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Cited by 21Plant Stress Responses and TolerancePlant Molecular Biology ResearchSeed Germination and Physiology

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Evolutionary analysis of angiosperm dehydrin gene family reveals three orthologues groups associated to specific protein domains

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Melgar, Alejandra E., Zelada, Alicia M.·2021·Scientific Reports
DOI 10.1038/s41598-021-03066-5PMC PMC8669000

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Abstract

Dehydrins (DHNs) are a family of plant proteins that play important roles on abiotic stress tolerance and seed development. They are classified into five structural subgroups: K-, SK-, YK-, YSK-, and KS-DHNs, according to the presence of conserved motifs named K-, Y- and S- segments. We carried out a comparative structural and phylogenetic analysis of these proteins, focusing on the less-studied KS-type DHNs. A search for conserved motifs in DHNs from 56 plant genomes revealed that KS-DHNs possess a unique and highly conserved N-terminal, 15-residue amino acid motif, not previously described. This novel motif, that we named H-segment, is present in DHNs of angiosperms, gymnosperms and lycophytes, suggesting that HKS-DHNs were present in the first vascular plants. Phylogenetic and microsynteny analyses indicate that the five structural subgroups of angiosperm DHNs can be assigned to three groups of orthologue genes, characterized by the presence of the H-, F- or Y- segments. Importantly, the hydrophilin character of DHNs correlate with the phylogenetic origin of the DHNs rather than to the traditional structural subgroups. We propose that angiosperm DHNs can be ultimately subdivided into three orthologous groups, a phylogenetic framework that should help future studies on the evolution and function of this protein family.

