Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.
Citation: Zolotarov Y, Strömvik M (2015) De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes. PLoS ONE 10(6): e0129016. https://doi.org/10.1371/journal.pone.0129016
Academic Editor: Haibing Yang, Purdue University, UNITED STATES
Received: January 11, 2015; Accepted: May 4, 2015; Published: June 26, 2015
Copyright: © 2015 Zolotarov, Strömvik. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Data Availability: All relevant data are within the paper, its Supporting Information files, or via GitHub (https://github.com/zolotarov/dehydrin_promoters).
Funding: This work was supported by a grant from Natural Sciences and Engineering Research Council of Canada (NSERC) (Grant no. 283303) to M.V.S.
Competing interests: The authors have declared that no competing interests exist.
Plants have developed specific mechanisms that allow them to prepare for and survive drastic changes in their environment. One of the better-studied mechanisms is cold acclimation, which allows plants to develop freezing tolerance [1,2]. During exposure to low non-freezing temperatures gene expression is modulated and numerous solutes, known as osmoprotectants, and protective proteins accumulate in plant tissues. Dehydrins or dehydration proteins, (DHN) belong to group II LEA (late embryogenesis abundant) proteins. They are often found among those protective proteins and they are ubiquitous in transcriptomes of plants under osmotic stress, such as cold, drought and high salinity [3–7]. All dehydrins contain a 15 amino acid K-segment, rich in lysine residues, represented by EKKGIMDKIKEKLPG conserved sequence . The K-segment forms an amphipathic α-helix that allows dehydrins to stabilize plant membranes and proteins during dehydration stresses [9–12]. In addition to the K-segment, dehydrins can contain a Y-segment (T/VDEYGNP) and an S-segment (3+ serines) . The S-segment is thought to be involved in ion binding and dehydrin phosphorylation, which induces a conformational change in dehydrins [14,15]. Currently, the function of the Y-segment is unknown. The dehydrins are categorized into 5 subclasses (Kn, KS, SKn, YnKn and YnSKn) based on the presence and location of the 3 conserved segments . Members of each subclass are expressed in response to a different set of stimuli. However, there is no clear link between subclass types and expression triggers .
As defined by Close, 1997, dehydrins must contain a K-segment. According to that definition, dehydrins are only found in plants. There are other proteins described as dehydrins, for example from Escherichia coli (GenBank: AAB18249.1), a fungus Pneumocystis carinii (GenBank: CAC43457.1)  or from whitish truffle Tuber borchii (GenBank: ABC33908.1) . However, these proteins do not contain the K-segment or any of the other conserved dehydrin segments and therefore should not be considered to be proper dehydrins.
Stress response in plants can be regulated in an abscisic acid (ABA) dependent and/or independent manner . Multiple transcription factors, such as C-repeat binding factor/dehydration responsive element binding protein (CBF/DREB) and ABA response element binding protein (AREB), participate in water stress response, by binding to cis-regulatory elements in the promoters of their respective regulons. The CBF1-3 are transcription factors that participate in ABA independent cold and dehydration induced gene expression  and they bind a C-repeat (CRT) cis-regulatory element core (CCGAC), also known as dehydration response element (DRE). Members of the CBF regulon include well-studied A. thaliana genes, such as LTI78/COR78 , COR15A and COR47 (an SKn dehydrin) . However, not all members of the CBF regulon have the CRT cis-regulatory element in their promoters , hence there are yet undiscovered motifs that are involved in cold and drought response. Numerous transcription factors participate in the ABA dependent stress response and they bind several cis-regulatory elements with a TACGTG core . Many members of the CBF regulon are also upregulated in response to drought and ABA exposure, demonstrating a cross-talk between stress-induced pathways . For example, in barley (Hordeum vulgare L.), a Kn dehydrin is strongly upregulated in response to cold, dehydration and ABA, and its promoter contains CRT and abscisic acid response elements (ABREs) cis-regulatory elements, whereas a barley SKn dehydrin, whose promoter contains multiple CRTs and no ABREs is only weakly upregulated in response to ABA, but shows a significant upregulation in response to cold . The expression of CBFs, and, in turn, their regulons, is modulated by photoperiod through phytochrome B and phytochrome-interacting factors [25,26].
In this study, we tested whether the different classes of dehydrin genes house specific and conserved cis-regulatory elements in their promoters that could contribute to gene characterization. De novo motif discovery, a computational approach to identify statistically overrepresented sequence motifs within a promoter sequence, was used to analyze a total of 350 dehydrin promoters. For each of the five dehydrin classes, statistically significant motifs were identified, and matched to experimentally validated cis-regulatory elements known from literature. Motifs linked to ABA-dependent and ABA-independent stress response pathways were detected in the promoters of dehydrin genes from various, distant plant lineages, which indicates that the stress response pathways regulating dehydrin expression are conserved.
Plant genomes used in the computational analyses
Permission to use data from genomes that are not published was obtained from members of sequencing consortia, where stated. In other cases, published data was used.
