The Transcription Factor bZIP60 Links the Unfolded Protein Response to the Heat Stress Response in Maize

A network-enabled pipeline for gene discovery and validation in non-model plant species

Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 (CSLF6), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum. Our analyses uncover regulators of CSLF6 and also shed light on the evolutionary conservation or divergence of gene regulatory elements among grass species. These results highlight NEEDLE's capability to provide biologically relevant TF predictions and demonstrate its value for non-model plant species with dynamic transcriptome datasets.

The molecular mechanism by which heat stress during the grain filling period inhibits maize grain filling and reduces yield

High temperatures significantly impair plant growth and development by restricting maize grain filling; however, the molecular mechanisms underlying heat stress remain poorly understood. In this study, 350 maize inbred lines were evaluated under field conditions, leading to the identification of heat-tolerant Zheng58 and heat-sensitive Qi319. The two inbred lines were exposed to controlled conditions of 30°C/20°C (optimal) and 42°C/30°C (heat stress) during the grain filling period. Heat stress significantly reduced thousand-kernel weight and seed setting rates, with Qi319 experiencing more pronounced declines. In contrast, Zheng58 showed superior performance, with a grain filling rate 48% higher and seed setting rate 57% greater than Qi319. Transcriptome analysis showed that heat stress disrupted starch biosynthesis and hormonal homeostasis, notably affecting abscisic acid and auxin pathways. Additionally, photosynthetic and transpiration rates in panicle leaves were reduced due to the downregulation of genes related to light-harvesting complexes, photosystem I subunits, and water transport. These findings highlight the critical roles of starch metabolism, hormonal regulation, and photosynthetic efficiency in heat tolerance, offering valuable insights for developing heat-resilient maize varieties to mitigate yield losses under high-temperature conditions.

Genome-Wide Analysis of the Hsf Gene Family in Rosa chinensis and RcHsf17 Function in Thermotolerance

Heat shock transcription factors (Hsfs) play an important role in response to high temperatures by binding to the promoter of the heat shock protein gene to promote its expression. As an important ornamental plant, the rose often encounters heat stress during the flowering process. However, there are few studies on the Hsf family in roses (Rosa. chinensis). In the current study, 19 Hsf genes were identified from R. chinensis and grouped into three main subfamilies (A, B, and C) according to their structural characteristics and phylogenetic analysis. The expression patterns of RcHsf genes were detected in different tissues by quantitative real-time PCR. The RcHsf genes exhibited distinct expression patterns at high temperatures, with RcHsf17 having the highest expression level. RcHsf17 was localized in the nucleus and had transcriptional activity. The overexpression of RcHsf17 increased thermotolerance in Arabidopsis, suggesting the potential role of RcHsf17 in the regulation of the high-temperature response. In addition, RcHsf17 overexpressed in Arabidopsis could enhance the response of transgenic Arabidopsis to methyl jasmonate. Collectively, this study identified and screened RcHsfs in response to high temperatures in roses, providing new insights into the functional divergence of RcHsfs and a basis for screening new varieties of rose.

SpbZIP60 confers cadmium tolerance by strengthening the root cell wall compartmentalization in Sedum plumbizincicola

Cadmium (Cd) is a prominent heavy metal pollutant that inhibits plant growth and poses risks to human health. Sedum plumbizincicola, as a Cd/Zn/Pb hyperaccumulator species, exhibits robust resistance to heavy metals and effective enrichment capacities. In our previous study, overexpressing SpbZIP60 in Arabidopsis enhanced Cd tolerance; however, the underlying the molecular mechanism remains to be elucidated. Here, we identified SpbZIP60 as a representative Cd stress response factor with nuclear localization and transcriptional activation activity. SpbZIP60 underwent conservative splicing in response to endoplasmic reticulum (ER) stress, while its response to Cd stress is independent of the ER stress-mediated unfolded protein response pathway. Overexpression of SpbZIP60 in S. alfredii increased the Cd tolerance and antioxidant activity. Furthermore, SpbZIP60 increased the content of cell wall components and thickened cell wall under Cd stress. Transcriptome analysis indicated a significant enrichment of differentially expressed genes within the phenylpropanoid metabolism pathway. Besides, the binding of SpbZIP60 to the promoter region of SpBglu resulted in the activation of gene expression, thereby enhancing the process of lignin deposition. Collectively, our results elucidated a molecular regulatory model in which SpbZIP60 increased the thickness of the root cell wall to impede Cd entry into the cell, consequently improving Cd tolerance.

RtHSFA9s of Rhodomyrtus tomentosa Positively Regulate Thermotolerance by Transcriptionally Activating RtHSFA2s and RtHSPs

Heat shock transcription factors (HSFs) are crucial components in heat stress response. However, the contribution of the HSFs governing the inherent thermotolerance in Rhodomyrtus tomentosa has barely been investigated. We here compared the roles of RtHSFA9a, RtHSFA9b, and RtHSFA9c in heat stress tolerance. These three genes are the results of gene duplication events, but there exist vast variations in their amino acid sequences. They are all localized to the nucleus. Arabidopsis thaliana plants with overexpressed RtHSFA9a and RtHSFA9c outperformed the wild-type plants, while the over-accumulation of RtHSFA9b had little impact on plant thermotolerance. By transiently overexpressing RtHSFA9a, RtHSFA9b, and RtHSFA9c in R. tomentosa seedlings, the mRNA abundance of heat shock response genes, including RtHSFA2a, RtHSFA2b, RtHSP17.4, RtHSP21.8, RtHSP26.5, and RtHSP70, were upregulated. Transactivation assays confirmed that there exist regulatory divergences among these three genes, viz., RtHSFA9a has the highest transcription activity in regulating RtHSFA2a, RtHSFA2b, RtHSP21.8, and RtHSP70; RtHSFA9c can transcriptionally activate RtHSFA2b, RtHSP21.8, and RtHSP70; RtHSFA9b makes limited contributions to the accumulation of RtHSFA2b, RtHSP21.8, and RtHSP70. Our results indicate that the RtHSFA9 genes make crucial contributions to the thermal adaption of R. tomentosa by positively regulating the RtHSFA2a, RtHSFA2b, and RtHSP genes, which provides novel insights into the RtHSFA9 subfamily.

Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets

Research on the dynamic expression of genes in plants is important for understanding different biological processes. We used the large amounts of transcriptomic data from various plant sample sources that are publicly available to investigate whether the expression levels of a subset of highly variable genes (HVGs) can be used to accurately identify the phenotypes of plants. Using maize (Zea mays L.) as an example, we built machine learning (ML) models to predict phenotypes using a gene expression dataset of 21 612 bulk RNA sequencing samples. We showed that the ML models achieved excellent prediction accuracy using only the HVGs to identify different phenotypes, including tissue types, developmental stages, cultivars and stress conditions. By ML models, several important functional genes were found to be associated with different phenotypes. We performed a similar analysis in rice (Orzya sativa L.) and found that the ML models could be generalized across species. However, the models trained from maize did not perform well in rice, probably because of the expression divergence of the conserved HVGs between the two species. Overall, our results provide an ML framework for phenotype prediction using gene expression profiles, which may contribute to precision management of crops in agricultural practices.

