Genome-wide investigation and analysis of U-box Ubiquitin–Protein ligase gene family in apple: Expression profiles during Penicillium expansum infection process

Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

“…At last, 62 PUB genes with complete U-box domain were obtained for further analysis. The number of PUB genes in pear are similar to the number of PUB genes in apple (69) [ 18 ]. Based on the location order of PUB genes, we named 62 PbrPUB genes (Table 1 ).…”

“…As a family of ubiquitin ligases, U-box genes encode a conserved U-box motif of about 70 amino acids and regulated the ubiquitination of the substrates [ 23 ]. U-box genes were widely distributed in the plants and reported to participate in many biological processes including plant hormone signaling regulations [ 6 ], self-incompatible or pseudo-self-compatibility regulations [ 18 ] as well as in biotic stress[ 19 – 21 ] and abiotic stress [ 5 , 22 , 23 ]. Due to PUB gene play an important role during plant development, PUB genes have been identified in different plant species, such as Arabidopsis thaliana (61) [ 9 , 10 ], rice (77) [ 11 ], tomato (62) [ 12 ], cotton (93) [ 13 ], and banana (91) [ 14 ].…”

“…For example, 125 GmPUB genes in soybean proteins were classified into six groups using phylogenetic tree analysis [ 17 ]. In apple, 69 U-box genes were clustered into seven groups [ 18 ]. Through the phylogenetic relationship analysis, it showed that PbrPUB s exhibited closer relations with SIU-boxs compared with AtPUBs .…”

“…In addition to the U-box domain, 62 PbrPUB proteins are found to bind to different domains including armadillo (ARM) repeats, the tetratricopeptide (TPR) domain and WD40 repeats. The majority of PUB proteins that have been elucidated for biological functions are from the U-box proteins with ARM repeats [ 18 ]. The ARM repeats have been shown primarily mediating the interaction with substrates, suggesting that interaction make the substrates available for ubiquitination [ 23 ].…”

“…In Arabidopsis thaliana , about 61 plant U-box genes were predicted [ 9 , 10 ], while 77 were found in Oryza sativa [ 11 ], 62 in Solanum lycopersicum [ 12 ], 93 in Gossypium raimondii [ 13 ], 91 in Musa acuminate [ 14 ], 61 in Medicago truncatula [ 15 ] 101 in Brassica rapa [ 16 ] and 125 in soybean [ 17 ]. In apple[ 18 ], 69 PUB genes were identified, and were divided into seven subgroups based on phylogenetic tree of PUB proteins from apple and Arabidopsis thaliana . Many previous studies have shown that PUB proteins are involved in biological processes such as plant hormone signaling regulations [ 6 ], self-incompatible or pseudo-self-compatibility regulations [ 19 ] as well as in biotic stress [ 20 – 22 ] and abiotic stress [ 5 , 23 , 24 ].…”