Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis
© Giorno et al.; licensee BioMed Central Ltd. 2012
Received: 13 June 2012
Accepted: 8 November 2012
Published: 20 November 2012
Heat shock transcriptional factors (Hsfs) play a crucial role in plant responses to biotic and abiotic stress conditions and in plant growth and development. Apple (Malus domestica Borkh) is an economically important fruit tree whose genome has been fully sequenced. So far, no detailed characterization of the Hsf gene family is available for this crop plant.
A genome-wide analysis was carried out in Malus domestica to identify heat shock transcriptional factor (Hsf) genes, named MdHsfs. Twenty five MdHsfs were identified and classified in three main groups (class A, B and C) according to the structural characteristics and to the phylogenetic comparison with Arabidopsis thaliana and Populus trichocarpa. Chromosomal duplications were analyzed and segmental duplications were shown to have occurred more frequently in the expansion of Hsf genes in the apple genome. Furthermore, MdHsfs transcripts were detected in several apple organs, and expression changes were observed by quantitative real-time PCR (qRT-PCR) analysis in developing flowers and fruits as well as in leaves, harvested from trees grown in the field and exposed to the naturally increased temperatures.
The apple genome comprises 25 full length Hsf genes. The data obtained from this investigation contribute to a better understanding of the complexity of the Hsf gene family in apple, and provide the basis for further studies to dissect Hsf function during development as well as in response to environmental stimuli.
KeywordsHsf Malus domestica Gene expression High temperature Apple fruit/ flower
Trees are sessile organisms with long lifespans that regularly experience climatic fluctuations in their native environment. Therefore, survival and reproduction is dependent upon an array of protective mechanisms that involve the activation of a wide range of transcriptional factors, and their products are considered to play a central role in response to extreme physiological conditions. There is evidence that members of the heat shock transcriptional factor (Hsf) family are important regulators in sensing and signaling of different environmental stresses. Similarly to many other transcription factors, the Hsfs have a modular structure containing signature domains structurally and functionally conserved throughout the eukaryotic kingdom. A common core structure in the Hsfs is composed of an N-terminal DNA binding domain (DBD), characterized by a central helix-turn-helix motif that specifically binds to the heat shock elements (HSE) in the target promoters, and an adjacent bipartite oligomerization domain (HR-A/B) composed of hydrophobic heptad repeats. Hsf trimerization via the formation of a triple stranded alpha-helical coiled-coil is a prerequisite for high affinity DNA binding and, subsequently, for transcriptional activity. Other Hsf functional modules include clusters of basic amino acids essential for nuclear import (NLS), leucine-rich export sequences important for nuclear export (NES), and a less conserved C-terminal activator domain (CTAD) rich in aromatic, hydrophobic and acidic amino acids, the so-called AHA motifs[2, 3].
In contrast to Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster, that each possesses only a single Hsf gene, plant genomes contain large numbers of Hsf genes, up to 52[1, 4, 5]. Based on structural characteristics and phylogenetic comparisons, plant Hsfs are grouped into classes A, B and C[2, 6]. All class A and C Hsfs have an extended HR-A/B region due to the insertion of 21 (Class A) or seven (class C) amino acid residues between A and B parts of the HR-A/B region. On the contrary, in class B Hsfs, the HR-A/B region does not contain insertions. In addition, sequence comparisons and structural analyses indicate that the combination of a AHA motif with an adjacent nuclear export signal NES represents a peculiar signature domain for many plant class A Hsfs[6, 7].
After the release of the whole genomic sequences of several plant organisms, including rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa), medicago (Medicago truncatula), tomato (Solanum lycopersicon), the Hsfs family was analyzed extensively, both to place each member in an organized nomenclature system and to provide maps of their expression[7–10].
Recently, the full genome sequence of the domesticated apple (Malus domestica Borkh) has been published. This provides a useful genomic tool to study this economically important fruit crop. As transcriptional factors, Hsfs are involved in different aspects of plant life including tolerance to biotic/abiotic stresses and developmental processes[12–14]. Therefore, this gene family represents an important group of transcriptional factors to investigate and to characterize. Genome scale analyses of the transcriptional response during development and to environmental stimuli require a precise and complete annotation of genes in order to provide reliable and exhaustive data. Therefore, the aim of this study was to annotate the full length Hsf genes in apple, and to analyze their expression profiles by quantitative real time PCR (qRT-PCR) in different organs/tissues from plants grown in the field and exposed to natural environmental conditions. The results of this work provide a foundation to better understand the functional structure and genomic organization of the Hsf gene family in apple, and will be undoubtedly useful in future gene cloning and functional studies.