Optimized irrigation and fertilization can mitigate negative CO2 impacts on seed yield and vigor of hybrid maize

Seed yield and vigor of hybrid maize determine the planting, yield, and quality of maize, and consequently affect food, nutrition, and livelihood security; however, the response of seed yield and vigor to climate change is still unclear. We established an optimization-simulation framework consisting of a water‑nitrogen crop production function, a seed vigor and a gridded process-based model to optimize irrigation and nitrogen fertilization management, and used it to evaluate seed yield and vigor in major seed production locations of China, the USA, and Mexico. This framework could reflect the influence of water and nitrogen inputs at different stages on seed yield and vigor considering the spatio-temporal variability of climate and soil properties. Projected seed yield and vigor decreased by 5.8-9.0 % without adaptation by the 2050s, due to the 1.3-5.8 % decrease in seed number and seed protein concentration. Seed yield was positively correlated with CO2 and negatively correlated with temperature, while seed vigor depended on the response of components of seed vigor to climatic factors. Under optimized management, the direct positive effects of temperature on seed protein concentration and CO2 on seed number were strengthened, and the direct negative effects of temperature on seed number and CO2 on seed protein concentration were weakened, which mitigated the reductions in both seed yield and vigor. Elevated CO2 was projected to exacerbate the 2.6 % seed vigor reduction and mitigate the 2.9 % seed yield loss without adaptation, while optimized management could increase seed yield by 4.1 % and mitigate the 2.2 % seed vigor reduction in the Hexi Corridor of China, and decrease the seed yield and vigor reduction by 2.4-5.8 % in the USA and Mexico. Optimized management can strengthen the positive and mitigate the negative effects of climate change on irrigated hybrid maize and inform high-yield and high-quality seed production globally.

Comparative analysis of IRE1s in plants: insights into heat stress adaptation in Triticum aestivum

BACKGROUND

The unfolded protein response (UPR) pathway serves as a crucial mechanism enabling plants to perceive, respond to, and shield themselves from adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1) is one of the key players of the UPR, and resides in the endoplasmic reticulum (ER) within the cell. This study provides a comprehensive analysis of 195 IRE1 genes across 90 diverse plant species, with a focus on their identification and characterization.

RESULTS

To decipher the functions of IRE1 family members, we investigated the evolution and spread of IREs in plants and analysed their structural and localization characteristics. Our detailed cis-element analysis revealed unique IRE1 regulation patterns in different plant species. Furthermore, gene expression analysis revealed tissue-specific and heat stress-responsive expression patterns of TaIRE1s, which were subsequently confirmed via quantitative gene expression analysis. TaIRE1-6A was upregulated in response to dithiothreitol (DTT) treatment as well as heat stress. This finding suggests that IRE1 might play a role in linking the UPR pathway and the heat stress response (HSR).

CONCLUSIONS

Our findings provide a comprehensive understanding of the evolution and expansion of IRE1 genes in different plant species. These findings provide a foundation for further in-depth research on the functional diversity of IREs in nutritious crops following polyploidization. By linking the UPR with HSR, IRE1 could be a key contributor to wheat's resilience against heat stress. Additionally, this connection offers important insights for future functional studies in other crops. Thus, this knowledge could be used for engineering climate resilience in crops such as wheat.

ZmHsp18 screened from the ZmHsp20 gene family confers thermotolerance in maize

Heat stress has become one of the abiotic stresses that pose an increasing threat to maize production due to global warming. The Hsp20 gene family confers tolerance to various abiotic stresses in plants. However, very few Hsp20s have been identified in relation to maize thermotolerance. In this study, we conducted a comprehensive study of Hsp20s involved in thermotolerance in maize. A total of 33 maize Hsp20 genes (ZmHsp20s) were identified through scanning for a conserved α-crystalline domain (ACD), and they were categorized into 14 subfamilies based on phylogenetic analysis. These genes are distributed across all maize chromosomes and nine of them are in regions previously identified as heat-tolerance quantitative trait loci (hrQTL). These hrQTL-associated ZmHsp20s show variation in tissue-specific expression profiles under normal conditions, and seven of them possess 1-5 heat stress elements in their promoters. The integration of RNA-seq data with real-time RT-PCR analysis indicated that ZmHsp23.4, ZmHsp22.8B and ZmHsp18 were dramatically induced under heat stress. Additionally, these genes exhibited co-expression patterns with key ZmHsfs, which are crucial in the heat tolerance pathway. When a null mutant carrying a frame-shifted ZmHsp18 gene was subjected to heat stress, its survival rate decreased significantly, indicating a critical role of ZmHsp18 in maize thermotolerance. Our study lays the groundwork for further research into the roles of ZmHsp20s in enhancing maize's thermotolerance.

Heat Shock Factor HSFA6b Mediates Mitochondrial Unfolded Protein Response in Arabidopsis thaliana

Mitochondria are important organelles in eukaryotes and are involved in various metabolic processes. Mitochondrial proteotoxic stress triggers the mitochondrial unfolded protein response (UPRmt) to restore mitochondrial protein homeostasis and maintain normal life activities. However, the regulatory mechanism of plant UPRmt remains to be revealed in Arabidopsis. Based on the fact that UPRmt activates heat shock protein (HSP) genes, we identified the heat shock transcription factor HSFA6b as a key regulator mediating UPRmt through reverse genetics. HSFA6b responded to mitochondrial proteotoxic stress and regulated mitochondrial heat shock proteins' genes' (mtHSPs) expression. HSFA6b translocated to the nuclear after treatment with doxycycline (Dox)-a mitochondrial ribosome translation inhibitor. HSFA6b binds to the mtHSPs promoters and activates mtHSPs expression. The HSFA6b mutation blocked the UPRmt signals to promote root growth under mitochondrial proteotoxic stress and accelerated leaf senescence during development. Our study reveals a novel signal-regulating mechanism in the UPRmt pathways and provides new insights regarding the regulation of plant growth and development and stress resistance by the UPRmt pathways.

Genome editing prospects for heat stress tolerance in cereal crops

The world population is steadily growing, exerting increasing pressure to feed in the future, which would need additional production of major crops. Challenges associated with changing and unpredicted climate (such as heat waves) are causing global food security threats. Cereal crops are a staple food for a large portion of the world's population. They are mostly affected by these environmentally generated abiotic stresses. Therefore, it is imperative to develop climate-resilient cultivars to support the sustainable production of main cereal crops (Rice, wheat, and maize). Among these stresses, heat stress causes significant losses to major cereals. These issues can be solved by comprehending the molecular mechanisms of heat stress and creating heat-tolerant varieties. Different breeding and biotechnology techniques in the last decade have been employed to develop heat-stress-tolerant varieties. However, these time-consuming techniques often lack the pace required for varietal improvement in climate change scenarios. Genome editing technologies offer precise alteration in the crop genome for developing stress-resistant cultivars. CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeat/Cas9), one such genome editing platform, recently got scientists' attention due to its easy procedures. It is a powerful tool for functional genomics as well as crop breeding. This review will focus on the molecular mechanism of heat stress and different targets that can be altered using CRISPR/Cas genome editing tools to generate climate-smart cereal crops. Further, heat stress signaling and essential players have been highlighted to provide a comprehensive overview of the topic.

Heat stress transcription factors as the central molecular rheostat to optimize plant survival and recovery from heat stress

Heat stress transcription factors (HSFs) are the core regulators of the heat stress (HS) response in plants. HSFs are considered as a molecular rheostat: their activities define the response intensity, incorporating information about the environmental temperature through a network of partner proteins. A prompted activation of HSFs is required for survival, for example the de novo synthesis of heat shock proteins. Furthermore, a timely attenuation of the stress response is necessary for the restoration of cellular functions and recovery from stress. In an ever-changing environment, the balance between thermotolerance and developmental processes such as reproductive fitness highlights the importance of a tightly tuned response. In many cases, the response is described as an ON/OFF mode, while in reality, it is very dynamic. This review compiles recent findings to update existing models about the HSF-regulated HS response and address two timely questions: How do plants adjust the intensity of cellular HS response corresponding to the temperature they experience? How does this adjustment contribute to the fine-tuning of the HS and developmental networks? Understanding these processes is crucial not only for enhancing our basic understanding of plant biology but also for developing strategies to improve crop resilience and productivity under stressful conditions.

