Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice ( Oryza sativa )

• Published in: International journal of molecular sciences 2021-11, Vol.22 (21), p.12088
• Main Authors: Kim, Me-Sun, Kang, Kwon-Kyoo, Cho, Yong-Gu
• Format: Article
• Language: English
• Subjects: Abiotic stress; Amino acids; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Cellular stress response; Chromosomes; Drought; Droughts; E3 ligase; Enzymes; Functional analysis; Gene expression; Genes; Genome editing; genome-wide; Genomes; Hormones; Kinases; Molecular weight; Mutation; Oryza - enzymology; Oryza - genetics; Oryza - growth & development; Oryza - metabolism; Oryza sativa; OsPUB; Phylogenetics; Phylogeny; Plant Breeding; Plant Proteins - genetics; Plant Proteins - metabolism; Plants, Genetically Modified; Polypeptides; Proteins; Regulatory sequences; Reliability analysis; Rice; Salinity; Sequence analysis; Signal transduction; Stress, Physiological; Transcription; Transcriptome; Transcriptomes; Ubiquitin; Ubiquitin-protein ligase; Ubiquitin-Protein Ligase Complexes - genetics; Ubiquitin-Protein Ligase Complexes - metabolism; Ubiquitination
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms222112088

Proteins encoded by U-box type ubiquitin ligase (PUB) genes in rice are known to play an important role in plant responses to abiotic and biotic stresses. Functional analysis has revealed a detailed molecular mechanism involving PUB proteins in relation to abiotic and biotic stresses. In this study, characteristics of 77 genes in rice were identified. Systematic and comprehensive analyses of the gene family were then performed, including analysis of conserved domains, phylogenetic relationships, gene structure, chromosome location, cis-acting elements, and expression patterns. Through transcriptome analysis, we confirmed that 16 genes show similar expression patterns in drought stress and blast infection response pathways. Numerous cis-acting elements were found in promoter sequences of 16 genes, indicating that the genes might be involved in complex regulatory networks to control hormones, stress responses, and cellular development. We performed qRT-PCR on 16 genes under drought stress and blast infection to further identify the reliability of transcriptome and cis-element analysis data. It was confirmed that the expression pattern was similar to RNA-sequencing analysis results. The transcription of under various stress conditions indicates that the PUB gene might have various functions in the responses of rice to abiotic and biotic stresses. Taken together, these results indicate that the genome-wide analysis of genes can provide a solid basis for the functional analysis of U-box E3 ubiquitin ligase genes. The molecular information of the U-box E3 ubiquitin ligase gene family in rice, including gene expression patterns and cis-acting regulatory elements, could be useful for future crop breeding programs by genome editing.