Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera

Genome‑wide identification and expression analysis of the UBC gene family in wheat (Triticum aestivum L.)

BACKGROUND

Ubiquitination is an important regulatory step of selective protein degradation in the plant UPS (ubiquitin-proteasome system), which is involved in various biological processes in eukaryotes. Ubiquitin-conjugating enzymes play an intermediate role in the process of protein ubiquitination reactions and thus play an essential role in regulating plant growth and response to adverse environmental conditions. However, a genome-wide analysis of the UBC gene family in wheat (Triticum aestivum L.) has not yet been performed.

RESULTS

In this study, the number, physiochemical properties, gene structure, collinearity, and phylogenetic relationships of TaUBC family members in wheat were analyzed using bioinformatics methods. The expression pattern of TaUBC genes in different tissues/organs and developmental periods, as well as the transcript levels under abiotic stress treatment, were analyzed using RNA-Seq data and qRT-PCR. Meanwhile, favorable haplotypes of TaUBC25 were investigated based on wheat resequencing data of 681 wheat cultivars from the Wheat Union Database. The analyses identified a total of 93 TaUBC family members containing a UBC domain in wheat genome. These genes were unevenly distributed across 21 chromosomes, and numerous duplication events were observed between gene members. Based on phylogenetic analysis, the TaUBC family was divided into 13 E2 groups and a separate UEV group. We investigated the expression of TaUBC family genes under different tissue/organ and stress conditions by quantitative real-time PCR (qRT-PCR) analysis. The results showed that some TaUBC genes were specifically expressed in certain tissues/organs and that most TaUBC genes responded to NaCl, PEG6000, and ABA treatment with different levels of expression. In addition, we performed association analysis for the two haplotypes based on key agronomic traits such as thousand-kernel weight (TKW), kernel length (KL), kernel weight (KW), and kernel thickness (KT), examining 122 wheat accessions at three environmental sites. The results showed that TaUBC25-Hap II had significantly higher TKW, KL, KW, and KT than TaUBC25-Hap I. The distribution analysis of haplotypes showed that TaUBC25-Hap II was preferred in the natural population of wheat.

CONCLUSION

Our results identified 93 members of the TaUBC family in wheat, and several genes involved in grain development and abiotic stress response. Based on the SNPs detected in the TaUBC sequence, two haplotypes, TaUBC25-Hap I and TaUBC25-Hap II, were identified among wheat cultivars, and their potential value for wheat breeding was validated by association analysis. The above results provide a theoretical basis for elucidating the evolutionary relationships of the TaUBC gene family and lay the foundation for studying the functions of family members in the future.

Transcriptomic analysis of alternative splicing events for different stages of growth and development in Sistan Yaghooti grape clusters

Sistan Yaghooti grape variety, despite characteristics such as early ripening, is vulnerable to cluster rot due to small berries and dense clusters. In this regard, AS may serve as a regulatory mechanism during developmental processes and in response to environmental signals. RNA-Seq analysis was performed to measure gene expression and the extent of AS events in the cluster growth and development stages of Sistan Yaghooti grape. The number of AS events increased during stages, suggesting that it contributes to the grapevine's adaptability to various stresses. In addition, DEG and DAS genes showed little overlap in cluster growth stages. Functional analysis of 19,194 DAS -gene sets showed that VIT_06s0004g06670 gene is involved in the activation of calcium channels (Ca2+) through the activation of 5 PLC biosynthetic pathways. Among the 27,229 DEG -sets, VIT_07s0005g05320 gene showed higher expression. Interestingly, this gene is involved in the synthesis of an EF -hand domain-containing protein capable of binding to Ca2+ by activating 4 biochemical pathways. These genes increase cytosolic Ca2+ concentration, enhancing plant stress tolerance and resistance to cracking. These results show that AS can respond independently to different types of stress. Among the other DAS genes, the GA2ox gene (VvGA2ox) showed an increase in AS events during cluster development. This gene is critical for initiating the degradation process of GA and plays a crucial role in different stages of seed development. Therefore, it is very likely that this gene is one of the main factors responsible for the density and seedlessness of Sistan Yaghooti grape.

