A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

SCFOsFBK1 E3 ligase mediates jasmonic acid-induced turnover of OsATL53 and OsCCR14 to regulate lignification of rice anthers and roots

The rice F-box protein OsFBK1, which mediates the turnover of a cinnamoyl CoA-reductase, OsCCR14, has previously been shown to regulate anther and root lignification. Here, we identify OsATL53, a member of the ATL family of RING-H2 proteins that interacts with OsCCR14 in the cytoplasm. OsATL53 was identified in the same yeast two-hybrid library screening as reported previously for OsCCR14, and we show it to have cytoplasmic localization and E3 ligase ubiquitination properties. SCFOsFBK1 mediates turnover of OsATL53 in the cytoplasm and the nucleus, and that of OsCCR14 only in the nucleus, as shown by cell-free degradation assays. Confocal fluorescence lifetime imaging microscopy analyses demonstrate that in presence of jasmonic acid (JA), which plays a role in anther dehiscence, OsATL53-OsCCR14 undergoes conformational changes that trigger the complex to accumulate around the nuclear periphery and signals OsFBK1 to initiate degradation of the proteins in the respective cellular compartments. OsATL53 decreases the enzymatic activity of OsCCR14 and sequesters it in the cytoplasm, thereby regulating the lignification process. Transgenic rice with knockdown of OsATL53 display increased lignin deposition in the anthers and roots compared to the wild type, whilst knockdown of OsCCR14 results in decreased lignin content. Our results show that OsATL53 affects the activity of OsCCR14, and that their JA-induced degradation by SCFOsFBK1 regulates lignification of rice anthers and roots.

The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6

NAC transcription factors (TFs) play critical roles in plant immunity by modulating the expression of downstream genes via binding to specific cis-elements in promoters. Here, we report the function and regulatory network of a pathogen- and defense phytohormone-inducible NAC TF gene, ONAC083, in rice (Oryza sativa) immunity. ONAC083 localizes to the nucleus and exhibits transcriptional activation activity that depends on its C-terminal region. Knockout of ONAC083 enhances rice immunity against Magnaporthe oryzae, strengthening pathogen-induced defense responses, and boosting chitin-induced pattern-triggered immunity (PTI), whereas ONAC083 overexpression has opposite effects. We identified ONAC083-binding sites in the promoters of 82 genes, and showed that ONAC083 specifically binds to a conserved element with the core sequence ACGCAA. ONAC083 activated the transcription of the genes OsRFPH2-6, OsTrx1, and OsPUP4 by directly binding to the ACGCAA element. OsRFPH2-6, encoding a RING-H2 protein with an N-terminal transmembrane region and a C-terminal typical RING domain, negatively regulated rice immunity against M. oryzae and chitin-triggered PTI. These data demonstrate that ONAC083 negatively contributes to rice immunity against M. oryzae by directly activating the transcription of OsRFPH2-6 through the ACGCAA element in its promoter. Overall, our study provides new insight into the molecular regulatory network of NAC TFs in rice immunity.

Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Background

RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat.

Results

In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X₂-R-X₁₄-Cys-X₁-H-X₂-Cys-X₂-Cys-X₁₀-Cys-X₂-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties.

Conclusions

Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08905-x.

Ubiquitin ligase OsRINGzf1 regulates drought resistance by controlling the turnover of OsPIP2;1

Water is crucial for plant growth and survival. The transcellular water movement is facilitated by aquaporins (AQPs) that rapidly and reversibly modify water permeability. The abundance of AQPs is regulated by its synthesis, redistribution and degradation. However, the molecular mechanism of proteasomal degradation of AQPs remains unclear. Here, we demonstrate that a novel E3 ligase, OsRINGzf1, mediated the degradation of AQPs in rice. OsRINGzf1 is the candidate gene from a drought-related quantitative trait locus (QTL) on the long arm of chromosome 4 in rice (Oryza sativa) and encodes a Really Interesting New Gene (RING) zinc finger protein 1. OsRINGzf1 possesses the E3 ligase activity, ubiquitinates and mediates OsPIP2;1 degradation, thus reducing its protein abundance. The content of OsPIP2;1 protein was decreased in OsRINGzf1 overexpression (OE) plants. The degradation of OsPIP2;1 was inhibited by MG132. The OsRINGzf1 OE plants, with higher leaf-related water content (LRWC) and lower leaf water loss rate (LWLR), exhibited enhanced drought resistance, whereas the RNAi and knockout plants of OsRINGzf1 were more sensitive to drought. Together, our data demonstrate that OsRINGzf1 positively regulates drought resistance through promoting the degradation of OsPIP2;1 to enhance water retention capacity in rice.

