regulator of JUB1. AtHB13 has previously been reported to act as a positive regulator of drought tolerance. AtHB13 and JUB1 thereby establish a joint drought stress control module.