The following genome sequences were obtained from Phytozome v10 (http://phytozome.jgi.doe.gov)  using BioMart : Amborella trichopoda , Aquilegia coerulea (Aquilegia coerulea Genome Sequencing Project, http://www.phytozome.net/, permission obtained from Dr. Scott Hodges), Arabidopsis halleri (Arabidopsis halleri v1.1, DOE-JGI, http://www.phytozome.net/ahalleri), Arabidopsis lyrata , Arabidopsis thaliana , Boechera stricta (Boechera stricta v1.2, DOE-JGI, http://www.phytozome.net/bstricta), Brachypodium distachyon , turnip mustard (Brassica rapa L.) [33,34], papaya (Carica papaya) , Capsella grandiflora and Capsella rubella , clementine (Citrus clementina) and, sweet orange (Citrus sinensis) , cucumber (Cucumis sativus) (permission obtained from Dr. Yiqun Weng), Eucalyptus grandis , Eutrema salsugineum (formerly Thellungiella halophila) , strawberry (Fragaria vesca) , soybean (Glycine max) , cotton (Gossypuim raimondii) , flax (Linum usitatissimum) , apple (Malus domestica) , cassava (Manihot esculenta) , barrel medic (Medicago truncatula) , monkey flower (Mimulus guttatus) , rice (Oryza sativa) , swtichgrass (Panicum virgatum v1.0, DOE-JGI, http://www.phytozome.net/pvirgatum), common bean (Phaseolus vulgaris L.) , moss (Physcomitrella patens) , peach (Prunus persica) , poplar (Populus trichocarpa) , castor bean (Ricinus communis) , foxtail millet (Setaria italica) , Shrub willow (Salix purpurea v1.0, DOE-JGI, http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spurpurea), tomato (Solanum lycopersicum) , potato (Solanum tuberosum) , greater duckweed (Spirodela polyrhiza) , cocoa (Theobroma cacao) , grape (Vitis vinifera) , maize (Zea mays) .
The following genomes were obtained from other sources: kiwifruit (Actinidia chinensis) , sugar beet (Beta vulgaris) ; pigeonpea (Cajanus cajan)  http://www.icrisat.org/gt-bt/iipg/genomedata.zip; pepper (Capsicum annuum) ; chickpea (Cicer arietinum)  http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip; Lotus japonicus  ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/; banana (Musa acuminata) ; Oryza brachyantha ; date palm (Phoenix dactylifera, Draft Sequence Version 3)  http://qatar-weill.cornell.edu/research/datepalmGenome/download.html; Norway spruce (Picea abies) ; loblolly pine (Pinus taeda) .
Identification of dehydrin genes
A custom solution was used to identify all dehydrin genes found in the plant genomes described above. Amino acid sequences of several known dehydrins were obtained from NCBI GenBank  and sequences of their K-segment were used to populate a seed FASTA file. A Python script was written that used Biopython  Motif module to scan all amino acid sequence for proteins containing a sequence similar to the K-segment, based on its position frequency matrix (PFM). After each round of search new K-segment sequences were added to the original FASTA file. The Y-segment sequence file was constructed in a similar manner using identified dehydrin protein sequences. Identified dehydrins were categorized based on the occurrence of conserved segments using either their PFMs (K- and Y-segments) or a regular expression that described a simpler S-segment. All identified dehydrins were divided into five categories: Kn, KS, SKn, YnKn, YnSKn and 1000 bps upstream of the transcription start site (where data was available, otherwise upstream from the start site) were obtained from Phytozome BioMart or they were directly extracted from the genomes using custom scripts. Oxytropis arctobia and Oxytropis splendens KS dehydrin gene sequences were obtained from NCBI GenBank (accessions: AEV59613 and AEV59617, respectively ). 1000 bp of O. arctobia and O. splendens promoters were obtained by amplifying GenomeWalker libraries and sequencing PCR products (Zolotarov et. al., unpublished).
To validate that the identified genes can actually be considered dehydrins, phmmer, as implemented on the HMMER web server  was used to search sequences on UniProt Knowledgebase  that have a significant similarity to putative dehydrins discovered using our custom method. The top ten significant hits were taken for each putative dehydrin and their domain annotation was extracted. Additionally, Needleman-Wunsch  pairwise alignment was used to compare 15 putative KS dehydrin to a known Arabidopsis KS dehydrin (AT1G54410). The closest match to every putative dehydrin in the NCBI GenBank non-redundant database was searched for using BLAST .
All the scripts and sequence data used in this paper are available from https://github.com/zolotarov/dehydrin_promoters
Intrinsic disorder and hydrophilicity analysis
The identified dehydrin sequences were compared for intrinsic disorder and hydrophilicity with random plant protein sequences to assess the classification as a dehydrin. To calculate the grand average of hydrophilicity, Biopython ProtParam module was used. To calculate disorder proportion, IUPred  scores were calculated for each amino acid. The proportion of amino acids with the score above 0.5 (indicating disorder) was calculated. Statistical comparison was performed using t-test implemented in the scipy library [79,80]. The same number of random protein sequences was obtained for each species as the number of dehydrins used in this study. The sequences were downloaded using NCBI Entrez Direct E-utilities .
De novo motif discovery
Motifs were discovered using MEME v4.9.1 , Seeder v0.01  and Weeder v1.4.2 , and using the five sets of sequences as separate input. Significant motifs were selected based on following parameters: E-value ≤ 0.05 for MEME, Q-value ≤ 0.01 for Seeder and the top 3 motifs recommended by Weeder adviser. All promoters that were available through Phytozome BioMart from all species included in the analyses, was used as a background set (a total of 1029220 promoters). A separate parser was written to extract significant PFMs from result files produced by each program. The PFMs produced for each dehydrin class were entered into the STAMP  website to group matrices by similarity and to identify significant (E-value ≤ 0.05) matches in PLACE . A representative member from a tree node of matrices grouped by similarity was selected and its sequence logo was generated using WebLogo 3.3 .
