Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses
© Zhang et al.; licensee BioMed Central. 2015
Received: 4 October 2014
Accepted: 24 February 2015
Published: 14 March 2015
Heat 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.
Here, 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.
The 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.
During their growth, plants are subjected not only to abiotic stresses, such as irradiation, temperature, salinity, and drought, but also biotic stresses, such as herbivore and pathogen attacks. These stress factors can simultaneously act on the plants causing cell injury and producing secondary stresses [1,2]. As sessile organisms, plants cannot move to avoid these stresses, and thus have developed mechanisms, such as morphological adaptation, to tolerate these stresses .
Along with other stresses, heat stress can trigger the expression of certain genes that were not expressed under “normal” conditions [4-6]. Heat shock proteins (Hsps) accumulate when the expression of their genes is triggered by heat, as well as other stresses [7-9]. Hsps are molecular chaperones that regulate the folding, localization, accumulation, and degradation of protein molecules in both plant and animal species . The expression of Hsps is controlled and regulated by specific types of transcription factors called heat shock factors (Hsfs), which normally exist as inactive proteins .
Plant Hsps are classified into five families based on their approximate molecular weights: small Hsp (sHsp), Hsp60, Hsp70, Hsp90, and Hsp100. Genes encoding Hsfs and Hsps have been well characterized in some model plants, such as Arabidopsis and rice [12,13]. In Arabidopsis, 21, 27, 18, 18, 7, and 4 genes have been identified as Hsf, sHsp, Hsp60, Hsp70, Hsp90, and Hsp100 family members, respectively [13-19].
To date, various stress responses and functions of Hsf and Hsp members have been reported. In Arabidopsis, HsfA1a, HsfA1b, and HsfA1d act as the main positive regulators of heat shock response . Arabidopsis HsfA2 was significantly increased under high light and heat stress or by H2O2 treatment. It is the key regulator in the induction of the defense system under several types of environmental stresses [21,22]. The cytosolic class I sHsp in Rosa chinensis, RcHsp17.8, was induced by heat, cold, salt, drought, osmotic, and oxidative stresses . A plastid nucleoid-localized sHsp (Hsp21) interacts with the plastid nucleoid protein pTAC5 and is essential for chloroplast development in Arabidopsis under heat stress . Hsp60 proteins as chaperones participate in the folding and aggregation of many proteins that are transported to organelles, such as chloroplasts and mitochondria [25,26]. Arabidopsis hsp60 mutants showed defects in chloroplast, embryo, and seedling development and also increased cell death [27,28]. Unlike other family members that are mainly expressed when the organism is subjected to environmental assaults, Hsp70s play essential functions in facilitating refolding and proteolytic degradation of abnormal proteins under both normal and stress conditions [29,30]. Hsp100 proteins belong to the Caseinolytic protease (Clp) family, which forms an ATP-dependent protease complex that is able to hydrolyze casein [19,31-33]. Tomatoes that have an antisense suppression of Hsp100/ClpB are more heat sensitive . Moreover, Lee et al.  noted that Arabidopsis mutant plants containing a chloroplast-localized Hsp100/ClpB-p knockout turned yellow after heat treatment. Hsps were not only transcriptionally regulated by Hsfs, but could also regulate the activity of Hsfs through a feedback loop caused by their physical interaction. In tomato, Hsp70 and Hsp90 regulate the Hsfs’ function by directly interacting with Hsfs. Hsp70 represses the activity of HsfA1 and HsfB1, while the DNA binding activity of HsfB1 is stimulated by Hsp90 in tomato . Above all, Hsfs and Hsps play crucial roles in plant development and various stress tolerances.
