XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues

Abstract

Background Fragaria vesca or ‘woodland strawberry’ has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit.ResultsThe search resulted in identification of 26 XTH-encoding genes named as FvXTHs. Genetic structure and phylogenetic analyses were performed allowing the classification of FvXTH genes into three phylogenetic groups: 17 in group I/II, 2 in group IIIA and 4 in group IIIB. Two sequences were included into the ancestral group. Through a comparative analysis, characteristic structural protein domains were found in FvXTH protein sequences. In complement, expression analyses of FvXTHs by qPCR were performed in fruit at different developmental and ripening stages, as well as, in other tissues. The results showed a diverse expression pattern of FvXTHs in several tissues, although most of them are highly expressed in roots. Their expression patterns are not related to their respective phylogenetic groups. In addition, most FvXTHs are expressed in ripe fruit, and interestingly, some of them (FvXTH 18 and 20, belonging to phylogenic group I/II, and FvXTH 25 and 26 to group IIIB) display an increasing expression pattern as the fruit ripens.ConclusionA discrete group of FvXTHs (18, 20, 25 and 26) increases their expression during softening of F. vesca fruit, and could take part in cell wall remodeling required for softening in collaboration with other cell wall degrading enzymes.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4255-8) contains supplementary material, which is available to authorized users.

Genome-Wide Identification, Characterization and Expression Analysis of Xyloglucan Endotransglucosylase/Hydrolase Genes Family in Barley (Hordeum vulgare)

“…The first glutamate residue (E) acts as catalytic nucleophile which initiates the enzymatic reaction and the second one as a base to activate the substrate. All members of HvXTH family, except HvXTH15 (ancestral group), had a conserved N -glycosylation site (marked with asterisks), which is proximal to the catalytic residues as reported in Fragaria vesca [12]. The N -glycosylation site domain (NxT/S/Y) is thought to play a role in protein stability.…”

“…Detailed three-dimensional structures of Tm-NXG1 and Tm-NXG2 revealed the major structural features of the active site regulating relative rates of hydrolysis to transglycosylation in GH16 xyloglucan-active enzymes transformation, suggesting that XTH genes evolved to have a role in cell wall remodeling [11]. A study of XTHs in Fragaria vesca also suggested a similar classification of XTH genes and revealed differing expression levels of XTHs during different developmental stages of fruit ripening and in different tissues [12].…”

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment

“…The XTHs can catalyze endolytic cleavage of xyloglucan polymers, thereby promoting fruit softening [86]. The XTH genes also participate in the degradation of cell walls [91] and are involved in fruit softening [92,93]. Yun et al [94] confirm that an XTH gene can promote the ripening of banana fruit by the degradation of hemicelluloses.…”

MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo (Citrus grandis Osbeck)

“…In the current study, mRNA for xyloglucan endotransglucosylase was highly abundant in MT fruit in the early developmental stages and xyloglucan endotransglucosylase was predicted as the target of miR9480a. A discrete group of FvXTHs increased their expression during softening of wild strawberry fruit, which was required for cell wall remodeling in fruit softening [42]. Expansin-A1 was up-regulated in MT fruit from S2 to S4, it is the target of miR8175 (Table 2).…”