Results and Discussion
In order to further understand how different dehydrins are regulated in response to environmental stress, motifs corresponding to conserved cis-regulatory elements were detected in the upstream regions of dehydrin genes in all five subclasses. Dehydrin proteins are by nature unstructured, and a custom identification strategy was employed to retrieve as many dehydrin genes with up to 1000 bp upstream region as possible. In total, 340 dehydrin promoters of size 1000 bp and eight dehydrin promoters of shorter length were retrieved from 51 plant genome sequences. In addition, two promoters from dehydrin genes isolated from two Oxytropis species were also included (Table 1, S1 Table). Out of the queried genomes, 10 were from monocotyledonous plants, 37 from dicotyledonous plants, one from a basal angiosperm (Amborella trichopoda), two from gymnosperms (Picea abies and Pinus taeda) and one from moss (Physcomitrella patens). The 350 sequences identified were confirmed to also match annotated dehydrins. For 330 out of 350 sequences, at least half of the top ten significant hits had “Dehydrin” as domain annotation. For the remaining 20 putative dehydrins, less than half of the top ten significant hits carried that annotation. Out of those, three were annotated as either a dehydrin or similar to dehydrin on NCBI GenBank and two were annotated as having a dehydrin domain on UniProtKB. The rest of the sequences were all short putative KS dehydrins. In these cases, all significant phmmer hits were analyzed. From 14.2% to 30.1% of significant hits had “Dehydrin” domain architecture, for sequences with lowest and highest number of significant hits with “Dehydrin” annotation, respectively. The rest of significant hits had no architecture annotation. When Needleman-Wunsch pairwise alignment was used to compare 15 putative KS dehydrin to a known Arabidopsis KS dehydrin (AT1G54410), sequence similarities ranged from 59.0% to 98.0%. This evidence supports the notion that the sequences extracted for the analyses can be classified as dehydrins.
Biochemical properties of dehydrins
Dehydrins are known to be intrinsically disordered and hydrophilic , making it difficult, if not impossible, to identify them by overall sequence homology. These properties are, however, important for their hypothesized function in protein stabilization through interaction with water molecules, as well as for their subcellular location in the cytosol and the nucleus and not within membranes [87,88]. To assess the identification of the dehydrins included in this study, the grand average of hydropathicity (GRAVY, ) and the proportions of amino acids in the disordered regions were compared between dehydrins and random plant proteins. It was found that the 350 dehydrin amino acid sequences analyzed, were significantly more hydrophilic than 350 random plant protein sequences (GRAVY -1.3470 for dehydrins, -0.2938 for random plant proteins, p-value < 0.001). The level of structural disorder indicated that in the dehydrins analyzed, the average proportion of amino acid sequences in the state of disorder was 99.32% compared to 15.95% in random plant proteins (p-value < 0.001).
Promoters of KS dehydrins have one conserved GATA motif
In total, 47 KS dehydrin promoters were included in the de novo motif discovery (Table 1). Using the de novo motif discovery tool Seeder [83,90], one single putative conserved regulatory motif was discovered in all 47 promoter sequences (Motif 1, Table 2, S2 Table). A similar motif was also discovered with Weeder . The KS dehydrins are known to be expressed in response to cold and dehydration, as well as being constitutively expressed [6,91–93]. Although the single identified overrepresented motif in KS dehydrin promoters does not directly match any typical cold or dehydration-related cis-regulatory elements in the PLACE database , it does match two motifs involved in light regulation and one involved in sugar regulation (Table 2): IBOXCORENT (I-box core) , REBETALGLHCB21  and SREATMSD , respectively. These three experimentally validated motifs share four nucleotides (GATA).
One of these motifs, the I-box (GATAAGR) can form a light-responsive conserved DNA modular array (CMA) together with a G-box (CACGTGGC) when located in close proximity to one another. In transgenic Arabidopsis and tobacco (Nicotiana tabacum) plants, the presence of this CMA in a promoter, drives GUS reporter gene expression when exposed to light. Interestingly, this expression seems to be mediated by phytochrome and cryptochrome photoreceptors .
Another of the motifs matching the motif discovered in the KS dehydrin promoters, the REBETALGLHCB21, also called REβ (CGGATA), was first identified in gibbous duckweed (Lemna gibba) . It is involved in phytochrome-mediated repression of promoter activity in darkness, when located in close proximity with REα (AACCAA). Although REα was not identified as a significantly overrepresented motif, it is found in 26 out of the 47 KS dehydrin promoters analyzed. The GATA part of the REβ was shown to be absolutely necessary for darkness-induced repression . Furthermore, in Arabidopsis, C-repeat (CCGAC, CRT)-linked cold and dehydration induced gene expression is mediated by phytochrome . While CRT was not found to be significantly overrepresented within the set of KS dehydrin promoters, it is noteworthy that 27 out of the 47 KS dehydrin promoters contain one or more copies of CRT or its reverse complement. Sixteen of the promoters contain both REα and REβ.
The motif discovered in the KS dehydrin promoters also matched a sugar-repressive element, SREATMSD (TTATCC, SRE), shown to be involved in sugar mediated gene repression in Arabidopsis . Sugars are known osmoprotectants that are produced by plants in response to cold . One of the suggested roles of dehydrins is in the stabilization of protein conformation. Sugars, such as sucrose and trehalose, can replace water molecules on the surface of a protein and can thus conserve its conformation. This allows cells to restore their function after rehydration .
