Hsf Genes Research Articles

Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar.

Heat shock transcription factor (Hsf) family is one of the most important regulators in the plant kingdom. Hsf has been demonstrated to be involved in various processes associated with plant growth, development as well as in response to hormone and abiotic stresses. In this study, we carried out a comprehensive analysis of Hsf family in desert poplar, Populus euphratica. Total of 32 genes encoding Hsf were identified and they were classified into three main classes (A, B, and C). Gene structure and conserved motif analyses indicated that the members in each class were relatively conserved. Total of 10 paralogous pairs were identified in PeuHsf family, in which nine pairs were generated by whole genome duplication events. Ka/Ks analysis showed that PeuHsfs underwent purifying selection pressure. In addition, various cis-acting elements involved in hormone and stress responses located in the promoter regions of PeuHsfs. Gene expression analysis indicated that several PeuHsfs were tissue-specific expression. Compared to Arabidopsis, more PeuHsf genes were significantly induced by heat, drought, and salt stresses (21, 19, and 22 PeuHsfs, respectively). Our findings are helpful in understanding the distinguished adaptability of P. euphratica to extreme environment and providing a basis for functional analysis of PeuHsfs in the future.

Overexpression of Heat Shock Factor Gene HsfA3 Increases Galactinol Levels and Oxidative Stress Tolerance in Arabidopsis.

Heat shock factors (Hsfs) are central regulators of abiotic stress responses, especially heat stress responses, in plants. In the current study, we characterized the activity of the Hsf gene HsfA3 in Arabidopsis under oxidative stress conditions. HsfA3 transcription in seedlings was induced by reactive oxygen species (ROS), exogenous hydrogen peroxide (H2O2), and an endogenous H2O2 propagator, 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). HsfA3-overexpressing transgenic plants exhibited increased oxidative stress tolerance compared to untransformed wild-type plants (WT), as revealed by changes in fresh weight, chlorophyll fluorescence, and ion leakage under light conditions. The expression of several genes encoding galactinol synthase (GolS), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), which function as antioxidants in plant cells, was induced in HsfA3 overexpressors. In addition, galactinol levels were higher in HsfA3 overexpressors than in WT under unstressed conditions. In transient transactivation assays using Arabidopsis leaf protoplasts, HsfA3 activated the transcription of a reporter gene driven by the GolS1 or GolS2 promoter. Electrophoretic mobility shift assays showed that GolS1 and GolS2 are directly regulated by HsfA3. Taken together, these findings provide evidence that GolS1 and GolS2 are directly regulated by HsfA3 and that GolS enzymes play an important role in improving oxidative stress tolerance by increasing galactinol biosynthesis in Arabidopsis.

Genome-Wide Identification and Function Analyses of Heat Shock Transcription Factors in Potato.

Heat shock transcription factors (Hsfs) play vital roles in the regulation of tolerance to various stresses in living organisms. To dissect the mechanisms of the Hsfs in potato adaptation to abiotic stresses, genome and transcriptome analyses of Hsf gene family were investigated in Solanum tuberosum L. Twenty-seven StHsf members were identified by bioinformatics and phylogenetic analyses and were classified into A, B, and C groups according to their structural and phylogenetic features. StHsfs in the same class shared similar gene structures and conserved motifs. The chromosomal location analysis showed that 27 Hsfs were located in 10 of 12 chromosomes (except chromosome 1 and chromosome 5) and that 18 of these genes formed 9 paralogous pairs. Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development. Promoter and quantitative real-time polymerase chain reaction (qRT-PCR) detections of StHsfs were conducted and demonstrated that these genes were all responsive to various stresses. StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions. A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.

Comparison of Copy Number of HSF Genes in Two Buffalo Genomes

ABSTRACTThe copy number variation (CNV) is the number of copies of a particular gene in the genotype of an individual. Recent evidences show that the CNVs can vary in frequency and occurrence between breeds. These variations reportedly allowed different breeds to adapt to different environments. As copy number variations follow Mendelian pattern of inheritance, identification and distribution of these variants between populations can be used to infer the evolutionary history of the species. In this study, we have examined the absolute copy number of four Heat shock factor genes viz. HSF-1, 2, 4, and 5 in two different breeds of buffalo species using real-time PCR. Here, we report that the absolute copy number of HSF2 varies between the two breeds. In contrast no significant difference was observed in the copy number for HSF-1, 4, and 5 between the two breeds. Our results provide evidence for the presence of breed specific differences in HSF2 genomic copy number. This seems to be the first step in delineating the genetic factors underlying environmental adaptation between the two breeds. Nevertheless, a more detailed study is needed to characterize the functional consequence of this variation.

