Ectopic expression of ubiquitin-conjugating enzyme gene from wild rice, OgUBC1, confers resistance against UV-B radiation and Botrytis infection in Arabidopsis thaliana

Ubiquitin-conjugating enzyme gene SgUBC2 confers manganese tolerance in Stylosanthes guianensis through antioxidant defense augmentation and manganese-responsive gene regulation

Stylo (Stylosanthes guianensis) is an important tropical legume with superior tolerance to manganese (Mn) toxicity, which severely constrains plant growth, especially in tropical acid soils. However, the mechanisms underlying Mn tolerance in stylo remain largely unknown. In this study, excess Mn-caused growth inhibition was observed in stylo shoots but not roots, accompanied by increased activities of superoxide dismutase and catalase, as well as elevated concentrations of ascorbate and glutathione, which may contribute to oxidative stress scavenging under Mn toxicity. SgUBC2, encoding a ubiquitin-conjugating enzyme, was functionally characterized. The results showed that the expression of SgUBC2 was significantly induced by excess Mn in stylo roots. Subcellular localization analysis revealed that SgUBC2 localized to both the cytosol and nucleus in Arabidopsis mesophyll protoplasts. Moreover, compared to the control plants, overexpression of SgUBC2 increased the shoot and root dry weights of the transgenic composite stylo plants under excess Mn conditions, likely due to reduced Mn accumulation and increased superoxide dismutase activity in roots. RNA-seq analysis showed that SgUBC2 overexpression altered the expression of multiple Mn-responsive genes, including those associated with antioxidant defense response, ion transporters and organic acid metabolism. Collectively, this study indicates that SgUBC2 plays critical roles in enhancing Mn tolerance in stylo, potentially through an elevated antioxidant defense system and coordinated regulation of Mn-responsive gene expression.

Genome-Wide Identification of the GbUBC Gene Family in Sea-Island Cotton (Gossypium barbadense) and the Active Regulation of Drought Resistance in Cotton by GbUBC23

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton.

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.

Transcriptome, Plant Hormone, and Metabolome Analysis Reveals the Mechanism of Purple Pericarp Formation in 'Zihui' Papaya (Carica papaya L.)

The color of the pericarp is a crucial characteristic that influences the marketability of papaya fruit. Prior to ripening, normal papaya exhibits a green pericarp, whereas the cultivar 'Zihui' displays purple ring spots on the fruit tip, which significantly affects the fruit's visual appeal. To understand the mechanism behind the formation of purple pericarp, this study performed a thorough examination of the transcriptome, plant hormone, and metabolome. Based on the UPLC-ESI-MS/MS system, a total of 35 anthocyanins and 11 plant hormones were identified, with 27 anthocyanins and two plant hormones exhibiting higher levels of abundance in the purple pericarp. In the purple pericarp, 14 anthocyanin synthesis genes were up-regulated, including CHS, CHI, F3H, F3'5'H, F3'H, ANS, OMT, and CYP73A. Additionally, through co-expression network analysis, three MYBs were identified as potential key regulators of anthocyanin synthesis by controlling genes encoding anthocyanin biosynthesis. As a result, we have identified numerous key genes involved in anthocyanin synthesis and developed new insights into how the purple pericarp of papaya is formed.

Tobacco NtUBC1 and NtUBQ2 enhance salt tolerance by reducing sodium accumulation and oxidative stress through proteasome activation in Arabidopsis

