Genome-Wide Analysis of U-box E3 Ubiquitin Ligase Family in Response to ABA Treatment in Salvia miltiorrhiza

Abstract

Plant U-box (PUB) proteins are ubiquitin ligases (E3) involved in multiple biological processes and in response to plant stress. However, the various aspects of the genome and the differences in functions between the U-box E3 (UBE3) ubiquitin ligases remain quite obscure in Salvia miltiorrhiza. The 60 UBE3 genes in the S. miltiorrhiza genome were recognized in the present study. The phylogenetic analysis, gene structure, motifs, promoters, and physical and chemical properties of the genes were also examined. Based on the phylogenetic relationship, the 60 UBE3 genes were categorized under six different groups. The U-box domain was highly conserved across the family of UBE3 genes. Analysis of the cis-acting element revealed that the UBE3 genes might play an important role in a variety of biological processes, including a reaction to the abscisic acid (ABA) treatment. To investigate this hypothesis, an ABA treatment was developed for the hairy roots of S. miltiorrhiza. Thirteen out of the UBE3 genes significantly increased after the ABA treatment. The co-expression network revealed that nine UBE3 genes might be associated with phenolic acids or tanshinone biosynthesis. The findings of the present study brought fresh and new understanding to the participation of the UBE3 gene family in plants, specifically in their biological responses mediated by the ABA. In S. miltiorrhiza, this gene family may be crucial during the ABA treatment. Significantly, the results of this study contribute novel information to the understanding of the ubiquitin ligase gene and its role in plant growth.

Cyclophilin effector Al106 of mirid bug Apolygus lucorum inhibits plant immunity and promotes insect feeding by targeting PUB33

“…S2). Plant U‐box proteins are widely found in a variety of plants, including Arabidopsis , rice, soybean, and apples (Chen et al ., 2022). U‐box motifs of approximately 70 amino acids are highly conserved in the PUB gene family; the family is divided into different subclasses based on the analysis of other domains present in these proteins (Yee & Goring, 2009; Trenner et al ., 2022).…”

Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

“…The young hairy roots were cut and cultured in liquid medium with persistent darkness at 25 °C and 120 rpm for 50 days, therewith treated with various exogenous inducers. Additional transcriptome data for this article can be downloaded by BioProject access numbers: PRJNA703309 (ABA), PRJNA393563 (MeJA), PRJNA301529 (SA), and PRJNA393563 (YE) [ 40 ].…”

Mining of the CULLIN E3 ubiquitin ligase genes in the whole genome of Salvia miltiorrhiza

“…All candidate CUL genes obtained from the result of HMMsearch were further submitted to SMART website ( http://smart.embl-heidelberg.de/ ) to determine completeness of CUL conserved domain ( Letunic and Bork 2018 ; Wang et al, 2021 ). In addition, ExPASy-Compute pI/Mw tool was used to calculate the amino acid number, molecular weight, theoretical pI, instability index, and aliphatic index as well as GRAVY (Grand Average of Hydropathicity) ( Chen et al, 2022 ). A Cell PLoc 2.0 prediction was introduced to determine the subcellular localization of CUL gene candidates ( http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/ ) ( Emanuelsson et al, 2000 ; Chen et al, 2022 ).…”

“…In addition, ExPASy-Compute pI/Mw tool was used to calculate the amino acid number, molecular weight, theoretical pI, instability index, and aliphatic index as well as GRAVY (Grand Average of Hydropathicity) ( Chen et al, 2022 ). A Cell PLoc 2.0 prediction was introduced to determine the subcellular localization of CUL gene candidates ( http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/ ) ( Emanuelsson et al, 2000 ; Chen et al, 2022 ).…”

“…Reverse transcription was performed with the cDNA Synthesis Kit (Clontech, USA) according to protocols. Double stranded cDNAs were separated on agarose gel, and were recovered for the RNA-seq ( Chen et al, 2022 ). Construction of the cDNA library was performed by the Majorbio Bio-pharm Technology (Shanghai, China) and was sequenced by Illumina HiSeq TM 2500 with PE100.…”