Heat Shock Factor Genes of Tall Fescue and Perennial Ryegrass in Response to Temperature Stress by RNA-Seq Analysis.

Heat shock factors (Hsfs) are important regulators of stress-response in plants. However, our understanding of Hsf genes and their responses to temperature stresses in two Pooideae cool-season grasses, Festuca arundinacea, and Lolium perenne, is limited. Here we conducted comparative transcriptome analyses of plant leaves exposed to heat or cold stress for 10 h. Approximately, 30% and 25% of the genes expressed in the two species showed significant changes under heat and cold stress, respectively, including subsets of Hsfs and their target genes. We uncovered 74 Hsfs in F. arundinacea and 52 Hsfs in L. perenne, and categorized these genes into three subfamilies, HsfA, HsfB, and HsfC based on protein sequence homology to known Hsf members in model organisms. The Hsfs showed a strong response to heat and/or cold stress. The expression of HsfAs was elevated under heat stress, especially in class HsfA2, which exhibited the most dramatic responses. HsfBs were upregulated by the both temperature conditions, and HsfCs mainly showed an increase in expression under cold stress. The target genes of Hsfs, such as heat shock protein (HSP), ascorbate peroxidase (APX), inositol-3-phosphate synthase (IPS), and galactinol synthase (GOLS1), showed strong and unique responses to different stressors. We comprehensively detected Hsfs and their target genes in F. arundinacea and L. perenne, providing a foundation for future gene function studies and genetic engineering to improve stress tolerance in grasses and other crops.

Transcriptome analysis of secondary cell wall development in Medicago truncatula.

BackgroundLegumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening in Arabidopsis, but such transcriptome data is lacking in legumes.ResultsA systematic microarray assay and high through-put real time PCR analysis of secondary cell wall development were performed along stem maturation in Medicago truncatula. More than 11,000 genes were differentially expressed during stem maturation, and were categorized into 10 expression clusters. Among these, 279 transcription factor genes were correlated with lignin/cellulose biosynthesis, therefore representing putative regulators of secondary wall development. The b-ZIP, NAC, WRKY, C2H2 zinc finger (ZF), homeobox, and HSF gene families were over-represented. Gene co-expression network analysis was employed to identify transcription factors that may regulate the biosynthesis of lignin, cellulose and hemicellulose. As a complementary approach to microarray, real-time PCR analysis was used to characterize the expression of 1,045 transcription factors in the stem samples, and 64 of these were upregulated more than 5-fold during stem maturation. Reverse genetics characterization of a cellulose synthase gene in cluster 10 confirmed its function in xylem development.ConclusionsThis study provides a useful transcriptome and expression resource for understanding cell wall development, which is pivotal to enhance biomass production in legumes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2330-6) contains supplementary material, which is available to authorized users.

Exposure time-dependent thermal effects of radiofrequency electromagnetic field exposure on the whole body of rats.

We investigated the thermal effects of radiofrequency electromagnetic fields (RF-EMFs) on the variation in core temperature and gene expression of some stress markers in rats. Sprague-Dawley rats were exposed to 2.14 GHz wideband code division multiple access (W-CDMA) RF signals at a whole-body averaged specific absorption rate (WBA-SAR) of 4 W/kg, which causes behavioral disruption in laboratory animals, and 0.4 W/kg, which is the limit for the occupational exposure set by the International Commission on Non-Ionizing Radiation Protection guideline. It is important to understand the possible in vivo effects derived from RF-EMF exposures at these intensities. Because of inadequate data on real-time core temperature analyses using free-moving animal and the association between stress and thermal effects of RF-EMF exposure, we analyzed the core body temperature under nonanesthetic condition during RF-EMF exposure. The results revealed that the core temperature increased by approximately 1.5°C compared with the baseline and reached a plateau till the end of RF-EMF exposure. Furthermore, we analyzed the gene expression of heat-shock proteins (Hsp) and heat-shock transcription factors (Hsf) family after RF-EMF exposure. At WBA-SAR of 4 W/kg, some Hsp and Hsf gene expression levels were significantly upregulated in the cerebral cortex and cerebellum following exposure for 6 hr/day but were not upregulated after exposure for 3 hr/day. On the other hand, there was no significant change in the core temperature and gene expression at WBA-SAR of 0.4 W/kg. Thus, 2.14-GHz RF-EMF exposure at WBA-SAR of 4 W/kg induced increases in the core temperature and upregulation of some stress markers, particularly in the cerebellum.