Genome-wide identification and transcriptome-based expression profiling of E2 gene family: Implication for potential roles in gonad development of Crassostrea gigas

In this study, we investigated the role of E2 ubiquitin conjugating enzymes (E2) in the Pacific oyster Crassostrea gigas, with a focus on their involvement in gonad development. We identified 34 E2 genes clustered into nine subgroups and 24 subfamilies. The gene structure and intron-exon location were conserved within the same subfamily, but motif variation suggested functional diversity. Tissue transcriptome analyses revealed that most E2 genes were broadly expressed, with UBE2CL showing specific expression in the female gonad. Expression profiling of E2 genes during early embryo-larvae development stages suggested that five E2 genes were highly expressed in early embryo development, indicating their involvement in cell division processes. Furthermore, by profiling the expression of E2 genes in different gonadal developmental stages, we observed a gradual increase in expression for four genes during gametogenesis, with significantly higher expression in the female gonad at the maturation stage. Similarly, five E2 genes displayed elevated expression levels in the male gonad at the maturation stage, indicating their crucial roles in gonadal development and gametogenesis. Our study provides valuable insights into the potential functions of the E2 gene family in C. gigas, shedding light on the molecular mechanisms underlying gonad development in oysters.

A Review of Potato Salt Tolerance

Potato is the world's fourth largest food crop. Due to limited arable land and an ever-increasing demand for food from a growing population, it is critical to increase crop yields on existing acreage. Soil salinization is an increasing problem that dramatically impacts crop yields and restricts the growing area of potato. One possible solution to this problem is the development of salt-tolerant transgenic potato cultivars. In this work, we review the current potato planting distribution and the ways in which it overlaps with salinized land, in addition to covering the development and utilization of potato salt-tolerant cultivars. We also provide an overview of the current progress toward identifying potato salt tolerance genes and how they may be deployed to overcome the current challenges facing potato growers.

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.

Functional characterization of the pUceS8.3 promoter and its potential use for ectopic gene overexpression

The pUceS8.3 is a constitutive gene promoter with potential for ectopic and strong genes overexpression or active biomolecules in plant tissues attacked by pests, including nematode-induced giant cells or galls. Soybean (Glycine max) is one of the most important agricultural commodities worldwide and a major protein and oil source. Herein, we identified the soybean ubiquitin-conjugating (E2) enzyme gene (GmUBC4; Glyma.18G216000), which is significantly upregulated in response to Anticarsia gemmatalis attack and Meloidogyne incognita-induced galls during plant parasitism by plant nematode. The GmUBC4 promoter sequence and its different modules were functionally characterized in silico and in planta using transgenic Arabidopsis thaliana and G. max lines. Its full-length transcriptional regulatory region (promoter and 5´-UTR sequences, named pUceS8.3 promoter) was able to drive higher levels of uidA (β-glucuronidase) gene expression in different tissues of transgenic A. thaliana lines compared to its three shortened modules and the p35SdAMV promoter. Notably, higher β-glucuronidase (GUS) enzymatic activity was shown in M. incognita-induced giant cells when the full pUceS8.3 promoter drove the expression of this reporter gene. Furthermore, nematode-specific dsRNA molecules were successfully overexpressed under the control of the pUceS8.3 promoter in transgenic soybean lines. The RNAi gene construct used here was designed to post-transcriptionally downregulate the previously characterized pre-mRNA splicing factor genes from Heterodera glycines and M. incognita. A total of six transgenic soybean lines containing RNAi gene construct were selected for molecular characterization after infection with M. incognita pre-parasitic second-stage (ppJ2) nematodes. A strong reduction in the egg number produced by M. incognita after parasitism was observed in those transgenic soybean lines, ranging from 71 to 92% compared to wild-type control plants. The present data demonstrated that pUceS8.3 is a gene promoter capable of effectively driving dsRNA overexpression in nematode-induced giant cells of transgenic soybean lines and can be successfully applied as an important biotechnological asset to generate transgenic crops with improved resistance to root-knot nematodes as well as other pests.

Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91-35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.

Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

BACKGROUND

E2 ubiquitin-conjugating (UBC) enzymes are an integral component of the ubiquitin proteasome system that play an important role in plant development, growth, and external stress responses. Several UBC genes have been identified in various plants. However, no studies exploring the functions of UBC genes in regulating fruit of strawberry have been reported. In the present study, a systematic analysis of the entire UBC family members were conducted in the genome of strawberry (Fragaria ×ananassa) based on bioinformatics method, and the gene functioning in strawberry ripening was explored.