As perennial species, poplars undergo seasonal variations and various environmental stresses frequently. The completion of the Populus trichocarpa genome sequencing project in 2006 makes it an ideal genetic model for studying tree development and physiology . To date, 28 Populus Hsfs have been reported based on the V2.2 P. trichocarpa genome database . In our previous study, we have reported the subcellular localization and expression, under various abiotic stresses, of 10 Hsp90 genes identified from the V3.0 P. trichocarpa genome database . However, the other Hsp families in poplar remain unclear, and little is known about the transcriptional regulatory relationships between Populus Hsfs and Hsps. Here, we provide a comprehensive analysis of the gene organization and expression of Populus Hsfs and other Hsp genes, including sHsp, Hsp60, Hsp70 and Hsp100, under different abiotic stresses. A complex transcriptional regulatory network between Populus Hsfs and Hsps has been generated based on their transcription patterns in poplar.
Identification and phylogenetic analysis of the Hsf and Hsp gene families in poplar
Numbers of Hsf and Hsp genes in Arabidopsis , Populus and rice
Structure of Hsf and Hsp genes and conserved motifs of Hsf and Hsp proteins in poplar
To gain further insights into the structural diversity of Hsf and Hsp genes in P. trichocarpa, we compared the exon/intron organization in the coding sequences between individual Hsf and Hsp genes of P. trichocarpa and Arabidopsis (Figures 1 and 2, middle panel). Most closely related members in the same Hsf or Hsp subfamilies shared similar intron numbers or exon length. In the PtHsp70 family, cytosolic Hsp70s have zero or one intron, ER-localized BIPs have six introns, mitochondrion-localized mtHsc70s have five introns and chloroplast-localized cpHsc70s have seven introns, while truncated Hsp70ts have no introns (Figure 2B). Interestingly, two cytosol-localized Hsp60 members, PtCpn60-8.1 and PtCpn60-8.2, have no introns in their coding regions while the other P. trichocarpa Hsp60s contain several introns (8–16) (Figure 2A). We then compared the intron phases with respect to the codons. The intron phases were remarkably well conserved within the same subfamilies in the detected PtHsf and PtHsp families.
We further detected the exon/intron structure of 42 paralogous pairs of the PtHsf and PtHsp genes (10, 9, 12, 9, and 2 pairs in P. trichocarpa Hsf, sHsp, Hsp60, Hsp70, and Hsp100 gene families, respectively, Additional file 3: Table S3). Although 36 paralogous pairs showed conserved intron numbers and gene lengths, one Hsf gene pair (PtHsfA8a/PtHsfA8b), four sHsp pairs (Pt17.8I-sHsp/Pt19.0I-sHsp, Pt12.2I-sHsp/Pt13.1I-sHsp, Pt14.5I-sHsp/Pt17.9I-sHsp, and Pt16.9VI-sHsp/Pt25.8VI-sHspI), and one Hsp60 pair (PtCpn60-a3/PtCpn60-a4) exhibited certain degrees of variation (Figures 1 and 2).
We then used the Multiple Expectation Maximization for Motif Elicitation (MEME)  to predict the conserved motifs shared among the related proteins within these families. In each family, 20 putative motifs were identified. The details of these motifs are listed in Additional file 4: Tables S4; Additional file 5: Tables S5; Additional file 6: Tables S6; Additional file 7: Tables S7 and Additional file 8: Tables S8. Most of the closely related members in the phylogenetic tree shared common motif compositions with each other (Figures 1 and 2, right panel).
Chromosomal location and duplication of Hsf and Hsp genes in poplar
The genome of P. trichocarpa has experienced at least two whole genome duplication (WGD) events, followed by a series of chromosomal reorganizations involving reciprocal tandem/terminal fusions and translocations . Approximately 84.7% (100 of 118) Hsf and Hsp genes were located in the replicated region, while 44 genes lacked copies on the corresponding duplicated blocks. A chromosome region containing two or more genes within 200 kb can be defined as a gene cluster . The gene clusters were distributed unevenly among Hsf and Hsp gene families. The sHsp, Hsp60, Hsp70, and Hsp100 families contain five, one, three, and one clusters, respectively (Figure 3 and Additional file 3: Table S3). The smallest tandem duplication clusters consisted of only two genes and the largest cluster, in the Hsp70 family, had five genes. Interestingly, none of the Hsf genes were represented in tandem clusters.