The ubiquitin/proteasome system plays a crucial role in the regulation of plant responses to environmental stress. Here, we studied the involvement of the UBC1 and UBQ2 genes encoding a ubiquitin conjugating enzyme (E2) and ubiquitin extension protein, respectively, in the response to salt stress. Our results showed that the constitutive expression of tobacco NtUBC1 and NtUBQ2 in Arabidopsis thaliana improved salt tolerance, along with the lower Na+ level and higher K+/Na+ ratio compared to control plants. Moreover, the expression levels of sodium transporters, including AtHKT1 (High-Affinity K+ Transporter1) and AtSOS1 (Salt Overly Sensitive 1), were higher in NtUBC1- and NtUBQ2-Arabidopsis. However, the transcript level of AtNHX1 (Na+/H+ Exchanger 1) was similar between control and transgenic plants. After salt exposure, the activity of the 26S proteasome markedly increased in NtUBC1- and NtUBQ2-expressing plants; however, ubiquitinated protein levels decreased compared to control plants. Furthermore, higher activity of antioxidant enzymes and lower ROS production were observed in UBC1- and UBQ2-expressing plants. We further challenged atubc1, atubc2, and atubq2 single mutants and atubc1ubc2 double mutant lines with salt stress; interestingly, the salt sensitivity and sodium levels of the studied mutants were enhanced, while the potassium levels were reduced. However, the atubc1ubc2 double mutant illustrated a more severe phenotype than the single mutants, probably due to the redundant function of UBC1 and UBC2 in Arabidopsis. Taken together, NtUBC1 and NtUBQ2 enhance salt tolerance by enhancing 26S proteasome activity and reducing Na+ accumulation, ROS, and ubiquitinated/salt-denatured proteins.

The Targeted Regulation of BDUbc and BDSKL1 Enhances Resistance to Blight in Bambusa pervariabilis × Dendrocalamopsis grandis

Arthrinium phaeospermum is the major pathogen responsible for the significant stem disease "blight" in B. pervariabilis × D. grandis. The interacting proteins of the key pathogenic factor ApCtf1β, BDUbc and BDSKL1, have previously been obtained by two-hybrid, BiFC, GST pull-down yeast assays. However, the functions of these interacting proteins remain unknown. This study successfully obtained transgenic plants overexpressing BDUbc, BDSKL1, and BDUbc + BDSKL1 via Agrobacterium-mediated gene overexpression. qRT-PCR analysis revealed significantly increased expression levels of BDUbc and BDSKL1 in the transgenic plants. After infection with the pathogenic spore suspension, the disease incidence and severity index significantly decreased across all three transgenic plants, accompanied by a marked increase in defense enzyme levels. Notably, the co-transformed plant, OE-BDUbc + BDSKL1, demonstrated the lowest disease incidence and severity index among the transgenic variants. These results not only indicate that BDUbc and BDSKL1 are disease-resistant genes, but also that these two genes may exhibit a synergistic enhancement effect, which further improves the resistance to blight in Bambusa pervariabilis × Dendrocalamopsis grandis.

Hormonal regulation of anthocyanin biosynthesis for improved stress tolerance in plants

Due to unprecedented climate change, rapid industrialization and increasing use of agrochemicals, abiotic stress, such as drought, low temperature, high salinity and heavy metal pollution, has become an increasingly serious problem in global agriculture. Anthocyanins, an important plant pigment, are synthesized through the phenylpropanoid pathway and have a variety of physiological and ecological functions, providing multifunctional and effective protection for plants under stress. Foliar anthocyanin accumulation often occurs under abiotic stress including high light, cold, drought, salinity, nutrient deficiency and heavy metal stress, causing leaf reddening or purpling in many plant species. Anthocyanins are used as sunscreens and antioxidants to scavenge reactive oxygen species (ROS), as metal(loid) chelators to mitigate heavy metal stress, and as crucial molecules with a role in delaying leaf senescence. In addition to environmental factors, anthocyanin synthesis is affected by various endogenous factors. Plant hormones such as abscisic acid, jasmonic acid, ethylene and gibberellin have been shown to be involved in regulating anthocyanin synthesis either positively or negatively. Particularly when plants are under abiotic stress, several plant hormones can induce foliar anthocyanin synthesis to enhance plant stress resistance. In this review, we revisit the role of plant hormones in anthocyanin biosynthesis and the mechanism of plant hormone-mediated anthocyanin accumulation and abiotic stress tolerance. We conclude that enhancing anthocyanin content with plant hormones could be a prospective management strategy for improving plant stress resistance, but extensive further research is essentially needed to provide future guidance for practical crop production.