The E3 ubiquitin ligase RING1 interacts with COP9 Signalosome Subunit 4 to positively regulate resistance to root-knot nematodes in Solanum lycopersicum L

Globally, root-knot nematodes (RKNs) cause massive production losses in all major crops. E3 ubiquitin ligases are involved in plant growth, development and immune response. But their roles in plant defense against RKNs are largely unclear. Here, we show that tomato E3 ubiquitin ligase RING1 interacts with COP9 Signalosome Subunit 4 (CSN4) which is essential for jasmonic acid (JA)-dependent basal defense against RKNs. Tissue-specific expression analysis showed that RING1 expression was the highest in tomato roots and the expression was significantly increased with RKN (Meloidogyne incognita) infection. Compared with the wild-type plants, the number of egg masses in roots significantly increased in the ring1 mutants, while RING1 overexpression conferred resistance against RKNs. Furthermore, RKN infection increased the accumulation of CSN4 protein in the roots of wild-type plants, which was largely compromised in the ring1 mutants but was enhanced in the RING1 overexpressing plants. The RKN-induced transcripts of JA biosynthetic and signaling genes as well as the accumulation of JA and JA-isoleucine were compromised in ring1 mutants but were increased in RING1 overexpressing plants. These results suggest that RING1 positively regulates JA-dependent basal defense against RKNs by interacting with CSN4 proteins.

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

BACKGROUND

Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown.

RESULTS

Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice (Oryza sativa L.) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1-OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity.

CONCLUSIONS

The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3-substrate interactome in plants.

Wheat E3 ubiquitin ligase TaGW2-6A degrades TaAGPS to affect seed size

TaGW2 has been identified as a key determinant of the grain weight in wheat (Triticum aestivum L.). In our previous study, we found that the grain size differs in Chinese Spring (CS) and its TaGW2-6A allelic variant (NIL31). In addition, the expression of the key starch biosynthesis enzyme gene TaAGPS differs significantly in the two materials. However, the underlying molecular mechanism associated with the action of TaGW2-6A has not been reported. In the present study, we found that TaGW2-6A-CS interacted with TaAGPS, whereas TaGW2-6A-NIL31 did not interact with it in vitro and in vivo. Furthermore, we found that the C-terminal LXLX domain (376-424 aa) of TaGW2-6A recognized TaAGPS. However, the TaGW2-6A allelic variant lacked this key interaction region due to premature translation termination. We also found that TaGW2-6A-CS can ubiquitinate TaAGPS and degrade it via the 26 S proteasome pathway. In addition, our analysis of the activity of ADP-glucose pyrophosphorylase (AGPase) indicated that the AGPase level in the endosperm cells was lower in CS than NIL31. Cytological observations demonstrated that the average number of starch granules and the average area of starch granules in endosperm cells were lower in CS than NIL31. The overexpression of TaAGPS positively regulated the seed size in transgenic Arabidopsis. Our findings provide novel insights into the molecular mechanism that allows TaGW2-6A-TaAGPS to regulate seed size via the starch synthesis pathway.

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.

RING Zinc Finger Proteins in Plant Abiotic Stress Tolerance

RING zinc finger proteins have a conserved RING domain, mainly function as E3 ubiquitin ligases, and play important roles in plant growth, development, and the responses to abiotic stresses such as drought, salt, temperature, reactive oxygen species, and harmful metals. RING zinc finger proteins act in abiotic stress responses mainly by modifying and degrading stress-related proteins. Here, we review the latest progress in research on RING zinc finger proteins, including their structural characteristics, classification, subcellular localization, and physiological functions, with an emphasis on abiotic stress tolerance. Under abiotic stress, RING zinc finger proteins on the plasma membrane may function as sensors or abscisic acid (ABA) receptors in abiotic stress signaling. Some RING zinc finger proteins accumulate in the nucleus may act like transcription factors to regulate the expression of downstream abiotic stress marker genes through direct or indirect ways. Most RING zinc finger proteins usually accumulate in the cytoplasm or nucleus and act as E3 ubiquitin ligases in the abiotic stress response through ABA, mitogen-activated protein kinase (MAPK), and ethylene signaling pathways. We also highlight areas where further research on RING zinc finger proteins in plants is needed.

Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Background

Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax.

Methods

Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax.

Results

We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.

Genome-wide analysis of RING-type E3 ligase family identifies potential candidates regulating high amylose starch biosynthesis in wheat (Triticum aestivum L.)