Among the 42 paralogous pairs of the Populus Hsf and Hsp families, 66.7% gene pairs (28 of 42 pairs) were generated by whole genome duplication and 19% (8 of 42 pairs) by tandem duplication (Additional file 3: Table S3). To verify whether Darwinian positive selection was involved in the Hsf and Hsp gene divergence after duplication, the nonsynonymous (Ka) versus synonymous (Ks) substitution rate ratios were calculated for the 42 paralogous pairs . A Ka/Ks ratio significantly lower than 0.5 suggests a purifying selection for both duplicates . The summary of Ka/Ks for the 42 Hsf and Hsp gene paralogous pairs is shown in Additional file 3: Table S3.
Expression patterns of Populus Hsf and Hsp genes
Publicly available Expressed Sequence Tags (ESTs) provide a useful tool to survey gene expression profiles using a digital northern blot . We conducted a preliminary expression analysis of Hsf and Hsp genes by counting the frequencies of ESTs obtained from different tissues and under various growth conditions in different Populus cDNA libraries (Additional file 9: Figure S1). A complete search of the digital expression profiles from PopGenIE (http://popgenie.org/)  yielded 77 Populus Hsf and Hsp genes in the cDNA libraries. The frequencies of these ESTs were relatively low, and most Hsf and Hsp genes were represented by only one EST in the cDNA libraries. Nevertheless, these expression profiles suggested that most of the PtHsf and PtHsp genes had broad expression patterns across different tissues.
Confirmation of Populus Hsf and Hsp gene expression levels by qRT-PCR
Populus Hsfs transcriptionally regulate the expression of different sets of Hsp genes
Duplications play major roles in the diversification of the Populus Hsf and Hsp gene families
Gene duplications represent the major mechanism for gene family expansion through either WGD or tandem duplications during evolution . Like most gene families, Hsf and Hsp appear to have undergone complicated evolutionary processes [11,13]. The abundance of Hsf and Hsp genes in P. trichocarpa may be the result of multiple gene duplication events, represented by a whole genome duplication following multiple segmental and tandem duplications . However, 44 of the 118 Hsf and Hsp genes lack copies in the corresponding duplicated blocks in the genome of P. trichocarpa (Figure 3). This suggested that dynamic rearrangements or segmental losses may have occurred following the segmental duplication. In plants, the exon/intron diversification of gene family members has played an important role in the evolution of multiple gene families . Only 6 of 42 paralogous pairs of Hsf and Hsp genes exhibited certain degrees of variation in P. trichocarpa (Figures 1 and 2). The differences might be derived from the single intron addition or subtraction events during the structural evolution of the Hsf or Hsp genes.
In P. trichocarpa, ~33.4% of predicted genes originated from whole genome duplication and 15.6% from tandem duplications . Our study indicates that the Hsf and Hsp gene families possess a higher whole genome duplication ratio (47.5%, 56 of 118 genes) and lower tandem duplication ratio (13.5%, 16 of 118 genes) in P. trichocarpa, which are dramatically different from the averages. This high retention rate of whole genome duplications and low retention rate of tandem duplications are also inconsistent with the previous studies on other families [52-56]. The low Ka/Ks ratio indicates that all gene pairs, except for two (PtHsf-A6a/PtHsf-A6b and Pt19.9CP-sHsp/Pt26.2CP-sHsp), might have evolved under the influence of purifying selection.
Populus Hsf and Hsp genes are vital players in plant development and in response to abiotic stresses
Plant Hsf and Hsp genes are implicated in a variety of biological processes [6,12,13,57]. The study on the Populus Hsf and Hsp gene families showed that these genes were differentially expressed in various analyzed tissues. Most Hsp60 and Hsp70 genes showed high expression levels in the upper stem (internode 2 and 3), indicating their putative roles in the primary stem growth of Populus (Figure 4). Our qRT-PCR results showed that all selected Populus Hsf and Hsp genes exhibited diverse expression levels in the five examined tissues (Figure 7), indicating that these Hsf and Hsp genes often participate in plant development. It is worth noting that the expression of Pt18.3I-sHsp was obviously higher in stem than in leaves and roots, indicating that it may have potential roles in stem development.