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.

Light-Induced Flavonoid Biosynthesis in Sinopodophyllum hexandrum with High-Altitude Adaptation

Sinopodophyllum hexandrum is a perennial alpine herb producing the anti-cancer metabolite podophyllotoxin (PPT). Although the adaptation of S. hexandrum to high altitudes has been demonstrated and the effects of temperature, precipitation, and UV-B light on plant growth and metabolite accumulation have been studied, knowledge on the role of flavonoid biosynthesis in adapting to high altitudes is limited. In this study, light intensity, amount and type of flavonoids, and differentially expressed proteins (DEPs) and genes (DEGs) at 2300 and 3300 m were analyzed by HPLC, proteomic, transcriptomic, and qRT-PCR analysis. We found that higher light intensity correlated with greater flavonoid, flavonol, and anthocyanin content as well as higher anthocyanin to total flavonoid and flavonol ratios observed at the higher altitude. Based on proteomic and transcriptomic analyses, nine DEPs and 41 DEGs were identified to be involved in flavonoid biosynthesis and light response at 3300 m. The relative expression of nine genes (PAL, CHS1, IFRL, ANS, MYB4, BHLH137, CYP6, PPO1, and ABCB19) involved in flavonoid biosynthesis and seven genes (HSP18.1, HSP70, UBC4, ERF5, ERF9, APX3, and EX2) involved in light stress were observed to be up-regulated at 3300 m compared with 2300 m. These findings indicate that light intensity may play a regulatory role in enhancing flavonoid accumulation that allows S. hexandrum to adapt to elevated-altitude coupled with high light intensity.

Proteomic analysis response of rice (Oryza sativa) leaves to ultraviolet-B radiation stress

Rice (Oryza sativa) is a human staple food and serves as a model organism for genetic and molecular studies. Few studies have been conducted to determine the effects of ultraviolet-B (UV-B) stress on rice. UV-B stress triggers morphological and physiological changes in plants. However, the underlying mechanisms governing these integrated responses are unknown. In this study, we conducted a proteomic response of rice leaves to UV-B stress using two-dimensional gel electrophoresis and identified the selected proteins by mass spectrometry analysis. Four levels of daily biologically effective UV-B radiation intensities were imposed to determine changes in protein accumulation in response to UV-B stress: 0 (control), 5, 10, and 15 kJ m^-2 d^-1in two cultivars, i.e., IR6 and REX. To mimic the natural environment, we conducted this experiment in Sunlit Soil-Plant-Atmosphere-Research (SPAR) chambers. Among the identified proteins, 11% of differentially expressed proteins were found in both cultivars. In the Rex cultivar, only 45% of proteins are differentially expressed, while only 27.5% were expressed in IR6. The results indicate that REX is more affected by UV-B stress than IR6 cultivars. The identified protein TSJT1 (spot 16) in both cultivars plays a crucial role in plant growth and development during stress treatment. Additionally, we found that UV-B stress altered many antioxidant enzymes associated with redox homeostasis and cell defense response. Another enzyme, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has been identified as spot 15, which plays an essential role in glycolysis and cellular energy production. Another vital protein identified is glycosyl hydrolase (GH) as spot 9, which catalyzes the hydrolysis of glycosidic bonds in cell wall polymers and significantly affects cell wall architecture. Some identified proteins are related to photosynthesis, protein biosynthesis, signal transduction, and stress response. The findings of our study provide new insights into understanding how rice plants are tailored to UV-B stress via modulating the expression of UV-B responsive proteins, which will help develop superior rice breeds in the future to combat UV-B stress. Data are available via ProteomeXchange with identifier PXD032163.

