Abstract
The largest group of deubiquitinases—ubiquitin-specific proteases (UBPs)—perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.
Highlights
Post-translational modifications (PTMs) of target proteins control many cellular processes [1,2], and ubiquitination is involved in many physiological events including DNA repair, cell-cycle control, abiotic or biotic stress tolerance, immune responses, endocytosis, and vesicle trafficking [3,4]
There are 27 putative ubiquitin-specific proteases (UBPs) family members in Arabidopsis thaliana classified into 14 sub-groups, and 21 in rice (Oryza sativa) classified into nine sub-groups [12,15]
We identified 67 PeUBP candidate genes, which were applied to confirm the existence of the conserved Ub carboxyl-terminal hydrolase (UCH) domain in UBP proteins using the Pfam database and the NCBI CD-search program
Summary
Post-translational modifications (PTMs) of target proteins control many cellular processes [1,2], and ubiquitination is involved in many physiological events including DNA repair, cell-cycle control, abiotic or biotic stress tolerance, immune responses, endocytosis, and vesicle trafficking [3,4]. Among the many types of DUBs, the highly conserved ubiquitin-specific proteases (UBPs) form the largest subfamily in plants. In addition to the conserved UCH domain, UBP proteins have additional non-UBP protein motifs such as the MYND-type zinc finger domain (ZnF-MYND) which has been reported to be a protein–protein interaction domain in mammalian cells, the zinc finger domain ZnF-UBPs, the meprin and TRAF homology (MATH) domains, the domain present in Ubiquitin-Specific Proteases (DUSPs), and Ubiquitin-associated (UBA) domains [13,14]. UBPs have multiple functions in cell proliferation [13,16], endoreplication [17], root hair elongation [18,19], mitochondria morphogenesis [20], deubiquitination of monoubiquitinated-H2A and -H2B [21,22], pollen development and transmission [22], canavanine resistance [12] and abscisic acid (ABA)-mediated resistance to salt and drought stress [23]
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