Molecular mechanisms underlying the negative effects of transient heatwaves on crop fertility

Transient heatwaves occurring more frequently as the climate warms, yet their impacts on crop yield are severely underestimated and even overlooked. Heatwaves lasting only a few days or even hours during sensitive stages, such as microgametogenesis and flowering, can significantly reduce crop yield by disrupting plant reproduction. Recent advances in multi-omics and GWAS analysis have shed light on the specific organs (e.g., pollen, lodicule, style), key metabolic pathways (sugar and reactive oxygen species metabolism, Ca2+ homeostasis), and essential genes that are involved in crop responses to transient heatwaves during sensitive stages. This review therefore places particular emphasis on heat-sensitive stages, with pollen development, floret opening, pollination, and fertilization as the central narrative thread. The multifaceted effects of transient heatwaves and their molecular basis are systematically reviewed, with a focus on key structures such as the lodicule and tapetum. A number of heat-tolerance genes associated with these processes have been identified in major crops like maize and rice. The mechanisms and key heat-tolerance genes shared among different stages may facilitate the more precise improvement of heat-tolerant crops.

LzSCL9, a Novel GRAS Transcription Factor in Lanzhou Lily (Lilium davidii var. unicolor), Participates in Regulation of Trichokonins-Primed Heat Stress Tolerance

In our previous research, we found that trichokonins' (TKs) employment improved the thermotolerance of the Lanzhou lily, a renowned edible crop species endemic to China that is relatively susceptible to high temperatures (HTs). Here, a novel Lanzhou lily GRAS gene, LzSCL9, was identified to respond to heat stress (HS) and HS+TKs treatment based on transcriptome and RT-qPCR analysis. TKs could improve the upregulation of LzSCL9 during long-term HS. The expression profile of LzSCL9 in response to HS with or without TKs treatment showed a significant positive correlation with LzHsfA2a-1, which was previously identified as a key regulator in TKs' conferred resilience to HT. More importantly, overexpression of LzSCL9 in the lily enhanced its tolerance to HTs and silencing LzSCL9 in the lily reduced heat resistance. Taken together, this study identified the positive role of LzSCL9 in TK-induced thermotolerance, thereby preliminarily establishing a molecular mechanism on TKs regulating the thermostability of the Lanzhou lily and providing a new candidate regulator for plant heat-resistant breeding.

The heat shock factor 20-HSF4-cellulose synthase A2 module regulates heat stress tolerance in maize

Temperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms underlying the plant heat stress response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors (TFs) that may contribute to the maize heat stress response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the inbred line B73. Co-expression network analysis highlighted several TFs, including the class B2a heat shock factor (HSF) ZmHSF20. Zmhsf20 mutant seedlings exhibited enhanced tolerance to heat stress. Furthermore, DNA affinity purification sequencing and Cleavage Under Targets and Tagmentation assays demonstrated that ZmHSF20 binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three class A Hsf genes, including ZmHsf4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 promote the heat stress response, with ZmHSF4 directly activating ZmCesA2 transcription. In agreement with the transcriptome analysis, ZmHSF20 inhibited cellulose accumulation and repressed the expression of cell wall-related genes. Importantly, the Zmhsf20 Zmhsf4 double mutant exhibited decreased thermotolerance, placing ZmHsf4 downstream of ZmHsf20. We proposed an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers seedling heat tolerance by repressing ZmHsf4 and ZmCesA2, thus balancing seedling growth and defense.

Dynamics of ER stress-induced gene regulation in plants

Endoplasmic reticulum (ER) stress is a potentially lethal condition that is induced by the abnormal accumulation of unfolded or misfolded secretory proteins in the ER. In eukaryotes, ER stress is managed by the unfolded protein response (UPR) through a tightly regulated, yet highly dynamic, reprogramming of gene transcription. Although the core principles of the UPR are similar across eukaryotes, unique features of the plant UPR reflect the adaptability of plants to their ever-changing environments and the need to balance the demands of growth and development with the response to environmental stressors. The past decades have seen notable progress in understanding the mechanisms underlying ER stress sensing and signalling transduction pathways, implicating the UPR in the effects of physiological and induced ER stress on plant growth and crop yield. Facilitated by sequencing technologies and advances in genetic and genomic resources, recent efforts have driven the discovery of transcriptional regulators and elucidated the mechanisms that mediate the dynamic and precise gene regulation in response to ER stress at the systems level.

Membralin is required for maize development and defines a branch of the endoplasmic reticulum-associated degradation pathway in plants

Endoplasmic reticulum (ER)-associated degradation (ERAD) plays key roles in controlling protein levels and quality in eukaryotes. The Ring Finger Protein 185 (RNF185)/membralin ubiquitin ligase complex was recently identified as a branch in mammals and is essential for neuronal function, but its function in plant development is unknown. Here, we report the map-based cloning and characterization of Narrow Leaf and Dwarfism 1 (NLD1), which encodes the ER membrane-localized protein membralin and specifically interacts with maize homologs of RNF185 and related components. The nld1 mutant shows defective leaf and root development due to reduced cell number. The defects of nld1 were largely restored by expressing membralin genes from Arabidopsis thaliana and mice, highlighting the conserved roles of membralin proteins in animals and plants. The excessive accumulation of β-hydroxy β-methylglutaryl-CoA reductase in nld1 indicates that the enzyme is a membralin-mediated ERAD target. The activation of bZIP60 mRNA splicing-related unfolded protein response signaling and marker gene expression in nld1, as well as DNA fragment and cell viability assays, indicate that membralin deficiency induces ER stress and cell death in maize, thereby affecting organogenesis. Our findings uncover the conserved, indispensable role of the membralin-mediated branch of the ERAD pathway in plants. In addition, ZmNLD1 contributes to plant architecture in a dose-dependent manner, which can serve as a potential target for genetic engineering to shape ideal plant architecture, thereby enhancing high-density maize yields.

Characterization of DREB family genes in Lotus japonicus and LjDREB2B overexpression increased drought tolerance in transgenic Arabidopsis

BACKGROUND

Drought stress affects plant growth and development. DREB proteins play important roles in modulating plant growth, development, and stress responses, particularly under drought stress. To study the function of DREB transcription factors (TFs), we screened key DREB-regulating TFs for drought in Lotus japonicus.

RESULTS

Forty-two DREB TFs were identified, and phylogenetic analysis of proteins from L. japonicus classified them into five subfamilies (A1, A2, A4, A5, A6). The gene motif composition of the proteins is conserved within the same subfamily. Based on the cis-acting regulatory element analysis, we identified many growth-, hormone-, and stress-responsive elements within the promoter regions of DREB. We further analyzed the expression pattern of four genes in the A2 subfamily in response to drought stress. We found that the expression of most of the LjDREB A2 subfamily genes, especially LjDREB2B, was induced by drought stress. We further generated LjDREB2B overexpression transgenic Arabidopsis plants. Under drought stress, the growth of wild-type (WT) and overexpressing LjDREB2B (OE) Arabidopsis lines was inhibited; however, OE plants showed better growth. The malondialdehyde content of LjDREB2B overexpressing lines was lower than that of the WT plants, whereas the proline content and antioxidant enzyme activities in the OE lines were significantly higher than those in the WT plants. Furthermore, after drought stress, the expression levels of AtP5CS1, AtP5CS2, AtRD29A, and AtRD29B in the OE lines were significantly higher than those in the WT plants.