Rice ubiquitin-conjugating enzyme OsUBC26 is essential for immunity to the blast fungus Magnaporthe oryzae

The functions of ubiquitin-conjugating enzymes (E2) in plant immunity are not well understood. In this study, OsUBC26, a rice ubiquitin-conjugating enzyme, was characterized in the defence against Magnaporthe oryzae. The expression of OsUBC26 was induced by M. oryzae inoculation and methyl jasmonate treatment. Both RNA interference lines and CRISPR/Cas9 null mutants of OsUBC26 reduced rice resistance to M. oryzae. WRKY45 was down-regulated in OsUBC26 null mutants. In vitro E2 activity assay indicated that OsUBC26 is an active ubiquitin-conjugating enzyme. Yeast two-hybrid assays using OsUBC26 as bait identified the RING-type E3 ligase UCIP2 as an interacting protein. Coimmunoprecipitation assays confirmed the interaction between OsUBC26 and UCIP2. The CRISPR/Cas9 mutants of UCIP2 also showed compromised resistance to M. oryzae. Yeast two-hybrid screening using UCIP2 as bait revealed that APIP6 is a binding partner of UCIP2. Moreover, OsUBC26 working with APIP6 ubiquitinateds AvrPiz-t, an avirulence effector of M. oryzae, and OsUBC26 null mutation impaired the proteasome degradation of AvrPiz-t in rice cells. In summary, OsUBC26 plays important roles in rice disease resistance by regulating WRKY45 expression and working with E3 ligases such as APIP6 to counteract the effector protein AvrPiz-t from M. oryzae.

More Than Just Cleaning: Ubiquitin-Mediated Proteolysis in Fungal Pathogenesis

Ubiquitin-proteasome mediated protein turnover is an important regulatory mechanism of cellular function in eukaryotes. Extensive studies have linked the ubiquitin-proteasome system (UPS) to human diseases, and an array of proteasome inhibitors have been successfully developed for cancer therapy. Although still an emerging field, research on UPS regulation of fungal development and virulence has been rapidly advancing and has generated considerable excitement in its potential as a target for novel drugs. In this review, we summarize UPS composition and regulatory function in pathogenic fungi, especially in stress responses, host adaption, and fungal pathogenesis. Emphasis will be given to UPS regulation of pathogenic factors that are important for fungal pathogenesis. We also discuss future potential therapeutic strategies for fungal infections based on targeting UPS pathways.

The sweetpotato GIGANTEA gene promoter is co-regulated by phytohormones and abiotic stresses in Arabidopsis thaliana

GIGANTEA (GI) is known to play significant roles in various molecular pathways. Nevertheless, the underlying mechanism of the transcriptional regulation of GI remains obscure in sweetpotato. In the present study, a 1518-bp promoter sequence was obtained from the Ipomoea batatas GIGANTEA (IbGI) gene, and several potential cis-elements responsive to light, phytohormones and abiotic stresses were identified by in silico analysis. In order to functionally validate the IbGI promoter, the 5' deletion analysis of the promoter was performed by cloning the full-length promoter (D0) and its four deletion fragments, D1 (1235 bp), D2 (896 bp), D3 (549 bp) and D4 (286 bp), upstream of the β-glucuronidase (GUS) reporter gene. Then, these were stably transformed in Arabidopsis plants. All transgenic seedlings exhibited stable GUS activity in the condition of control, but with decreased activity in the condition of most treatments. Interestingly, merely D1 seedlings that contained an abscisic acid responsive cis-element (ABRE-element) had an extremely powerful GUS activity under the treatment of ABA, which implies that fragment spanning nucleotides of -1235 to -896 bp might be a crucial component for the responses of ABA. Eight different types of potential transcriptional regulators of IbGI were isolated by Y1H, including TGA2.2, SPLT1 and GADPH, suggesting the complex interaction mode of protein-DNA on the IbGI promoter. Taken together, these present results help to better understand the transcriptional regulation mechanism of the IbGI gene, and provides an insight into the IbGI promoter, which can be considered as an alternation for breeding transgenic plants.

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.