RESULTS

A total of 191 UBC genes were identified in the genome of cultivated strawberry. These genes were unevenly distributed across the 28 chromosomes from the 4 subgenomes of cultivated strawberry, ranging from 3 to 11 genes per chromosome. Moreover, the expansion of FaUBC genes in strawberry was mainly driven by WGD. All the FaUBC genes were clarified into 13 groups and most of them were included in the group VI. The gene structure analysis showed that the number of exons varied from 1 to 23, and the structure of genes had few differences within the same groups but a distinction in different groups. Identification of the cis-acting elements of the promoter revealed multiple regulatory elements that responded to plant growth and development, phytohormone responsive, and abiotic and biotic stress. Data from functional annotation indicated that FaUBC genes play a role in a variety of biological processes. The RNA-seq data showed that FaUBC genes displayed different expression pattern during the fruit ripening process and clarified into 6 clusters. In particular, cluster 3 exhibiting a sudden expression increase in the turning red stage were speculated to be involved in fruit ripening. Hence, two FaUBC genes (FaUBC76 and FaUBC78) were selected for gene function analysis by transient over-expression method. The results indicated that FaUBC76 has a positive effect on the fruit development and ripening in strawberry by up-regulating accumulation of anthocyanins. Moreover, expression of some maturity-related genes were also significantly increased, further supporting a role for FaUBC76 in the regulation of fruit ripening or softening. On the contrary, the overexpression of FaUBC78 significantly increased the firmness of strawberry fruit, indicating that FaUBC78 had a positive role in inhibiting the decrease of strawberry fruit firmness.

CONCLUSION

Our study not only provide comprehensive information on system evolution and function on UBC genes, but also give a new insight into explore the roles of FaUBC genes in the regulation of strawberry ripening.

Overexpression of A Biotic Stress-Inducible Pvgstu Gene Activates Early Protective Responses in Tobacco under Combined Heat and Drought

Drought and heat stresses are major factors limiting crop growth and productivity, and their effect is more devastating when occurring concurrently. Plant glutathione transferases (GSTs) are differentially expressed in response to different stimuli, conferring tolerance to a wide range of abiotic stresses. GSTs from drought-tolerant Phaseolus vulgaris var. "Plake Megalosperma Prespon" is expected to play an important role in the response mechanisms to combined and single heat and drought stresses. Herein, we examined wild-type N. tabacum plants (cv. Basmas Xanthi) and T1 transgenic lines overexpressing the stress-induced Pvgstu3-3 and Pvgstu2-2 genes. The overexpression of Pvgstu3-3 contributed to potential thermotolerance and greater plant performance under combined stress. Significant alterations in the primary metabolism were observed in the transgenic plants between combined stress and stress-free conditions. Stress-responsive differentially expressed genes (DEGs) and transcription factors (TFs) related to photosynthesis, signal transduction, starch and sucrose metabolism, osmotic adjustment and thermotolerance, were identified under combined stress. In contrast, induction of certain DEGs and TF families under stress-free conditions indicated that transgenic plants were in a primed state. The overexpression of the Pvgstu3-3 is playing a leading role in the production of signaling molecules, induction of specific metabolites and activation of the protective mechanisms for enhanced protection against combined abiotic stresses in tobacco.

Transcriptomic analysis of grapevine Dof transcription factor gene family in response to cold stress and functional analyses of the VaDof17d gene

Dof genes enhance cold tolerance in grapevine and VaDof17d is tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides. DNA-binding with one finger (Dof) proteins comprise a large family that plays important roles in the regulation of abiotic stresses. No in-depth analysis of Dof genes has been performed in the grapevine. In this study, we analyzed a total of 25 putative Dof genes in grapevine at genomic and transcriptomic levels, compiled expression profiles of 11 selected VaDof genes under cold stress and studied the potential function of the VaDof17d gene in grapevine calli. The 25 Dof proteins can be classified into four phylogenetic groups. RNA-seq and qRT-PCR results demonstrated that a total of 11 VaDof genes responded to cold stress. Comparative mRNA sequencing of 35S::VaDof17d grape calli showed that VaDof17d was tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides (RFOs), as observed by the up-regulation of galactinol synthase (GolS) and raffinose synthase genes. We found that the Dof17d-ED (CRISPR/Cas9-mediated mutagenesis of Dof17d-ED) mutant had low cold tolerance with a decreased RFOs level during cold stress. These results formed the fundamental knowledge for further analysis of the biological roles of Dof genes in the grapevine's adaption to cold stresses.

