Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress

Background

The heat shock factor (Hsf) and small heat shock protein (sHsp, also called Hsp20) complex has been identified as a primary component in the protection of plant cells from ubiquitous stresses, particularly heat stress. Our study aimed to characterize and analyze the Hsf and Hsp genes in Brachypodium distachyon, an annual temperate grass and model plant in cereal and grass studies.

Results

We identified 24 Hsf and 18 Hsp20 genes in B. distachyon and explored their evolution in gene organization, sequence features, chromosomal localization, and gene duplication. Our phylogenetic analysis showed that BdHsfs could be divided into three categories and BdHsp20s into ten subfamilies. Further analysis showed that the 3’UTR length of BdHsp20 genes had a negative relationship with their expression under heat stress. Expression analyses indicated that BdHsp20s and BdHsfs were strongly and rapidly induced by high-temperature treatment. Additionally, we constructed a complex regulatory network based on their expression patterns under heat stress. Morphological analysis suggested that the overexpression of five BdHsp20 genes enhanced the seed germination rate and decreased cell death under high temperatures.

Conclusion

Ultimately, our study provided important evolutionary and functional characterizations for future research on the regulatory mechanisms of BdHsp20s and BdHsfs in herbaceous plants under environmental stress.

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Heat shock transcription factors (HSFs) are central elements in the regulatory network that controls plant heat stress response. They are involved in multiple transcriptional regulatory pathways and play important roles in heat stress signaling and responses to a variety of other stresses. We identified 41 members of the HSF gene family in moso bamboo, which were distributed non-uniformly across its 19 chromosomes. Phylogenetic analysis showed that the moso bamboo HSF genes could be divided into three major subfamilies; HSFs from the same subfamily shared relatively conserved gene structures and sequences and encoded similar amino acids. All HSF genes contained HSF signature domains. Subcellular localization prediction indicated that about 80% of the HSF proteins were located in the nucleus, consistent with the results of GO enrichment analysis. A large number of stress response-associated cis-regulatory elements were identified in the HSF upstream promoter sequences. Synteny analysis indicated that the HSFs in the moso bamboo genome had greater collinearity with those of rice and maize than with those of Arabidopsis and pepper. Numerous segmental duplicates were found in the moso bamboo HSF gene family. Transcriptome data indicated that the expression of a number of PeHsfs differed in response to exogenous gibberellin (GA) and naphthalene acetic acid (NAA). A number of HSF genes were highly expressed in the panicles and in young shoots, suggesting that they may have functions in reproductive growth and the early development of rapidly-growing shoots. This study provides fundamental information on members of the bamboo HSF gene family and lays a foundation for further study of their biological functions in the regulation of plant responses to adversity.

Enhancing phytoremediation of hazardous metal(loid)s using genome engineering CRISPR-Cas9 technology

Rapid and drastic changes in the global climate today have given a strong impetus to developing newer climate-resilient phytoremediation approaches. These methods are of great public and scientific importance given the urgency of this environmental crisis. Climate change has adverse effects on the growth, outputs, phenology, and overall productivity of plants. Contamination of soil with metal(loid)s is a major worldwide problem. Some metal(loids) are carcinogenic pollutants that have a long half-life and are non-degradable in the environment. There are many instances of the potential link between chronic heavy metal exposure and human disease. The adaptation of plants in the changing environment is, however, a major concern in phytoremediation practice. The creation of climate-resistant metal hyperaccumulation plants using molecular techniques could provide new opportunities to mitigate these problems. Consequently, advancements in molecular science would accelerate our knowledge of adaptive plant remediation/resistance and plant production in the context of global warming. Genome modification using artificial nucleases has the potential to enhance phytoremediation by modifying genomes for a sustainable future. This review focuses on biotechnology to boost climate change tolerant metallicolous plants and the future prospects of such technology, particularly the CRISPR-Cas9 genome editing system, for enhancing phytoremediation of hazardous pollutants.

Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes

Heat shock transcription factors (HSFs) are involved in environmental stress response and plant development, such as heat stress and flowering development. According to the structural characteristics of the HSF gene family, HSF genes were classified into three major types (HSFA, HSFB, and HSFC) in plants. Using conserved domains of HSF genes, we identified 621 HSF genes among 13 cotton genomes, consisting of eight diploid and five tetraploid genomes. Phylogenetic analysis indicated that HSF genes among 13 cotton genomes were grouped into two different clusters: one cluster contained all HSF genes of HSFA and HSFC, and the other cluster contained all HSF genes of HSFB. Comparative analysis of HSF genes in Arabidopsis thaliana, Gossypium herbaceum (A1), Gossypium arboreum (A2), Gossypium raimondii (D5), and Gossypium hirsutum (AD1) genomes demonstrated that four HSF genes were inherited from a common ancestor, A0, of all existing cotton A genomes. Members of the HSF gene family in G. herbaceum (A1) genome indicated a significant loss compared with those in G. arboretum (A2) and G. hirsutum (AD1) A genomes. However, HSF genes in G. raimondii (D5) showed relative loss compared with those in G. hirsutum (AD1) D genome. Analysis of tandem duplication (TD) events of HSF genes revealed that protein-coding genes among different cotton genomes have experienced TD events, but only the two-gene tandem array was detected in Gossypium thurberi (D1) genome. The expression analysis of HSF genes in G. hirsutum (AD1) and Gossypium barbadense (AD2) genomes indicated that the expressed HSF genes were divided into two different groups, respectively, and the expressed HSF orthologous genes between the two genomes showed totally different expression patterns despite the implementation of the same abiotic stresses. This work will provide novel insights for the study of evolutionary history and expression characterization of HSF genes in different cotton genomes and a widespread application model for the study of HSF gene families in plants.

Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus)

Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.

Genome wide identification, classification and functional characterization of heat shock transcription factors in cultivated and ancestral cottons (Gossypium spp.)

Heat shock transcription factors (HSF) have been demonstrated to play a significant transcriptional regulatory role in plants and considered as an integral part of signal transduction pathways against environmental stresses especially heat stress. Despite of their importance, HSFs have not yet been identified and characterized in all cotton species. In this study, we report the identification of 42, 39, 67, and 79 non-redundant HSF genes from diploid cottons G. arboreum (A2) and G. raimondii (D5), and tetraploid cottons G. barbadense (AD2) and G. hirsutum (AD1) respectively. The chromosome localization of identified HSFs revealed their random distribution on all the 13 chromosomes of A and D genomes of cotton with few regions containing HSFs in clusters. The genes structure and conserved domain analysis revealed the family-specific conservation of intron/exon organization and conserved domains in HSFs. Various abiotic stress-related cis-regulatory elements were identified from the putative promoter regions of cotton HSFs suggesting their possible role in mediating abiotic stress tolerance. The combined phylogenetic analysis of all the cotton HSFs grouped them into three subfamilies; with 145 HSFs belong to class A, 85 to class B, and 17 to class C subfamily. Moreover, a detailed analysis of HSF gene family in four species of cotton elucidated the role of allopolyploid and hybridization during evolutionary cascade of allotetraploid cotton. Comparatively, existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Phylogenetic, collinearity and multiple synteny analyses exhibited dispersed, segmental, proximal, and tandem gene duplication events in HSF gene family. Duplication of gene events suggests that HSF gene family of cotton evolution was under strong purifying selection. Expression analysis revealed that GarHSF04 were found to be actively involved in PEG and salinity tolerance in G. arboreum. GhiHSF14 upregulated in heat and downregulated in salinity whilst almost illustrated similar behavior under cold and PEG treatments and GhiHSF21 exhibited down regulation almost across all the stresses in G. hirsutum. Overwhelmingly, present study paves the way to better understand the evolution of cotton HSF TFs and lays a foundation for future investigation of HSFs in improving abiotic stress tolerance in cotton.

Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum

Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum.

Priming by High Temperature Stress Induces MicroRNA Regulated Heat Shock Modules Indicating Their Involvement in Thermopriming Response in Rice

Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures.

Impacts of Heat Stress-Induced Oxidative Stress on the Milk Protein Biosynthesis of Dairy Cows

Heat stress (HS) is one of the most important factors posing harm to the economic wellbeing of dairy industries, as it reduces milk yield as well as milk protein content. Recent studies suggest that HS participates in the induction of tissue oxidative stress (OS), as elevated levels of reactive oxygen species (ROS) and mitochondrial dysfunction were observed in dairy cows exposed to hot conditions. The OS induced by HS likely contributes to the reduction in milk protein content, since insulin resistance and apoptosis are promoted by OS and are negatively associated with the synthesis of milk proteins. The apoptosis in the mammary gland directly decreases the amount of mammary epithelial cells, while the insulin resistance affects the regulation of insulin on mTOR pathways. To alleviate OS damages, strategies including antioxidants supplementation have been adopted, but caution needs to be applied as an inappropriate supplement with antioxidants can be harmful. Furthermore, the complete mechanisms by which HS induces OS and OS influences milk protein synthesis are still unclear and further investigation is needed.

High temperature-mediated disturbance of carbohydrate metabolism and gene expressional regulation in rice: a review

Global warming has induced higher frequencies of excessively high-temperature weather episodes, which pose damage risk to rice growth and production. Past studies seldom specified how high temperature-induced carbohydrate metabolism disturbances from both source and sink affect rice fertilization and production. Here we discuss the mechanism of heat-triggered damage to rice quality and production through disturbance of carbohydrate generation and consumption under high temperatures. Furthermore, we provide strong evidence from past studies that rice varieties that maintain high photosynthesis and carbohydrate usage efficiencies under high temperatures will suffer less heat-induced damage during reproductive developmental stages. We also discuss the complexity of expressional regulation of rice genes in response to high temperatures, while highlighting the important roles of heat-inducible post-transcriptional regulations of gene expression. Lastly, we predict future directions in heat-tolerant rice breeding and also propose challenges that need to be conquered in the future.

Genome-Wide Analysis of Heat Shock Transcription Factors in Ziziphus jujuba Identifies Potential Candidates for Crop Improvement Under Abiotic Stress

Plant heat shock transcription factors (Hsfs) play a significant role in adoption under abiotic stress conditions by modulating the expression of several stress-responsive genes. Analysis of the Hsf gene family will serve to understand the molecular mechanism which is involved in response to abiotic stress. The Ziziphus species grows in warm and dry regions and is inherently tolerant to abiotic stress conditions; thus, Ziziphus is a highly enriched source of genes conferring abiotic stress tolerance. Therefore, the present study provides a comprehensive genome-wide analysis of the Hsf gene family in Z. jujuba. Identified 21 non-redundant Hsf genes were grouped into three major classes (classes A, B, and C) based on the phylogenetic analysis. Promoter and gene ontology analysis suggested that ZjHsfs perform diverse functions in response to abiotic stress conditions. Two paralogous pairs resulting from tandem gene duplication events were identified. Also, physio-chemical properties of chromosomal locations, gene structure, motifs, and protein domain organization of Hsfs were analyzed. Real-time PCR expression analyses revealed that most of the Z. jujuba Hsf genes are differentially expressed in response to heat stress. The analysis suggested ZjHsf-2, ZjHsf-3, ZjHsf-5, ZjHsf-7, ZjHsf-8, ZjHsf-10, ZjHsf-12, ZjHsf-17, and ZjHsf-18 were the outstanding candidate genes for imparting heat stress tolerance and for future functional analysis. The present analysis laid the foundation for understanding the molecular mechanism of the Hsf gene family regulating Z. jujuba development and tolerance to abiotic stress conditions.

CaHsfA1d Improves Plant Thermotolerance via Regulating the Expression of Stress- and Antioxidant-Related Genes

Heat shock transcription factor (Hsf) plays an important role in regulating plant thermotolerance. The function and regulatory mechanism of CaHsfA1d in heat stress tolerance of pepper have not been reported yet. In this study, phylogenetic tree and sequence analyses confirmed that CaHsfA1d is a class A Hsf. CaHsfA1d harbored transcriptional function and predicted the aromatic, hydrophobic, and acidic (AHA) motif mediated function of CaHsfA1d as a transcription activator. Subcellular localization assay showed that CaHsfA1d protein is localized in the nucleus. The CaHsfA1d was transcriptionally up-regulated at high temperatures and its expression in the thermotolerant pepper line R9 was more sensitive than that in thermosensitive pepper line B6. The function of CaHsfA1d under heat stress was characterized in CaHsfA1d-silenced pepper plants and CaHsfA1d-overexpression Arabidopsis plants. Silencing of the CaHsfA1d reduced the thermotolerance of the pepper, while CaHsfA1d-overexpression Arabidopsis plants exhibited an increased insensitivity to high temperatures. Moreover, the CaHsfA1d maintained the H2O2 dynamic balance under heat stress and increased the expression of Hsfs, Hsps (heat shock protein), and antioxidant gene AtGSTU5 (glutathione S-transferase class tau 5) in transgenic lines. Our findings clearly indicate that CaHsfA1d improved the plant thermotolerance via regulating the expression of stress- and antioxidant-related genes.

Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)

BACKGROUND

Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata.

RESULTS

In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species.

CONCLUSIONS

The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.

Genome-Wide Analysis of the Heat Shock Transcription Factor Gene Family in Brassica juncea: Structure, Evolution, and Expression Profiles

Heat shock transcription factor (HSF) is ubiquitous in the whole biological world and plays an important role in regulating growth and development and responses to environment stress. In this study, a total of 60 HSF transcription factors in Brassica juncea genome were identified and analyzed. Phylogenetic analysis showed that HSF genes were divided into three groups namely: A, B, and C, of which group A was further divided into nine subgroups (A1-A9). The analysis of gene structure and conserved motifs showed that some homologous genes are highly conserved. There was strong conservative microcollinearity among Brassica rapa, B. juncea, and Brassica oleracea, which provides a basis for studying the replication of gene families. Moreover, the results revealed that the promoter regions of BjuHSF genes were rich in cis-elements related to growth and development, hormone signal, and stress response. The prediction of protein interaction results showed that HSFs could interact with multiple transcription factors and proteins in the genome, while functional annotation revealed that BjuHSF genes were involved in many biological processes. The expression patterns of BjuHSF genes were analyzed by qPCR, and the results showed that these genes were closely linked to stress response, hormones, and development process. These results are a foundation for further analysis of the regulation mechanism of HSF gene family.