Motifs discovered in promoters of Kn match abscisic acid and low temperature response elements
A total of 39 Kn dehydrin promoters were included in the de novo regulatory motif discovery analysis (Table 1). The Kn dehydrins are expressed in response to high salinity, abscisic acid (ABA), cold and dehydration [3,5,99,100]. A total of three putative regulatory motifs were identified in this set of promoters (Table 3, S2 Table)—two were discovered using MEME (Motif 2: GGCAGGAC/GTGGTGCC; and Motif 3: ATGTCGGC/GCCGACAT) and one using Seeder (Motif 4: TCGCCGACAT/ATGTCGGCGA). Motif 2 (GGCAGGAC) has a significant match to the SITEIIBOSPCNA (TGGTCCCAC) motif in the PLACE database. This motif is linked with meristematic tissue-specific gene expression in rice (Oryza sativa)  and it was found in 31 out of the 39 promoters. Motifs 3 and 4, found in all analyzed Kn dehydrin promoters, match DREDR1ATRD29AB motif (TACCGACAT)  and LTREATLTI78 (ACCGACA) , two low temperature response elements (LTREs) involved in cold response in A. thaliana. Additionally, Motif 3 matches an ABRE found in wheat and rice- ABREOSRAB21 (ACGTSSSC) . The presence of both LTREs and an ABRE indicates that Kn dehydrins, similarly to SKn and YnSKn dehydrins, could be expressed in ABA-dependent and independent manner in response to osmotic stresses.
SKn dehydrins contain multiple cold/dehydration, abscisic acid and light regulated response elements
A total of 120 SKn dehydrin promoters were analyzed (Table 1). Six de novo discovered putative regulatory motifs are presented in Table 4 and S2 Table. MEME and Seeder each discovered three motifs. The SKn dehydrins are known to be expressed in response to cold, ABA, dehydration and salt [3,5,14,105]. Three out of six motifs (motifs 5–7) have matches in PLACE that are known ABREs. Motif 5 (CCACGTGTC/GACACGTGG) matches ABREs from wheat (Triticum aestivum)  and canola (Brassica napus) . Motif 6 (CCGACGCG/CGCGTCGG) matches ABREs from maize , and rice . Motif 7 (CCAACGCG/CGCGTTGG) matches an ABRE from barley  and rice . Motifs 6, 8 (CACCGACC/GGTCGGTG) and 9 (TGGTCGGT/ACCGACCA) match low temperature response elements known as C-repeats (CRT, consensus sequence: RCCGAC), found in numerous species [110–112].
The presence of these significantly overrepresented motifs indicates that the SKn dehydrins are regulated at the transcriptional level and their expression is modulated in response to cold and ABA. SKn dehydrins should also be expressed in response to drought, since CRT, which is also called dehydration responsive element , is found in their promoters. The circadian clock controls cold induction of C-repeat binding factors (CBFs), which in turn bind CRT/DRE elements . Phytochrome and cryptochrome genes are also regulated by a circadian clock in Arabidopsis . COR27, a cold-induced gene, is regulated by circadian clock related evening elements (EE) . In addition to EE, the COR27 promoter also contains multiple ABREs and G-boxes, to which motifs 5 and 6 also match. The core EE (AATATCT)  is found in 18 out of 73 SKn gene promoters analyzed. Motifs involved in light-induced regulation of gene expression found in the promoters of SKn genes could participate in modulation of these genes by the circadian clock. It has been shown previously, using bioinformatics methods, that the promoters of cold-regulated genes contain CRTs and ABREs [112,121] and our data also support those findings.
Motifs 5 and 10 match an auxin response element found in soybean GmAux28  and SAUR15A promoter, respectively . It has been shown previously that numerous genes related to auxin response in Arabidopsis are modulated in response to cold, such as auxin response factor ARF7 or the PINOID-binding protein 1 that is involved in hormone signaling and stress response .
YnSKn dehydrins promoters contain multiple ABREs, light REs and a CRT
YnSKn dehydrins represent the largest subclass out of the five dehydrin classes analyzed. A total of 123 YnSKn gene promoters were analyzed (Table 1). The YnSKn dehydrins are expressed in response to ABA, dehydration and high salinity [3,5,100]. The two motifs presented in Table 5 and S2 Table (Motifs 11 and 12) match numerous elements in the PLACE database and both were discovered using a Seeder. Motif 11 (GACACGTGGC) is very similar to Motif 5 (GACACGTGT), found in the SKn dehydrin promoters and they both match several of the same motifs in PLACE database, namely ABREs, G-box and light response elements. Motif 13 (CACCGAC) is almost identical to Motif 8 (CACCGACC) discovered in the SKn dehydrin promoters, which matches CRT/DRE necessary for CBF mediated cold and dehydration response . Overall, motifs found YnSKn dehydrin promoters are very similar to those found in SKn dehydrin promoters indicating that they possibly have a similar function, and that these two classes may have diverged more recently than the other classes. While the function of the Y-segment in the gene products of YnSKn and YnKn dehydrins is not known, it shows similarity to the nucleotide binding domain of plant chaperones . The gene products of the other dehydrin classes do not have any such domains. In addition, there are evolutive constraints on the Y-segment in a dehydrin from arctic Oxytropis species compared with temperate species , suggesting that the Y-segment might carry an important function that differentiates YnSKn from SKn dehydrins. Some of the published data shows that YnSKn dehydrins are not expressed in response to cold [3,5], however there is evidence that after a period of acclimation they do accumulate in Red-Osier Dogwood (Cornus sericea L.)  and apple trees . It is possible that cold-induced YnSKn dehydrin expression was not detected in some data sets due to a limited time of exposure to low temperature.
YnKn dehydrins promoters contain ABREs and light REs
YnKn dehydrins represent the smallest subgroup, with only 21 members found in 51 plant genomes (Table 1). YnKn dehydrins are known to be expressed in response to cold [129,130], and two motifs were detected in their promoters (Table 6, S2 Table). One was identified using Seeder and the other using MEME. Both motifs match several ABREs and light REs in the PLACE database. Motif 13 (TAACACGTGTC/GACACGTGTTA) is similar to motif 11 (GACACGTGGC/GCCACGTGTC) identified in YnSKn dehydrins and it matches the some of the same motifs in PLACE. Motif 14 (ACGTGGCA/TGCCACGT) is similar to motif 11 (GACACGTGGC) found in YnSKn dehydrin. The lack of CRTs in the promoters of YnKn dehydrins suggests that they might be expressed in response to cold in ABA-dependent manner, not linked with the CBF transcription factors .