Identification of heat-tolerance QTLs and high-temperature stress-responsive genes through conventional QTL mapping, QTL-seq and RNA-seq in tomato

BACKGROUND

High temperature is one of the major abiotic stresses in tomato and greatly reduces fruit yield and quality. Identifying high-temperature stress-responsive (HSR) genes and breeding heat-tolerant varieties is an effective way to address this issue. However, there are few reports on the fine mapping of heat-tolerance quantitative trait locus (QTL) and the identification of HSR genes in tomato. Here, we applied three heat tolerance-related physiological indexes, namely, relative electrical conductivity (REC), chlorophyll content (CC) and maximum photochemical quantum efficiency (Fv/Fm) of PSII (photosystem II), as well as the phenotypic index, the heat injury index (HII), and conventional QTL analysis combined with QTL-seq technology to comprehensively detect heat-tolerance QTLs in tomato seedlings. In addition, we integrated the QTL mapping results with RNA-seq to identify key HSR genes within the major QTLs.

RESULTS

A total of five major QTLs were detected: qHII-1-1, qHII-1-2, qHII-1-3, qHII-2-1 and qCC-1-5 (qREC-1-3). qHII-1-1, qHII-1-2 and qHII-1-3 were located, respectively, in the intervals of 1.43, 1.17 and 1.19 Mb on chromosome 1, while the interval of qHII-2-1 was located in the intervals of 1.87 Mb on chromosome 2. The locations observed with conventional QTL mapping and QTL-seq were consistent. qCC-1-5 and qREC-1-3 for CC and REC, respectively, were located at the same position by conventional QTL mapping. Although qCC-1-5 was not detected in QTL-seq analysis, its phenotypic variation (16.48%) and positive additive effect (0.22) were the highest among all heat tolerance QTLs. To investigate the genes involved in heat tolerance within the major QTLs in tomato, RNA-seq analysis was performed, and four candidate genes (SlCathB2, SlGST, SlUBC5, and SlARG1) associated with heat tolerance were finally detected within the major QTLs by DEG analysis, qRT-PCR screening and biological function analysis.

CONCLUSIONS

In conclusion, this study demonstrated that the combination of conventional QTL mapping, QTL-seq analysis and RNA-seq can rapidly identify candidate genes within major QTLs for a complex trait of interest to replace the fine-mapping process, thus greatly shortening the breeding process and improving breeding efficiency. The results have important applications for the fine mapping and identification of HSR genes and breeding for improved thermotolerance.

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.

Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in Two Pyrus Species

Ripening affects the nutritional contents and quality of fleshy fruits, and it plays an important role during the process of fruit development. Studies have demonstrated that ubiquitin-conjugating (UBC or E2) genes can regulate fruit ripening, but the characterization of UBCs in pear is not well documented. The recently published genome-wide sequences of Pyrus bretschneideri and Pyrus communis have allowed a comprehensive analysis of this important gene family in pear. Using bioinformatics approaches, we identified 83 (PbrUBCs) and 84 (PcpUBCs) genes from P. bretschneideri and P. communis, respectively, which were divided into 13 subfamilies. In total, 198 PbrUBC paralogous, 215 PcpUBC paralogous, and 129 orthologous gene pairs were detected. Some paralogous gene pairs were found to be distributed on the same chromosome, suggesting that these paralogs may be caused by tandem duplications. The expression patterns of most UBC genes were divergent between Pyrus bretschneideri and Pyrus communis during pear fruit development. Remarkably, the transcriptome data showed that UBC genes might play a more important role in fruit ripening for further study. This is the first report on the systematic analysis of two Pyrus UBC gene families, and these data will help further study the role of UBC genes in fruit development and ripening, as well as contribute to the functional verification of UBC genes in pear.

The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses

Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up- or down-regualted in the cultivar “Sijimi” (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were up- or down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan.