In ubiquitin-mediated post-translational modifications, RING finger families are emerged as important E3 ligases in regulating biological processes. Amylose and amylopectin are two major constituents of starch in wheat seed endosperm. Studies have been found the beneficial effects of high amylose or resistant starch on health. The ubiquitin-mediated post-translational regulation of key enzymes for amylose/amylopectin biosynthesis (GBSSI and SBEII) is still unknown. In this study, the genome-wide analysis identified 1272 RING domains in 1255 proteins in wheat, which is not reported earlier. The identified RING domains classified into four groups—RING-H2, RING-HC, RING-v, RING-G, based on the amino acid residues (Cys, His) at metal ligand positions and the number of residues between them with the predominance of RING-H2 type. A total of 1238 RING protein genes were found to be distributed across all 21 wheat chromosomes. Among them, 1080 RING protein genes were identified to show whole genome/segmental duplication within the hexaploid wheat genome. In silico expression analysis using transcriptome data revealed 698 RING protein genes, having a possible role in seed development. Based on differential gene expression and correlation analysis of 36 RING protein genes in diverse (high and low) amylose mutants and parent, 10 potential RING protein genes found to be involved in high amylose biosynthesis and significantly associated with two starch biosynthesis genes; GBSSI and SBEIIa. Characterization of mutant lines using next-generation sequencing method identified unique mutations in 698 RING protein genes. This study signifies the putative role of RING-type E3 ligases in amylose biosynthesis and this information will be helpful for further functional validation and its role in other biological processes in wheat.

The Rice Abscisic Acid-Responsive RING Finger E3 Ligase OsRF1 Targets OsPP2C09 for Degradation and Confers Drought and Salinity Tolerance in Rice

Drought and salinity are major important factors that restrain growth and productivity of rice. In plants, many really interesting new gene (RING) finger proteins have been reported to enhance drought and salt tolerance. However, their mode of action and interacting substrates are largely unknown. Here, we identified a new small RING-H2 type E3 ligase OsRF1, which is involved in the ABA and stress responses of rice. OsRF1 transcripts were highly induced by ABA, salt, or drought treatment. Upregulation of OsRF1 in transgenic rice conferred drought and salt tolerance and increased endogenous ABA levels. Consistent with this, faster transcriptional activation of key ABA biosynthetic genes, ZEP, NCED3, and ABA4, was observed in OsRF1-OE plants compared with wild type in response to drought stress. Yeast two-hybrid assay, BiFC, and co-immunoprecipitation analysis identified clade A PP2C proteins as direct interacting partners with OsRF1. In vitro ubiquitination assay indicated that OsRF1 exhibited E3 ligase activity, and that it targeted OsPP2C09 protein for ubiquitination and degradation. Cell-free degradation assay further showed that the OsPP2C09 protein is more rapidly degraded by ABA in the OsRF1-OE rice than in the wild type. The combined results suggested that OsRF1 is a positive player of stress responses by modulating protein stability of clade A PP2C proteins, negative regulators of ABA signaling.

The apple RING-H2 protein MdCIP8 regulates anthocyanin accumulation and hypocotyl elongation by interacting with MdCOP1

COP1, an important RING ubiquitin ligase E3, is a molecular switch for light regulation in plant development. As an interacting protein of COP1, CIP8 contains a RING-H2 domain, but its biological function is unclear. Here, the apple MdCIP8 was identified based on its homology with AtCIP8 in Arabidopsis. MdCIP8 was constitutively expressed at different levels in various apple tissues, and the expression level of MdCIP8 was not affected by light and dark conditions. MdCIP8 reversed the short hypocotyl phenotype of the cip8 mutant under light conditions. Furthermore, the yeast two-hybrid experiment showed that MdCIP8 interacted with the RING domain of MdCOP1 through its RING-H2 domain. MdCIP8-OX/cop1-4 exhibited the phenotype of the cop1-4 mutant, indicating that CIP8 acts upstream of COP1. In addition, an apple transient injection experiment showed that MdCIP8 inhibited anthocyanin accumulation in an MdCOP1-dependent pathway. Overall, our findings reveal that CIP8 plays an inhibitory role in the light-regulation responses of plants.

Molecular characterization of a RING E3 ligase SbHCI1 in sorghum under heat and abscisic acid stress

Molecular function ofRING E3 ligase SbHCI1is involved in ABA-mediated basal heat stress tolerancein sorghum. Global warming generally reduces plant survival, owing to the negative effects of high temperatures on plant development. However, little is known about the role of Really Interesting New Gene (RING) E3 ligase in the heat stress responses of plants. As such, the aim of the present study was to characterize the molecular functions of the Sorghum bicolor ortholog of the Oryza sativa gene for Heat- and Cold-Induced RING finger protein 1 (SbHCI1). Subcellular localization revealed that SbHCI1 was mainly associated with the cytosol and that it moved to the Golgi apparatus under heat stress conditions. The fluorescent signals of SbHCI1 substrate proteins were observed to migrate to the cytoplasm under heat stress conditions. Bimolecular fluorescence complementation (BiFC) and yeast two-hybrid (Y2H) assays revealed that SbHCI1 physically interacted with OsHCI1 ortholog partner proteins in the cytoplasm. Moreover, an in vitro ubiquitination assay revealed that SbHCI1 polyubiquitinated each of the three interacting proteins. The ectopic overexpression of SbHCI1 in Arabidopsis revealed that the protein was capable of inducing abscisic acid (ABA)-hypersensitivity and basal heat stress tolerance. Therefore, SbHCI1 possesses E3 ligase activity and may function as a positive regulator of heat stress responses through the modulation of interacting proteins.

