Genome-wide identification and expression analysis of Ubiquitin-specific protease gene family in maize (Zea mays L.)

Abstract

Background Ubiquitin-specific proteases (UBPs) are a large family of deubiquitinating enzymes (DUBs). They are widespread in plants and are critical for plant growth, development, and response to external stresses. However, there are few studies on the functional characteristics of the UBP gene family in the important staple crop, maize (Zea mays L.). Results In this study, we performed a bioinformatic analysis of the entire maize genome and identified 45 UBP genes. Phylogenetic analysis indicated that 45 ZmUBP genes can be divided into 15 subfamilies. Analysis of evolutionary patterns and divergence levels indicated that ZmUBP genes were present before the isolation of dicotyledons, were highly conserved and subjected to purifying selection during evolution. Most ZmUBP genes exhibited different expression levels in different tissues and developmental stages. Based on transcriptome data and promoter element analysis, we selected eight ZmUBP genes whose promoters contained a large number of plant hormones and stress response elements and were up-regulated under different abiotic stresses for RT-qPCR analysis, results showed that these genes responded to abiotic stresses and phytohormones to varying degrees, indicating that they play important roles in plant growth and stress response. Conclusions In this study, the structure, location and evolutionary relationship of maize UBP gene family members were analyzed for the first time, and the ZmUBP genes that may be involved in stress response and plant growth were identified by combining promoter element analysis, transcriptome data and RT-qPCR analysis. This study informs research on the involvement of maize deubiquitination in stress response.

An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response

“…The number of UBP members varies with the genome size of different plants, but given their highly conserved functions, such variation is limited ( Table 2 ). For example, there are 44 UBPs in rice ( Oryza sativa ), 44 in Populus trichocarpa , 45 in maize ( Zea mays ), 21 in Vernicia fordii , and 48 in Moso bamboo ( Wang et al., 2018 ; Wu et al., 2019a ; Zheng and Du, 2021 ; Cao et al., 2022 ; Fu et al., 2024 ). Here, we constructed a phylogenetic tree for UBPs from five representative plant species: the dicotyledonous herb A. thaliana , the monocotyledonous O. sativa , the dicotyledonous woody tree P. trichocarpa , the lycophyte Selaginella moellendorffii , and the bryophyte Physcomitrium patens .…”