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

Owing to a sessile lifestyle in nature, plants are routinely faced with diverse hostile environments such as various abiotic and biotic stresses, which lead to accumulation of free radicals in cells, cell damage, protein denaturation, etc., causing adverse effects to cells. During the evolution process, plants formed defense systems composed of numerous complex gene regulatory networks and signal transduction pathways to regulate and maintain the cell homeostasis. Among them, ubiquitin-proteasome pathway (UPP) is the most versatile cellular signal system as well as a powerful mechanism for regulating many aspects of the cell physiology because it removes most of the abnormal and short-lived peptides and proteins. In this system, the ubiquitin-conjugating enzyme (E2) plays a critical role in transporting ubiquitin from the ubiquitin-activating enzyme (E1) to the ubiquitin-ligase enzyme (E3) and substrate. Nevertheless, the comprehensive study regarding the role of E2 enzymes in plants remains unexplored. In this review, the ubiquitination process and the regulatory role that E2 enzymes play in plants are primarily discussed, with the focus particularly put on E2's regulation of biological functions of the cell.

Chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in Volvariella volvacea

In Volvariella volvacea, an important edible mushroom species, cryogenic autolysis is a typical part of abnormal metabolism; however, the underlying mechanisms remain unclear. Ubiquitylome analysis revealed that chilling stress (CS) affected protein translation and degradation by ubiquitination. Comparative proteomics analysis showed that CS downregulated protein expression in V. volvacea V23 instead of VH3 (improved chilling stress resistance strain). The integrative ubiquitylome, proteomics, and transcriptome analyses indicated that CS reduced protein translation by the ubiquitination of ribosomal proteins. An activity assay of the 20S proteasome showed that CS decreased the degradation efficiency of the ubiquitin-proteasome system. UBEV2, one type of ubiquitin-conjugating enzyme E2 (UBE2) in V. volvacea, was upregulated after cold stress treatment using western blot analysis. GST pull-down experiments of UBEV2 provided evidence that CS affected protein translation by the ubiquitination of ribosomal proteins. Co-IP experiments confirmed that UBEV2 bound to the ubiquitinated SSB2, a ribosome-associated molecular chaperone. An anti-freezing experiment demonstrated that the UBE2 inhibitor could improve the cold stress resistance of V. volvacea. Our observations revealed that CS triggered ubiquitination-mediated autolysis associated with a decrease in protein translation and highlighted the mechanistic role of UBEV2 in facilitating cryogenic autolysis in V. volvacea. SIGNIFICANCE: Volvariella volvacea, the edible straw mushroom, is a highly nutritious food source widely cultivated on a commercial scale in tropical and subtropical regions. The challenges associated with the cryogenic autolysis preservation of V. volvacea have limited its marketability. This issue of cryogenic autolysis is both an interesting scientific problem to solve and a practical economic matter. Integrative ubiquitylome, proteomics, and transcriptome analyses, together with GST pulldown and Co-IP experiments, indicated that chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in V. volvacea. This study significantly contributes to our understanding of ubiquitination-mediated autolysis associated with a decrease in protein translation in V. volvacea. Our data highlight the mechanistic role of UBEV2 in facilitating the cryogenic autolysis of V. volvacea. We provided a new idea for the preservation of V. volvacea by inhibiting UBEV2 to increase its marketability.

Evolution and expression analysis of the sorghum ubiquitin-conjugating enzyme family

Ubiquitin-conjugating enzymes (UBCs), which catalyse the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. Current knowledge regarding the sorghum (Sorghum bicolor (L.) Moench) ubiquitin-conjugating enzyme (SbUBC) family remains very limited. We identified 53 UBC-encoding genes in the sorghum genome and divided these into 18 groups according to their phylogenetic relationship with Arabidopsis thaliana (L.) Heynh., which was further supported by conserved motif and gene structure analyses. Different expression levels under a variety of abiotic stresses suggested that these might participate in distinct signalling pathways and that they underwent functional divergence during evolution. Furthermore, several SbUBC genes responded to single treatments, and individual SbUBC genes responded to multiple treatments, suggesting that sorghum UBCs may mediate crosstalk among different signalling pathways. Overall, the results provide valuable information for better understanding the classification and putative functions of sorghum UBC-encoding genes.