Numerous dehydrins were identified in 51 plant genomes, many of which are not found in protein databases such as InterPro or PROSITE, or they are not annotated in Phytozome. The identified dehydrins were categorized into five subclasses based on the occurrence of conserved protein segments. Three de novo motif discovery software tools were used to find statistically significant overrepresented motifs in the promoters of each group of dehydrins. These motifs were matched to known cis-regulatory elements in the PLACE database to help explain the regulation of dehydrin expression in response to different environmental stimuli.
Dehydrins are expressed in response to multiple stress stimuli. Although there is overlap in expression triggers between dehydrin subclasses, there are differences in the pattern of expression. Some of the dehydrins are expressed constitutively in all tissues [3,5] and more specifically in seeds [131,132]. The presence of ABREs, CRTs and light REs in the promoters of YnSKn and SKn dehydrins indicates that they could be expressed in response to dehydration and cold in both ABA-dependent and independent pathway and that this expression is modulated by light.
While YnSKn and SKn dehydrin are found in most species, often in several copies, the other three subclasses are encountered less often. It is probable that they either have specialized functions or they are expressed together with YnSKn and SKn dehydrins to increase the overall protective effect against dehydration. It is important to note that the number of discovered dehydrins is probably an underestimation due to incompleteness of genome assembly and errors inherent in sequencing.
Dehydrins play an important role in the survival of plants facing various stresses. Motifs matching cis-regulatory elements linked to both ABA-dependent and independent stress response pathways, as well as light response pathways were detected in dehydrins from many different plant families. The implication of this finding is that the regulation of dehydrins is conserved in the plant lineages included in this study and that stress-linked selection pressure preserved cis-regulatory elements in the promoters of dehydrins through stabilizing selection.
S1 Table. Annotation and meta-data about the dehydrins included in the study.
Each identified dehydrin was further analyzed by BLAST to find the closest match at NCBI GenBank non-reduntant database. The fields are 1. Species; 2. Gene; 3. Dehydrin subgroup; 4. BLAST top hit e-value; 5. BLAST top hit accession; 6. BLAST top hit description; 7. K-segment location; 8. Y-segment location; 9. S-segment location.
S2 Table. Motif logos of motifs discovered in dehydrin promoters.
The authors wish to thank Paul Harrison for helpful discussions on disordered proteins.
Conceived and designed the experiments: MS YZ. Performed the experiments: YZ. Analyzed the data: YZ. Contributed reagents/materials/analysis tools: MS. Wrote the paper: MS YZ.
- 1. Hannah MA, Heyer AG, Hincha DK (2005) A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet 1: e26. pmid:16121258
- 2. Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, et al. (2009) Metabolic Pathways Involved in Cold Acclimation Identified by Integrated Analysis of Metabolites and Transcripts Regulated by DREB1A and DREB2A. Plant Physiol 150: 1972–1980. pmid:19502356
- 3. Choi DW, Close TJ, Zhu B (1999) The barley (Hordeum vulgare L.) dehydrin multigene family: sequences, allele types, chromosome assignments, and expression characteristics of 11 Dhn genes of cv Dicktoo. Theor Appl Genet 98: 1234–1247–1247.
- 4. Allagulova CR, Gimalov FR, Shakirova FM, Vakhitov VA (2003) The Plant Dehydrins: Structure and Putative Functions. Biochemistry (Moscow) 68: 945–951. pmid:14606934
- 5. Hundertmark M, Hincha DK (2008) LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 9: 118. pmid:18318901
- 6. Archambault A, Strömvik MV (2011) PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic. Funct Integr Genomic 11: 497–505. pmid:21499864
- 7. Yamasaki Y, Koehler G, Blacklock BJ, Randall SK (2013) Dehydrin expression in soybean. Plant Physiol and Bioch 70: 213–220. pmid:23792826
- 8. Close TJ (1996) Dehydrins: Emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97: 795–803.
- 9. Rorat T (2006) Plant dehydrins—tissue location, structure and function. Cell Mol Biol Lett 11: 536–556. pmid:16983453
- 10. Koag MC, Wilkens S, Fenton RD, Resnik J, Vo E, Close TJ (2009) The K-Segment of Maize DHN1 Mediates Binding to Anionic Phospholipid Vesicles and Concomitant Structural Changes. Plant Physiol 150: 1503–1514. pmid:19439573
- 11. Drira M, Saibi W, Brini F, Gargouri A, Masmoudi K, Hanin M (2012) The K-Segments of the Wheat Dehydrin DHN-5 are Essential for the Protection of Lactate Dehydrogenase and β-Glucosidase Activities In Vitro. Mol Biotechnol 54: 643–650.
- 12. Rahman LN, McKay F, Giuliani M, Quirk A, Moffatt BA, Harauz G, et al. (2013) Interactions of Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 with membranes at cold and ambient temperatures—Surface morphology and single-molecule force measurements show phase separation, and reveal tertiary and quaternary associations. BBA—Biomembranes 1828: 967–980.
- 13. Close TJ (1997) Dehydrins: A commonalty in the response of plants to dehydration and low temperature. Physiol Plant 100: 291–296.