Identification, classification and duplication of Hsf genes in the Malus domestica genome
List of Hsfs genes in the Malus domestica genome
Analysis of conserved domains in the apple Hsf proteins
Functional motifs of apple Hsfs
AHA (454) DIEAFLKDWDD
AHA (482) DIFWEQFLTAS
AHA (486) DIFWEQFLTAS
AHA (516) DIEAFLKDWDD
AHA1 (318) ETIWEELWSD AHA2 (360) DWGKDLQD
AHA1 (315) ETIWEELWSD AHA2 (355) DWGEDLQD
AHA1 (431) EDIWSMGFGV AHA2 (450) ELWGNPVNY AHA3(470) LDVWDIGPLQ AHA4 (486) IDKWPAHDS
AHA1 (500) EDIWSMNFDV AHA2 (518) NELWGNPXNY AHA3 (539) LDVWDIDPLQ AHA4 (555) INKWPAHES
AHA1 (252) LTFWEDTIHD AHA2 (356) DGFWEQFLTE
AHA (431) DVFWEQFLTE
AHA (431) DVFWEQFLTE
AHA (308) DGAWEQFLLA
AHA (306) DGAWEQLLLG
(179) KRKCK (223) RKRKR
( 204) KKRR
Motif sequences identified by MEME tools in apple Hsfs
Best possible match
Phylogenetic analysis of apple Hsf proteins
In silico expression analyses of MdHsf genes
Digital expression of MdoHsf genes
Tissue and organ type (DFCI Apple Gene Index)
Of the group A1, MdHsfA1a and MdHsfA1d, were the most represented as their expression was detected in leaf, flower, fruit, shoot and phloem. Similarly, MdHsfB1a and MdHsfB1b of B class were expressed in several apple tissues. Interestingly, MdHsfA9b was the only Hsf specific for seed, whereas MdHsfA9a was found in leaf. Furthermore, expression restricted to only a single tissue type was observed also for other members of the MdHsf family; all A3-type MdHsfs were expressed in shoot and both members of the class C were found in root. In addition, the analysis of digital data showed that duplicated genes located on different chromosomes had identical expression patterns (e.g. MdHsfB4a and MdHsfB4b, MdHsfC1a and MdHsfC1b).
Expression analysis of MdHsf genes in apple organs under natural environmental conditions
To further characterize the expression of Hsf family genes in apple, the quantitative real-time PCR analysis was extended to leaf samples harvested from field-grown trees exposed to naturally increased temperatures. Leaf samples were taken during the summer period, at two different temperature ranges: at 26°C/12°C (day/night; max/min) on 30th July 2011, which were used as reference, and at high temperature average of 32°C/17°C (day/night; max/min) on the 21st August 2011 (Additional file1: Figure S1).
In plants, members of the Hsf family have been described as key regulators in molecular and cellular responses to stress conditions[1, 7]. Furthermore, data from tomato and Arabidopsis have shown that the Hsfs are important components involved in developmental signalling[13, 14]. Both size and composition of the Hsf family have been analyzed and characterized in different plant species. The present study investigates for the first time this gene family in the economically relevant domesticated apple and shows that its genome contains 25 full length Hsf genes. This number is similar to that of Populus trichocarpa for which 28 loci encoding Hsf proteins were found. Velasco et al.  have shown that genome wide duplications had occurred in apple causing the expansion of several gene classes. Indeed, it was found that the enlargement of the MdHsf family is in particular originated from segmental duplications between different chromosomes. This situation is similar in maize and in Populus, in which segmental Hsf gene duplications were more prevalent than those of tandem duplications[9, 10]. Gene duplications have an important role not only in the genomic rearrangement and expansion but also in diversification of gene function. In particular, genes encoding for nucleic acid binding proteins, among which transcription factors, originated mostly by segmental duplication. In contrast, membrane proteins and proteins involved in the stress response are encoded by genes mainly duplicated in tandem[18, 19]. Therefore, the prevalence of segmental duplication events in MdHsf expansion may be associated to the fact that these genes act as transcriptional regulators.