Hsfs, as transcriptional activators of Hsps, cooperated with Hsps to form a network responding to various stresses. They play a broad role in the tolerance to multiple environmental stress treatments apart from heat stress [6,35]. The response of Hsfs and Hsps to heat and other abiotic stresses overlaps extensively, indicating that Hsfs and Hsps are important in the cross-talk of multiple environmental stress response pathways [12,13]. Interestingly, under drought stress, most members of the Populus Hsf, Hsp60, Hsp70, and Hsp100 families were not regulated, while only members of the sHsp family were significantly up-regulated (especially Populus C-I sHsp genes) in the hybrid poplar (Figure 6). The specific response to drought stress of Populus C-I sHsp might be related to the member expansion of the Populus C-I sHsp subfamily, but the mechanisms need to be further examined. The expression of Hsps could be down-regulated to their initial levels when plants recovered from high temperatures . However, the Populus sHsps remained at a high expression level 2 h after the plants’ recovery from 37°C (Figure 8). This indicated that Populus sHsps play an irreplaceable role compared with other Hsps (Hsp60, Hsp70, and Hsp100 genes) in response to heat and drought stress.
Complex transcriptional regulatory network between Populus Hsfs and Hsps
Several PtHsfs, including PtHsfA2, PtHsfA6a, and PtHsfB2a, showed high coexpression levels with PtHsps, indicating that these PtHsfs might be the key regulators among the numerous PtHsfs. Nishizawa et al.  showed that Arabidopsis HsfA2 is a key regulator in the induction of the defense system under several types of environmental stresses. In our study, the overexpression of PtHsfA2 induced the expression of 11 of 12 Hsps (Figure 10A), indicating that PtHsfA2 is also an activator of the downstream Hsps. The expression of PtHsfA2 was induced under nitrogen deprivation, drought, and heat stresses (Figures 5 and 6), implying that PtHsfA2 is a key regulator under various stresses in poplars. A set of PtHsps could be simultaneously induced by the transient overexpression of PtHsfA6a, PtHsfB2a, or PtHsfB2b, indicating that these Hsps were generally regulated by the three Hsfs (Figure 10B, D, and E). Recently, Ikeda et al.  reported that HsfB1 and HspB2b suppress the general heat shock response under non-heat-stress conditions and in the attenuating period. However, HsfB1 and HsfB2b appear to be necessary for the expression of heat stress-inducible Hsps under heat stress conditions, which is necessary for acquired thermotolerance. In this study, most detected Hsps could not be activated by the overexpression of PtHsfB1 (Figure 10C), while they could be activated by overexpressing PtHsfB2a or PtHsfB2b (Figure 10D and E). These results indicated that PtHsfB1 is not a direct activator of these Hsps. Under heat stress, PtHsfB1 was also induced dramatically, indicating that although PtHsfB1 could not regulate the downstream Hsps directly, it might be involved in the heat stress response in some indirect manner. Tomato (Solanum lycopersicum) HsfB proteins may be coactivators of HsfAs . In Arabidopsis, the heat stress response is finely regulated by activation and repression activities of Hsfs . The expression of a particular Populus Hsfs can induce the expression of a different set of Hsps, suggesting a complex transcriptional regulatory network between Populus Hsfs and Hsps. Additionally, the Hsps might also be regulated by both the activation and the repression mechanisms during the heat stress response in Populus. However, the precise regulatory mechanisms among Hsfs and Hsps of woody plants during development and stress responses require further investigation.