- 14. Kovacs D, Kalmar E, Torok Z, Tompa P (2008) Chaperone Activity of ERD10 and ERD14, Two Disordered Stress-Related Plant Proteins. Plant Physiol 147: 381–390. pmid:18359842
- 15. Rahman LN, Smith GST, Bamm VV, Voyer-Grant JAM, Moffatt BA, Dutcher JR, et al. (2011) Phosphorylation of Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 facilitates cation-induced conformational changes and actin assembly. Biochemistry 50: 9587–9604. pmid:21970344
- 16. Eriksson SK, Harryson P (2011) Dehydrins: Molecular Biology, Structure and Function. In: Lüttge U, Beck E, Bartels D, editors. Ecological Studies. Ecological Studies. Berlin, Heidelberg: Springer Berlin Heidelberg, Vol. 215. pp. 289–305. https://doi.org/10.1007/978-3-642-19106-0_14
- 17. Abba S, Ghignone S, Bonfante P (2006) A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins. BMC Genomics 7: 39. pmid:16512918
- 18. Agarwal PK, Jha B (2010) Transcription factors in plants and ABA dependent and independent abiotic stress signalling. Biol Plant 54: 201–212.
- 19. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi-Shinozaki K (2002) DNA-Binding Specificity of the ERF/AP2 Domain of Arabidopsis DREBs, Transcription Factors Involved in Dehydration- and Cold-Inducible Gene Expression. Biochem Bioph Res Co 290: 998–1009.
- 20. Knight H, Trewavas AJ, Knight MR (1997) Calcium signalling in Arabidopsis thaliana responding to drought and salinity. Plant J 12: 1067–1078. pmid:9418048
- 21. Thomashow MF, Gilmour SJ, Stockinger EJ, Jaglo-Ottosen KR, Zarka DG (2001) Role of the Arabidopsis CBF transcriptional activators in cold acclimation. Physiol Plant 112: 171–175.
- 22. Fowler S, Thomashow MF (2002) Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway. Plant Cell 14: 1675–1690. pmid:12172015
- 23. Higo K (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297–300. pmid:9847208
- 24. Chinnusamy V, Schumaker K, Zhu J-K (2004) Molecular genetic perspectives on cross‐talk and specificity in abiotic stress signalling in plants. J Exp Bot 55: 225–236. pmid:14673035
- 25. Kim H-J, Kim Y-K, Park J-Y, Kim J (2002) Light signalling mediated by phytochrome plays an important role in cold-induced gene expression through the C-repeat/dehydration responsive element (C/DRE) in Arabidopsis thaliana. Plant J 29: 693–704. pmid:12148528
- 26. Lee C-M, Thomashow MF (2012) Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. P Natl Acad Sci USA 109: 15054–15059. pmid:22927419
- 27. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: D1178–D1186. pmid:22110026
- 28. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, et al. (2009) BioMart—biological queries made easy. BMC Genomics 10: 22. pmid:19144180
- 29. Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342: 1241089. pmid:24357323
- 30. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, Clark RM, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43: 476–481. pmid:21478890
- 31. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815. pmid:11130711
- 32. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763–768. pmid:20148030
- 33. Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, et al. (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11: 136. pmid:21995777
- 34. The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43: 1035–1039. pmid:21873998
- 35. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991–996. pmid:18432245
- 36. Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo Y-L, et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45: 831–835. pmid:23749190
- 37. Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, et al. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32: 656–662. pmid:24908277
- 38. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, et al. (2014) The genome of Eucalyptus grandis. Nature 510: 356–362. pmid:24919147
- 39. Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, et al. (2013) The Reference Genome of the Halophytic Plant Eutrema salsugineum. Front Plant Sci 4.
- 40. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, et al. (2010) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43: 109–116. pmid:21186353
- 41. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183. pmid:20075913
- 42. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, et al. (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423–427. pmid:23257886
- 43. Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, et al. (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72: 461–473. pmid:22757964
- 44. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, et al. (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42: 833–839. pmid:20802477
- 45. Prochnik S, Marri PR, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, et al. (2012) The Cassava Genome: Current Progress, Future Directions. Trop Plant Biol 5: 88–94. pmid:22523606
- 46. Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, et al. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520–524. pmid:22089132
- 47. Hellsten U, Wright KM, Jenkins J, Shu S, Yuan Y, Wessler SR, et al. (2013) Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proc Natl Acad Sci USA 110: 19478–19482. pmid:24225854
- 48. Kawahara Y, la Bastide de M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, et al. (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6: 4. pmid:24280374
- 49. Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, et al. (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46: 707–713. pmid:24908249
- 50. Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, et al. (2013) Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 14: 498. pmid:23879659
- 51. The International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45: 487–494. pmid:23525075
- 52. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. (2006) The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596–1604. pmid:16973872
- 53. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, et al. (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 28: 951–956. pmid:20729833
- 54. Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, et al. (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30: 549–554. pmid:22580950
- 55. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641. pmid:22660326
- 56. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 189–195. pmid:21743474
- 57. Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, et al. (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 5: 3311. pmid:24548928
- 58. Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D, Cornejo O, et al. (2013) The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 14: R53. pmid:23731509
- 59. The French—Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463–467. pmid:17721507
- 60. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. (2009) The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326: 1112–1115. pmid:19965430
- 61. Huang S, Ding J, Deng D, Tang W, Sun H, Liu D, et al. (2013) Draft genome of the kiwifruit Actinidia chinensis. Nat Commun 4: 2640. pmid:24136039
- 62. Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, et al. (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505: 546–549. pmid:24352233
- 63. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, et al. (2011) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30: 83–89. pmid:22057054
- 64. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, et al. (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111: 5135–5140. pmid:24591624
- 65. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, et al. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31: 240–246. pmid:23354103
- 66. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, et al. (2008) Genome Structure of the Legume, Lotus japonicus. DNA Res 15: 227–239. pmid:18511435
- 67. D’Hont A, Denoeud F, Aury J- M, Baurens F- C, Carreel F, Garsmeur O, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213–217. pmid:22801500
- 68. Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, et al. (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4: 1–9.