CONCLUSIONS

Our results facilitate further functional analysis of L. japonicus DREB. LjDREB2B overexpression improves drought tolerance in transgenic Arabidopsis. These results indicate that DREB holds great potential for the genetic improvement of drought tolerance in L. japonicus.

The complex transcriptional regulation of heat stress response in maize

As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth and reduces productivity. To mitigate the heat-induced damages and adapt to high temperature environment, plants have evolved a series of molecular mechanisms to sense, respond and adapt high temperatures and heat stress. In this review, we summarized recent advances in molecular regulations underlying high temperature sensing, heat stress response and memory in maize, especially focusing on several important pathways and signals in high temperature sensing, and the complex transcriptional regulation of ZmHSFs (Heat Shock Factors) in heat stress response. In addition, we highlighted interactions between ZmHSFs and several epigenetic regulation factors in coordinately regulating heat stress response and memory. Finally, we laid out strategies to systematically elucidate the regulatory network of maize heat stress response, and discussed approaches for breeding future heat-tolerance maize.

ATP homeostasis and signaling in plants

ATP is the primary form of energy for plants, and a shortage of cellular ATP is generally acknowledged to pose a threat to plant growth and development, stress resistance, and crop quality. The overall metabolic processes that contribute to the ATP pool, from production, dissipation, and transport to elimination, have been studied extensively. Considerable evidence has revealed that in addition to its role in energy supply, ATP also acts as a regulatory signaling molecule to activate global metabolic responses. Identification of the eATP receptor DORN1 contributed to a better understanding of how plants cope with disruption of ATP homeostasis and of the key points at which ATP signaling pathways intersect in cells or whole organisms. The functions of SnRK1α, the master regulator of the energy management network, in restoring the equilibrium of the ATP pool have been demonstrated, and the vast and complex metabolic network mediated by SnRK1α to adapt to fluctuating environments has been characterized. This paper reviews recent advances in understanding the regulatory control of the cellular ATP pool and discusses possible interactions among key regulators of ATP-pool homeostasis and crosstalk between iATP/eATP signaling pathways. Perception of ATP deficit and modulation of cellular ATP homeostasis mediated by SnRK1α in plants are discussed at the physiological and molecular levels. Finally, we suggest future research directions for modulation of plant cellular ATP homeostasis.

A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress

The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.

A novel maize F-bZIP member, ZmbZIP76, functions as a positive regulator in ABA-mediated abiotic stress tolerance by binding to ACGT-containing elements

The group F-bZIP transcription factors (TFs) in Arabidopsis are involved in nutrient deficiency or salt stress responses. Nevertheless, our learning about the functions of group F-bZIP genes in maize remains limited. Here, we cloned a new F-bZIP gene (ZmbZIP76) from maize inbred line He344. The expression of ZmbZIP76 in maize was dramatically induced by high salt, osmotic stress and abscisic acid. Accordingly, overexpression of ZmbZIP76 increased tolerance of transgenic plants to salt and osmotic stress. In addition, ZmbZIP76 functions as a nuclear transcription factor and upregulates the expression of a range of abiotic stress-responsive genes by binding to the ACGT-containing elements, leading to enhanced reactive oxygen species (ROS) scavenging capability, increased abscisic acid level, proline content, and ratio of K+/Na+, reduced water loss rate, and membrane damage. These physiological changes caused by ZmbZIP76 ultimately enhanced tolerance of transgenic plants to salt and osmotic stress.

Specific ABA-independent tomato transcriptome reprogramming under abiotic stress combination

Crops often have to face several abiotic stresses simultaneously, and under these conditions, the plant's response significantly differs from that observed under a single stress. However, up to the present, most of the molecular markers identified for increasing plant stress tolerance have been characterized under single abiotic stresses, which explains the unexpected results found when plants are tested under real field conditions. One important regulator of the plant's responses to abiotic stresses is abscisic acid (ABA). The ABA signaling system engages many stress-responsive genes, but many others do not respond to ABA treatments. Thus, the ABA-independent pathway, which is still largely unknown, involves multiple signaling pathways and important molecular components necessary for the plant's adaptation to climate change. In the present study, ABA-deficient tomato mutants (flacca, flc) were subjected to salinity, heat, or their combination. An in-depth RNA-seq analysis revealed that the combination of salinity and heat led to a strong reprogramming of the tomato transcriptome. Thus, of the 685 genes that were specifically regulated under this combination in our flc mutants, 463 genes were regulated by ABA-independent systems. Among these genes, we identified six transcription factors (TFs) that were significantly regulated, belonging to the R2R3-MYB family. A protein-protein interaction network showed that the TFs SlMYB50 and SlMYB86 were directly involved in the upregulation of the flavonol biosynthetic pathway-related genes. One of the most novel findings of the study is the identification of the involvement of some important ABA-independent TFs in the specific plant response to abiotic stress combination. Considering that ABA levels dramatically change in response to environmental factors, the study of ABA-independent genes that are specifically regulated under stress combination may provide a remarkable tool for increasing plant resilience to climate change.

SlCathB2 as a negative regulator mediates a novel regulatory pathway upon high-temperature stress response in tomato

High-temperature stress (HS) is a major abiotic stress that affects the yield and quality of plants. Cathepsin B-like protease 2 (CathB2) has been reported to play a role in developmental processes and stress response, but its involvement in HS response has not been identified. Here, overexpression, virus-induced gene silencing (VIGS)and RNA-sequencing analysis were performed to uncover the functional characteristics of SlCathB2-1 and SlCathB2-2 genes for HS response in tomato. The results showed that overexpression of SlCathB2-1 and SlCathB2-2 resulted in reduced heat tolerance of tomato to HS while silencing the genes resulted in enhanced heat tolerance. RNA-sequencing analysis revealed that the heat shock proteins (HSPs) exhibited higher expression in WT than in SlCathB2-1 and SlCathB2-2 overexpression lines. Furthermore, the possible molecular regulation mechanism underlying SlCathB2-1 and SlCathB2-2-mediated response to HS was investigated. We found that SlCathB2-1 and SlCathB2-2 negatively regulated antioxidant capacity by regulating a set of genes involved in antioxidant defence and reactive oxygen species (ROS) signal transduction. We also demonstrated that SlCathB2-1 and SlCathB2-2 positively regulated ER-stress-induced PCD (ERSID) by regulating unfolded protein response (UPR) gene expression. Furthermore, SlCathB2-1 and SlCathB2-2 interacting with proteasome subunit beta type-4 (PBA4) was identified in the ERSID pathway using yeast two-hybrid (Y2H) analysis and bimolecular fluorescence complementation (BiFC) screening. Overall, the study identified both SlCathB2-1 and SlCathB2-2 as new negative regulators to HS and presented a new HS response pathway. This provided the foundation for the construction of heat-tolerant molecular mechanisms and breeding strategies aiming to improve the thermotolerance of tomato plants.

Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice

High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA-target gene pairs in rice heat-sensitive and heat-tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat-sensitive line and heat-tolerant line, and functional enrichment analysis revealed that these genes were involved in heat-related processes and pathways. The miRNAs-mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs-222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat-tolerant and the heat-sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature-responsive miRNAs targeted these mRNAs involved in many heat-related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA-mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.

Heat-Resistant Inbred Lines Coordinate the Heat Response Gene Expression Remarkably in Maize (Zea mays L.)