Malus, Arabidopsis and Populus belong to the Rosid lineage and they are grouped in two distinct clades, namely Fabids (Malus and Populus) and Malvids (Arabidopsis). It was observed in the present study that the majority of the MdHsfs had a closer phylogenetic relationship to the PtHsfs than to the AtHsfs. This may be attributable to the fact that Malus and Populus belong to the same Fabids clade, and as they are both trees may have adapted to prolonged and repeated environmental constraints, unlike Arabidopsis.
Functional diversification of multifamily duplicated genes has been observed in trees. For example, the family of the glutathione S-transferase in Populus has a clear divergence in expression patterns in response to different stress treatments. Therefore the presence of many duplicated Hsf genes in the apple genome may be related to the fact that a sub-functionalization has taken place especially to cope with prolonged and specific stress conditions.
MdHsf genes were found to be expressed in several apple tissues. In particular, members belonging to the A1 and B1 subclasses, such as MdHsfA1a, MdHsfA1d, MdHsfB1a, MdHsfB1b, were constitutively expressed in different tissues. A similar situation was found in other plants like Arabidopsis where A1-type Hsfs were involved in house-keeping processes under normal conditions, being ready for the fast activation of other Hsfs genes following stress treatment[22, 23]. Furthermore, expression data from flower and fruit tissues indicated that some duplicated gene pairs, e.g. MdHsfA9a and MdHsfA9b, exhibited differences in their expression levels. This suggests that they may be subjected to a different regulation in apple tissue[1, 7].
In contrast, the expression of MdHsfA2a and MdHsfA2b was mainly detected in full bloom flowers. AtHsfA9 and LeHsfA2a (Le, Lycopersicon esculentum) were found expressed in seed and developing pollen grains[13, 14, 24]. It was shown that the presence of these Hsfs during plant development is important for heat shock protein activation. This suggests that MdHsfA2a and MdHsfA2b may be important during pollination and fertilization, which occurs at anthesis.
Effects of heat stress (HS) on Hsf gene expression has been examined in several plant species, but no data are available about Hsf expression in trees exposed to naturally increased temperatures. Under laboratory settings, it was shown that AtHsfA1a and AtHsfA1b regulate the early response to HS in Arabidopsis[22, 25]. AtHsfA2 is rapidly induced by HS, and it is involved in enhancing and maintaining of HS-response when plants are exposed to prolonged or repeated cycles of HS[26, 27]. Similarly to AtHsfA2, AtHsfA3 is involved in thermo-tolerance mechanisms[7, 28, 29]. The A1-type MdHsfs were expressed at the same level also in leaves from plants growing in field and exposed to different temperature conditions. MdHsfA2a b, MdHsfA3b c were instead strongly induced. This may suggest that these types of MdHsfs could be involved in maintaining the stress response when apple trees are exposed to prolonged periods of high temperature conditions.
In contrast to class A Hsfs, genes assigned to the B and C classes have so far not been fully characterized. Members of the B class were shown to act mainly as repressors of the expression of HS inducible genes[30, 31]. Some of them form a complex with Hsf A-types to maintain housekeeping gene expression during HS regimes. Therefore, the strong transcriptional activation in apple may indicate that some of them may have a role in the response to the high temperatures also in this species. For the majority of MdHsfs, increased messenger RNA levels were observed under naturally increased temperatures. However, MdHsfA9b and MdHsfB4a-b were the only Hsf genes showing low transcript abundance. Although proteomic data are not available for all MdHsfs genes, their activation or repression may suggest that these transcripts could have a high hierarchy of molecular events induced by the high temperatures.
The complexity of the Hsf family has been object of many investigations in different plant species. Here, 25 full length Hsfs genes were identified in the apple genome. Based on structural characteristics of the proteins and on the comparison with homologues from other species, the 25 MdHsfs were grouped in three different classes. Segmental and tandem duplications were examined and contributed to the expansion of the Hsf family in the apple genome. The expression profiles in flowers/fruits at different developmental stages as well as in leaves exposed to naturally increased temperature indicated that MdHsfs may play a role in different aspects of apple growth/development.