- 69. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, et al. (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29: 521–527. pmid:21623354
- 70. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, et al. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579–584. pmid:23698360
- 71. Wegrzyn JL, Liechty JD, Stevens KA, Wu L-S, Loopstra CA, Vasquez-Gross HA, et al. (2014) Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation. Genetics 196: 891–909. pmid:24653211
- 72. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38: D46–D51. pmid:19910366
- 73. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423. pmid:19304878
- 74. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 39: W29–W37. pmid:21593126
- 75. Magrane M, UniProt Consortium (2011) UniProt Knowledgebase: a hub of integrated protein data. Database 2011: bar009–bar009. pmid:21447597
- 76. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443–453. pmid:5420325
- 77. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. pmid:2231712
- 78. Dosztányi Z, Csizmók V, Tompa P, Simon I (2005) The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins. J Mol Biol 347: 827–839. pmid:15769473
- 79. Millman KJ, Aivazis M (2011) Python for Scientists and Engineers. Comput Sci Eng 13: 9–12.
- 80. Oliphant TE (2007) Python for Scientific Computing. Comput Sci Eng 9: 10–20.
- 81. Kans J (2013) Entrez Direct: E-utilities on the UNIX Command Line. In: Entrez Programming Utilities Help (Internet). Bethesda (MD): National Center for Biotechnology Information (US); 2010-. Available: http://www.ncbi.nlm.nih.gov/books/NBK179288/. Accessed 11 January 2015.
- 82. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–W208. pmid:19458158
- 83. Fauteux F, Blanchette M, Strömvik MV (2008) Seeder: discriminative seeding DNA motif discovery. Bioinformatics 24: 2303–2307. pmid:18718942
- 84. Pavesi G, Mauri G, Pesole G (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17: S207–S214. pmid:11473011
- 85. Mahony S, Benos PV (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35: W253–W258. pmid:17478497
- 86. Crooks GE, Hon G, Chandonia J-M, Brenner SE (2004) WebLogo: A Sequence Logo Generator. Genome Res 14: 1188–1190. pmid:15173120
- 87. Close TJ (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97: 795–803.
- 88. Tunnacliffe A, Wise MJ (2007) The continuing conundrum of the LEA proteins. Naturwissenschaften 94: 791–812–812. pmid:17479232
- 89. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105–132. pmid:7108955
- 90. Fauteux F, Strömvik MV (2009) Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. BMC Plant Biol 9: 126. pmid:19843335
- 91. Rorat T, Grygorowicz WJ, Irzykowski W, Rey P (2003) Expression of KS-type dehydrins is primarily regulated by factors related to organ type and leaf developmental stage during vegetative growth. Planta 218: 878–885. pmid:14685858
- 92. Tommasini L, Svensson J, Rodriguez E, Wahid A, Malatrasi M, Kato K, et al. (2008) Dehydrin gene expression provides an indicator of low temperature and drought stress: transcriptome-based analysis of barley (Hordeum vulgare L.). Funct Integr Genomic 8: 387–405–405. pmid:18512091
- 93. Hara M, Shinoda Y, Kubo M, Kashima D, Takahashi I, Kato T, et al. (2011) Biochemical characterization of the Arabidopsis KS-type dehydrin protein, whose gene expression is constitutively abundant rather than stress dependent. Acta Physiol Plant 33: 2103–2116–2116.
- 94. Martínez-Hernández A, López-Ochoa L, Argüello-Astorga G, Herrera-Estrella L (2002) Functional properties and regulatory complexity of a minimal RBCS light-responsive unit activated by phytochrome, cryptochrome, and plastid signals. Plant Physiol 128: 1223–1233. pmid:11950971
- 95. Degenhardt J, Tobin EM (1996) A DNA binding activity for one of two closely defined phytochrome regulatory elements in an Lhcb promoter is more abundant in etiolated than in green plants. Plant Cell 8: 31–41. pmid:8597658
- 96. Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E (2005) Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol 138: 757–766. pmid:15908603
- 97. Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, et al. (2004) Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 136: 4159–4168. pmid:15557093
- 98. Hoekstra FA, Golovina EA, Buitink J (2001) Mechanisms of plant desiccation tolerance. Trends Plant Sci 6: 431–438. pmid:11544133
- 99. Ohno R, Takumi S, Nakamura C (2003) Kinetics of transcript and protein accumulation of a low-molecular-weight wheat LEA D-11 dehydrin in response to low temperature. J Plant Physiol 160: 193–200. pmid:12685035
- 100. Šunderlíková V, Salaj J, Kopecky D, Salaj T, Wilhem E, Matušíková I (2009) Dehydrin genes and their expression in recalcitrant oak (Quercus robur) embryos. Plant Cell Rep 28: 1011–1021. pmid:19466427
- 101. Kosugi S, Suzuka I, Ohashi Y (1995) Two of three promoter elements identified in a rice gene for proliferating cell nuclear antigen are essential for meristematic tissue-specific expression. Plant J 7: 877–886. pmid:7599648
- 102. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17: 287–291. pmid:10096298
- 103. Nordin K, Vahala T, Palva ET (1993) Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana (L.) Heynh. Plant Mol Biol 21: 641–653. pmid:8448363
- 104. Busk PK, Pagès M (1998) Regulation of abscisic acid-induced transcription. Plant Mol Biol 37: 425–435–435. pmid:9617810
- 105. Deng Z, Pang Y, Kong W, Chen Z, Wang X, Liu X, et al. (2013) A novel ABA-dependent dehydrin ERD10 gene from Brassica napus. Mitochondr DNA 16: 28–35.