High temperatures are increasingly becoming a prominent environmental factor accelerating the adverse influence on the growth and development of maize (Zea mays L.). Therefore, it is critical to identify the key genes and pathways related to heat stress (HS) tolerance in maize. Great challenges have been faced in dissecting genetic mechanisms and uncovering master genes for HS tolerance. Here, Z58D showed more thermotolerance than AF171 at the seedling stage with a lower wilted leaf rate and H2O2 accumulation under HS conditions. Transcriptomic analysis identified 3006 differentially expressed genes (DEGs) in AF171 and 4273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that commonly upregulated genes in AF171 and Z58D were significantly enriched in the following biological processes, including protein folding, response to heat, response to temperature stimulus and response to hydrogen peroxide. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus were significantly over-represented for the 1234 upregulated genes in Z58D. Furthermore, more commonly upregulated genes exhibited higher expression levels in Z58D than AF171. In addition, maize inbred CIMBL55 was verified to be more tolerant than B73, and more commonly upregulated genes also showed higher expression levels in CIMBL55 than B73 under HS. These consistent results indicate that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among five inbred lines via comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at the expression levels. These candidate genes may confer thermotolerance in maize.

Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii

High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.

Asparagine-rich protein (NRP) mediates stress response by regulating biosynthesis of plant secondary metabolites in Arabidopsis

The plant-specific stress response protein NRP (asparagine-rich protein) is characterized by an asparagine-rich domain at its N-terminus and a conserved development and cell death (DCD) domain at its C-terminus. Previous transcriptional studies and phenotypic analyses have demonstrated the involvement of NRP in response to severe stress conditions, such as high salt and ER Endoplasmic reticulum-stress. We have recently identified distinct roles for NRP in biotic- and abiotic-stress signaling pathways, in which NRP interacts with different signaling proteins to change their subcellular localizations and stability. Here, to further explore the function of NRP, a transcriptome analysis was carried out on nrp1nrp2 knock-out lines at different life stages or under different growing conditions. The most significant changes in the transcriptome at both stages and conditions turned out to be the induction of the synthesis of secondary metabolites (SMs). Such an observation implicates that NRP is a general stress-responsive protein involved in various challenges faced by plants during their life cycle, which might involve a broad alteration in the distribution of SMs.

CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance

Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.

Genetic and molecular exploration of maize environmental stress resilience: Toward sustainable agriculture

Global climate change exacerbates the effects of environmental stressors, such as drought, flooding, extreme temperatures, salinity, and alkalinity, on crop growth and grain yield, threatening the sustainability of the food supply. Maize (Zea mays) is one of the most widely cultivated crops and the most abundant grain crop in production worldwide. However, the stability of maize yield is highly dependent on environmental conditions. Recently, great progress has been made in understanding the molecular mechanisms underlying maize responses to environmental stresses and in developing stress-resilient varieties due to advances in high-throughput sequencing technologies, multi-omics analysis platforms, and automated phenotyping facilities. In this review, we summarize recent advances in dissecting the genetic factors and networks that contribute to maize abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient maize varieties.

It is time to move: Heat-induced translocation events

Climate change-induced temperature fluctuations impact agricultural productivity through short-term intense heat waves or long-term heat stress. Plants have evolved sophisticated strategies to deal with heat stress. Understanding perception and transduction of heat signals from outside to inside cells is essential to improve plant thermotolerance. In this review, we will focus on translocation of molecules and proteins associated with signal transduction to understand how plant cells decode signals from the environment to trigger a suitable response.

Maize heat shock proteins-prospection, validation, categorization and in silico analysis of the different ZmHSP families

Among the plant molecular mechanisms capable of effectively mitigating the effects of adverse weather conditions, the heat shock proteins (HSPs), a group of chaperones with multiple functions, stand out. At a time of full progress on the omic sciences, they look very promising in the genetic engineering field, especially in order to conceive superior genotypes, potentially tolerant to abiotic stresses (AbSts). Recently, some works concerning certain families of maize HSPs (ZmHSPs) were published. However, there was still a lack of a study that, with a high degree of criteria, would fully conglomerate them. Using distinct but complementary strategies, we have prospected as many ZmHSPs candidates as possible, gathering more than a thousand accessions. After detailed data mining, we accounted for 182 validated ones, belonging to seven families, which were subcategorized into classes with potential for functional parity. In them, we identified dozens of motifs with some degree of similarity with proteins from different kingdoms, which may help explain some of their still poorly understood means of action. Through in silico and in vitro approaches, we compared their expression levels after controlled exposure to several AbSts' sources, applied at diverse tissues, on varied phenological stages. Based on gene ontology concepts, we still analyzed them from different perspectives of term enrichment. We have also searched, in model plants and close species, for potentially orthologous genes. With all these new insights, which culminated in a plentiful supplementary material, rich in tables, we aim to constitute a fertile consultation source for those maize researchers attracted by these interesting stress proteins.

Crosstalk between endoplasmic reticulum and cytosolic unfolded protein response in tomato

Conditions that cause proteotoxicity like high temperature trigger the activation of unfolded protein response (UPR). The cytosolic (CPR) and endoplasmic reticulum (ER) UPR rely on heat stress transcription factor (HSF) and two members of the basic leucine zipper (bZIP) gene family, respectively. In tomato, HsfA1a is the master regulator of CPR. Here, we identified the core players of tomato ER-UPR including the two central transcriptional regulators, namely bZIP28 and bZIP60. Interestingly, the induction of ER-UPR genes and the activation of bZIP60 are altered in transgenic plants where HsfA1a is either overexpressed (A1aOE) or suppressed (A1CS), indicating an interplay between CPR and ER-UPR systems. Several ER-UPR genes are differentially expressed in the HsfA1a transgenic lines either exposed to heat stress or to the ER stress elicitor tunicamycin (TUN). The ectopic expression of HsfA1a is associated with higher tolerance against TUN. On the example of the ER-resident Hsp70 chaperone BIP3, we show that the presence of cis-elements required for HSF and bZIP regulation serves as a putative platform for the co-regulation of these genes by both CPR and ER-UPR mechanisms, in the case of BIP3 in a stimulatory manner under high temperatures. In addition, we show that the accumulation of HsfA1a results in higher levels of three ATG genes and a more sensitized induction of autophagy in response to ER stress which also supports the increased tolerance to ER stress of the A1aOE line. These findings provide a basis for the coordination of protein homeostasis in different cellular compartments under stress conditions.

Identification and functional analysis of ZmDLS associated with the response to biotic stress in maize

Terpenes are the main class of secondary metabolites produced in response to pest and germ attacks. In maize (Zea mays L.), they are the essential components of the herbivore-induced plant volatile mixture, which functioned as a direct or indirect defense against pest and germ attacks. In this study, 43 maize terpene synthase gene (ZmTPS) family members were systematically identified and analyzed through the whole genomes of maize. Nine genes, including Zm00001d032230, Zm00001d045054, Zm00001d024486, Zm00001d004279, Zm00001d002351, Zm00001d002350, Zm00001d053916, Zm00001d015053, and Zm00001d015054, were isolated for their differential expression pattern in leaves after corn borer (Ostrinia nubilalis) bite. Additionally, six genes (Zm00001d045054, Zm00001d024486, Zm00001d002351, Zm00001d002350, Zm00001d015053, and Zm00001d015054) were significantly upregulated in response to corn borer bite. Among them, Zm00001d045054 was cloned. Heterologous expression and enzyme activity assays revealed that Zm00001d045054 functioned as d-limonene synthase. It was renamed ZmDLS. Further analysis demonstrated that its expression was upregulated in response to corn borer bites and Fusarium graminearum attacks. The mutant of ZmDLS downregulated the expressions of Zm00001d024486, Zm00001d002351, Zm00001d002350, Zm00001d015053, and Zm00001d015054. It was more attractive to corn borer bites and more susceptible to F. graminearum infection. The yeast one-hybrid assay and dual-luciferase assay showed that ZmMYB76 and ZmMYB101 could upregulate the expression of ZmDLS by binding to the promoter region. This study may provide a theoretical basis for the functional analysis and transcriptional regulation of terpene synthase genes in crops.