Malus domestica represents an economically important woody plant whose genome has been fully sequenced and whose commercial value is due to fruit production in the field. Therefore, understanding the role of protective genes as the Hsfs during development and under stress conditions is important. The results of this research will be undoubtedly useful for future gene cloning and functional studies and, in turn, for producing apple cultivars with improved genetic traits.
Identification and classification of Hsfs in Malus domestica
The recently sequenced apple genome was investigated for putative genes encoding for MdHsfs (Md: Malus domestica) based on BLASTN and BLASTP in NCBI and TIGR-Apple databases[11, 15]. Physical localization of all candidate MdHsfs was analyzed in order to reject redundant sequences with the same chromosome location. In order to identify signature domains, the MdHsf sequences were compared to the Hsf proteins of Arabidopsis and tomato by amino acid sequence alignment using ClustalW (version 1.83). Presence of DBD domains and coiled-coil structures were checked by SMART and MARCOIL programs[33, 34]. In addition, identification of putative domain motifs in the full-length amino acid sequences of the MdHsfs was also performed by MEME tools. Visualization of the Meme motifs in the MdHsfs was performed by using Expasy tools (http://prosite.expasy.org/mydomains). MdHsf names were assigned on the basis of the original nomenclature as worked out for the Arabidopsis thaliana Hsf family, and later applied to other plant Hsf families[2, 7]. Classification into three different groups A, B and C was based on the information of oligomerization domains.
Phylogenetic analysis and gene duplication of MdHsfs
Gene duplications in the apple genome were analyzed by testing the similarity of all MdHsf genes using ClustalW. A gene duplication was defined according to the following criteria: (1) the length of the sequence alignment covered ≥ 80 % of the longest gene, and (2) the similarity of the aligned gene regions was ≥ 80 %[36, 37]. Data were then plotted using Circos software.
To understand the evolutionary relationships of the MdHsf proteins, a phylogenetic tree was constructed. The N-terminal Hsf protein sequences containing the DBD and HR-A/B regions from Malus domestica, Arabidopsis thaliana and Populus trichocarpa[7, 10] were aligned using ClustalW. A phylogenetic tree was constructed using the Neighbor Joining (NJ) method in MEGA (version 5.0). Based on the results of the model selection analysis, the Jones-Taylor-Thornton matrix-based method was used to compute evolutionary distances. The rate variation among sites was modeled with a gamma distribution (shape parameter = 0.67). Bootstrap analysis was conducted with 1000 replicates to assess statistical support for each node.
Digital and EST expression analysis
The analysis of MdHsfs expression profiles was investigated at the transcriptional level. MdHsfs expression patterns were searched with the BLAST program in TIGR-Apple EST libraries using the following parameters: maximum identity > 95%, length > 200 bp and E-value <10-10.
Experiments were carried out in 2011 on 18-year-old apple trees (cultivar ‘Golden Delicious’ on M9 rootstock) trained with standard horticultural practices at the experimental farm of the Research Centre for Agriculture and Forestry Laimburg (South Tyrol, Italy). Samples were taken from 24 homogeneous trees grouped in 3 biological replicates each containing 8 trees distributed in the same block of the orchard. Tissue samples were collected between April and August 2011 from trees grown under field environmental conditions and exposed to natural variations of temperature and solar radiation. Temperature data are reported in the Additional file1. Young leaves (3–5 cm in length) as well as developing flowers corresponding to the tight cluster (FLS1), pink (FLS2) and full bloom (anthesis, FLS3) stages were harvested from the plants during spring period and under max-minimum temperature average in the range of 23°C/7°C (day/night; max/ min). From the same trees developing fruits of 10 mm (FUS1), 15 mm (FUS2) and 20 mm (FUS3) in length were also collected under max-minimum temperatures of 23°C/14°C (day/night; max/min). For testing Hsfs gene expression under naturally increased temperature conditions, leaf samples were taken during the summer period, at two different temperature ranges: at 26°C/12°C (day/night; max/min) on 30th July, 2011, which were used as reference, and at high temperature average of 32°C/17°C (day/night; max/min) on the 21st August, 2011 (Additional file1: Figure S1). All samples used in gene expression analyses were harvested at midday (12:00 am) and were positioned around 1.60 m in height from the soil.