Molecular dissection of two homoeologous wheat genes encoding RING H2-type E3 ligases: TaSIRFP-3A and TaSIRFP-3B

Two homoeologous wheat genes, TaSIRFP-3A and TaSIRFP-3B, encode the RING-HC-type E3 ligases that play an inhibitory role in sucrose metabolism in response to cold stress. In higher plants, the attachment of ubiquitin (Ub) and the subsequent recognition and degradation by the 26S proteasome affects a variety of cellular functions that are essential for survival. Here, we characterized the two homoeologous wheat genes encoding the really interesting new gene (RING) HC-type E3 ligases: TaSIRFP-3A and TaSIRFP-3B (Triticum aestivum SINA domain including RING finger protein 1 and 2), which regulate target proteins via the Ub/26S proteasome system. The TaSIRFP-3A gene was highly expressed under cold stress. In contrast, its homoeologous gene, TaSIRFP-3B, showed only a slight increase in expression levels in shoots. Despite these differences, both the proteins exhibited E3 ligase activity with the cytosol- and nucleus-targeted localization, demonstrating their conserved molecular function. Heterogeneous overexpression of TaSIRFP-3A or TaSIRFP-3B in Arabidopsis showed delayed plant growth causing a reduction in sucrose synthase enzymatic activity and photosynthetic sucrose synthesis, by regulating sucrose synthase proteins. TaSIRFP-3A- or TaSIRFP-3B-overexpressing plants showed higher hypersensitivity under cold stress than WT plants with an accumulation of reactive oxygen species (ROS). These results suggest that the negative regulation of TaSIRFP-3A and TaSIRFP-3B in response to cold stress is involved in sucrose metabolism.

The AlRabring7 E3-Ub-ligase mediates AlRab7 ubiquitination and improves ionic and oxidative stress tolerance in Saccharomyces cerevisiae

The maintenance of ROS homeostasis, membrane biogenesis and recycling of molecules are common stress responses involving specific and complex regulatory network. Ubiquitination is an important and common mechanism which facilitates environmental adaptation in eukaryotes. In the present study we have cloned the AlRabring7, an E3-Ub-ligase, previously identified as AlRab7 interacting partner. The role of AlRabring7 for ubiquitinating AlRab7 and facilitating stress tolerance is analysed. The AlRabring7, with an open-reading frame of 702 bp encodes a protein of 233 amino acids, with RING-HC domain of 40 amino acids. In silico analysis shows that AlRabring7 is a C3HC4-type RING E3 Ub ligase. The protein - protein docking show interaction dynamics between AlRab7-AlRabring7-Ubiquitin proteins. The AlRab7 and AlRabring7 transcript showed up-regulation in response to different salts i.e: NaCl, KCl, CaCl₂, NaCl + KCl, NaCl + CaCl₂, imposing ionic as well as hyperosmotic stress, and also with oxidative stress by H₂O₂ treatment. Interestingly, the AlRabring7 showed early transcript expression with maximum expression in shoots on combinatorial stresses. The AlRab7 showed delayed and maximum expression with NaCl + CaCl₂ stress treatment. The AlRab7 complements yeast ypt7Δ mutants and restored the fragmented vacuole. The in vitro ubiquitination assay revealed that AlRabring7 function as E3 ubiquitin ligase and mediates AlRab7 ubiquitination. Overexpression of AlRab7 and AlRabring7 independently and when co-transformed enhanced the growth of yeast cells during stress conditions. Further, the bimolecular fluorescence complementation assay shows the in planta interaction of the two proteins. Our results suggest that AlRab7 and AlRabring7 confers enhanced stress tolerance in yeast.

Zinc Finger Proteins in the Human Fungal Pathogen Cryptococcus neoformans

Zinc is one of the essential trace elements in eukaryotes and it is a critical structural component of a large number of proteins. Zinc finger proteins (ZNFs) are zinc-finger domain-containing proteins stabilized by bound zinc ions and they form the most abundant proteins, serving extraordinarily diverse biological functions. In recent years, many ZNFs have been identified and characterized in the human fungal pathogen Cryptococcus neoformans, a fungal pathogen causing fatal meningitis mainly in immunocompromised individuals. It has been shown that ZNFs play important roles in the morphological development, differentiation, and virulence of C. neoformans. In this review, we, first, briefly introduce the ZNFs and their classification. Then, we explain the identification and classification of the ZNFs in C. neoformans. Next, we focus on the biological role of the ZNFs functionally characterized so far in the sexual reproduction, virulence factor production, ion homeostasis, pathogenesis, and stress resistance in C. neoformans. We also discuss the perspectives on future function studies of ZNFs in C. neoformans.

Research Progress on Plant RING-Finger Proteins

E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.

