Utility of the Amborella trichopoda expansin superfamily in elucidating the history of angiosperm expansins

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

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.

Ectopic expression of an expansin-like B gene from wild Arachis enhances tolerance to both abiotic and biotic stresses

Plant expansins are structural cell wall-loosening proteins implicated in several developmental processes and responses to environmental constraints and pathogen infection. To date, there is limited information about the biological function of expansins-like B (EXLBs), one of the smallest and less-studied subfamilies of plant expansins. In the present study, we conducted a functional analysis of the wild Arachis AdEXLB8 gene in transgenic tobacco (Nicotiana tabacum) plants to clarify its putative role in mediating defense responses to abiotic and biotic stresses. First, its cell wall localization was confirmed in plants expressing an AdEXLB8:eGFP fusion protein, while nanomechanical assays indicated cell wall reorganization and reassembly due to AdEXLB8 overexpression without compromising the phenotype. We further demonstrated that AdEXLB8 increased tolerance not only to isolated abiotic (drought) and biotic (Sclerotinia sclerotiorum and Meloidogyne incognita) stresses but also to their combination. The jasmonate and abscisic acid signaling pathways were clearly favored in transgenic plants, showing an activated antioxidative defense system. In addition to modifications in the biomechanical properties of the cell wall, we propose that AdEXLB8 overexpression interferes with phytohormone dynamics leading to a defense primed state, which culminates in plant defense responses against isolated and combined abiotic and biotic stresses.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in watermelon (Citrullus lanatus)

Expansins are plant cell-wall loosening proteins involved in cell enlargement, adaptive responses to environmental stimuli, and various developmental processes. Although expansins have been characterized in many plant species, little is reported on this family in watermelon. In this study, 30 expansin genes in the watermelon genome (ClEXPs) were identified. These genes which were divided into four subfamilies (7 ClEXLAs, 2 ClEXLBs, 18 ClEXPAs, and 3 ClEXPBs) are unevenly distribute on 10 of 11 watermelon chromosomes. Chromosome mapping suggested that tandem duplication events may have played important roles in the expanding of watermelon expansins. Gene structure and motif identification revealed that same subfamily and subgroup have conserved gene structure and motif. Detection of cis-acting elements revealed that ClEXPs gene promoter regions were enriched with light-responsive elements, hormone-responsive, environmental stress-related, and development-related elements. Expression patterns of ClEXPs were investigated by qRT-PCR. The results showed that expression patterns of 15 ClEXP genes differed in three tissues. Through our own and public RNA-seq analysis, we found that ClEXPs had different expression patterns in fruit flesh, fruit rind, and seed at various developmental stages, and most of ClEXPs were highly responsive to abiotic and biotic stresses. Remarkably, 7 ClEXPs (ClEXLA1, ClEXLA6, ClEXLB1, ClEXLB2, ClEXPA5, ClEXPA10, and ClEXPA16) exhibited positive response to at least three kinds of stresses, suggesting that they might play important roles in the crosstalk of stress signal pathways. The results of this study provide useful insights for the functional identification of expansin gene family in watermelon.

Phylogenetic comparison of 5' splice site determination in central spliceosomal proteins of the U1-70K gene family, in response to developmental cues and stress conditions

Intron-containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding the eukaryotic transcriptome and proteome. In eukaryotic cells, precursor mRNA (pre-mRNA) splicing is performed by a mega-macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5'-splice site recognition. Its central component, named U1-70K, has been extensively characterized in animals and yeast. Very few investigations on U1-70K genes have been conducted in plants, however. To this end, we performed a comprehensive study to systematically identify 115 U1-70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that the expansion of the plant U1-70K gene family was likely to have been driven by whole-genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1-70Ks are likely to preserve their conserved molecular function across plant lineages and play an important functional role in response to environmental stresses. Furthermore, genetic analysis using T-DNA insertion mutants suggested that Arabidopsis U1-70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source for future mechanistic studies on this U1 snRNP-specific splicing factor.

Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica

Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.

Expansin gene loss is a common occurrence during adaptation to an aquatic environment

Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene

Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.

Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)

Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants' ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.