Endoplasmic stress sensor Ire1 is involved in cytosolic/nuclear protein quality control in Pichia pastoris cells independent of HAC1

In eukaryotic species, dysfunction of the endoplasmic reticulum (ER), namely, ER stress, provokes a cytoprotective transcription program called the unfolded protein response (UPR). The UPR is triggered by transmembrane ER-stress sensors, including Ire1, which acts as an endoribonuclease to splice and mature the mRNA encoding the transcription factor Hac1 in many fungal species. Through analyses of the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii), we revealed a previously unknown function of Ire1. In P. pastoris cells, the IRE1 knockout mutation (ire1Δ) and HAC1 knockout mutation (hac1Δ) caused only partially overlapping gene expression changes. Protein aggregation and the heat shock response (HSR) were induced in ire1Δ cells but not in hac1Δ cells even under non-stress conditions. Moreover, Ire1 was further activated upon high-temperature culturing and conferred heat stress resistance to P. pastoris cells. Our findings cumulatively demonstrate an intriguing case in which the UPR machinery controls cytosolic protein folding status and the HSR, which is known to be activated upon the accumulation of unfolded proteins in the cytosol and/or nuclei.

Enhancing heat stress tolerance in Lanzhou lily (Lilium davidii var. unicolor) with Trichokonins isolated from Trichoderma longibrachiatum SMF2

Lanzhou lily (Lilium davidii var. unicolor) is a renowned edible crop produced in China and relatively sensitive to high temperature (HT). Trichokonins (TKs) are antimicrobial peptaibols secreted from Trichoderma longibrachiatum strain SMF2. Here, we report that TKs application improves the thermotolerance of Lanzhou lily. The activity of the antioxidant enzyme system (SOD, CAT, and POD), the level of heat-resistance-associated phytohormones (ABA, SA, and JA), the relative water content (RWC), the content of chlorophyll (Chl), and the net photosynthetic rate (P _n) were promoted by TKs treatment in Lanzhou lily plants subjected to heat stress (HS). TKs treatment also mitigated cell injury as shown by a lower accumulation of malondialdehyde (MDA) and relative electrolyte leakage (REL) under HS conditions. RNA-seq data analysis showed that more than 4.5 times differentially expressed genes (DEGs) responded to TKs treatment under HS compared to non-HS, and TKs treatment reduced protein folding and enhanced cellular repair function under HS conditions. The analyses of DEGs involved in hormone (ABA, SA and JA) synthesis and signaling pathways suggested that TKs might improve Lanzhou lily heat tolerance by promoting ABA synthesis and signal transduction. TKs highly induced DEGs of the HSF-HSP pathway under HS, in which HSFA2 accounted for most of the HSF family. Furthermore, TKs treatment resulted in the upregulation of heat-protective genes LzDREB2B, LzHsfA2a, LzMBF1c, LzHsp90, and LzHsp70 involved in HSF-HSP signal pathway after long-term HS. LzHsfA2a-1 likely plays a key role in acquisition of TKs-induced thermotolerance of Lanzhou lily as evidenced by the sustained response to HS, the enhanced response to TKs treatment under long-term HS, and the high sequence similarity to LlHsfA2a which is a key regulator for the improvement of heat tolerance in Lilium longiflorum. Our results reveal the underlying mechanisms of TKs-mediated thermotolerance in Lanzhou lily and highlight an attractive approach to protecting crop plants from damage caused by HS in a global warming future.

A pan-grass transcriptome reveals patterns of cellular divergence in crops

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.

Integrated ATAC-Seq and RNA-Seq Data Analysis to Reveal OsbZIP14 Function in Rice in Response to Heat Stress

Transcription factors (TFs) play critical roles in mediating the plant response to various abiotic stresses, particularly heat stress. Plants respond to elevated temperatures by modulating the expression of genes involved in diverse metabolic pathways, a regulatory process primarily governed by multiple TFs in a networked configuration. Many TFs, such as WRKY, MYB, NAC, bZIP, zinc finger protein, AP2/ERF, DREB, ERF, bHLH, and brassinosteroids, are associated with heat shock factor (Hsf) families, and are involved in heat stress tolerance. These TFs hold the potential to control multiple genes, which makes them ideal targets for enhancing the heat stress tolerance of crop plants. Despite their immense importance, only a small number of heat-stress-responsive TFs have been identified in rice. The molecular mechanisms underpinning the role of TFs in rice adaptation to heat stress still need to be researched. This study identified three TF genes, including OsbZIP14, OsMYB2, and OsHSF7, by integrating transcriptomic and epigenetic sequencing data analysis of rice in response to heat stress. Through comprehensive bioinformatics analysis, we demonstrated that OsbZIP14, one of the key heat-responsive TF genes, contained a basic-leucine zipper domain and primarily functioned as a nuclear TF with transcriptional activation capability. By knocking out the OsbZIP14 gene in the rice cultivar Zhonghua 11, we observed that the knockout mutant OsbZIP14 exhibited dwarfism with reduced tiller during the grain-filling stage. Under high-temperature treatment, it was also demonstrated that in the OsbZIP14 mutant, the expression of the OsbZIP58 gene, a key regulator of rice seed storage protein (SSP) accumulation, was upregulated. Furthermore, bimolecular fluorescence complementation (BiFC) experiments uncovered a direct interaction between OsbZIP14 and OsbZIP58. Our results suggested that OsbZIP14 acts as a key TF gene through the concerted action of OsbZIP58 and OsbZIP14 during rice filling under heat stress. These findings provide good candidate genes for genetic improvement of rice but also offer valuable scientific insights into the mechanism of heat tolerance stress in rice.

Grapevine bZIP transcription factor bZIP45 regulates VvANN1 and confers drought tolerance in Arabidopsis

Drought is a severe environmental condition that restricts the vegetative growth and reduces the yield of grapevine (Vitis vinifera L.). However, the mechanisms underlying grapevine response and adaptation to drought stress remain unclear. In the present study, we characterized an ANNEXIN gene, VvANN1, which plays a positive role in the drought stress response. The results indicated that VvANN1 was significantly induced by osmotic stress. Expression of VvANN1 in Arabidopsis thaliana enhanced osmotic and drought tolerance through modulating the level of MDA, H₂O₂, and O₂ ^·- at the seedling stage, implying that VvANN1 might be involved in the process of ROS homeostasis under drought or osmotic stress conditions. Moreover, we used yeast one-hybridization and chromatin immunoprecipitation assays to show that VvbZIP45 could regulate VvANN1 expression by directly binding to the promoter region of VvANN1 in response to drought stress. We also generated transgenic Arabidopsis that constitutively expressed the VvbZIP45 gene (35S::VvbZIP45) and further produced VvANN1Pro::GUS/35S::VvbZIP45 Arabidopsis plants via crossing. The genetic analysis results subsequently indicated that VvbZIP45 could enhance GUS expression in vivo under drought stress. Our findings suggest that VvbZIP45 may modulate VvANN1 expression in response to drought stress and reduce the impact of drought on fruit quality and yield.

