Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses

Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance

With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.

Expression Profiling Reveals the Possible Involvement of the Ubiquitin-Proteasome Pathway in Abiotic Stress Regulation in Gracilariopsis lemaneiformis

Gracilariopsis lemaneiformis is an economically important red macroalga, the cultivation of which is affected by abiotic stresses. This research intends to study the response mechanism of various components of the ubiquitin-protease pathway to abiotic stress in G. lemaneiformis. The algae were treated with five common external stresses (high temperature, low temperature, O3, PEG, and water shortage) to study the macroscopic and microscopic manifestations of the ubiquitin-proteasome pathway. Firstly, the changes in soluble protein and ubiquitin were detected during the five treatments, and the results showed that the content of soluble protein and ubiquitin significantly increased under most stresses. The content of the soluble protein increased the most on the second day after 20% PEG treatment, which was 1.38 times higher than that of the control group, and the content of ubiquitin increased the most 30 min after water shortage treatment, which was 3.6 times higher than that of the control group. Then, 12 key genes (E1, E2, UPL1, HRD1, UFD1, Cul3, Cul4, DDB2, PIAS1, FZR1, APC8, and COP1) of the ubiquitin-proteasome pathway were studied, including an estimation of the probably regulatory elements in putative promoter regions and an analysis of transcript levels. The results showed that CAAT box, LTR, GC motif, and MBS elements were present in the putative promoter regions, which might have endowed the genes with the ability to respond to stress. The transcript analysis showed that under high temperature, low temperature, PEG, O3, and water shortage, all of the genes exhibited instant and significant up-regulation, and different genes had different response levels to different stresses. Many of them also showed the synergistic effect of transcript up-regulation under various stress treatments. In particular, E1, E2, Cul3, Cul4, UPL1, HRD1, and COP1 performed most significantly under the five stresses. Collectively, our exploration of the ubiquitin-proteasome pathway and the transcript levels of key genes suggest a significant role to cope with adversity, and potential candidate genes can be selected for transformation to obtain stress-resistant strains.

HECT ubiquitin ligases as accessory proteins of the plant proteasome

The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome's ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.

Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

Background

DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear.

Methods

The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results.

Results

A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17­ were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17­-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum

The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways.

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1-CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16-17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.

Growth, physiological and transcriptomic analysis of the perennial ryegrass Lolium perenne in response to saline stress

Salinization of soil is a global environmental concern. To bioremediate or use saline-alkali lands, most studies focused on screening of halophytes and breeding of saline-tolerant non-halophyte vegetables. Seldom studies investigated effects of salinity on general landscape plants, which are important for landscape construction in urban areas. In the present study, effects of salinity on seed germination and seedling growth of the perennial ryegrass Lolium perenne were investigated. The final seed germination rate was not affected at salinity up to 6.4‰. Partial seedlings wilted in all saline treatments and the mortality of L. perenne was positively correlated with salinity. Treatments with salinity equal to or lower than 1.6‰ did not affect length and dry weight of shoot and root. These results suggested that L. perenne could be sowed and then grow well in low-salinity areas. To explore the underlying physiological mechanisms, contents of photosynthetic pigments and antioxidant indices were determined. The results showed that contents of chlorophyll a, b and carotenoid significantly decreased in all saline treatments, in comparison to the control. Similarly, activities of superoxide dismutase and peroxidase decreased and contents of glutathione and malondialdehyde increased in saline treatments. Additionally, transcriptome analysis identified 792 differentially expressed genes (DEGs) in L. perenne shoots between 6.4‰ saline treatment and the control. Compared with the control, genes in relation to iron transportation and amino acid metabolism were downregulated, but genes participating in energy metabolism were upregulated. These changes would inhibit toxicity of ion accumulation and provide more energy for plants to resist saline stress.

Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties

Background

Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach.

Results

In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed.

Conclusions

The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

Genome-wide identification, phylogenetic and expression analysis of the maize HECT E3 ubiquitin ligase genes

HECT (homologous to the E6AP carboxyl terminus) ubiquitin ligase genes (E3s) are enzymes with diverse functions influencing plant growth, development, and responses to abiotic stresses. However, there is relatively little information available regarding the maize HECT E3 gene family. In the present study, 12 maize HECT E3 genes (ZmUPL1 to ZmUPL12) were identified at the whole-genome level. The phylogenetic relationships, structures, and expression levels of the maize HECT E3 genes were then analyzed. On the basis of the constructed maximum likelihood phylogenetic tree, the HECT E3 genes were divided into six groups. The quantitative real-time polymerase chain reaction assay results revealed that all of the maize ZmUPL genes were expressed in most of the examined tissues and were responsive to three abiotic stresses. Considered together, the study results may provide a useful foundation for future investigations of maize stress-tolerance genes as well as functional analyses of the E3 enzymes in diverse agriculturally important crop species.

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L

The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of HECT genes in Brassica rapa and Brassica oleracea, followed by analysis of phylogeny, gene structure, additional domains, putative cis-regulatory elements, chromosomal location, synteny, and expression. Ten and 13 HECT genes were respectively identified in B. rapa and B. oleracea and then resolved into seven groups along with their Arabidopsis orthologs by phylogenetic analysis. This classification is well supported by analyses of gene structure, motif composition within the HECT domain and additional protein domains. Ka/Ks ratio analysis showed that these HECT genes primarily underwent purifying selection with varied selection pressures resulting in different rates of evolution. RNA-Seq data analysis showed that the overwhelming majority of them were constitutively expressed in all tested tissues. qRT-PCR based expression analysis of the 10 B. rapa HECT genes under salt and drought stress conditions showed that all of them were responsive to the two stress treatments, which was consistent with their promoter sequence analysis revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. Our study provides useful information and lays the foundation for further functional determination of each HECT gene across the Brassica species.

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice

Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.

SorghumFDB: sorghum functional genomics database with multidimensional network analysis

Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C₄ grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein–protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.

Database URL:http://structuralbiology.cau.edu.cn/sorghum/index.html.