Genome-wide identification and expression profiling reveal the regulatory role of U-box E3 ubiquitin ligase genes in strawberry fruit ripening and abiotic stresses resistance

Abstract

The plant U-box (PUB) proteins are a type of E3 ubiquitin ligases well known for their functions in response to various stresses. They are also related to fruit development and ripening. However, PUB members possess such roles that remain unclear in strawberry. In this study, 155 PUB genes were identified in octoploid strawberry and classified into four groups. Their promoters possessed a variety of cis-acting elements, most of which are associated with abiotic stresses, followed by phytohormones response and development. Protein-protein interaction analysis suggested that FaU-box members could interact with each other as well as other proteins involved in hormone signaling and stress resistance. Transcriptome-based and RT-qPCR expression analysis revealed the potential involvement of FaU-box genes in resistance to stresses and fruit ripening. Of these, FaU-box98 and FaU-box136 were positively while FaU-box52 was negatively related to strawberry ripening. FaU-box98 comprehensively participated in resistance of ABA, cold, and salt, while FaU-box83 and FaU-box136 were broadly associated with drought and salt stresses. FaU-box18 and FaU-box52 were ABA-specific; FaU-box3 was specific to salt stress. In addition, the functional analysis of a randomly selected FaU-box (FaU-box127) showed that the transient overexpression of FaU-box127 promoted the ripening of strawberry fruit, along with significant changes in the expression levels of some ripening-related genes and the content of organic acid and soluble sugar. Overall, these findings provided comprehensive information about the FaU-box gene family and identified the potential FaU-box members participating in stress resistance and strawberry fruit ripening regulation.

Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress

“…Currently, plant U-box type E3 ubiquitin ligases, as members of the single-subunit group, are widely distributed in eukaryotic organisms. The U-box domain contains about 70 amino acids, which is structurally related to RING-type [ 10 ]. Plant U-box (PUB) proteins are identified in an increasing number of plant species with different gene numbers.…”

“…In strawberry ( Fragaria × ananassa Duch. ), the PUB genes FaU-box83 , FaU-box3 , FaU-box98 and FaU-box136 are continuously induced by salt stress [ 10 ]. Overexpression of wheat ( Triticum aestivum L.) TaPUB26 in Brachypodium distachyon disrupts intracellular ion homeostasis while decreasing the activity of antioxidant enzymes, which in turn reduces the salt tolerance of transgenic B. distachyon [ 19 ].…”

“…Overexpression of the TaPUB1 gene in wheat can maintain a low Na + /K + ratio and regulate antioxidant enzyme activity to improve salt tolerance in transgenic wheat [ 19 ]. Although the biological functions of PUB genes with regard to salt stress tolerance have been reported in some plants [ 10 , 14 , 20 ], the functions of PUB genes have not yet been reported in perennial halophytes, and the regulation mechanism of PUB genes in response to salt stress in different plants remains to be further elucidated.…”

“…Currently, the studies on the molecular mechanisms of salt tolerance in Zoysia plants are mainly associated with the identification of genes and their biological function [ 27 , 28 , 29 , 30 ]. To date, the U-box E3 ubiquitin ligase genes have not been studied in Z. japonica , although PUB genes have been reported to be associated with salt tolerance in many other plants [ 10 , 17 ]. The present study conducted the genome-wide identification, cis -element analysis, and protein interaction prediction of PUB genes under salt stress in Z. japonica , and investigated their evolutionary relationships, gene structures, and expression patterns.…”

Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)

“…In crop plants, U-box genes have been identified in the genomes of various plants, including rice, cabbage, soybean, tomato, barley, cotton ( G. barbadense ), wheat, sorghum, potato, Brassica oleracea L., wild emmer wheat and Solanum tuberosum , with a total of 41 to 213 genes, respectively [ 23 – 34 ]. In fruit plants such as banana, stony hard peach, white pear, apple and strawberry, with a total of 62 to 765 U-box genes have been identified, respectively [ 35 – 39 ].…”