Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis

Abstract

The U-box gene encodes a ubiquitin ligase that contains a U-box domain. The plant U-box (PUB) protein plays an important role in the plant stress response; however, very few studies have investigated the role of these proteins in Moso bamboo (Phyllostachys edulis). Thus, more research on PUB proteins is necessary to understand the mechanisms of stress tolerance in P. edulis. In this study, we identified 121 members of the PUB family in P. edulis (PePUB), using bioinformatics based on the P. edulis V2 genome build. The U-box genes of P. edulis showed an uneven distribution among the chromosomes. Phylogenetic analysis of the U-box genes between P. edulis and Arabidopsis thaliana suggested that these genes can be classified into eight subgroups (Groups I–VIII) based on their structural and phylogenetic features. All U-box genes and the structure of their encoded proteins were identified in P. edulis. We further investigated the expression pattern of PePUB genes in different tissues, including the leaves, panicles, rhizomes, roots, and shoots. The qRT-PCR results showed that expression of three genes, PePUB15, PePUB92, and PePUB120, was upregulated at low temperatures compared to that at 25°C. The expression levels of two PePUBs, PePUB60 and PePUB120, were upregulated under drought stress. These results suggest that the PePUB genes play an important role in resistance to low temperatures and drought in P. edulis. This research provides new insight into the function, diversity, and characterization of PUB genes in P. edulis and provides a basis for understanding their biological roles and molecular mechanisms.

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

“…SbPUB13 in Group 3 contained two WD40 repeats, which might participate in transcriptional regulation and signaling (Villamil et al, 2013;Jain and Pandey, 2018). In addition, six SbPUB genes in Group 5 had the USP, Pkinase, and TRR domains, indicating that these proteins are involved in signal transduction via phosphorylation and play an important role in PPIs (Fiedler et al, 1993;Zhou et al, 2021).…”

Identification and expression analysis of the lipid phosphate phosphatases gene family reveal their involvement in abiotic stress response in kiwifruit

“…Research shows that TGACG-motif, TGA-element, ABRE, G-box, MBS and GT1-motif have regulatory effects under salt stress (Yamniuk and Vogel, 2004 ). Studies have shown that these cis-acting elements are able to respond to changes in external stimuli and rapidly regulate gene expression (Zhou et al, 2021 ). These findings provide a basis for our in-depth understanding of the molecular mechanisms underlying the function of the AcLPP genes.…”

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

“…SbPUB13 in Group 3 contained two WD40 repeats, which might participate in transcriptional regulation and signaling [44,45]. In addition, six SbPUB genes in Group 5 had the USP, Pkinase, and TRR domains, indicating that these proteins are in involved in signal transduction via phosphorylation and play an important role in PPIs [46,47].…”