In this study, 118 members of Populus Hsf and Hsp (including sHsp, Hsp60, Hsp70 and Hsp100) gene families were identified. A comprehensive analysis of these genes, including phylogeny, chromosomal location, gene structure, expression profiling and heat stress responses, was performed. In the phylogenetic tree, the majority of subfamilies contained members from both Populus and Arabidopsis, which suggested that the functions of most of Hsfs and Hsps were conserved during evolution. In addition, a gene duplication analysis revealed that the class I cytosolic sHsp subfamily had expanded more than that of Arabidopsis, showing both the conservation and divergence of gene families during the evolution. An extensive expression analysis indicated that Populus Hsf and Hsp genes may play various conserved roles in different biological processes in plants. Moreover, the coexpression network and transient overexpression of PtHsfs imply that there is a complex transcriptional regulatory network between Populus Hsfs and Hsps. The present study established a solid foundation for functional research on the Populus Hsf and Hsp gene families and has improved our understanding of the functions of Hsf and Hsp genes in woody plants.
Sequence retrieval and phylogenetic reconstruction
Published Arabidopsis Hsf and Hsp sequences  were retrieved and were used as queries in BLAST searches against the Populus trichocarpa genome database (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa, release 3.0) to identify potential Populus Hsfs and Hsps. WoLF PSORT (http://psort.hgc.jp/) was used to predict their protein subcellular localizations . The isoelectric points and molecular weights were estimated using the Compute pI/Mw tool from ExPASy (http://web.expasy.org/compute_pi). The phylogenetic trees were constructed using the neighbor-joining method  in the MEGA package V5.1  with bootstrap values from 1,000 replicates indicated at each node. To predict putative orthologous genes, a reciprocal Best Blast Hit search was used. The gene names of Populus Hsfs are according to Scharf et al.  and the gene names of Populus sHsps were revised according to their molecular weights in the P. trichocarpa genome V3.0 based on Water et al. .
Chromosomal locations, gene structures, and a conserved motif analysis
The chromosomal locations of the Hsf and Hsp genes were determined using the Populus genome browser (http://www.phytozome.net/poplar). Homologous chromosome segments resulting from whole-genome duplication events were identified as described previously . The exon and intron structures were illustrated using Gene Structure Display Server (GSDS, http://gsds.cbi.pku.edu.cn)  by aligning the cDNA sequences with the corresponding genomic DNA sequences from Phytozome (http://www.phytozome.net). The conserved motifs in the encoded proteins were analyzed by MEME online program (http://meme.sdsc.edu, v4.9.0) . MEME was run locally with the following parameters: number of repetitions = any, maximum number of motifs = 20, and optimum motif width = 30 to 70 residues for Hsf, Hsp60, Hsp70 and Hsp100. Because of the short sHsp protein length, we set an optimum motif width of between 10 and 40.
Publicly available microarray data analyses and coexpression network generation
For abiotic and hormonal treatments, the Affymetrix microarray data available in the NCBI GEO database under the series accession numbers GSE26199 (heat stress), GSE17230 (drought stress), and GSE16786 were analyzed [47,66,67]. GSE16786 is composed of the following five subsets: GSE14893 (nitrogen limitation, genotype 1979), GSE14515 (nitrogen limitation, genotype 3200), GSE16783 (1 week after leaf wounding), GSE16785 (90 h after leaf wounding), and GSE16773 (methyl jasmonate-elicited suspension cell cultures). Probe sets corresponding to Populus Hsf and Hsp genes were identified using the online Probe Match tool POParray (http://aspendb.uga.edu/poparray). For genes with more than one probe sets, the median of expression values was considered. The expression data were gene-wise normalized. The data was normalized using the Gene Chip Robust Multiarray Analysis (GCRMA) algorithm followed by log transformation and average calculations. After normalization and log transformation of data for all the Populus genes present on the chip, the log signal intensity values for Populus probe set IDs corresponding to Hsf and Hsp genes were extracted for further analyses. The expression profiles were performed in MultiExperiment Viewer (MeV) v4.7.4 .