Transcriptomic Analysis Reveals Important Roles of Lignin and Flavonoid Biosynthetic Pathways in Rice Thermotolerance During Reproductive Stage

Rice is one of the major staple cereals in the world, but heat stress is increasingly threatening its yield. Analyzing the thermotolerance mechanism from new thermotolerant germplasms is very important for rice improvement. Here, physiological and transcriptome analyses were used to characterize the difference between two germplasms, heat-sensitive MH101 and heat-tolerant SDWG005. Two genotypes exhibited diverse heat responses in pollen viability, pollination characteristics, and antioxidant enzymatic activity in leaves and spikelets. Through cluster analysis, the global transcriptomic changes indicated that the ability of SDWG005 to maintain a steady-state balance of metabolic processes played an important role in thermotolerance. After analyses of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, we found that the thermotolerance mechanism in SDWG00 was associated with reprogramming the cellular activities, such as response to abiotic stress and metabolic reorganization. In contrast, the down-regulated genes in MH101 that appeared to be involved in DNA replication and DNA repair proofreading, could cause serious injury to reproductive development when exposed to high temperature during meiosis. Furthermore, we identified 77 and 11 differentially expressed genes (DEGs) involved in lignin and flavonoids biosynthetic pathways, respectively. Moreover, we found that more lignin deposition and flavonoids accumulation happened in SDWG005 than in MH101 under heat stress. The results indicated that lignin and flavonoid biosynthetic pathways might play important roles in rice heat resistance during meiosis.

Identification of chalcone synthase genes and their expression patterns reveal pollen abortion in cotton

Chalcone synthase (CHS) is a key enzyme and producing flavonoid derivatives as well play a vital roles in sustaining plant growth and development. However, the systematic and comprehensive analysis of CHS genes in island cotton (G. barbadense) has not been reported yet especially response to cytoplasmic male sterility (CMS). To fill this knowledge gap, a genome-wide investigation of CHS genes were studied in island cotton. A total of 20 GbCHS genes were identified and grouped into five GbCHSs. The gene structure analysis revealed that most of GbCHS genes consisted of two exons and one intron, and 20 motifs were identified. Twenty five pairs duplicated events (12 GbCHS genes) were identified including 23 segmental duplication pairs and two tandem duplication events, representing that GbCHS gene family amplification mainly owned to segmental duplication events and evolving slowly. Gene expression analysis exhibited that the GbCHS family genes presented a diversity expression patterns in various organs of cotton. Coupled with functional predictions and gene expression, the abnormal expression of GbCHS06, 10, 16 and 19 might be associated with pollen abortion of CMS line in island cotton. Conclusively, GbCHS genes exhibited diversity and conservation in many aspects, which will help to better understand functional studies and a reference for CHS research in island cotton and other plants.

Genomic analyses of heat stress transcription factors (HSFs) in simulated drought stress response and storage root deterioration after harvest in cassava

Heat shock factors (HSFs) play crucial roles in various plant stress responses. However, the current knowledge about HSFs in cassava, an important crop, is still insufficient. In this research, we identified 32 cassava HSF genes (MeHSFs) and clustered them into three groups (A, B, C) based on phylogenetic analysis and structural characteristics. Conserved motif analyses showed that MeHSFs display domains characteristic to HSF transcription factors. Gene structure analyses suggested that 29 MeHSFs contained only two exons. All identified 32 cassava MeHSFs were distributed on 13 chromosomes. Their expression profiles revealed that the different MeHSFs were expressed differentially in different tissues, most high expression genes belonged to group A. The similar MeHSFs were up-regulated after treatment with both PEG and abscisic acid (ABA), which implied that these MeHSFs may participate in resistance to simulated drought stress associated with the ABA signaling pathway. In addition, several MeHSFs were induced during postharvest physiological deterioration (PPD) in cassava. Our results provided basic but important knowledge for future gene function analysis of MeHSFs toward efforts in improving tolerance to abiotic stress and PPD in cassava.

Genome-Wide Identification and Functional Characterization of the Heat Shock Factor Family in Eggplant (Solanum melongena L.) under Abiotic Stress Conditions

Plant heat shock factors (Hsfs) play crucial roles in various environmental stress responses. Eggplant (Solanum melongena L.) is an agronomically important and thermophilic vegetable grown worldwide. Although the functions of Hsfs under environmental stress conditions have been characterized in the model plant Arabidopsis thaliana and tomato, their roles in responding to various stresses remain unclear in eggplant. Therefore, we characterized the eggplant SmeHsf family and surveyed expression profiles mediated by the SmeHsfs under various stress conditions. Here, using reported Hsfs from other species as queries to search SmeHsfs in the eggplant genome and confirming the typical conserved domains, we identified 20 SmeHsf genes. The SmeHsfs were further classified into 14 subgroups on the basis of their structure. Additionally, quantitative real-time PCR revealed that SmeHsfs responded to four stresses—cold, heat, salinity and drought—which indicated that SmeHsfs play crucial roles in improving tolerance to various abiotic stresses. The expression pattern of SmeHsfA6b exhibited the most immediate response to the various environmental stresses, except drought. The genome-wide identification and abiotic stress-responsive expression pattern analysis provide clues for further analysis of the roles and regulatory mechanism of SmeHsfs under environmental stresses.

Wheat Heat Shock Factor TaHsfA6f Increases ABA Levels and Enhances Tolerance to Multiple Abiotic Stresses in Transgenic Plants

Abiotic stresses are major constraints limiting crop growth and production. Heat shock factors (Hsfs) play significant roles in mediating plant resistance to various environmental stresses, including heat, drought and salinity. In this study, we explored the biological functions and underlying mechanisms of wheat TaHsfA6f in plant tolerance to various abiotic stresses. Gene expression profiles showed that TaHsfA6f has relatively high expression levels in wheat leaves at the reproductive stage. Transcript levels of TaHsfA6f were substantially up-regulated by heat, dehydration, salinity, low temperature, and multiple phytohormones, but was not induced by brassinosteroids (BR). Subcellular localization analyses revealed that TaHsfA6f is localized to the nucleus. Overexpression of the TaHsfA6f gene in Arabidopsis results in improved tolerance to heat, drought and salt stresses, enhanced sensitivity to exogenous abscisic acid (ABA), and increased accumulation of ABA. Furthermore, RNA-sequencing data demonstrated that TaHsfA6f functions through up-regulation of a number of genes involved in ABA metabolism and signaling, and other stress-associated genes. Collectively, these results provide evidence that TaHsfA6f participates in the regulation of multiple abiotic stresses, and that TaHsfA6f could serve as a valuable gene for genetic modification of crop abiotic stress tolerance.

Functional characterization of maize heat shock transcription factor gene ZmHsf01 in thermotolerance

BACKGROUND

Heat waves can critically influence maize crop yields. Plant heat shock transcription factors (HSFs) play a key regulating role in the heat shock (HS) signal transduction pathway.

METHOD

In this study, a homologous cloning method was used to clone HSF gene ZmHsf01 (accession number: MK888854) from young maize leaves. The transcript levels of ZmHsf01 were detected using qRT-PCR in different tissues and treated by HS, abscisic acid (ABA), hydrogen peroxide (H2O2), respectively, and the functions of gene ZmHsf01 were studied in transgenic yeast and Arabidopsis.

