Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L. Beauv)

E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.

Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)

BACKGROUND

The U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress.

RESULTS

In this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus.

CONCLUSIONS

Overall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.

Genome-wide identification, evolution and expression pattern analysis of the GATA gene family in Sorghum bicolor

The GATA family of transcription factors is zinc finger DNA binding proteins involved in a variety of biological processes, including plant growth and development and response to biotic/abiotic stresses, and thus play an essential role in plant response to environmental changes. However, the GATA gene family of Sorghum (SbGATA) has not been systematically analyzed and reported yet. Herein, we used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 33 SbGATA genes identified. These SbGATA genes, distributed on 10 chromosomes, are classified into four subfamilies (I-IV) containing one pair of tandem duplications and nine pairs of segment duplications, which are more closely related to the monocot Brachypodium distachyon and Oryza sativa GATA genes. The physicochemical properties of the SbGATAs are significantly different among the subfamilies, while the protein structure and conserved protein motifs are highly conserved in the subfamilies. In addition, the transcription of SbGATAs is tissue-specific during Sorghum growth and development, which allows for functional diversity in response to stress and hormones. Collectively, our study lays a theoretical foundation for an in-depth analysis of the functions, mechanisms and evolutionary relationships of SbGATA during plant growth and development.

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.