High infestation levels of Schizotetranychus oryzae severely affects rice metabolism

High levels of Schizotetranychus oryzae phytophagous mite infestation on rice leaves can severely affect productivity. Physiological characterization showed that S. oryzae promotes a decrease in chlorophyll concentration and the establishment of a senescence process in rice leaves. Late-infested leaves also present high levels of superoxide radical and hydrogen peroxide accumulation, along with high levels of membrane integrity loss, which is indicative of cell death. To better understand the rice molecular responses to high levels of mite infestation, we employed the Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We identified 83 and 88 proteins uniquely present in control and late-infested leaves, respectively, along with 11 and one proteins more abundant in control and late-infested leaves, respectively. S. oryzae infestation induces a decreased abundance of proteins related to translation, protease inhibition, and photosynthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation. Our results also suggest that S. oryzae infestation interferes with intracellular transport, DNA structure maintenance, and amino acid and lipid metabolism in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of late-infested rice leaves and suggest several targets which could be tested in future biotechnological approaches aiming to avoid the population increase of phytophagous mite in rice plants.

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of RNA sequencing data revealed expression profile of tomato E2 genes in seedling, root, leaf, seed, fruit, and flower tissues. Our study aid in the understanding of distribution, expansion, evolutionary relation and probable participation in plant biological processes of tomato E2 enzymes that will facilitate strong base for future research on ubiquitin-mediated regulations in tomato and other plant systems.

Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya

Background

Ripening affects the quality and nutritional contents of fleshy fruits and is a crucial process of fruit development. Although several studies have suggested that ubiquitin-conjugating enzyme (E2s or UBC enzymes) are involved in the regulation of fruit ripening, little is known about the function of E2s in papaya (Carica papaya).

Methodology/Principal findings

In the present study, we searched the papaya genome and identified 34 putative UBC genes, which were clustered into 17 phylogenetic subgroups. We also analyzed the nucleotide sequences of the papaya UBC (CpUBC) genes and found that both exon-intron junctions and sequence motifs were highly conserved among the phylogenetic subgroups. Using real-time PCR analysis, we also found that all the CpUBC genes were expressed in roots, stems, leaves, male and female flowers, and mature fruit, although the expression of some of the genes was increased or decreased in one or several specific organs. We also found that the expression of 13 and two CpUBC genes were incresesd or decreased during one and two ripening stages, respectively. Expression analyses indicates possible E2s playing a more significant role in fruit ripening for further studies.

Conclusions

To the best of our knowledge, this is the first reported genome-wide analysis of the papaya UBC gene family, and the results will facilitate further investigation of the roles of UBC genes in fruit ripening and will aide in the functional validation of UBC genes in papaya.

The banana E2 gene family: Genomic identification, characterization, expression profiling analysis

The E2 is at the center of a cascade of Ub1 transfers, and it links activation of the Ub1 by E1 to its eventual E3-catalyzed attachment to substrate. Although the genome-wide analysis of this family has been performed in some species, little is known about analysis of E2 genes in banana. In this study, 74 E2 genes of banana were identified and phylogenetically clustered into thirteen subgroups. The predicted banana E2 genes were distributed across all 11 chromosomes at different densities. Additionally, the E2 domain, gene structure and motif compositions were analyzed. The expression of all of the banana E2 genes was analyzed in the root, stem, leaf, flower organs, five stages of fruit development and under abiotic stresses. All of the banana E2 genes, with the exception of few genes in each group, were expressed in at least one of the organs and fruit developments, which indicated that the E2 genes might involve in various aspects of the physiological and developmental processes of the banana. Quantitative RT-PCR (qRT-PCR) analysis identified that 45 E2s under drought and 33 E2s under salt were induced. To the best of our knowledge, this report describes the first genome-wide analysis of the banana E2 gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.

Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize

BACKGROUND

Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays).

METHODOLOGY/PRINCIPAL FINDINGS

In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress.

CONCLUSIONS

Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize.