RESULT

ZmHsf01 had a coding sequence (CDS) of 1176 bp and encoded a protein consisting of 391 amino acids. The homologous analysis results showed that ZmHsf01 and SbHsfA2d had the highest protein sequence identities. Subcellular localization experiments confirmed that ZmHsf01 was localized in the nucleus. ZmHsf01 was expressed in many maize tissues. It was up-regulated by HS, and up-regulated in roots and down-regulated in leaves under ABA and H2O2treatments. ZmHsf01-overexpressing yeast cells showed increased thermotolerance. In Arabidopsis seedlings, ZmHsf01 compensated for the thermotolerance defects of mutant athsfa2, and ZmHsf01-overexpressing lines showed enhanced basal and acquired thermotolerance. When compared to wild type (WT) seedlings, ZmHsf01-overexpressing lines showed higher chlorophyll content and survival rates after HS. Heat shock protein (HSP) gene expression levels were more up-regulated in ZmHsf01-overexpressing Arabidopsis seedlings than WT seedlings. These results suggest that ZmHsf01 plays a vital role in response to HS in plant.

Rice OsHSFA3 Gene Improves Drought Tolerance by Modulating Polyamine Biosynthesis Depending on Abscisic Acid and ROS Levels

Drought is a serious problem, which causes heavy yield losses for rice. Heat-shock factors (HSFs) had been implicated in tolerance to drought and high temperature. However, there has not been much functional characterization and mechanism clarification in rice. Previously, we found an HSF gene, OsHSFA3, was highly related with drought tolerance after screening from 10,000 different samples. Herein, we cloned the OsHSFA3 from rice and overexpressed it in Arabidopsis thaliana to study its regulatory mechanism of drought tolerance. Phenotypic and physiological assays of the transgenic Arabidopsis lines showed that overexpression of OsHSFA3 confers drought tolerance by reducing water loss and reactive oxygen species (ROS) levels, whereas it increases abscisic acid (ABA) levels. However, enzymatic antioxidants such as activity levels of superoxide dismutase, peroxidase and catalase were not significantly different between wild type and transgenic lines. Instead, we observed a significant increase in polyamine content, which was correlated with increased AtADC1, AtADC2, SPDS1 and SPMS expression levels. In silico and in vivo analyses confirmed that OsHSFA3 is a nuclear-localized gene. In addition, OsHSFA3 can bind to the promoter of AtADC1 and OsADC via a yeast one-hybrid assay. Overall, this study reveals that OsHSFA3 improves drought tolerance in Arabidopsis not only by increasing ABA levels, but also by modulating polyamine levels to maintain ROS homeostasis, therefore it could be a strong candidate to develop drought-tolerant rice cultivars.

TaHsfA2-1, a new gene for thermotolerance in wheat seedlings: Characterization and functional roles

Heat shock transcription factors (Hsfs) play an important role in regulating heat stress response in plants. Our previous study found that there were 82 non-redundant Hsfs in wheat, 18 of which belonged to subclass A2. In this study, we cloned an A2 member, TaHsfA2-1, which encoded a protein of 346 amino acid residues in wheat. The fusion protein TaHsfA2-1-GFP was localized in the nucleus under normal growth conditions. TaHsfA2-1 was expressed in nearly all the measured tissues, most highly in mature leaves. The expression level of TaHsfA2-1 can be enhanced by heat stress, PEG stress, and signal molecules such as H₂O₂ and SA. Yeast cells transformed with TaHsfA2-1 improved thermotolerance compared to those with the empty vector. TaHsfA2-1-overexpressing Arabidopsis displayed a better growth state with more green leaves than wild-type seedlings after heat stress. Accordingly, the chlorophyll content and survival rate in the transgenic lines were higher than in the wild type, and relative conductivity in the transgenic lines was lower than in the wild type. Further research found that TaHsfA2-1-overexpressing Arabidopsis up-regulated the expression of some heat shock protein genes (Hsps) compared to wild type after heat stress. These results suggested that TaHsfA2-1 is a new gene that improves thermotolerance in plants by mediating the expression of Hsps. A functional gene was provided for molecular breeding in the subsequent research.

Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)

The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.

Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat (Triticum aestivum L.) and Possible Roles in Anther Development

Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Recently, HSFs have been shown to play roles in anther development. Thus, investigating the HSF family members and identifying their protective roles in anthers are essential for the further development of male sterile wheat breeding. In the present study, 61 wheat HSF genes (TaHsfs) were identified in the whole wheat genome and they are unequally distributed on 21 chromosomes. According to gene structure and phylogenetic analyses, the 61 TaHsfs were classified into three categories and 12 subclasses. Genome-wide duplication was identified as the main source of the expansion of the wheat HSF gene family based on 14 pairs of homeologous triplets, whereas only a very small number of TaHsfs were derived by segmental duplication and tandem duplication. Heat shock protein 90 (HSP90), HSP70, and another class of chaperone protein called htpG were identified as proteins that interact with wheat HSFs. RNA-seq analysis indicated that TaHsfs have obvious period- and tissue-specific expression patterns, and the TaHsfs in classes A and B respond to heat shock, whereas the C class TaHsfs are involved in drought regulation. qRT-PCR identified three TaHsfA2bs with differential expression in sterile and fertile anthers, and they may be candidate genes involved in anther development. This comprehensive analysis provides novel insights into TaHsfs, and it will be useful for understanding the mechanism of plant fertility conversion.

Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum)

Background

Heat shock transcription factor (Hsfs) is widely found in eukaryotes and prokaryotes. Hsfs can not only help organisms resist high temperature, but also participate in the regulation of plant growth and development (such as involved in the regulation of seed maturity and affects the root length of plants). The Hsf gene was first isolated from yeast and then gradually found in plants and sequenced, such as Arabidopsis thaliana, rice, maize. Tartary buckwheat is a rutin-rich crop, and its nutritional value and medicinal value are receiving more and more attention. However, there are few studies on the Hsf genes in Tartary buckwheat. With the whole genome sequence of Tartary buckwheat, we can effectively study the Hsf gene family in Tartary buckwheat.

Results

According to the study, 29 Hsf genes of Tartary buckwheat (FtHsf) were identified and renamed according to location of FtHsf genes on chromosome after removing a redundant gene. Therefore, only 29 FtHsf genes truly had the functional characteristics of the FtHsf family. The 29 FtHsf genes were located on 8 chromosomes of Tartary buckwheat, and we found gene duplication events in the FtHsf gene family, which may promote the expansion of the FtHsf gene family. Then, the motif compositions and the evolutionary relationship of FtHsf proteins and the gene structures, cis-acting elements in the promoter, synteny analysis of FtHsf genes were discussed in detail. What’s more, we found that the transcription levels of FtHsf in different tissues and fruit development stages were significantly different by quantitative real-time PCR (qRT-PCR), implied that FtHsf may differ in function.

Conclusions

In this study, only 29 Hsf genes were identified in Tartary buckwheat. Meanwhile, we also classified the FtHsf genes, and studied their structure, evolutionary relationship and the expression pattern. This series of studies has certain reference value for the study of the specific functional characteristics of Tartary buckwheat Hsf genes and to improve the yield and quality of Tartary buckwheat in the future.