RNA isolation and quantitative real-time PCR (qRT-PCR) analyses
Total RNA was isolated from apple tissues with the hot phenol method. RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer, and its quality was checked by agarose gel electrophoresis. For reverse transcription, total RNA was incubated with RNase-free DNase (RQ1; Promega, Madison, WI), and 1 μg was used for reverse transcription according to the manufacturer’s instructions (Superscript Vilo cDNA Synthesis kit; Invitrogen).
The qRT-PCR analyses were carried out on a 7500 Fast Real-time PCR System (Applied Biosystems) with the ROX Reference Dye. Each reaction contained 12.5 μl SYBR GreenER qPCR SuperMix Universal (Invitrogen), 20 ng of cDNA and 400 nM of each specific primer. The qRT-PCRs were performed using a controlled temperature program starting with 10 min at 95°C, followed by 40 cycles of 15 s at 95°C and 60 s at 60°C. To verify the presence of a specific product, the melting temperature of the amplified products was determined. In addition, each PCR mixture was analyzed on a 2% agarose/ethidium bromide stained gel to verify the size of the amplified DNA fragment. The primers used for the qRT-PCRs were designed using Quantprime software and are reported in the Additional file2. The qRT-PCRs were performed in duplicated technical reactions and repeated on three independent biological replicates. Relative mRNA levels of the target genes were calculated based on Vandesompele et al. . The genes encoding for elongation factor 1 alpha subunit (eF-1 alpha; accession number AJ223969.1), Importin alpha Isoform9 (IMPA-9; accession number CN909679) and Tip-41 like protein (Tip-41 CN941833) were used as references in the qRT-PCR analyses.
Heat shock transcriptional factor
Adjacent bipartite oligomerization domain
C-terminal activation domain
Heat shock element
Nuclear export signal
Nuclear localization signal
Quantitative reverse transcription real-time PCR.
The authors wish to thank Nunzio D’Agostino for suggestions during manuscript preparation and for his useful contribution in drawing the Circos Figure1. Christine Kerschbamer is very thanked for the technical assistance, Philipp Brunner to assist with apple growth and Alberto Storti for his kind support during this research.
The authors are grateful to the Foundation for Research and Innovation of the Autonomous Province of Bozen/Bolzano for covering the Open Access publication costs.
This work was partially funded by the Autonomous Province of Bozen/Bolzano, Italy (Departments 31 and 33). The South Tyrolean Fruit Growers' Co-operatives, in particularly VOG and VIP, are acknowledged for co-financing the Strategic Project on Apple Proliferation – APPL.
- von Koskull-Döring P, Scharf KD, Nover L: The diversity of plant heat stress transcription factors. Trends Plant Sci. 2007, 12: 452-457. 10.1016/j.tplants.2007.08.014.View ArticlePubMedGoogle Scholar
- Nover L, Bharti K, Döring P, Mishra SK, Ganguli A, Scharf KD: Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need?. Cell Stress Chaperone. 2001, 6: 177-189. 10.1379/1466-1268(2001)006<0177:AATHST>2.0.CO;2.View ArticleGoogle Scholar
- Döring P, Treuter E, Kistner C, Lyck R, Chen A, Nover L: The role of AHA motifs in the activator function of tomato heat stress transcription factors HsfA1a and HsfA2. Plant Cell. 2000, 12: 265-278.PubMed CentralView ArticlePubMedGoogle Scholar
- Morimoto RI: Regulation of the heat shock transcriptional response: crosstalk between a family of heat shock factors, molecular chaperones and negative regulators. Genes Dev. 1998, 12: 3788-3796. 10.1101/gad.12.24.3788.View ArticlePubMedGoogle Scholar
- Pirkkala L, Nykanen P, Sistonen L: Roles of the heat shock transcription factors in regulation of the heat shock response and beyond. FASEB J. 2001, 15: 1118-1131. 10.1096/fj00-0294rev.View ArticlePubMedGoogle Scholar