Identification and expression analysis of heat shock transcription factors in the wild Chinese grapevine (Vitis pseudoreticulata)

Heat shock transcription factors (Hsfs) are known to play pivotal roles in the adaptation of plants to heat stress and other stress stimuli. While grapevine (Vitis vinifera L.) is one of the most important fruit crops worldwide, little is known about the Hsf family in Vitis spp. Here, we identified nineteen putative Hsf genes (VviHsfs) in Vitis spp based on the 12 × grape genome (V. vinifera L.). Phylogenetic analysis revealed three classes of grape Hsf genes (classes A, B, and C). Additional comparisons between grape and Arabidopsis thaliana demonstrated that several VviHsfs genes occurred in corresponding syntenic blocks of Arabidopsis. Moreover, we examined the expression profiles of the homologs of the VviHsfs genes (VpHsfs) in the wild Chinese Vitis pseudoreticulata accession Baihe-35-1, which is tolerant to various environmental stresses. Among the nineteen VpHsfs, ten VpHsfs displayed lower transcript levels under non-stress conditions and marked up-regulation during heat stress treatment; several VpHsfs also displayed altered expression levels in response to cold, salt, and hormone treatments, suggesting their versatile roles in response to stress stimuli. In addition, eight VpHsf-GFP fusion proteins showed differential subcellular localization in V. pseudoreticulata mesophyll protoplasts. Taken together, our data may provide an important reference for further studies of Hsf genes in Vitis spp.

The heat shock factor gene family in Salix suchowensis: a genome-wide survey and expression profiling during development and abiotic stresses.

Heat shock transcription factors (Hsfs), which act as important transcriptional regulatory proteins, play crucial roles in plant developmental processes, and stress responses. Recently, the genome of the shrub willow Salix suchowensis was fully sequenced. In this study, a total of 27 non-redundant Hsf genes were identified from the S. suchowensis genome. Phylogenetic analysis revealed that the members of the SsuHsf family can be divided into three groups (class A, B, and C) based on their structural characteristics. Promoter analysis indicated that the SsuHsfs promoters included various cis-acting elements related to hormone and/or stress responses. Furthermore, the expression profiles of 27 SsuHsfs were analyzed in different tissues and under various stresses (heat, drought, salt, and ABA treatment) using RT-PCR. The results demonstrated that the SsuHsfs were involved in abiotic stress responses. Our results contribute to a better understanding of the complexity of the SsuHsf gene family, and will facilitate functional characterization in future studies.

Identification, isolation, and expression analysis of heat shock transcription factors in the diploid woodland strawberry Fragaria vesca.

Heat shock transcription factors (Hsfs) are known to play dominant roles in plant responses to heat, as well as other abiotic or biotic stress stimuli. While the strawberry is an economically important fruit plant, little is known about the Hsf family in the strawberry. To explore the functions of strawberry Hsfs in abiotic and biotic stress responses, this study identified 17 Hsf genes (FvHsfs) in a wild diploid woodland strawberry (Fragaria vesca, 2n = 2x = 14) and isolated 14 of these genes. Phylogenetic analysis divided the strawberry FvHsfs genes into three main groups. The evolutionary and structural analyses revealed that the FvHsf family is conserved. The promoter sequences of the FvHsf genes contain upstream regulatory elements corresponding to different stress stimuli. In addition, 14 FvHsf-GFP fusion proteins showed differential subcellular localization in Arabidopsis mesophyll protoplasts. Furthermore, we examined the expression of the 17 FvHsf genes in wild diploid woodland strawberries under various conditions, including abiotic stresses (heat, cold, drought, and salt), biotic stress (powdery mildew infection), and hormone treatments (abscisic acid, ethephon, methyl jasmonate, and salicylic acid). Fifteen of the seventeen FvHsf genes exhibited distinct changes on the transcriptional level during heat treatment. Of these 15 FvHsfs, 8 FvHsfs also exhibited distinct responses to other stimuli on the transcriptional level, indicating versatile roles in the response to abiotic and biotic stresses. Taken together, the present work may provide the basis for further studies to dissect FvHsf function in response to stress stimuli.

