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Evolution of the modular, disordered stress proteins known as dehydrins.

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.

SUBMITTER: Riley AC

PROVIDER: S-EPMC6364937 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Evolution of the modular, disordered stress proteins known as dehydrins.

Riley Andrew C AC Ashlock Daniel A DA Graether Steffen P SP

PloS one 20190206 2

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 ...[more]

PMID: 30726271

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Project description:Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity (>85%, 85-60%, and 60-40%), were inferred for each type of protein structure. The substitution matrices for disordered and ordered proteins differed significantly at each level of sequence similarity. The disordered matrices reflected a greater likelihood of evolutionary changes, relative to the ordered matrices, and these changes involved nonconservative substitutions. Glutamic acid and asparagine were interesting exceptions to this result. Important differences between the substitutions that are accepted in disordered proteins relative to ordered proteins were also identified. In general, disordered proteins have fewer evolutionary constraints than ordered proteins. However, some residues like tryptophan and tyrosine are highly conserved in disordered proteins. This is due to their important role in forming protein-protein interfaces. Finally, the amino acid frequencies for disordered proteins, computed during the development of the matrices, were compared with amino acid frequencies for different categories of secondary structure in ordered proteins. The highest correlations were observed between the amino acid frequencies in disordered proteins and the solvent-exposed loops and turns of ordered proteins, supporting an emerging structural model for disordered proteins.

Dataset Information

Evolution of the modular, disordered stress proteins known as dehydrins.

Publications

Evolution of the modular, disordered stress proteins known as dehydrins.

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