Molecular Functions of Rice Cytosol-Localized RING Finger Protein 1 in Response to Salt and Drought and Comparative Analysis of Its Grass Orthologs

In higher plants, the post-translational modification of target proteins via the attachment of molecules such as ubiquitin (Ub) mediates a variety of cellular functions via the Ub/26S proteasome system. Here, a really interesting new gene (RING)-H2 type E3 ligase, which regulates target proteins via the Ub/26S proteasome system, was isolated from a rice plant, and its other grass orthologs were examined to determine the evolution of its molecular function during speciation. The gene encoding Oryza sativa cytoplasmic-localized RING finger protein 1 (OsCLR1) was highly expressed under salt and drought stresses. By contrast, the three grass orthologs, SbCLR1 from Sorghum bicolor, ZmCLR1 from Zea mays and TaCLR1 from Triticum aestivum, showed different responses to these stresses. Despite these differences, all four orthologs exhibited E3 ligase activity with cytosol-targeted localization, demonstrating conserved molecular functions. Although OsCLR1-overexpressing plants showed higher survival rates under both salt and drought stresses than that of the wild type (WT) plants, this pattern was not observed in the other orthologs. In addition, OsCLR1-overexpressing plants exhibited lower germination rates in ABA than that of WT plants, whereas the three ortholog CLR1-overexpressing plants showed rates similar to the WT plants. These results indicate the positive regulation of OsCLR1 in response to salt and drought in an ABA-dependent manner. Despite the molecular functions of the three CLR1 orthologs remaining largely unknown, our results provide an insight into the evolutionary fate of CLR1 grass orthologs during speciation after the divergence from a common ancestor.

A rice really interesting new gene H2-type E3 ligase, OsSIRH2-14, enhances salinity tolerance via ubiquitin/26S proteasome-mediated degradation of salt-related proteins

Salinity is a deleterious abiotic stress factor that affects growth, productivity, and physiology of crop plants. Strategies for improving salinity tolerance in plants are critical for crop breeding programmes. Here, we characterized the rice (Oryza sativa) really interesting new gene (RING) H2-type E3 ligase, OsSIRH2-14 (previously named OsRFPH2-14), which plays a positive role in salinity tolerance by regulating salt-related proteins including an HKT-type Na⁺ transporter (OsHKT2;1). OsSIRH2-14 expression was induced in root and shoot tissues treated with NaCl. The OsSIRH2-14-EYFP fusion protein was predominately expressed in the cytoplasm, Golgi, and plasma membrane of rice protoplasts. In vitro pull-down assays and bimolecular fluorescence complementation assays revealed that OsSIRH2-14 interacts with salt-related proteins, including OsHKT2;1. OsSIRH2-14 E3 ligase regulates OsHKT2;1 via the 26S proteasome system under high NaCl concentrations but not under normal conditions. Compared with wild type plants, OsSIRH2-14-overexpressing rice plants showed significantly enhanced salinity tolerance and reduced Na⁺ accumulation in the aerial shoot and root tissues. These results suggest that the OsSIRH2-14 RING E3 ligase positively regulates the salinity stress response by modulating the stability of salt-related proteins.

Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum

RING domain proteins generally have E3 ubiquitin ligase activity and are involved in degrading their substrate proteins. The roles of these proteins in growth, development, and responses to different abiotic stresses have been described well in various plant species, but little is available on tomatoes. Here, we identified 474 RING domains in 469 potential proteins encoded in the tomato genome. These RING genes were found to be located in 12 chromosomes and could be divided into 51 and 11 groups according to the conserved motifs outside the RING domain and phylogenetic analysis, respectively. Segmental duplication could be the major driver in the expansion of the tomato RING gene family. Further comparative syntenic analysis suggested that there have been functional divergences of RING genes during plant evolution and most of the RING genes in various species are under negative selection. Expression profiles derived from a transcriptomic analysis showed that most tomato RING genes exhibited tissue-specific expression patterning. Further RT-qPCR validation showed that almost all genes were upregulated by salt treatment, which was consistent with the microarray results. This study provides the first comprehensive understanding of the RING gene family in the tomato genome. Our results pave the way for further investigation of the classification, evolution, and potential functions of the RING domain genes in tomato.

Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes

E3 ubiquitin ligases of the ubiquitin proteasome system (UPS) mediate recognition of substrates and later transfer the ubiquitin (Ub). They are the most expanded components of the system. The Really Interesting New Gene (RING) domain contains 40-60 residues that are highly represented among E3 ubiquitin ligases. The Arabidopsis thaliana E3 ubiquitin ligases with a RING finger primarily contain RING-HC or RING-H2 type domains or less frequently RING-v, RING-C2, RING-D, RING-S/T and RING-G type domains. Our previous work on three E3 ubiquitin ligase families with a RING-H2 type domain, ATL, BTL, and CTL, suggested that a phylogenetic distribution based on the RING domain allowed for the creation a catalog of known domains or unknown conserved motifs. This work provided a useful and comprehensive view of particular families of RING E3 ubiquitin ligases. We updated the annotation of A. thaliana RING proteins and surveyed RING proteins from 30 species across eukaryotes. Based on domain architecture profile of the A. thaliana proteins, we catalogued 4711 RING finger proteins into 107 groups, including 66 previously described gene families or single genes and 36 novel families or undescribed genes. Forty-four groups were specific to a plant lineage while 41 groups consisted of proteins found in all eukaryotic species. Our present study updates the current classification of plant RING finger proteins and reiterates the importance of these proteins in plant growth and adaptation.