Molecular characterization and expression of HSP70, HSF and HSBP genes in Octopus vulgaris during thermal stress

Temperature is an important environmental factor that affects the growth and survival of Octopus vulgaris, the common octopus. To understand the protective mechanism that O. vulgaris exhibits under heat stress, we used rapid amplification of cDNA ends (RACE) to obtain full-length sequences of three heat stress response related genes: (1) the heat shock protein 70 (OvHSP70), (2) the heat shock transcription factor (OvHSF), and (3) the heat shock factor-binding protein (OvHSBP) of O. vulgaris. The OvHSP70, OvHSF, and OvHSBP proteins contained 2 222 bp, 2 264 bp, 841 bp that encoded for 635, 458 and 90 amino acids, respectively. The results of multiple sequence alignment showed that the amino acid sequences of OvHSP70 were highly conserved with respect to other species. Similarly, the DNA binding domain, the trimerization domain of OvHSF, and the coiled coil region of OvHSBP also had highly conserved regions. The real-time polymerase chain reaction (PCR) results indicated that OvHSP70 was temperature-dependent and time-dependent, showing a positive response to heat stress. On exposure to 28°C and to 30°C, the mRNA expression levels of OvHSF and OvHSBP were higher than those in the control group at 24°C. The mRNA expression of OvHSBP significantly increased with heat treatment at 26°C, while the mRNA expression of OvHSF decreased. The experimental results indicated that the expression of OvHSP70, OvHSF and OvHSBP were all sensitive to heat stress, which suggests that these three genes may play an important role for O. vulgaris in responding to environmental stress. Thus, this study sets a theoretical foundation for further in-depth studies on the molecular protective mechanisms of the heat response in O. vulgaris.

Genome-wide analysis, expression profile of heat shock factor gene family (CaHsfs) and characterisation of CaHsfA2 in pepper (Capsicum annuum L.).

BackgroundHeat shock factors (Hsfs) play crucial roles in plant developmental and defence processes. The production and quality of pepper (Capsicum annuum L.), an economically important vegetable crop, are severely reduced by adverse environmental stress conditions, such as heat, salt and osmotic stress. Although the pepper genome has been fully sequenced, the characterization of the Hsf gene family under abiotic stress conditions remains incomplete.ResultsA total of 25 CaHsf members were identified in the pepper genome by bioinformatics analysis and PCR assays. They were grouped into three classes, CaHsfA, B and C, based on highly conserved Hsf domains, were distributed over 11 of 12 chromosomes, with none found on chromosome 11, and all of them, except CaHsfA5, formed a protein–protein interaction network. According to the RNA-seq data of pepper cultivar CM334, most CaHsf members were expressed in at least one tissue among root, stem, leaf, pericarp and placenta. Quantitative real-time PCR assays showed that all of the CaHsfs responded to heat stress (40 °C for 2 h), except CaHsfC1 in thermotolerant line R9 leaves, and that the expression patterns were different from those in thermosensitive line B6. Many CaHsfs were also regulated by salt and osmotic stresses, as well as exogenous Ca2+, putrescine, abscisic acid and methyl jasmonate. Additionally, CaHsfA2 was located in the nucleus and had transcriptional activity, consistent with the typical features of Hsfs. Time-course expression profiling of CaHsfA2 in response to heat stress revealed differences in its expression level and pattern between the pepper thermosensitive line B6 and thermotolerant line R9.ConclusionsTwenty-five Hsf genes were identified in the pepper genome and most of them responded to heat, salt, osmotic stress, and exogenous substances, which provided potential clues for further analyses of CaHsfs functions in various kinds of abiotic stresses and of corresponding signal transduction pathways in pepper.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0512-7) contains supplementary material, which is available to authorized users.

Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses.

BackgroundHeat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear.ResultsHere, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.ConclusionsThe comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1398-3) contains supplementary material, which is available to authorized users.