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

Background

Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited.

Results

In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response.

Conclusions

These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus)

Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.

Ethylene-mediated signaling confers thermotolerance and regulates transcript levels of heat shock factors in rice seedlings under heat stress

BACKGROUND

Agriculture is highly dependent on climate. Increases in temperature caused by global warming pose challenges for crop production. Heat stress induces oxidative damage to cell membranes and then causes cell death. Plants have developed various responses to elevated temperatures, including hormone signaling pathways and heat shock factors that elevate their thermotolerance. In response to heat stress, the gaseous hormone ethylene is produced through regulation of the expression of signaling-related genes to modulate resource allocation dynamics. For comprehensive understanding of the role of ethylene, this study used an ethylene precursor to analyze the ethylene signaling pathway involved in adjustment of the homeostasis of the antioxidant system and to evaluate heat shock factor expression in rice seedlings under heat stress.

RESULTS

Levels of cell membrane oxidation and ion leakage were reduced in rice seedlings under heat treatment combined with ethylene precursor treatment, conferring enhanced thermotolerance. Reduction of the fresh weight and chlorophyll a/b ratio in rice seedlings was lower in rice seedlings under heat stress with ethylene precursor treatment than in those under heat stress only. Moreover, reduction of antioxidant response caused by heat stress was ameliorated by treatment with ethylene precursors such as catalase and total peroxidase. Quantitative reverse transcriptase-polymerase chain reaction showed higher expression levels of heat shock factors such as HSFA1a and HSFA2a, c, d, e, and f and ethylene-signaling-related genes such as ethylene insensitive 2, ethylene insensitive-like 1, and ethylene insensitive-like 2 in rice seedlings under heat stress with ethylene precursor treatment than in rice seedlings under heat stress only.

CONCLUSION

Ethylene-mediated signaling was involved in the reduction of oxidative damage, maintenance of chlorophyll content, and enhancement of thermotolerance in rice seedlings under heat stress. Furthermore, this study revealed heat shock factors and ethylene-signaling-related genes involved in complex network regulation that confers thermotolerance to rice seedlings.

Genome wide transcriptome analysis reveals vital role of heat responsive genes in regulatory mechanisms of lentil (Lens culinaris Medikus)

The present study reports the role of morphological, physiological and reproductive attributes viz. membrane stability index (MSI), osmolytes accumulations, antioxidants activities and pollen germination for heat stress tolerance in contrasting genotypes. Heat stress increased proline and glycine betaine (GPX) contents, induced superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione peroxidase (GPX) activities and resulted in higher MSI in PDL-2 (tolerant) compared to JL-3 (sensitive). In vitro pollen germination of tolerant genotype was higher than sensitive one under heat stress. In vivo stressed pollens of tolerant genotype germinated well on stressed stigma of sensitive genotype, while stressed pollens of sensitive genotype did not germinate on stressed stigma of tolerant genotype. De novo transcriptome analysis of both the genotypes showed that number of contigs ranged from 90,267 to 104,424 for all the samples with N50 ranging from 1,755 to 1,844 bp under heat stress and control conditions. Based on assembled unigenes, 194,178 high-quality Single Nucleotide Polymorphisms (SNPs), 141,050 microsatellites and 7,388 Insertion-deletions (Indels) were detected. Expression of 10 genes was evaluated using quantitative Real Time Polymerase Chain Reaction (RT-qPCR). Comparison of differentially expressed genes (DEGs) under different combinations of heat stress has led to the identification of candidate DEGs and pathways. Changes in expression of physiological and pollen phenotyping related genes were also reaffirmed through transcriptome data. Cell wall and secondary metabolite pathways are found to be majorly affected under heat stress. The findings need further analysis to determine genetic mechanism involved in heat tolerance of lentil.

Genome-wide identification and classification of the Hsf and sHsp gene families in Prunus mume, and transcriptional analysis under heat stress

The transcriptional activation of heat shock proteins (Hsps) by heat shock transcription factors (Hsfs) is presumed to have a pivotal role in plant heat stress (HS) response. Prunus mume is an ornamental woody plant with distinctive features, including rich varieties and colors. In this study, 18 Hsfs and 24 small Hsps (sHsps) were identified in P. mume. Their chromosomal locations, protein domains, conserved motifs, phylogenetic relationships, and exon–intron structures were analyzed and compared with Arabidopsis thaliana Hsfs or sHsps. A total of 18 PmHsf members were classified into three major classes, A, B, and C. A total of 24 PmsHsps were grouped into eight subfamilies (CI to CIII, P, endoplasmic reticulum, M, and CI- or P-related). Quantitative reverse transcription PCR analysis revealed that members of the A2, A7, and A9 groups became the prominent Hsfs after heat shock, suggesting their involvement in a key regulatory role of heat tolerance. Most of the PmsHsp genes were up-regulated upon exposure to HS. Overall, our data contribute to an improved understanding of the complexity of the P. mume Hsf and sHsp gene families, and provide a basis for directing future systematic studies investigating the roles of the Hsf and sHsp gene families.

Genome-wide identification, phylogenetic and expression analysis of the heat shock transcription factor family in bread wheat (Triticum aestivum L.)

Background

Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of Cd in edible tissues, which poses a major hazard to human health. It has been reported that heat shock transcription factor A 4a (HsfA4a) of wheat and rice conferred Cd tolerance by upregulating metallothionein gene expression. However, genome-wide identification, classification, and comparative analysis of the Hsf family in wheat is lacking. Further, because of the promising role of Hsf genes in Cd tolerance, there is need for an understanding of the expression of this family and their functions on wheat under Cd stress. Therefore, here we identify the wheat TaHsf family and to begin to understand the molecular mechanisms mediated by the Hsf family under Cd stress.

Results

We first identified 78 putative Hsf homologs using the latest available wheat genome information, of which 38 belonged to class A, 16 to class B and 24 to class C subfamily. Then, we determined chromosome localizations, gene structures, conserved protein motifs, and phylogenetic relationships of these TaHsfs. Using RNA sequencing data over the course of development, we surveyed expression profiles of these TaHsfs during development and under different abiotic stresses to characterise the regulatory network of this family. Finally, we selected 13 TaHsf genes for expression level verification under Cd stress using qRT-PCR.

Conclusions

To our knowledge, this is the first report of the genome organization, evolutionary features and expression profiles of the wheat Hsf gene family. This work therefore lays the foundation for targeted functional analysis of wheat Hsf genes, and contributes to a better understanding of the roles and regulatory mechanism of wheat Hsfs under Cd stress.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5876-x) contains supplementary material, which is available to authorized users.

Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach

Among the significant transcription factors (TFs), HSF proteins play pivotal roles in the regulation of hormonal signal transduction and different abiotic stress (AbS) responses. Hence considering its importance, global omics expression analysis of HSF candidates was performed in rice (OsHSF). The current study identified 25 HSF family members and physically plotted them against the rice genome. These proteins were systematically analyzed for their physicochemical features, organization and expression signatures. Further, heatmap of both spatio-temporal and global plant hormones revealed the developmental tissues and hormone specific expression profiling of these genes respectively. Comparative genome mapping between OsHSF players in interrelated C4 grass species revealed the chromosome level synteny. Signalome analysis revealed the protein - protein interactions of OsHSF. Expression profiling of key players in response to stresses exhibited the new involvement in combined AbS (CAbS) responses. Our results are significantly valuable to decipher their functional analysis of CAbS tolerant in rice.