Genome-wide survey, characterization, and expression analysis of RING finger protein genes in Brassica oleracea and their syntenic comparison to Brassica rapa and Arabidopsis thaliana

The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B. oleracea. Comparison of these results with B. rapa and A. thaliana revealed some common as well as species-specific features. Our results showed that the differential gene loss following the whole genome triplication has largely contributed to the RING protein gene number variation among these species, although other factors such as tandem duplication, RING domain loss, or modification had also contributed to this variation. Analysis of RNA-seq data showed that these RING protein genes were functionally diversified and involved in all the stages of plant growth and development, and that the triplicated members were also diverged in expression with one member often more dominantly expressed over the two others in the majority of cases. Our study lays the foundation for further functional determination of each RING protein gene among species of the genus Brassica.

Characterization of a novel zinc finger transcription factor (TaZnF) from wheat conferring heat stress tolerance in Arabidopsis

C3HC4-type zinc finger proteins are known to play important roles in various plant processes including regulation of growth and development, signaling networks, responses to abiotic stresses etc. The current study identifies and explores the involvement of TaZnF in plant stress response, mainly heat stress. TaZnF belongs to C4HC3-type zinc finger transcription factor. Phylogenetic analysis of TaZnF revealed strong sequence similarity to Brachypodium distachyon, a model system for crop species. Gene expression studies have revealed its role under diverse stress conditions including heat and cold conditions. The transcript level of TaZnF was found to be highest in seed and starts at the post anthesis period 3-5DAA, a more sensitive stage resulting in a negative influence on the yield of crop species. TaZnF possesses transcriptional activity. Overexpression of TaZnF in Arabidopsis thaliana conferred improved tolerance to both basal and high-temperature stress as observed from various assays examining their growth and development. The transgenics were recovered and showed early flowering compared to wild-type. They had larger primary roots, more lateral branching, bigger, and more numerous leaves, resulting in heavier fresh weight. Enhanced growth and early recovery resulted in bigger plants with more yield. Additionally, the overexpression Arabidopsis transgenics also showed considerable tolerance to cold and oxidative stress. These observations suggest that TaZnF acts as a positive regulator of thermal stress and thus can be of great significance in understanding and improving temperature stress tolerance in plants.

CTLs, a new class of RING-H2 ubiquitin ligases uncovered by YEELL, a motif close to the RING domain that is present across eukaryotes

RING ubiquitin E3 ligases enclose a RING domain for ubiquitin ligase activity and associated domains and/or conserved motifs outside the RING domain that collectively facilitate their classification and usually reveal some of key information related to mechanism of action. Here we describe a new family of E3 ligases that encodes a RING-H2 domain related in sequence to the ATL and BTL RING-H2 domains. This family, named CTL, encodes a motif designed as YEELL that expands 21 amino acids next to the RING-H2 domain that is present across most eukaryotic lineages. E3 ubiquitin ligase BIG BROTHER is a plant CTL that regulates organ size, and SUMO-targeted ubiquitin E3 ligase RNF111/ARKADIA is a vertebrate CTL. Basal animal and vertebrate, as well as fungi species, encode a single CTL gene that constraints the number of paralogs observed in vertebrates. Conversely, as previously described in ATL and BTL families in plants, CTL genes range from a single copy in green algae and 3 to 5 copies in basal species to 9 to 35 copies in angiosperms. Our analysis describes key structural features of a novel family of E3 ubiquitin ligases as an integral component of the set of core eukaryotic genes.

Molecular characterization of rice arsenic-induced RING finger E3 ligase 2 (OsAIR2) and its heterogeneous overexpression in Arabidopsis thaliana

Arsenic (As) accumulation adversely affects the growth and productivity of plants and poses a serious threat to human health and food security. In this study, we identified one As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase gene from rice root tissues during As stress. We named it Oryza sativa As-Induced RING E3 ligase 2 (OsAIR2). Expression of OsAIR2 was induced under various abiotic stress conditions, including heat, salt, drought and As exposure. Results of an in vitro ubiquitination assay showed that OsAIR2 possesses an E3 ligase activity. Within the cell, OsAIR2 was found to be localized to the Golgi apparatus. Using yeast two-hybrid (Y2H) assay, the 3-ketoacyl-CoA thiolase (KAT) protein was identified as an interaction partner. We found that the O. sativa KAT1 (OsKAT1) is localized to the cytosol and peroxisomes. Moreover, in vitro pull-down assay verified the physical interaction between OsAIR2 and OsKAT1. Interestingly, in vitro ubiquitination assay and in vivo proteasomal degradation assay revealed that OsAIR2 ubiquitinates OsKAT1 and promotes the degradation of OsKAT1 via the 26S proteasome degradation pathway. Heterogeneous overexpression of OsAIR2 in Arabidopsis improved the seed germination and increased the root length under arsenate stress conditions. Therefore, these results suggest that OsAIR2 may be associated with the plant response to As stress and acts as a positive regulator of As stress tolerance.

Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.

Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

This study was designed to investigate at the molecular level how a transgenic version of rice "Nipponbare" obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and a transgenic version (erf71) that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF) family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.

Molecular dissection of Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress

Ubiquitination-mediated protein degradation via Really Interesting New Gene (RING) E3 ligase plays an important role in plant responses to abiotic stress conditions. Many plant studies have found that RING proteins regulate the perception of various abiotic stresses and signal transduction. In this study, Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1) gene was selected randomly from 44 Oryza sativa RING Finger Proteins (OsRFPs) genes highly expressed in rice roots exposed to salinity stress. Transcript levels of OsSIRP1 in rice leaves after various stress treatments, including salt, heat, drought and hormone abscisic acid (ABA), were observed. Poly-ubiquitinated products of OsSIRP1 were investigated via an in vitro ubiquitination assay.35S:OsSIRP1-EYFP was distributed in the cytosol of untreated and salt-treated rice protoplasts. Heterogeneous overexpression of OsSIRP1 in Arabidopsis reduced tolerance for salinity stress during seed germination and root growth. Our findings indicate that OsSIRP1 acts as a negative regulator of salinity stress tolerance mediated by the ubiquitin 26S proteasome system.

Overexpression of GhSARP1 encoding a E3 ligase from cotton reduce the tolerance to salt in transgenic Arabidopsis

Ubiquitination plays a very important role in the response to abiotic stresses of plant. To identify key regulators of salt stress, a gene GhSARP1(Salt-Associated Ring finger Protein)encoding C3H2C3-type E3 ligase, was cloned from cotton. Transcription level of GhSARP1 was high in leaf, flower and fiber of 24,27 and 27DPA (Days Post-Anthesis), but low in root and stem. Except PEG6000 treatment, the expression of GhSARP1 was down-regulated by NaCl, cold and ABA after being treated for 1 h. GhSARP1-GFP fusion protein located on the plasma membrane, which was dependent on trans-membrane motif. In vitro ubiquitination assay showed that GhSARP1 had E3 ligase activity. Heterogeneous overexpression of GhSARP1reduced salt tolerance of transgenic Arabidopsis in germination and post-germination stage. Our results suggested that the GhSARP1 might negatively regulate the response to salt stress mediated by the ubiquitination in cotton.

The evolutionary landscape of PRC1 core components in green lineage

The origin and evolution of plant PRC1 core components. Polycomb repressive complex1 (PRC1) plays critical roles in epigenetic silencing of homeotic genes and determination of cell fate. Animal PRC1 has been well investigated for a long time, whereas plant PRC1 was just confirmed in recent years. It is enigmatic whether PRC1 core components in plants share a common ancestor with those in animals. We evaluated the origin of plant PRC1 RING-finger proteins (RING1 and BMI1) through comparing with the homologs in some representative unikonts and using BMI1- and RING1-like proteins as reciprocal outgroup, finding both PRC1 RING-finger proteins have the earliest origin in mosses, similar to LHP1. Additionally, the gene structure, copy number, and domain organization were analyzed to deeply understand the evolutionary history of plant PRC1 complex. In conclusion, PRC1 RING-finger proteins have independent origins in plants and animals, but convergent evolution might attribute to the conservation of PRC1 complex in plants and animals. Plant LHP1 as the homolog of non-PRC1 protein HP1 was recruited to fulfill the role of Pc counterpart. Gene duplication followed by functional divergence makes a great contribution to evolutionary progress of PRC1 in green plants.

Molecular characterization of Oryza sativa arsenic-induced RING E3 ligase 1 (OsAIR1): Expression patterns, localization, functional interaction, and heterogeneous overexpression

High levels of arsenic (As) in plants are a serious threat to human health, and arsenic accumulation affects plant metabolism and ultimately photosynthesis, growth, and development. We attempted to isolate As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase genes from rice, and we have designated one such gene Oryza sativa arsenic-induced RING E3 ligase 1 (OsAIR1). OsAIR1 expression was induced under abiotic stress conditions, including drought, salt, heat, and As exposure. Results from an in vitro ubiquitination assay showed that OsAIR1 possesses E3 ligase activity. Within the cell, the expression of this gene was found to be localized to the vacuole. In a network-based analysis, we found significantly enriched gene ontology (GO) functions, which included ribonucleoprotein complexes such as ribosomes, suggesting that the function of OsAIR1 are related to translation. Differences in the proportion of seedlings with expanded cotyledons and root lengths, and the lack of differences in germination rates between OsAIR1-overexpressing lines and control plants under AsV stress, suggest that OsAIR1 may positively regulate post-germination plant growth under stress conditions.