- Baniwal SK, Bharti K, Chan KY, Fauth M, Ganguli A, Kotak S, Mishra SK, Nover L, Port M, Scharf KD, Tripp J, Weber C, Zielinski D, Döring P: Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. J Biosci. 2004, 29: 471-487. 10.1007/BF02712120.View ArticlePubMedGoogle Scholar
- Scharf KD, Berberich T, Ebersberger I, Nover L: The plant heat stress transcription factor (Hsf) family: Structure, function and evolution. Biochim Biophys Acta. 2012, 1819 (2): 104-119. 10.1016/j.bbagrm.2011.10.002.View ArticlePubMedGoogle Scholar
- Chauhan H, Khurana N, Agarwal P, Khurana P: Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress. Mol Genet Genomics. 2011, 286 (2): 171-187. 10.1007/s00438-011-0638-8.View ArticlePubMedGoogle Scholar
- Lin YX, Jiang HY, Chu ZX, Tang XL, Zhu SW, Cheng BJ: Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics. 2011, 12: 76-10.1186/1471-2164-12-76.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang F, Dong Q, Jiang H, Zhu S, Chen B, Xiang Y: Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula. Mol Biol Rep. 2012, 39 (2): 1877-1886. 10.1007/s11033-011-0933-9.View ArticlePubMedGoogle Scholar
- Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, et al: The genome of the domesticated apple (Malus domestica Borkh). Nat Genet. 2010, 42 (10): 833-839. 10.1038/ng.654.View ArticlePubMedGoogle Scholar
- Frank G, Pressman E, Ophir R, Althan L, Shaked R, Freedman M, Shen S, Firon N: Transcriptional profiling of maturing tomato (Solanum lycopersicum L.) microspores reveals the involvement of heat shock proteins, ROS scavengers, hormones, and sugars in the heat stress response. J Exp Bot. 2009, 60 (13): 3891-3908. 10.1093/jxb/erp234.PubMed CentralView ArticlePubMedGoogle Scholar
- Giorno F, Wolters-Arts M, Grillo S, Scharf KD, Vriezen WH, Mariani C: Developmental and heat stress-regulated expression of HsfA2 and small heat shock proteins in tomato anthers. J Exp Bot. 2010, 61 (2): 453-462. 10.1093/jxb/erp316.PubMed CentralView ArticlePubMedGoogle Scholar
- Kotak S, Vierling E, Bäumlein H, von Koskull-Döring P: A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis. Plant Cell. 2007, 19: 182-195. 10.1105/tpc.106.048165.PubMed CentralView ArticlePubMedGoogle Scholar
- Vision TJ, Brown DG, Tanksley SD: The origins of genomic duplications in Arabidopsis. Science. 2000, 290 (5499): 2114-2117. 10.1126/science.290.5499.2114.View ArticlePubMedGoogle Scholar
- Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH: Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 2008, 148 (2): 993-1003. 10.1104/pp.108.122457.PubMed CentralView ArticlePubMedGoogle Scholar
- Rizzon C, Ponger L, Gaut BS: Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol. 2006, 2: e115-10.1371/journal.pcbi.0020115.PubMed CentralView ArticlePubMedGoogle Scholar
- Judd WS, Olmstead RG: A survey of tricolpate (eudicot) phylogenetic relationships. Am J Bot. 2004, 91 (10): 1627-1644. 10.3732/ajb.91.10.1627.View ArticlePubMedGoogle Scholar
- Lan T, Yang ZL, Yang X, Liu YJ, Wang XR, Zeng QY: Extensive functional diversification of the Populus glutathione S-transferase supergene family. Plant Cell. 2009, 21 (12): 3749-3766. 10.1105/tpc.109.070219.PubMed CentralView ArticlePubMedGoogle Scholar
- Busch W, Wunderlich M, Schöffl F: Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J. 2005, 41 (1): 1-14.View ArticlePubMedGoogle Scholar
- Mishra SK, Tripp J, Winkelhaus S, Tschiersch B, Theres K, Nover L, Scharf KD: In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato. Genes Dev. 2002, 16 (12): 1555-1567. 10.1101/gad.228802.PubMed CentralView ArticlePubMedGoogle Scholar