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Figures

Figure 1 DHNs identified in Viridiplantae genomes by different HMM profiles. Sequences retrieved from species genomes using F-HMM, Y-HMM, KS-HMM profiles constructed in this study and Pfam00257 the Pfam profile for dehydrin family proteins are displayed as a Venn diagram. White numbers indicate the number of KS-DHNs present in each subset. Note that most KS-DHNs are not recovered using Pfam00257.
Figure 1 DHNs identified in Viridiplantae genomes by different HMM profiles. Sequences retrieved from species genomes using F-HMM, Y-HMM, KS-HMM profiles constructed in this study and Pfam00257 the Pfam profile for dehydrin family proteins are displayed as a Venn diagram. White numbers indicate the number of KS-DHNs present in each subset. Note that most KS-DHNs are not recovered using Pfam00257.CC BY · PubMed Central
Figure 2 Identification of conserved protein motifs and structural classification of DHNs. (a) LOGO representation of the different conserved motifs detected by MEME in the set of DHNs of the unbiased database. (b) Number of members of each angiosperm DHN structural subgroup identified in the unbiased database. We distinguished FSK2 and FSK3 structural subgroups in accordance to Strimbeck6. All classified DHNs belonging to 19 angiosperm families are listed in Supplementary Data S1. The dotted pattern indicates monocots, while the filled pattern indicates eudicots.
Figure 2 Identification of conserved protein motifs and structural classification of DHNs. (a) LOGO representation of the different conserved motifs detected by MEME in the set of DHNs of the unbiased database. (b) Number of members of each angiosperm DHN structural subgroup identified in the unbiased database. We distinguished FSK2 and FSK3 structural subgroups in accordance to Strimbeck6. All classified DHNs belonging to 19 angiosperm families are listed in Supplementary Data S1. The dotted pattern indicates monocots, while the filled pattern indicates eudicots.CC BY · PubMed Central
Figure 3 Conservation of KS-DHNs in vascular plants. Multiple sequence alignment of KS-DHNs (HKS-DHNs) of representative angiosperms (A. trichopoda, S. bicolor, N. nucifera, A. thaliana, M. truncatula) and non-angiosperms (the lycophyte S. moellendorffii and the gymnosperm G. biloba) performed with T-Coffee and visualised with Jalview. The H-, K-, B and S-segments are indicated. Note that the general structure of the proteins is conserved in all vascular plant groups.
Figure 3 Conservation of KS-DHNs in vascular plants. Multiple sequence alignment of KS-DHNs (HKS-DHNs) of representative angiosperms (A. trichopoda, S. bicolor, N. nucifera, A. thaliana, M. truncatula) and non-angiosperms (the lycophyte S. moellendorffii and the gymnosperm G. biloba) performed with T-Coffee and visualised with Jalview. The H-, K-, B and S-segments are indicated. Note that the general structure of the proteins is conserved in all vascular plant groups.CC BY · PubMed Central
Figure 4 Disorder prediction plots for representative angiosperm H-DHNs (KS-DHN). Disorder of A. trichopoda, S. bicolor and A. thaliana H-DHN proteins were predicted by the IUPred2A program. Note that all proteins are predicted as fully disordered (score > 0.5), however, regions corresponding to the H- and K-motifs display reduced disorder tendency. The H-, K-, B and S-segments are indicated.
Figure 4 Disorder prediction plots for representative angiosperm H-DHNs (KS-DHN). Disorder of A. trichopoda, S. bicolor and A. thaliana H-DHN proteins were predicted by the IUPred2A program. Note that all proteins are predicted as fully disordered (score > 0.5), however, regions corresponding to the H- and K-motifs display reduced disorder tendency. The H-, K-, B and S-segments are indicated.CC BY · PubMed Central
Figure 5 Unrooted phylogenetic tree of angiosperm DHN proteins. Amino acid sequences of DHN proteins from angiosperms were aligned and an approximately maximum-likelihood reconstruction of the phylogenetic relationships was generated using IQ-TREE. Branches with bootstrap support over 90% are indicated by a violet dot. The motifs of each protein are indicated by coloured boxes, as indicated. Note that all H-DHNs (KS-DHNs) are grouped together in a branch with high support, and most F- and Y-DHNs are also grouped together, forming three groups. DHN proteins from the angiosperm A. trichopoda (red) and the eudicot N. nucifera (blue) are indicated to show that they possess one DHN in each group. The tree is unrooted and shows the relative relatedness of the sequences, meaning that the position of the apparent root is arbitrary.
Figure 5 Unrooted phylogenetic tree of angiosperm DHN proteins. Amino acid sequences of DHN proteins from angiosperms were aligned and an approximately maximum-likelihood reconstruction of the phylogenetic relationships was generated using IQ-TREE. Branches with bootstrap support over 90% are indicated by a violet dot. The motifs of each protein are indicated by coloured boxes, as indicated. Note that all H-DHNs (KS-DHNs) are grouped together in a branch with high support, and most F- and Y-DHNs are also grouped together, forming three groups. DHN proteins from the angiosperm A. trichopoda (red) and the eudicot N. nucifera (blue) are indicated to show that they possess one DHN in each group. The tree is unrooted and shows the relative relatedness of the sequences, meaning that the position of the apparent root is arbitrary.CC BY · PubMed Central
Figure 6 Microsynteny analysis of angiosperm H-DHNs genes. The genomic neighbourhood of the H-DHN gene of A. trichopoda (LOC18421535) is compared to that of other angiosperms. H-DHN genes are indicated as black dots, and a colour code indicates homologous genes present in the other species. Grey dots indicate genes only present in A. trichopoda. Some intervening genes in species other than A. trichopoda are not shown for clarity.
Figure 6 Microsynteny analysis of angiosperm H-DHNs genes. The genomic neighbourhood of the H-DHN gene of A. trichopoda (LOC18421535) is compared to that of other angiosperms. H-DHN genes are indicated as black dots, and a colour code indicates homologous genes present in the other species. Grey dots indicate genes only present in A. trichopoda. Some intervening genes in species other than A. trichopoda are not shown for clarity.CC BY · PubMed Central
Figure 7 Distribution of biochemical and biophysical properties of angiosperm DHNs. Scatter plots show the distribution of molecular weight (a), isoelectric point (b and f), glycine content (c), GRAVY index (d), Fold Index (e) or glycine content, GRAVY and Fold index simultaneously (g) in orthologous or structural subgroups of DHNs. Members of the three orthologous groups of DHNs are colour-coded: Y- (green), F- (orange) and H-DHNs (violet).
Figure 7 Distribution of biochemical and biophysical properties of angiosperm DHNs. Scatter plots show the distribution of molecular weight (a), isoelectric point (b and f), glycine content (c), GRAVY index (d), Fold Index (e) or glycine content, GRAVY and Fold index simultaneously (g) in orthologous or structural subgroups of DHNs. Members of the three orthologous groups of DHNs are colour-coded: Y- (green), F- (orange) and H-DHNs (violet).CC BY · PubMed Central

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Metadata

Authors
Melgar, A. E., & Zelada, A. M.
Affiliations
Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
Corresponding author
Zelada, Alicia M.
ORCID
Zelada, Alicia M.
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2021-12-13
Volume
11
Issue
1
Pages
23869-23869
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-021-03066-5
PMC
PMC8669000
OpenAlex
W4200094692
Cited by
21
References
75
Citations by year
2026: 4 · 2025: 8 · 2024: 6 · 2023: 2 · 2022: 1
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Greater South Information System
Funders
Consejo Nacional de Investigaciones Científicas y Técnicas (PIP 11220150100584)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Stress Responses and Tolerance
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Seed Germination and Physiology
Keywords
dehydrins, flowering plants, phylogenetic analysis, conserved motifs, abiotic stress tolerance, seed development, microsynteny, protein family evolution, gymnosperms, lycophytes
MeSH terms
Protein Domains, Multigene Family, Phylogeny, Plant Proteins, Evolution, Molecular, Magnoliopsida, Amino Acid Motifs

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CoChat. (2026). Citation check: Evolutionary analysis of angiosperm dehydrin gene family reveals three orthologues groups associated to specific protein domains. https://app.cochat.ai/papers/10.1038/s41598-021-03066-5
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Melgar, A. E., & Zelada, A. M. (2021). Evolutionary analysis of angiosperm dehydrin gene family reveals three orthologues groups associated to specific protein domains. Scientific Reports. https://doi.org/10.1038/s41598-021-03066-5

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