- 106. Ezcurra I, Ellerström M, Wycliffe P, Stålberg K, Rask L (1999) Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression. Plant Mol Biol 40: 699–709. pmid:10480393
- 107. Busk PK, Pagès M (1997) Protein binding to the abscisic acid-responsive element is independent of VIVIPAROUS1 in vivo. Plant Cell 9: 2261–2270. pmid:11407411
- 108. Ono A, Izawa T, Chua N-H, Shimamoto K (1996) The rab16B promoter of rice contains two distinct abscisic acid-responsive elements. Plant Physiol. 112, 483–491. pmid:8883374
- 109. Straub PF, Shen Q, Ho TD (1994) Structure and promoter analysis of an ABA- and stress-regulated barley gene, HVA1. Plant Mol Biol 26: 617–630. pmid:7948917
- 110. Qin F, Sakuma Y, Li J, Liu Q, Li Y-Q, Shinozaki K, et al. (2004) Cloning and Functional Analysis of a Novel DREB1/CBF Transcription Factor Involved in Cold-Responsive Gene Expression in Zea mays L. Plant Cell Physiol 45: 1042–1052. pmid:15356330
- 111. Skinner JS, Zitzewitz J, Szűcs P, Marquez-Cedillo L, Filichkin T, Amundsen K, et al. (2005) Structural, Functional, and Phylogenetic Characterization of a Large CBF Gene Family in Barley. Plant Mol Biol 59: 533–551. pmid:16244905
- 112. Suzuki M, Ketterling MG, McCarty DR (2005) Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis. Plant Physiol 139: 437–447. pmid:16113229
- 113. Giuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, Cashmore AR (1988) An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci USA 85: 7089–7093. pmid:2902624
- 114. Donald RGK, Cashmore AR (1990) Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J 9: 1717. pmid:2347304
- 115. Ngai N, Tsai F-Y, Coruzzi G (1997) Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and transfactors. Plant J 12: 1021–1034. pmid:9418044
- 116. Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94: 1035–1040. pmid:9023378
- 117. Fowler SG, Cook D, Thomashow MF (2005) Low Temperature Induction of Arabidopsis CBF1, 2, and 3 Is Gated by the Circadian Clock. Plant Physiol 137: 961–968. pmid:15728337
- 118. Tóth R, Kevei E, Hall A, Millar AJ, Nagy F, Kozma-Bognár L (2001) Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. Plant Physiol 127: 1607–1616. pmid:11743105
- 119. Mikkelsen MD, Thomashow MF (2009) A role for circadian evening elements in cold-regulated gene expression in Arabidopsis. Plant J 60: 328–339. pmid:19566593
- 120. Rawat R, Xu Z-F, Yao K-M, Chye M-L (2005) Identification of cis-elements for ethylene and circadian regulation of the Solanum melongena gene encoding cysteine proteinase. Plant Mol Biol 57: 629–643. pmid:15988560
- 121. Kreps J, Budworth P, Goff S, Wang R (2003) Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm. Plant Biotechnol J 1: 345–352. pmid:17166133
- 122. Hong JC, Cheong YH, Nagao RT, Bahk JD, Key JL, Cho MJ (1995) Isolation of two soybean G-box binding factors which interact with a G-box sequence of an auxin-responsive gene. Plant J 8: 199–211. pmid:7670504
- 123. Xu N, Hagen G, Guilfoyle T (1997) Multiple auxin response modules in the soybean SAUR 15A promoter. Plant Sci 126: 193–201.
- 124. Lee B-H, Henderson DA, Zhu J-K (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell 17: 3155–3175. pmid:16214899
- 125. Shih M-D, Hoekstra FA, Hsing Y-IC (2008) Late Embryogenesis Abundant Proteins. In: Delseny J-CKAM, editor. Advances in Botanical Research. Advances in Botanical Research. Academic Press, Vol. Volume 48. pp. 211–255.
- 126. Archambault A, Strömvik MV (2011) The Y-segment of novel cold dehydrin genes is conserved and codons in the PR-10 genes are under positive selection in Oxytropis (Fabaceae) from contrasting climates. Mol Genet Genomics 287: 123–142. pmid:22183143
- 127. Sarnighausen E, Karlson DT, Zeng Y, Goldsbrough PB, Raghothama KG, Ashworth EN (2004) Characterization of a Novel YnSKn Class of Dehydrin-Like cDNAs from Cold Acclimated Red-Osier Dogwood (Cornus sericea L.) Xylem. J Crop Improv 10: 17–35.
- 128. Garcia-Bañuelos ML, Gardea AA, Winzerling JJ, Vazquez-Moreno L (2009) Characterization of a Midwinter-Expressed Dehydrin (DHN) Gene from Apple Trees (Malus domestica). Plant Mol Biol Rep 27: 476–487.
- 129. Welling A, Rinne P, Vihera-Aarnio A, Kontunen-Soppela S, Heino P, Palva TE (2004) Photoperiod and temperature differentially regulate the expression of two dehydrin genes during overwintering of birch (Betula pubescens Ehrh.). J Exp Bot 55: 507–516. pmid:14739271
- 130. Wisniewski ME, Bassett CL, Renaut J, Farrell R, Tworkoski T, Artlip TS (2006) Differential regulation of two dehydrin genes from peach (Prunus persica) by photoperiod, low temperature and water deficit. Tree Physiol 26: 575–584. pmid:16452071
- 131. Finch-Savage WE, Pramanik SK, Bewley JD (1994) The expression of dehydrin proteins in desiccation-sensitive (recalcitrant) seeds of temperate trees. Planta 193: 478–485.
- 132. Delahaie J, Hundertmark M, Bove J, Leprince O, Rogniaux H, Buitink J (2013) LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance. J Exp Bot.