ZmHsf05, a new heat shock transcription factor from Zea mays L. improves thermotolerance in Arabidopsis thaliana and rescues thermotolerance defects of the athsfa2 mutant

High temperature directly affects the yield and quality of crops. Plant Hsfs play vital roles in plant response to heat shock. In the present study, ZmHsf05 was isolated from maize (Zea mays L.) using homologous cloning methods. The sequencing analysis demonstrated that CDS of ZmHsf05 was 1080 bp length and encoded a protein containing 359 amino acids. The putative amino acid sequence of ZmHsf05 contained typical Hsf domains, such as DBD, OD, NLS and AHA motif. Subcellular localization assays displayed that the ZmHsf05 is localized to the nucleus. ZmHsf05 was expressed in many maize tissues and its expression level was increased by heat stress treatment. ZmHsf05 rescued the reduced thermotolerance of the athsfa2 mutant in Arabidopsis seedlings. Arabidopsis seedlings of ZmHsf05-overexpressing increased both the basal and acquired thermotolerances. After heat stress, the ZmHsf05-overexpressing lines showed enhanced survival rate and chlorophyll content compared with WT seedlings. The expression of Hsps was up-regulated in the ZmHsf05-overexpressing Arabidopsis lines after heat stress treatment. These results suggested that ZmHsf05 plays an important role in both basal and acquired thermotolerance in plants.

Improving Potato Stress Tolerance and Tuber Yield Under a Climate Change Scenario - A Current Overview

Global climate change in the form of extreme heat and drought poses a major challenge to sustainable crop production by negatively affecting plant performance and crop yield. Such negative impact on crop yield is likely to be aggravated in future because continued greenhouse gas emissions will cause further rise in temperature leading to increased evapo-transpiration and drought severity, soil salinity as well as insect and disease threats. This has raised a major challenge for plant scientists on securing global food demand, which urges an immediate need to enhance the current yield of major food crops by two-fold to feed the increasing population. As a fourth major food crop, enhancing potato productivity is important for food security of an increasing population. However, potato plant is highly prone to high temperature, drought, soil salinity, as well as insect and diseases. In order to maintain a sustainable potato production, we must adapt our cultivation practices and develop stress tolerant potato cultivars that are appropriately engineered for changing environment. Yet the lack of data on the underlying mechanisms of potato plant resistance to abiotic and biotic stress and the ability to predict future outcomes constitutes a major knowledge gap. It is a challenge for plant scientists to pinpoint means of improving tuber yield under increasing CO2, high temperature and drought stress including the changing patterns of pest and pathogen infestations. Understanding stress-related physiological, biochemical and molecular processes is crucial to develop screening procedures for selecting crop cultivars that can better adapt to changing growth conditions. Elucidation of such mechanism may offer new insights into the identification of specific characteristics that may be useful in breeding new cultivars aimed at maintaining or even enhancing potato yield under changing climate. This paper discusses the recent progress on the mechanism by which potato plants initially sense the changes in their surrounding CO2, temperature, water status, soil salinity and consequently respond to these changes at the molecular, biochemical and physiological levels. We suggest that future research needs to be concentrated on the identification and characterization of signaling molecules and target genes regulating stress tolerance and crop yield potential.

Genome-wide identification and characterization of the metal tolerance protein (MTP) family in grape (Vitis vinifera L.)

Metal tolerance proteins (MTPs) play an important role in the transport of metals at the cellular, tissue and whole plant levels. In the present study, 11 MTP genes were identified and these clustered in three major sub-families Fe/Zn-MTP, Zn-MTP, and Mn-MTP, and seven groups, which are similar to the grouping of MTP genes in both Arabidopsis and rice. Vitis vinifera metal tolerance proteins (VvMTP) ranged from 366 to 1092 amino acids, were predicted to be located in the cell vacuole, and had four to six putative TMDs, except for VvtMTP12 and VvMTP1. The VvMTPs had putative cation diffusion facilitator (CDF) domains and the putative Mn-MTPs also had zinc transporter dimerization domains (ZD-domains). V. vinifera Mn-MTPs had gene structures and motif distributions similar to those of the Fe/Zn-MTP and Zn-MTP sub-families. The upstream regions of VvMTP genes had variable frequencies of cis-regulatory elements that could indicate regulation at different developmental stages and/or differential regulation in response to stress. Comparison of the VvMTP coding sequences with known miRNAs found in various plant species indicated the presence of 13 putative miRNAs, with 7 of these associated with VvMTPs. Temporal and spatial expression profiling indicates a potential role for VvMTP genes during growth and development in grape plants, as well as the involvement of these genes in plant responses to environmental stress, especially osmotic stress. The data generated from this study provides a basis for further investigation of the roles of MTP genes in grapes.

Capsicum annuum HsfB2a Positively Regulates the Response to Ralstonia solanacearum Infection or High Temperature and High Humidity Forming Transcriptional Cascade with CaWRKY6 and CaWRKY40

The responses of pepper (Capsicum annuum) plants to inoculation with the pathogenic bacterium Ralstonia solanacearum and to high-temperature-high-humidity (HTHH) conditions were previously found to be coordinated by the transcription factors CaWRKY6 and CaWRKY40; however, the underlying molecular mechanism was unclear. Herein, we identified and functionally characterized CaHsfB2a, a nuclear-localized heat shock factor involved in pepper immunity to R. solanacearum inoculation (RSI) and tolerance to HTHH. CaHsfB2a is transcriptionally induced in pepper plants by RSI or HTHH and by exogenous application of salicylic acid (SA), methyl jasmonate (MeJA), ethylene (ETH), or abscisic acid (ABA). Virus-induced gene silencing (VIGS) of CaHsfB2a significantly impaired pepper immunity to RSI, hampered HTHH tolerance, and curtailed expression of immunity- and thermotolerance-associated marker genes such as CaHIR1, CaNPR1, CaABR1, and CaHSP24. Likewise, transient overexpression of CaHsfB2a in pepper leaves induced hypersensitive response (HR)-like cell death and H2O2 accumulation and upregulated the above-mentioned marker genes as well as CaWRKY6 and CaWRKY40. Chromatin immunoprecipitation (ChIP) and microscale thermophoresis (MST) analysis revealed that CaHsfB2a bound the promoters of both CaWRKY6 and CaWRKY40. In a parallel experiment, we determined by ChIP-PCR and MST that CaHsfB2a was regulated directly by CaWRKY40 but indirectly by CaWRKY6. Cumulatively, our results suggest that CaHsfB2a positively regulates plant immunity against RSI and tolerance to HTHH, via transcriptional cascades and positive feedback loops involving CaWRKY6 and CaWRKY40.