Response of Tradescantia plants to oxidative stress induced by heavy metal pollution of soils from industrial areas

Numerous investigations have demonstrated that even soil in which concentrations of individual elements do not exceed permissible limits can cause harmful effects in living organisms. In the present study, polluted-soil-induced oxidative stress was evaluated using Tradescantia clone 4430, which is widely used for genotoxicity evaluations, employing biochemical (superoxide dismutase (SOD), contents of ascorbic acid (AA), carotenoids (Car), hydrogen peroxide (H₂O₂), chlorophyll (Chl) a/b ratio), and molecular (RAPD and differential display (DD-PCR)) markers after long-term exposure. The activity (staining intensity) of SOD isoforms in Tradescantia leaves was higher in plants grown in all heavy-metal-polluted test soils compared to the control. No direct link between the soil pollution category and the contents of AA, Car, Chl a/b in Tradescantia leaves was revealed, but the concentration of H₂O₂ was shown to be a sensitive biochemical indicator that may appropriately reflect the soil contamination level. Both short-term (treatment of cuttings with H₂O extracts of soil) and long-term (0.5 and 1.0 year) exposure increased MN frequencies, but the coincidence of the MN induction and the soil pollution level was observed only in some cases of long-term exposure. Soil (geno)toxin-induced polymorphism in the RAPD profile was determined with two primers in plants after long-term exposure to soils of an extremely hazard category. Transcript profiling of plants after long-term cultivation in test soils using DD-PCR showed that the majority of differentially expressed transcript-derived fragments (TDFs) were homologous to genes directly or indirectly participating in photosynthesis, the abiotic stress response, and signal transduction cascades.

Genome-wide identification and expression analysis of the E2 gene family in potato

E2 (ubiquitin conjugating enzymes) is an important part of the ubiquitin-proteasome pathway. These enzymes have a significant role to play during plant growth and development, which can response to various stresses. To date, the E2 family has been reported in some high plants, but the genome-wide characterization of this gene family in potato remains unknown. In the present study, 57 putative StUBCs were identified, which were clustered into eight subgroups based on phylogeny. The introns varied in numbers 0 to 9. The highest numbers of introns were 5, which accounted for 31.57%. The analysis of gene duplication showed that 22 StUBC genes were involved in 13 segmental duplication events, while no tandem duplication was found in StUBC genes. According to gene ontology analysis (GO), StUBC family major function is protein binding and ion binding. The RNA sequencing data revealed that 15 StUBC genes were highly expressed in different organs and tubers. 27 StUBC genes were up-regulated under 50 µM ABA treatments. Moreover, the RNA-seq data and qRT-PCR analysis indicated that 17 StUBC genes responded to heat stress. 8 StUBC genes responded to salt stress according to qRT-PCR analysis, and StUBC2, StUBC12, StUBC30 and StUBC13 were predominant expression. The result of this research could provide valuable information to insight into potato E2 family and establish a foundation for further to elucidate function of E2 genes.

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in Brassica rapa

To understand ubiquitination mechanism, E2s (ubiquitin conjugating enzymes) have crucial part as they play a major role in regulating many biological processes in plants. Meanwhile, Brassica rapa is an important leafy vegetable crop and therefore its characterization along with the expression pattern of E2s under various stresses is imperative. In this study, a total of 83 genes were identified in B. rapa and were classified into four different classes based on domain information. Here, we analyzed phylogenetic relationships, collinear correlation, gene duplication, interacting network, and expression patterns of E2 genes in B. rapa. Furthermore, RT-PCR analysis for 8 multiple abiotic and hormone treatments (namely, ABA, GA, JA, BR, PEG, NaCl, and heat and cold stress) illustrated striking expression pattern under one or more treatments, speculating that these might be stress-responsive genes. The cis-elements and interaction network analyses implicate valuable clues of important function of E2 genes in development and multiple stress responses in B. rapa. This study will further facilitate functional analysis of E2s for improving stress resistance mechanism in B. rapa.