Heat shock transcription factors expression during fruit development and under hot air stress in Ponkan (Citrus reticulata Blanco cv. Ponkan) fruit

Heat shock transcription factors (Hsfs) play a role in plant responses to stress. Citrus is an economically important fruit whose genome has been fully sequenced. So far, no detailed characterization of the Hsf gene family is available for citrus. A genome-wide analysis was carried out in Citrus clementina to identify Hsf genes, named CcHsfs. Eighteen CcHsfs were identified and classified into three main clades (clades A, B and C) according to the structural characteristics and the phylogenetic comparison with Arabidopsis and tomato. MEME motif analysis highlighted the conserved DBD and HR-A/B domains, which were similar to Hsf protein structures in other species. Gene expression analysis in Ponkan (Citrus reticulata Blanco cv. Ponkan) fruit identified 14 Hsf genes, named CrHsf, as important candidates for a role in fruit development and ripening, and showed seven genes to be expressed in response to hot air stress. CrHsfB2a and CrHsfB5 were considered to be important regulators of citrate content and showed variation in both developmentally-related and hot air-triggered citrate degradation processes. In summary, the data obtained from this investigation provides the basis for further study to dissect Hsf function during fruit development as well as in response to heat stress and also emphasizes the potential importance of CrHsfs in regulation of citrate metabolism in citrus fruit.

Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis).

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetable crops grown worldwide, and various methods exist for selection, propagation, and cultivation. The entire Chinese cabbage genome has been sequenced, and the heat shock transcription factor family (Hsfs) has been found to play a central role in plant growth and development and in the response to biotic and abiotic stress conditions, particularly in acquired thermotolerance. We analyzed heat tolerance mechanisms in Chinese cabbage. In this study, 30 Hsfs were identified from the Chinese cabbage genome database. The classification, phylogenetic reconstruction, chromosome distribution, conserved motifs, expression analysis, and interaction networks of the Hsfs were predicted and analyzed. Thirty BrHsfs were classified into 3 major classes (class A, B, and C) according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 8 subclasses. Distribution mapping results showed that Hsf genes were located on 10 Chinese cabbage chromosomes. The expression profile indicated that Hsfs play differential roles in 5 organs in Chinese cabbage, and likely participate in the development of underground parts and regulation of reproductive growth. An orthologous gene interaction network was constructed, and included MBF1C, ROF1, TBP2, CDC2, and HSP70 5 genes, which are closely related to heat stress. Our results contribute to the understanding of the complexity of Hsfs in Chinese cabbage and provide a basis for further functional gene research.

Genome-wide identification and characterization of heat shock factor genes from pigeonpea (<i>Cajanus cajan</i>)

Genome-wide analysis of heat shock factor ( H s f ) g e n e s was ca r r ied out in p i g e on p e a ( Cajanus cajan ) in order to understand their structure and function. A tot a l of 23 Hsfs w e r e p re dict e d using FGENESH a nd l a b e led a s C c Hsf . Out of the 2 3 g e n e s, 14 unique sequences w e r e s e l ec t e d a nd c h a r a c t er i z e d for t h e ir p re sumed str u c tur e s s u c h a s p r ote i n doma in a nd mo t if o r g a ni z a t i on. The p h y l o g e n e t ic r e lationships a nd e x p re ss i on p r o f i l ing of C cHsf g e n e s under heat-stress w as studied. Phylogenetic analysis showed that CcH s f g e n e s w e r e di s t r i b ut e d i n to eight g r o u p s. I n th i s st u d y , c lasses A, B, and C were f u r ther subdivi d e d in t o subcl a sses such a s A1, A2, A 3, A4, A5, A6, A8, A 9, B1, B 2, B 3 , B 4 and C1. E x p r e ss i on p r o f ili n g of all 14 genes w a s ca r r i e d out by s e m i - q u a nt i ta t ive P CR, among which C c H sfA - 1d and C c HsfA - 2 w e r e observed to be highly upregulated duri n g heat-stress . R e l a t i ve qu a nt i f i ca t i on with qRT- P C R showed that C cHsfA - 1d i s up r e g ul a t e d 2 - 6 h r s af t e r heat-stress indicating its significant role as an early response factor. Our study provides a glimpse of the Hsf gene family in pigeonpea and this information can be utilized to gain more insight into the heat-response mechanism in pigeonpea. Abbreviations: AHA - Aromatic/ Hydrophobic /Acidic; Hsf - Heat Shock Factors; IRRK- Isoleucine, Arginine, Arginine, Lysine; NLS - Nuclear Localization Signal; NES - Nuclear Export Signal

Cloning and sequence analysis of hsf, an outer membrane protein gene of Pasteurella multocida serotype B:2

Aim: The present study was undertaken to clone, sequence and analyze the hsf, an outer membrane protein gene of Pasteurella multocida serotype B:2 Materials and Methods: hsf gene was amplified from genomic DNA of P. multocida. Polymerase chain reaction (PCR) product was cloned in pET-32a vector and was characterized. hsf gene was sequenced, analyzed and phylogenetic tree was constructed taking sequences of other strains. Results: Amplicon size was found to be 785 bp. Recombinant got characterized through colony PCR and restriction enzyme analysis. Conclusion: hsf gene of P. multocida serotype B is similar to serotype A, but different from serotype D. Further work is needed to evaluate role of Hsf protein in protection studies and to study the antigenic properties of this recombinant protein as a candidate for vaccine.

Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses.

BackgroundHigh temperature affects organism growth and metabolic activity. Heat shock transcription factors (Hsfs) are key regulators in heat shock response in eukaryotes and prokaryotes. Under high temperature conditions, Hsfs activate heat shock proteins (Hsps) by combining with heat stress elements (HSEs) in their promoters, leading to defense of heat stress. Since the first plant Hsf gene was identified in tomato, several plant Hsf family genes have been thoroughly characterized. Although soybean (Glycine max), an important oilseed crops, genome sequences have been available, the Hsf family genes in soybean have not been characterized accurately.ResultWe analyzed the Hsf genetic structures and protein function domains using the GSDS, Pfam, SMART, PredictNLS, and NetNES online tools. The genome scanning of dicots (soybean and Arabidopsis) and monocots (rice and maize) revealed that the whole-genome replication occurred twice in soybean evolution. The plant Hsfs were classified into 3 classes and 16 subclasses according to protein structure domains. The A8 and B3 subclasses existed only in dicots and the A9 and C2 occurred only in monocots. Thirty eight soybean Hsfs were systematically identified and grouped into 3 classes and 12 subclasses, and located on 15 soybean chromosomes. The promoter regions of the soybean Hsfs contained cis-elements that likely participate in drought, low temperature, and ABA stress responses. There were large differences among Hsfs based on transcriptional levels under the stress conditions. The transcriptional levels of the A1 and A2 subclass genes were extraordinarily high. In addition, differences in the expression levels occurred for each gene in the different organs and at the different developmental stages. Several genes were chosen to determine their subcellular localizations and functions. The subcellular localization results revealed that GmHsf-04, GmHsf-33, and GmHsf-34 were located in the nucleus. Overexpression of the GmHsf-34 gene improved the tolerances to drought and heat stresses in Arabidopsis plants.ConclusionsThis present investigation of the quantity, structural features, expression characteristics, subcellular localizations, and functional roles provides a scientific basis for further research on soybean Hsf functions.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1009) contains supplementary material, which is available to authorized users.

Genome-wide cloning, identification, classification and functional analysis of cotton heat shock transcription factors in cotton (Gossypium hirsutum).

BackgroundHeat shock transcriptional factors (Hsfs) play important roles in the processes of biotic and abiotic stresses as well as in plant development. Cotton (Gossypium hirsutum, 2n = 4x = (AD)2 = 52) is an important crop for natural fiber production. Due to continuous high temperature and intermittent drought, heat stress is becoming a handicap to improve cotton yield and lint quality. Recently, the related wild diploid species Gossypium raimondii genome (2n = 2x = (D5)2 = 26) has been fully sequenced. In order to analyze the functions of different Hsfs at the genome-wide level, detailed characterization and analysis of the Hsf gene family in G. hirsutum is indispensable.ResultsEST assembly and genome-wide analyses were applied to clone and identify heat shock transcription factor (Hsf) genes in Upland cotton (GhHsf). Forty GhHsf genes were cloned, identified and classified into three main classes (A, B and C) according to the characteristics of their domains. Analysis of gene duplications showed that GhHsfs have occurred more frequently than reported in plant genomes such as Arabidopsis and Populus. Quantitative real-time PCR (qRT-PCR) showed that all GhHsf transcripts are expressed in most cotton plant tissues including roots, stems, leaves and developing fibers, and abundantly in developing ovules. Three expression patterns were confirmed in GhHsfs when cotton plants were exposed to high temperature for 1 h. GhHsf39 exhibited the most immediate response to heat shock. Comparative analysis of Hsfs expression differences between the wild-type and fiberless mutant suggested that Hsfs are involved in fiber development.ConclusionsComparative genome analysis showed that Upland cotton D-subgenome contains 40 Hsf members, and that the whole genome of Upland cotton contains more than 80 Hsf genes due to genome duplication. The expression patterns in different tissues in response to heat shock showed that GhHsfs are important for heat stress as well as fiber development. These results provide an improved understanding of the roles of the Hsf gene family during stress responses and fiber development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-961) contains supplementary material, which is available to authorized users.

Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes.

Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species.