Heat shock transcription factor 3 regulates plant immune response through modulation of salicylic acid accumulation and signalling in cassava

As the terminal components of signal transduction, heat stress transcription factors (Hsfs) mediate the activation of multiple genes responsive to various stresses. However, the information and functional analysis are very limited in non-model plants, especially in cassava (Manihot esculenta), one of the most important crops in tropical areas. In this study, 32 MeHsfs were identified from the cassava genome; the evolutionary tree, gene structures and motifs were also analysed. Gene expression analysis found that MeHsfs were commonly regulated by Xanthomonas axonopodis pv. manihotis (Xam). Amongst these MeHsfs, MeHsf3 was specifically located in the cell nucleus and showed transcriptionally activated activity on heat stress elements (HSEs). Through transient expression in Nicotiana benthamiana leaves and virus-induced gene silencing (VIGS) in cassava, we identified the essential role of MeHsf3 in plant disease resistance, by regulating the transcripts of Enhanced Disease Susceptibility 1 (EDS1) and pathogen-related gene 4 (PR4). Notably, as regulators of defence susceptibility, MeEDS1 and MePR4 were identified as direct targets of MeHsf3. Moreover, the disease sensitivity of MeHsf3- and MeEDS1-silenced plants could be restored by exogenous salicylic acid (SA) treatment. Taken together, this study highlights the involvement of MeHsf3 in defence resistance through the transcriptional activation of MeEDS1 and MePR4.

Characterization and Functional Analysis of FaHsfC1b from Festuca arundinacea Conferring Heat Tolerance in Arabidopsis

Heat transcription factors (Hsfs) belong to a large gene family classified into A, B, and C groups, with classes A and B Hsfs being well-characterized and known for their roles in plant tolerance to abiotic stresses. The functions and roles of Class C Hsfs are not well-documented. The objectives of this study were to characterize a class C Hsf gene (FaHsfC1b) cloned from tall fescue (Festuca arundinacea), a perennial grass species, and to determine the physiological functions of FaHsfC1b in regulating heat tolerance by overexpressing FaHsfC1b in Arabidopsis thaliana. Full length cDNA of FaHsfC1b was cloned and the sequence alignment showed that it had high similarity to OsHsfC1b with typical DNA binding domain, hydrophobic oligomerization domain, and a nucleus localization signal. Transient expression with FaHsfC1b-eGFP in protoplasts of Arabidopsis leaves indicated its nucleus localization. qRT-PCR analysis showed that FaHsfC1b responded to heat, osmotic, salt, and cold stress in leaves and roots during 48-h treatment. Physiological analysis showed that FaHsfC1b overexpression enhanced plant survival rate, chlorophyll content, and photochemical efficiency, while it resulted in decreases in electrolyte leakage, H₂O₂ and O²⁻ content under heat stress. qRT-PCR showed that endogenous HsfC1 was induced in transgenic plants and the expression levels of heat protection protein genes, including several HSPs, AtGalSyn1, AtRof1, and AtHSA32, as well as ABA-synthesizing gene (NCED3) were significantly upregulated in transgenic plants overexpressing FaHsfC1b under heat stress. Our results first demonstrate that HsfC1b plays positive roles in plant tolerance to heat stress in association with the induction and upregulation of heat-protective genes. HsfC1b may be used as a candidate gene for genetic modification of cool-season plant species for improving heat tolerance.

Mapping of domains of heat stress transcription factor OsHsfA6a responsible for its transactivation activity

Elevated temperatures affect the growth and reproduction of crop plants and thus have become concern worldwide. Hsp101/ClpB protein is a major molecular chaperone, performing dis-aggregation of protein aggregates formed during heat stress. In rice, OsHsfA6a binds to the promoter of OsHsp101/ClpB-C and regulates its expression. In this study, analysis of C-terminal domains of ClassA OsHsfs revealed the presence of aromatic, hydrophobic, acidic (AHA) and nuclear export signal (NES) motifs in all the members. Using deletion constructs, we show that the activation potential of OsHsfA6a is confined in the C-terminal activation domain comprising of AHA and NES sequences. The results obtained in yeast were complemented with transient expression of reporter in protoplast (TERP) based assay. Detailed analysis of OsHsfA6a splice variants shows the presence of one full version and a DBD truncated smaller version whose existence needs experimental evidences. Phylogeny analysis revealed that OsHsfA6a has diverged from A6a/A6b forms of Arabidopsis and tomato and has no expressologs. OsHsfA6a in-silico network was enriched in MAP kinases along with Hsp70 and Hsp90 proteins. Thus, it appears that regulation of OsClpB-C by HsfA6a is unique in rice and activation potential of OsHsfA6a resides in the single AHA motif located in the C-terminal domain.

The roles of Arabidopsis HSFA2, HSFA4a, and HSFA7a in the heat shock response and cytosolic protein response

Previously, we found that Arabidopsis plants transformed with a construct containing the promoter of Oshsp17.3 from rice fused to the β-glucuronidase gene (GUS), Oshsp17.3Pro::GUS (Oshsp17.3p), showed a GUS signal after heat shock (HS) or azetidine-2-carboxylic acid (AZC) treatment. HS and AZC trigger the heat shock response (HSR) and cytosolic protein response (CPR), respectively, in the cytosol by modulating specific heat shock factor (HSF) activity. Here we further identified that AtHSFA2 (At2g26150), AtHSFA7a (At3g51910), AtHSFB2a (At5g62020), and AtHSFB2b (At4g11660) are HS- and AZC-inducible; AtHSFA4a (At4g18880) is AZC-inducible; and AtHSFA5 (At4g13980) is less AZC- and HS-inducible. To investigate the roles of these 6 AtHSFs in the HSR or CPR, we crossed two independent Oshsp17.3p transgenic Arabidopsis plants with the AtHSF-knockout mutants athsfa2 (SALK_008978), athsfa4a (GABI_181H12), athsfa5 (SALK_004385), athsfa7a (SALK_080138), athsfb2a (SALK_137766), and athsfb2b (SALK_047291), respectively. As compared with the wild type, loss-of-function mutation of AtHSFA2, AtHSFA4a, and AtHSFA7a decreased HS and AZC responsiveness, so these 3 AtHSFs are essential for the HSR and CPR. In addition, loss-of-function results indicated that AthsfB2b is involved in regulating the HSR in Arabidopsis. Furthermore, analysis of the relative GUS activity of two double knockout mutants, athsfA2/athsfA4a and athsfA2/athsfA7a, revealed that AtHSFA2, AtHSFA4a, and AtHSFA7a function differentially in the HSR and CPR. Transcription profiling in athsf mutants revealed positive or negative transcriptional regulation among the 6 AtHSFs in Arabidopsis plants under HS and AZC conditions. Tunicamycin treatment demonstrated that these 6 AtHSFs are not involved in the unfolded protein response.