Coordinated regulation of the mitochondrial retrograde response by circadian clock regulators and ANAC017

Mitochondrial retrograde signaling (MRS) supports photosynthetic function under a variety of conditions. Induction of mitochondrial dysfunction with myxothiazol (a specific inhibitor of the mitochondrial bc₁ complex) or antimycin A (an inhibitor of the mitochondrial bc₁ complex and cyclic electron transport in the chloroplast under light conditions) in the light and dark revealed diurnal control of MRS. This was evidenced by (1) significantly enhanced binding of ANAC017 to promoters in the light compared with the dark in Arabidopsis plants treated with myxothiazol (but not antimycin A), (2) overlap in the experimentally determined binding sites for ANAC017 and circadian clock regulators in the promoters of ANAC013 and AOX1a, (3) a diurnal expression pattern for ANAC017 and transcription factors it regulates, (4) altered expression of ANAC017-regulated genes in circadian clock mutants with and without myxothiazol treatment, and (5) a decrease in the magnitude of LHY and CCA1 expression in an ANAC017-overexpressing line and protein-protein interaction between ANAC017 and PIF4. This study also shows a large difference in transcriptome responses to antimycin A and myxothiazol in the dark: these responses are ANAC017 independent, observed in shoots and roots, similar to biotic challenge and salicylic acid responses, and involve ERF and ZAT transcription factors. This suggests that antimycin A treatment stimulates a second MRS pathway that is mediated or converges with salicylic acid signaling and provides a merging point with chloroplast retrograde signaling.

Maize cytolines as models to study the impact of different cytoplasms on gene expression under heat stress conditions

BACKGROUND

Crops are under constant pressure due to global warming, which unfolds at a much faster pace than their ability to adapt through evolution. Agronomic traits are linked to cytoplasmic-nuclear genome interactions. It thus becomes important to understand the influence exerted by the organelles on gene expression under heat stress conditions and profit from the available genetic diversity. Maize (Zea mays) cytolines allow us to investigate how the gene expression changes under heat stress conditions in three different cytoplasmic environments, but each having the same nucleus. Analyzing retrograde signaling in such an experimental set-up has never been done before. Here, we quantified the response of three cytolines to heat stress as differentially expressed genes (DEGs), and studied gene expression patterns in the context of existing polymorphism in their organellar genomes.

RESULTS

Our study unveils a plethora of new genes and GO terms that are differentially expressed or enriched, respectively, in response to heat stress. We report 19,600 DEGs as responding to heat stress (out of 30,331 analyzed), which significantly enrich 164 GO biological processes, 30 GO molecular functions, and 83 GO cell components. Our approach allowed for the discovery of a significant number of DEGs and GO terms that are not common in the three cytolines and could therefore be linked to retrograde signaling. Filtering for DEGs with a fold regulation > 2 (absolute values) that are exclusive to just one of the cytolines, we find a total of 391 up- and down-DEGs. Similarly, there are 19 GO terms with a fold enrichment > 2 that are cytoline-specific. Using GBS data we report contrasting differences in the number of DEGs and GO terms in each cytoline, which correlate with the genetic distances between the mitochondrial genomes (but not chloroplast) and the original nuclei of the cytolines, respectively.

CONCLUSIONS

The experimental design used here adds a new facet to the paradigm used to explain how gene expression changes in response to heat stress, capturing the influence exerted by different organelles upon one nucleus rather than investigating the response of several nuclei in their innate cytoplasmic environments.

A dynamic phosphoproteomic analysis provides insight into the C4 plant maize (Zea mays L.) response to natural diurnal changes

As sessile organisms, plants need to respond to rapid changes in numerous environmental factors, mainly diurnal changes of light, temperature, and humidity. Maize is the world's most grown crop, and as a C4 plant it exhibits high photosynthesis capacity, reaching the highest rate of net photosynthesis at midday; that is, there is no "midday depression." Revealing the physiological responses to diurnal changes and underlying mechanisms will be of great significance for guiding maize improvement efforts. In this study, we collected maize leaf samples and analyzed the proteome and phosphoproteome at nine time points during a single day/night cycle, quantifying 7424 proteins and 5361 phosphosites. The new phosphosites identified in our study increased the total maize phosphoproteome coverage by 8.5%. Kinase-substrate network analysis indicated that 997 potential substrates were phosphorylated by 20 activated kinases. Through analysis of proteins with significant changes in abundance and phosphorylation, we found that the response to a heat stimulus involves a change in the abundance of numerous proteins. By contrast, the high light at noon and rapidly changing light conditions induced changes in the phosphorylation level of proteins involved in processes such as chloroplast movement, photosynthesis, and C4 pathways. Phosphorylation is involved in regulating the activity of large number of enzymes; for example, phosphorylation of S55 significantly enhanced the activity of maize phosphoenolpyruvate carboxykinase1 (ZmPEPCK1). Overall, the database of dynamic protein abundance and phosphorylation we have generated provides a resource for the improvement of C4 crop plants.

Development of a GFP biosensor reporter for the unfolded protein response-signaling pathway in plants: incorporation of the bZIP60 intron into the GFP gene

The ability to measure the activation of the unfolded protein response (UPR) in plants is important when they are exposed to stressful environments. To this end, we developed a unique and versatile biosensor-reporter system to indicate the activation of UPR in living plant cells. The small cytoplasmically spliced intron from the bZIP60 locus was incorporated into the 5' end of the GFP gene, creating the 35S::bZIP60 intron:GFP construct. When this construct is transiently expressed in Arabidopsis protoplasts, the presence of the bZIP60 intron prevents GFP mRNA from being translated under non-UPR conditions. However, when UPR is activated, the IRE1 kinase/ribonuclease splices this intron from the GFP mRNA and its translation proceeds, generating GFP fluorescence. We demonstrated the utility of the system in Arabidopsis leaf protoplasts treated with DTT, which is a chemical inducer of UPR, followed by visualization and quantification using confocal microscopy. The 35S::bZIP60 intron:GFP construct was also expressed in protoplasts from an overexpressor line containing the coding sequence for the UPR-induced, protein folding chaperone, protein disulfide isomerase-9 (PDI9). PDI9 also influences the strength of the UPR signaling pathway. Protoplasts from WT and PDI9 overexpressor plants treated with DTT exhibited significantly higher GFP fluorescence relative to untreated protoplasts, indicating that the bZIP60 intron was spliced from the GFP mRNA in response to activation of UPR. RT-PCR further confirmed the higher induction of PDI9 and bZIP60 (total and spliced) mRNA levels in DTT-treated protoplasts relative to controls. This system can be adapted for monitoring crop stress and for basic studies dissecting the UPR signaling pathway.

Increased ATPase activity promotes heat-resistance, high-yield, and high-quality traits in rice by improving energy status

Heat stress during the reproductive stage results in major losses in yield and quality, which might be mainly caused by an energy imbalance. However, how energy status affected heat response, yield and quality remains unclear. No relationships were observed among the heat resistance, yield, and quality of the forty-nine early rice cultivars under normal temperature conditions. However, two cultivars, Zhuliangyou30 (ZLY30) and Luliangyou35 (LLY35), differing in heat resistance, yield, and quality were detected. The yield was higher and the chalkiness degree was lower in ZLY30 than in LLY35. Decreases in yields and increases in the chalkiness degree with temperatures were more pronounced in LLY35 than in ZLY30. The accumulation and allocation (ratio of the panicle to the whole plant) of dry matter weight and non-structural carbohydrates were higher in ZLY30 than in LLY35 across all sowing times and temperatures. The accumulation and allocation of dry matter weight and non-structural carbohydrates in panicles were higher in ZLY30 than in LLY35. Similar patterns were observed in the relative expression levels of sucrose unloading related genes SUT1 and SUT2 in grains. The ATP content was higher in the grains of LLY35 than in ZLY30, whereas the ATPase activity, which determined the energy status, was significantly lower in the former than in the latter. Thus, increased ATPase activity, which improved the energy status of rice, was the factor mediating the balance among heat-resistance, high-yield, and high-quality traits in rice.