Characterization of the Ubiquitin-Conjugating Enzyme Gene Family in Rice and Evaluation of Expression Profiles under Abiotic Stresses and Hormone Treatments

Ubiquitin-conjugating enzyme E2s (UBCs), which catalyze the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. However, little is known about the knowledge of UBC gene family in rice. In this study, a total of 39 UBC encoding genes, which all contained an UBC domain with a cysteine active site, were identified in the rice genome. These were classified into fifteen distinct subfamilies based upon their sequence similarity and phylogenetic relationships. A subset of 19 OsUBC genes exhibited chromosomal duplication; 4 and 15 OsUBC genes were tandemly and segmentally duplicated, respectively. Comprehensive analyses were performed to investigate the expression profiles of OsUBC genes in various stages of vegetative and reproductive development using data from EST, Microarrays, MPSS, and real-time PCR. Many OsUBC genes exhibited abundant and tissue-specific expression patterns. Moreover, 14 OsUBCs were found to be differentially expressed under treatments with drought, or salt stresses. The expression analysis after treatments with IAA, 6-BA, GA and ABA indicated that almost all OsUBC genes were responsive to at least two of the four hormones. Several genes were significantly down-regulated under all of the hormone treatments, and most of the genes reduced by 6-BA were also reduced by GA. This study will facilitate further studies of the OsUBC gene family and provide useful clues for functional validation of OsUBCs in rice.

An Acidic PATHOGENESIS-RELATED1 Gene of Oryza grandiglumis is Involved in Disease Resistance Response Against Bacterial Infection

Wild rice, Oryza grandiglumis shows hyper-resistance response to pathogen infection. In order to identify genes necessary for defense response in plants, we have carried out a subtractive hybridization coupled with a cDNA macroarray. An acidic PATHOGENESIS-RELATED1 (PR1) gene of the wild rice is highly identical to the acidic PR1 genes of different plant species. The OgPR1a cDNA has an apparent single open reading frame with a predicted molecular mass 40,621 Da and an isoelectic point of 5.14. Both in silico analysis and a transient expression assay in onion epidermal cells revealed that the OgPR1a protein could be localized in intercellular space in plants. The OgPR1a mRNA was strongly transcribed by the exogenous treatment with ethylene and jasmonic acid as well as protein phosphatase inhibitors. Additionally, ectopic expression of the OgPR1a conferred disease resistance on Arabidopsis to the bacterial and fungal infections.

Overexpression of VrUBC1, a Mung Bean E2 Ubiquitin-Conjugating Enzyme, Enhances Osmotic Stress Tolerance in Arabidopsis

The ubiquitin conjugating enzyme E2 (UBC E2) mediates selective ubiquitination, acting with E1 and E3 enzymes to designate specific proteins for subsequent degradation. In the present study, we characterized the function of the mung bean VrUBC1 gene (Vigna radiata UBC 1). RNA gel-blot analysis showed that VrUBC1 mRNA expression was induced by either dehydration, high salinity or by the exogenous abscisic acid (ABA), but not by low temperature or wounding. Biochemical studies of VrUBC1 recombinant protein and complementation of yeast ubc4/5 by VrUBC1 revealed that VrUBC1 encodes a functional UBC E2. To understand the function of this gene in development and plant responses to osmotic stresses, we overexpressed VrUBC1 in Arabidopsis (Arabidopsis thaliana). The VrUBC1-overexpressing plants displayed highly sensitive responses to ABA and osmotic stress during germination, enhanced ABA- or salt-induced stomatal closing, and increased drought stress tolerance. The expression levels of a number of key ABA signaling genes were increased in VrUBC1-overexpressing plants compared to the wild-type plants. Yeast two-hybrid and bimolecular fluorescence complementation demonstrated that VrUBC1 interacts with AtVBP1 (A. thalianaVrUBC1 Binding Partner 1), a C3HC4-type RING E3 ligase. Overall, these results demonstrate that VrUBC1 plays a positive role in osmotic stress tolerance through transcriptional regulation of ABA-related genes and possibly through interaction with a novel RING E3 ligase.