Research Article: Evolution of the modular, disordered stress proteins known as dehydrins

Date Published: February 6, 2019

Publisher: Public Library of Science

Author(s): Andrew C. Riley, Daniel A. Ashlock, Steffen P. Graether, Marc Robinson-Rechavi.

http://doi.org/10.1371/journal.pone.0211813

Abstract

Dehydrins, plant proteins that are upregulated during dehydration stress conditions, have modular sequences that can contain three conserved motifs (the Y-, S-, and K-segments). The presence and order of these motifs are used to classify dehydrins into one of five architectures: Kn, SKn, KnS, YnKn, and YnSKn, where the subscript n describes the number of copies of that motif. In this study, an architectural and phylogenetic analysis was performed on 426 dehydrin sequences that were identified in 53 angiosperm and 3 gymnosperm genomes. It was found that angiosperms contained all five architectures, while gymnosperms only contained Kn and SKn dehydrins. This suggests that the ancestral dehydrin in spermatophytes was either Kn or SKn, and the Y-segment containing dehydrins first arose in angiosperms. A high-level split between the YnSKn dehydrins from either the Kn or SKn dehydrins could not be confidently identified, however, two lower level architectural divisions appear to have occurred after different duplication events. The first likely occurred after a whole genome duplication, resulting in the duplication of a Y3SK2 dehydrin; the duplicate subsequently lost an S- and K- segment to become a Y3K1 dehydrin. The second split occurred after a tandem duplication of a Y1SK2 dehydrin, where the duplicate lost both the Y- and S- segment and gained four K-segments, resulting in a K6 dehydrin. We suggest that the newly arisen Y3K1 dehydrin is possibly on its way to pseudogenization, while the newly arisen K6 dehydrin developed a novel function in cold protection.

Partial Text

Due to their sessile nature, plants have evolved various methods for responding to biotic and abiotic stresses. Contact with abiotic (environmental) stresses can cause severe damage to plants, which can result in crop loss, growth impairment, and even death [1,2]. Dehydration, itself a significant abiotic stress in plants, can take many forms, such as drought, cold, and high salinity. Under such conditions, plants face numerous problems, including mechanical impairment, alterations in turgor pressure, and loss of cell integrity [1]. A group of proteins, known as dehydration proteins (dehydrins), have their expression correlated with dehydration stress and protection [3]. Dehydrins are a member of a protein family known as the late embryogenesis abundant (LEA) proteins [3–7]. The exact in vivo biochemical function of dehydrins is currently unknown, however in vitro experiments have given clues as to how they can protect plants. Experiments have shown that dehydrins may have roles in enzyme cryoprotection [8–14], membrane protection [15–17], and protection against reactive oxygen species [18–20].

After performing the filtering and iterative searching as described in the Material and Methods, a total of 426 dehydrin sequences were collected from 56 spermatophyte genomes. Of those dehydrins, 69 were the Kn architecture, 54 were KnS, 140 were SKn, 22 were YnKn, and 141 were YnSKn. In the three gymnosperm species, 22 Kn and 21 SKn architectures were identified. Aside from the three well-documented segments (Y-, S- and K-segments), only two other motifs were consistently detected (i.e. in at least ~100 sequences). The logo of one motif can be seen in Fig 1, and is similar to the F-segment that was previously described by Strimbeck [59], but the two segment definitions differ at the termini. The F-segment described in Fig 1 has an additional Glu at the N-terminal end, followed by two fairly variable residues, while the F-segment described by Strimbeck had an additional two Lys at the C-terminal end [59]. The F-segment was found in 121 sequences, of which 111 were SKn dehydrins and 10 were Kn dehydrins. The other motif that was detected is a string of Lys (11 residues of Lys interspersed with Arg, Asp and Glu), which was found in 94 sequences. In the 51 KnS dehydrins and 42 SKn dehydrins, the poly-Lys repeat was located between the S- and K-segments. It was also detected in one Kn dehydrin.

Gene duplication is a major contributor to plant evolution. The average number of genes in plants found to be paralogous is 64.5%, ranging from 45.5% in Physcomitrella patens to 84.4% in Malus domestica [68]. There are five main mechanisms that result in gene duplication: whole genome duplication (WGD), tandem duplication, transposon-mediated duplication, segmental duplication, and retroduplication [68,69]. After duplication, a gene is either lost or retained; a gene can be lost if it undergoes pseudogenization or if it is deleted from the genome [68,69]. This can occur for various reasons, for example, if the duplicated gene is redundant and its loss results in no decrease in fitness [68,69]. A duplicated gene is retained if it results in improved fitness, such as from a change in function [68,69]. The presence of multiple dehydrins in different plant species [21] suggests that the different copies most likely arose through duplication events. The different dehydrin architectures that arose also suggest that dehydrins may be gaining new functions or variations of their original function. The only dehydrin architectures that were found across all spermatophytes we studied were the Kn and SKn dehydrins. A lack of dehydrins containing the Y-segment in gymnosperms was previously described [70]. Expression data of Y-segment containing dehydrins was compared to SKn in A. thaliana, Populus trichocarpa, Oryza sativa, Zea mays, and Brachypodium distachyon [66,71–74]. We observed that during seed germination, Y-segment containing dehydrins were always upregulated to very high levels, whereas SKn dehydrins were not upregulated or only to a lower level (S2, S3, S4, S5 and S6 Tables). The absence of Y-segments in gymnosperms and the upregulation of Y-segment containing dehydrins in angiosperm seeds suggests the Y-segment has some role in coated seeds. Note that the F-segment was found in both angiosperm and gymnosperm SKn dehydrins [59]. These findings give rise to the possibility that the architecture of the ancestral dehydrins in spermatophytes is either a Kn or SKn dehydrin containing an F-segment, and that the YnSKn dehydrins arose after the angiosperms and gymnosperms division.

Two potential dehydrin architectural changes appeared after gene duplication. The first was a change from a Y3SK2 to a Y3K1 dehydrin, however the observed decrease in expression levels under similar conditions may be an indicator of the Y3K1 gene being pseudogenized. The second was a change from Y1SK2 to K6. The K6 dehydrin in A. thaliana had much higher expression during cold stress, and larger dehydrin constructs with higher numbers of K-segments have been shown to have improved enzyme cryoprotection [25]. These two duplications account for all of the Kn and YnKn dehydrins in the Brassicaceae family. Further work needs to be done to investigate what the architecture of the ancestral dehydrin was. Determining if and when the YnSKn dehydrins split from SKn may be important in answering this question.

 

Source:

http://doi.org/10.1371/journal.pone.0211813

 

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