Regulatory Mechanisms of Heat Stress Response and Thermomorphogenesis in Plants

As worldwide warming intensifies, the average temperature of the earth continues to increase. Temperature is a key factor for the growth and development of all organisms and governs the distribution and seasonal behavior of plants. High temperatures lead to various biochemical, physiological, and morphological changes in plants and threaten plant productivity. As sessile organisms, plants are subjected to various hostile environmental factors and forced to change their cellular state and morphological architecture to successfully deal with the damage they suffer. Therefore, plants have evolved multiple strategies to cope with an abnormal rise in temperature. There are two main mechanisms by which plants respond to elevated environmental temperatures. One is the heat stress response, which is activated under extremely high temperatures; the other is the thermomorphogenesis response, which is activated under moderately elevated temperatures, below the heat-stress range. In this review, we summarize recent progress in the study of these two important heat-responsive molecular regulatory pathways mediated, respectively, by the Heat Shock Transcription Factor (HSF)-Heat Shock Protein (HSP) pathway and PHYTOCHROME INTER-ACTING FACTOR 4 (PIF4) pathways in plants and elucidate the regulatory mechanisms of the genes involved in these pathways to provide comprehensive data for researchers studying the heat response. We also discuss future perspectives in this field.

A View into Seed Autophagy: From Development to Environmental Responses

Autophagy is a conserved cellular mechanism involved in the degradation and subsequent recycling of cytoplasmic components. It is also described as a catabolic process implicated in the specific degradation of proteins in response to several stimuli. In eukaryotes, the endoplasmic reticulum accumulates an excess of proteins in response to environmental changes, and is the major cellular organelle at the crossroads of stress responses. Return to proteostasis involves the activation of the Unfolded Protein Response (UPR) and eventually autophagy as a feedback mechanism to relieve protein overaccumulation. Recent publications have focused on the relevance of autophagy in two central processes of seed biology: (i) seed storage protein accumulation upon seed maturation and (ii) reserve mobilization during seed imbibition. Although ER-protein accumulation and the subsequent activation of autophagy resemble the Seed Storage Protein (SSP) deposition during seed maturation, the molecular connection between seed development, autophagy, and seed response to abiotic stresses is still an underexplored field. This mini-review presents current advances in autophagy in seeds, highlighting its participation in the normal course of seed development from embryogenesis to germination. Finally, the function of autophagy in response to the seed environment is also considered, as is its involvement in controlling seed dormancy and germination.

Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis

Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10-6), and individual QTL explained 4.80%-24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.

ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana

Background

Heat stress is a major abiotic stress affecting the growth and development of plants, including crop species. Plants have evolved various adaptive strategies to help them survive heat stress, including maintaining membrane stability, encoding heat shock proteins (HSPs) and ROS-scavenging enzymes, and inducing molecular chaperone signaling. Brassinosteroids (BRs) are phytohormones that regulate various aspects of plant development, which have been implicated also in plant responses to heat stress, and resistance to heat in Arabidopsis thaliana is enhanced by adding exogenous BR. Brassinazole resistant 1 (BZR1), a transcription factor and positive regulator of BR signal, controls plant growth and development by directly regulating downstream target genes. However, the molecular mechanism at the basis of BR-mediated heat stress response is poorly understood. Here, we report the identification of a new factor critical for BR-regulated heat stress tolerance.

Results

We identified ERF49 in a genetic screen for proteins required for BR-regulated gene expression. We found that ERF49 is the direct target gene of BZR1 and that overexpressing ERF49 enhanced sensitivity of transgenic plants to heat stress. The transcription levels of heat shock factor HSFA2, heat stress-inducible gene DREB2A, and three heat shock protein (HSP) were significantly reduced under heat stress in ERF49-overexpressed transgenic plants. Transcriptional activity analysis in protoplast revealed that BZR1 inhibits ERF49 expression by binding to the promoter of ERF49. Our genetic analysis showed that dominant gain-of-function brassinazole resistant 1-1D mutant (bzr1-1D) exhibited lower sensitivity to heat stress compared with wild-type. Expressing ERF49-SRDX (a dominant repressor reporter of ERF49) in bzr1-1D significantly decreased the sensitivity of ERF49-SRDX/bzr1-1D transgenic plants to heat stress compared to bzr1-1D.

Conclusions

Our data provide clear evidence that BR increases thermotolerance of plants by repressing the expression of ERF49 through BZR1, and this process is dependent on the expression of downstream heat stress-inducible genes. Taken together, our work reveals a novel molecular mechanism mediating plant response to high temperature stress.

Maize HEAT UP-REGULATED GENE 1 plays vital roles in heat stress tolerance

Increasing temperature is one of the major threats to maize growth and yield globally. Under heat stress conditions, intracellular protein homeostasis is seriously disturbed, leading to accumulation of abnormally folded proteins, especially in the endoplasmic reticulum (ER). Molecular chaperones are vital players in the renaturation process and in preventing protein aggregation. However, heat stress tolerance-associated chaperones are not well documented in maize. Here, we characterized the biological roles of HEAT UP-REGULATED GENE 1 (ZmHUG1) in maize. ZmHUG1 encodes a heat-inducible holdase-type molecular chaperone localized in the ER. Knockout mutant of ZmHUG1 exhibited remarkably enhanced sensitivity to heat stress. Accordingly, the zmhug1 mutant showed severe ER stress under high temperature. MAIZE PRENYLATED RAB ACCEPTOR 1.C1 (ZmPRA1.C1) was identified as a client of ZmHUG1, and heat-induced aggregation of ZmPRA1.C1 was accelerated in the zmhug1 mutant. Furthermore, the expression of ZmHUG1 was rapidly transactivated by ER stress sensor BASIC LEUCINE ZIPPER DOMAIN 60 (bZIP60) when heat stress occurred. This study reveals a ZmHUG1-based thermo-protective mechanism in maize.

ZmNAC074, a maize stress-responsive NAC transcription factor, confers heat stress tolerance in transgenic Arabidopsis

The harsh environment such as high temperature greatly limits the growth, development and production of crops worldwide. NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) play key regulatory roles in abiotic stress responses of plants. However, the functional roles of NAC TFs in heat stress response of maize remain elusive. In our present study, we identified and isolated a stress-responsive NAC transcription factor gene in maize, designated as ZmNAC074 and orthologous with rice OsNTL3. Further studies revealed that ZmNAC074 may encode a membrane-bound transcription factor (MTF) of NAC family in maize, which is comprised of 517 amino acid residues with a transmembrane domain at the C-terminus. Moreover, ZmNAC074 was highly expressed and induced by various abiotic stresses in maize seedlings, especially in leaf tissues under heat stress. Through generating ZmNAC074 transgenic plants, phenotypic and physiological analyses further displayed that overexpression of ZmNAC074 in transgenic Arabidopsis confers enhanced heat stress tolerance significantly through modulating the accumulation of a variety of stress metabolites, including reactive oxygen species (ROS), antioxidants, malondialdehyde (MDA), proline, soluble protein, chlorophyll and carotenoid. Further, quantitative real-time PCR analysis showed that the expression levels of most ROS scavenging and HSR- and UPR-associated genes in transgenic Arabidopsis were significantly up-regulated under heat stress treatments, suggesting that ZmNAC074 may encode a positive regulator that activates the expression of ROS-scavenging genes and HSR- and UPR-associated genes to enhance plant thermotolerance under heat stress conditions. Overall, our present study suggests that ZmNAC074 may play a crucial role in conferring heat stress tolerance in plants, providing a key candidate regulatory gene for heat stress tolerance regulation and genetic improvement in maize as well as in other crops.