Characterization of novel heat-responsive transcription factor (TaHSFA6e) gene involved in regulation of heat shock proteins (HSPs) - A key member of heat stress-tolerance network of wheat

Heat stress has an adverse effect on the quality and quantity of agriculturally important crops, especially wheat. The tolerance mechanism has not been explored much in wheat and very few genes/ TFs responsive to heat stress is available on public domain. Here, we identified, cloned and characterized a putative TaHSFA6e TF gene of 1.3 kb from wheat cv. HD2985. We observed an ORF of 368 aa with Hsf DNA binding signature domain in the amino acid sequence. Single copy number of TaHSFA6e was observed integrated in the genome of wheat. Expression analysis of TaHSFA6e under differential HS showed maximum transcripts in wheat cv. Halna (thermotolerant) in response to 38 °C for 2 h during pollination and grain-filling stages, as compared to PBW343, HD2329 and HD2985. Putative target genes of TaHSFA6e (HSP17, HSP70 and HSP90) showed upregulation in response to differential HS (30 & 38 °C, 2 h) during pollination and grain-filling stages. Small HSP17 was observed most triggered in Halna under HS. We observed increase in the catalase, guaiacol peroxidase, total antioxidant capacity (TAC), and decrease in the lipid peroxidation in thermotolerant cvs. (Halna, HD2985), as compared to thermosusceptible (PBW343, HD2329) under differential HS. Multiple stresses (heat - 38 °C, 2 h, and drought - 100 mL of 20% polyethylene Glycol 6000) during seedling stage of wheat showed positive correlation between the expression of TaHSFA6e, putative targets (HSP70, HSP90, HSP17) and TAC. Halna (thermotolerant) performed better, as compared to other contrasting cvs. TaHSFA6e TF can be used as promising candidate gene for manipulating the heat stress-tolerance network.

Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage

The heat stress transcription factors (Hsfs) play a prominent role in thermotolerance and eliciting the heat stress response in plants. Identification and expression analysis of Hsfs gene family members in chickpea would provide valuable information on heat stress responsive Hsfs. A genome-wide analysis of Hsfs gene family resulted in the identification of 22 Hsf genes in chickpea in both desi and kabuli genome. Phylogenetic analysis distinctly separated 12 A, 9 B, and 1 C class Hsfs, respectively. An analysis of cis-regulatory elements in the upstream region of the genes identified many stress responsive elements such as heat stress elements (HSE), abscisic acid responsive element (ABRE) etc. In silico expression analysis showed nine and three Hsfs were also expressed in drought and salinity stresses, respectively. Q-PCR expression analysis of Hsfs under heat stress at pod development and at 15 days old seedling stage showed that CarHsfA2, A6, and B2 were significantly upregulated in both the stages of crop growth and other four Hsfs (CarHsfA2, A6a, A6c, B2a) showed early transcriptional upregulation for heat stress at seedling stage of chickpea. These subclasses of Hsfs identified in this study can be further evaluated as candidate genes in the characterization of heat stress response in chickpea.

Identification, Expression Analysis of the Hsf Family, and Characterization of Class A4 in Sedum Alfredii Hance under Cadmium Stress

Sedum alfredii Hance, a cadmium (Cd)/zinc (Zn)/lead (Pb) co-hyperaccumulating species, is a promising phytoremediation candidate because it accumulates substantial amounts of heavy metal ions without showing any obvious signs of poisoning. The heat shock transcription factor (Hsf) family plays crucial roles in plant growth, development, and stress responses. Although the roles of some Hsfs in abiotic stress have been well studied in model plants, the Hsf family has not been systematically investigated in heavy metal hyperaccumulators. Here, we comprehensively analyzed the Hsf gene family in S. alfredii based on a transcriptome under Cd stress. There were 22 Hsf members that were identified and phylogenetically clustered into three classes, namely, SaHsfA, SaHsfB, and SaHsfC. All of the three classes shared similar motifs. The expression profiles of the 22 Hsf members showed significant differences: 18 SaHsfs were responsive to Cd stress, as were multiple SaHsp genes, including SaHsp18.1, SaHsp22, SaHsp26.5, SaHsp70, SaHsp90, and SaHsp101. Two class A4 members, SaHsfA4a and SaHsfA4c, exhibited transcriptional activation activities. Overexpression of SaHsfA4a and SaHsfA4c in transgenic yeast indicated an improved tolerance to Cd stress and Cd accumulation. Our results suggest SaHsfs play important regulatory roles in heavy metal stress responses, and provide a reference for further studies on the mechanism of heavy metal stress regulation by SaHsfs.

Overexpression of lily HsfA3s in Arabidopsis confers increased thermotolerance and salt sensitivity via alterations in proline catabolism

Although HsfA3 (heat-stress transcription factor A3) is well characterized in heat stress, its roles in other abiotic stresses are less clear. In this study, we isolated two homologous HsfA3 genes, LlHsfA3A and LlHsfA3B, from lily (Lilium longiflorum). Both genes were induced by heat stress, but not by salt stress. Overexpressing LlHsfA3A in Arabidopsis enhanced its basal and acquired thermotolerance, while overexpressing LlHsfA3B just enhanced its acquired thermotolerance. In both cases, overexpressing plants showed hypersensitivity to salt stress, and a lack of sucrose exacerbated this salt sensitivity. Using a transient assay, the opposite effects were observed in lily. Further analysis revealed that either LlHsfA3A or LlHsfA3B overexpression altered normal proline accumulation. During heat treatments, proline increased in wild-type Arabidopsis plants, but no such increase was detected in transgenic plants that showed better basal or acquired thermotolerance. Under salt stress, proline accumulation was decreased in Arabidopsis and lily with the overexpression of LlHsfA3A or LlHsfA3B. Proline catabolism was activated by overexpression, and both LlHsfA3A and LlHsfA3B affected proline oxidation via regulation of AtbZIP11, AtbZIP44, and AtbZIP53 to activate AtproDH1 and AtproDH2 in transgenic Arabidopsis. Taken together, our results suggested that overexpression of LlHsfA3A or LlHsfA3B caused opposite effects on heat and salt tolerance, which may implicate proline catabolism.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H₂O₂-dependent oxidation of a wide range of substrates in plants and animals. As is known, H₂O₂ acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H₂O₂ content assays revealed that cotton fiber kept high enzyme activity and the lowest H₂O₂ level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.

Heat shock factor C2a serves as a proactive mechanism for heat protection in developing grains in wheat via an ABA-mediated regulatory pathway

High temperature at grain filling can severely reduce wheat yield. Heat shock factors (Hsfs) are central regulators in heat acclimation. This study investigated the role of TaHsfC2a, a member of the monocot-specific HsfC2 subclass, in the regulation of heat protection genes in Triticum aestivum. Three TaHsfC2a homoeologous genes were highly expressed in wheat grains during grain filling and showed only transient up-regulation in the leaves by heat stress but were markedly up-regulated by drought and abscisic acid (ABA) treatment. Overexpression of TaHsfC2a-B in transgenic wheat resulted in up-regulation of a suite of heat protection genes (e.g. TaHSP70d and TaGalSyn). Most TaHsfC2a-B target genes were heat, drought and ABA inducible. Transactivation analysis of two representative targets (TaHSP70d and TaGalSyn) showed that TaHsfC2a-B activated expression of reporters driven by these target promoters. Promoter mutagenesis analyses revealed that heat shock element is responsible for transactivation by TaHsfC2a-B and heat/drought induction. TaHsfC2a-B-overexpressing wheat showed improved thermotolerance but not dehydration tolerance. Most TaHsfC2a-B target genes were co-up-regulated in developing grains with TaHsfC2a genes. These data suggest that TaHsfC2a-B is a transcriptional activator of heat protection genes and serves as a proactive mechanism for heat protection in developing wheat grains via the ABA-mediated regulatory pathway.