- Almoguera C, Rojas A, Díaz-Martín J, Prieto-Dapena P, Carranco R, Jordano J: A seed-specific heat-shock transcription factor involved in developmental regulation during embryogenesis in sunflower. J Biol Chem. 2002, 277 (46): 43866-43872. 10.1074/jbc.M207330200.View ArticlePubMedGoogle Scholar
- Lohmann C, Eggers-Schumacher G, Wunderlich M, Schöffl F: Two different heat shock transcription factors regulate immediate early expression of stress genes in Arabidopsis. Mol Genet Genomics. 2004, 271 (3): 376-10.1007/s00438-004-1001-0.View ArticleGoogle Scholar
- Charng YY, Liu HC, Liu NY, Chi WT, Wang CN, Chang SH, Wang TT: A heat-inducible transcription factor, HsfA2, is required for extension of acquired thermotolerance in Arabidopsis. Plant Physiol. 2007, 143 (1): 251-262.PubMed CentralView ArticlePubMedGoogle Scholar
- Meiri D, Breiman A: Arabidopsis ROF1 (FKBP62) modulates thermotolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. Plant J. 2009, 59 (3): 387-399. 10.1111/j.1365-313X.2009.03878.x.View ArticlePubMedGoogle Scholar
- Schramm F, Larkindale J, Kiehlmann E, Ganguli A, Englich G, Vierling E, von Koskull-Döring P: A cascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant J. 2008, 53 (2): 264-274.View ArticlePubMedGoogle Scholar
- Chen H, Hwang JE, Lim CJ, Kim DY, Lee SY, Lim CO: Arabidopsis DREB2C functions as a transcriptional activator of HsfA3 during the heat stress response. Biochem Biophys Res Commun. 2010, 401 (2): 238-244. 10.1016/j.bbrc.2010.09.038.View ArticlePubMedGoogle Scholar
- Czarnecka-Verner E, Yuan CX, Scharf KD, Englich G, Gurley WB: Plants contain a novel multi-member class of heat shock factors without transcriptional activator potential. Plant Mol Biol. 2000, 43: 459-471.View ArticlePubMedGoogle Scholar
- Ikeda M, Mitsuda N, Ohme-Takagi M: Arabidopsis HsfB1 and HsfB2b act as repressors of the expression of heat-inducible Hsfs but positively regulate the acquired thermotolerance. Plant Physiol. 2011, 157 (3): 1243-1254. 10.1104/pp.111.179036.PubMed CentralView ArticlePubMedGoogle Scholar
- Bharti K, Von Koskull-Döring P, Bharti S, Kumar P, Tintschl-Körbitzer A, Treuter E, Nover L: Tomato heat stress transcription factor HsfB1 represents a novel type of general transcription coactivator with a histone-like motif interacting with the plant CREB binding protein ortholog HAC1. Plant Cell. 2004, 16 (6): 1521-1535. 10.1105/tpc.019927.PubMed CentralView ArticlePubMedGoogle Scholar
- Bailey TL, Williams N, Misleh C, Li WW: MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34: W369-W373. 10.1093/nar/gkl198.PubMed CentralView ArticlePubMedGoogle Scholar
- Yang S, Zhang X, Yue JX, Tian D, Chen JQ: Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics. 2008, 280: 187-198. 10.1007/s00438-008-0355-0.View ArticlePubMedGoogle Scholar
- Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH: Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol. 2002, 19: 256-262. 10.1093/oxfordjournals.molbev.a004079.View ArticlePubMedGoogle Scholar
- Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19: 1639-1645. 10.1101/gr.092759.109.PubMed CentralView ArticlePubMedGoogle Scholar
- Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.View ArticlePubMedGoogle Scholar
- Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992, 8: 275-282.PubMedGoogle Scholar
- Gambino G, Perrone I, Gribaudo I: A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal. 2008, 19 (6): 520-525. 10.1002/pca.1078.View ArticlePubMedGoogle Scholar
- Arvidsson S, Kwasniewski M, Riaño-Pachón DM, Mueller-Roeber B: QuantPrime–a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinforma. 2008, 9: 465-10.1186/1471-2105-9-465.View ArticleGoogle Scholar
- Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology. 2002, 3 (7): 1-11. 3 RESEARCH0034View ArticleGoogle Scholar
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