The WGCNA package  provides a robust set of R functions for constructing weighted coexpression networks. The data from the microarray data and our RNA-seq data in Figures 4, 5, 6 were used for the coexpression analysis. The similarity matrix was transformed into an adjacency matrix using a method that employs a power function. The network picture was created using Cytoscape .
Plant material and growth conditions
One-year-old P. trichocarpa and hybrid poplar (P. alba × P. glandulosa) clones (84 K) were grown in a growth chamber under long-day conditions (16 h light/8 h dark) at 23°C. Plant materials for the qRT-PCR of different tissues and under heat treatment conditions were collected from 84 K. For the heat treatment used in RNA-seq, 1-year-old seedlings of P. alba × P. glandulosa were treated at 37°C for 8 h (10:00 a.m.-18:00 p.m.) and then recovered to 23°C. During the heat treatment, three time points (0 h, 2 h, and R2 h) were selected to sample collection for RNA-seq. At each time point, the 5th internodes of seedlings under both heat treatment and control conditions were collected separately. For the heat treatment used in the qRT-PCR, the chamber was heated to 37°C for 3 h (pretreatment), returned to 23°C for 2 h, heated to 45°C for 3 h (treatment), and then allowed to recover for 2 h. Leaves from three different plants were harvested at seven selected time points during heat stress treatments. For the transient overexpression of 35S::PtHsfs, P. trichocarpa leaves were infiltrated by Agrobacterium tumefaciens. Samples were harvested, frozen immediately in liquid nitrogen, and stored at −80°C for further analysis. Three biological replicates were performed.
Plasmid construction and transient overexpression in P. trichocarpa
The coding sequences of PtHsfA2, A6a, B1, B2a, and B2b were amplified from the cDNA of P. trichocarpa, and inserted into pMDC32 to produce the 35S::PtHsfs constructs using the Gateway cloning system (Invitrogen, Carlsbad, USA). Each 35S::PtHsfs construct was introduced into the A. tumefaciens GV3101 by electroporation. A sample of 1 mL from an overnight A. tumefaciens culture was centrifuged at 6,000 × g for 1 min, the supernatant was discarded and the pellet was resuspended in infiltration media (10 mM MgCl2 and 150 μM acetosyringone) (OD600 = 0.1). Then, the A. tumefaciens was infiltrated into P. trichocarpa epidermal cells. After 3 days, the infiltrated leaf regions were collected for RNA extraction.
RNA isolation and real-time qRT-PCR
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Venlo, Netherlands) with an on-column RNase-free DNase I (Qiagen, Venlo, Netherlands) treatment to remove any contamination of genomic DNA. The first-strand cDNA synthesis was carried out with ~1 μg RNA using the SuperScript III reverse transcription kit (Invitrogen, Carlsbad, USA) and random primers according to the manufacturer’s procedure. Primers with melting temperatures of 58–60°C and amplicon lengths of 150–250 bp were designed using Primer3 software (http://frodo.wi.mit.edu/primer3/input.htm). All primer sequences are listed in Additional file 11: Table S10. Real-time qRT-PCR was conducted on a 7500 Real Time PCR System (Applied Biosystems, CA, USA) using a SYBR Premix Ex Taq™ Kit (TaKaRa, Dalian, China) according to the manufacturer’s instructions. Relative expression levels were calculated using the 2-ΔΔCt method . The PtActin and PtTubulin genes were used as internal controls.
The statistical significance of differences in measured parameters was tested using the procedures of DPS (Zhejiang University, China). Differences between the means among different tissues or gene pairs were compared using Duncan’s test and Fisher’s protected least significant difference (LSD) test at 0.05 probability levels.
This work was supported by the National High Technology Research and Development Program of China [2013AA102702] and the National Natural Science Foundation of China  to JC, the National Key Basic Research Program of China [2012CB114500] and a Collaborative Innovation Plan of Jiangsu Higher Education to ML, the China Postdoctoral Science Foundation [2014 M550104] to JZ, and the lecture and study program for outstanding scholars from home and abroad (CAFYBB2011007).
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