The RING Finger Ubiquitin E3 Ligase OsHTAS Enhances Heat Tolerance by Promoting H2O2-Induced Stomatal Closure in Rice

Heat stress often results in the generation of reactive oxygen species, such as hydrogen peroxide, which plays a vital role as a secondary messenger in the process of abscisic acid (ABA)-mediated stomatal closure. Here, we characterized the rice (Oryza sativa) HEAT TOLERANCE AT SEEDLING STAGE (OsHTAS) gene, which plays a positive role in heat tolerance at the seedling stage. OsHTAS encodes a ubiquitin ligase localized to the nucleus and cytoplasm. OsHTAS expression was detected in all tissues surveyed and peaked in leaf blade, in which the expression was concentrated in mesophyll cells. OsHTAS was responsive to multiple stresses and was strongly induced by exogenous ABA. In yeast two-hybrid assays, OsHTAS interacted with components of the ubiquitin/26S proteasome system and an isoform of rice ascorbate peroxidase. OsHTAS modulated hydrogen peroxide accumulation in shoots, altered the stomatal aperture status of rice leaves, and promoted ABA biosynthesis. The results suggested that the RING finger ubiquitin E3 ligase OsHTAS functions in leaf blade to enhance heat tolerance through modulation of hydrogen peroxide-induced stomatal closure and is involved in both ABA-dependent and DROUGHT AND SALT TOLERANCE-mediated pathways.

Genome-wide analysis of RING finger proteins in the smallest free-living photosynthetic eukaryote Ostreococus tauri

RING finger proteins and ubiquitination marks are widely involved in diverse aspects of growth and development, biological processes, and stress or environmental responses. As the smallest free-living photosynthetic eukaryote known so far, the green alga Ostreococus tauri has become an excellent model for investigating the origin of different gene families in the green lineage. Here, 65 RING domains in 65 predicted proteins were identified from O. tauri and on the basis of one or more substitutions at the metal ligand positions and spacing between them they were divided into eight canonical or modified types (RING-CH, -H2, -v, -C2, -C3HCHC2, -C2HC5, -C3GC3S, and -C2SHC4), in which the latter four were newly identified and might represent the intermediate states between RING domain and other similar domains, respectively. RING finger proteins were classified into eight classes based on the presence of additional domains, including RING-Only, -Plus, -C3H1, -PHD, -WD40, -PEX, -TM, and -DEXDc classes. These RING family genes usually lack introns and are distributed over 17 chromosomes. In addition, 29 RING-finger proteins in O. tauri share different degrees of homology with those in the model flowering plant Arabidopsis, indicating they might be necessary for the basic survival of free-living eukaryotes. Therefore, our results provide new insight into the general classification and evolutionary conservation of RING domain-containing proteins in O. tauri.

Molecular dissection of a rice microtubule-associated RING finger protein and its potential role in salt tolerance in Arabidopsis

Although a number of RING E3 ligases in plants have been demonstrated to play key roles in a wide range of abiotic stresses, relatively few studies have detailed how RING E3 ligases exert their cellular actions. We describe Oryza sativa RING finger protein with microtubule-targeting domain 1 (OsRMT1), a functional RING E3 ligase that is likely involved in a salt tolerance mechanism. Functional characterization revealed that OsRMT1 undergoes homodimer formation and subsequently autoubiquitination-mediated protein degradation under normal conditions. By contrast, OsRMT1 is predominantly found in the nucleus and microtubules and its degradation is inhibited under salt stress. Domain dissection of OsRMT1 indicates that the N-terminal domain is required for microtubule targeting. Bimolecular fluorescence complementation analysis and degradation assay revealed that OsRMT1-interacted proteins localized in various organelles were degraded via the ubiquitin (Ub)/26S proteasome-dependent pathway. Interestingly, when OsRMT1 and its target proteins were co-expressed in N. benthamiana leaves, the protein-protein interactions appeared to take place mainly in the microtubules. Overexpression of OsRMT1 in Arabidopsis resulted in increased tolerance to salt stress. Our findings suggest that the abundance of microtubule-associated OsRMT1 is strictly regulated, and OsRMT1 may play a relevant role in salt stress response by modulating levels of its target proteins.

Rice RING E3 ligase may negatively regulate gamma-ray response to mediate the degradation of photosynthesis-related proteins

In this study, our findings regarding the regulation of GA irradiation-induced OsGIRP1 in relation to the levels of photosynthesis-related proteins such as OsrbcL1 and OsrbcS1 and hypersensitive responses of overexpressing plants to GR irradiation provide insight into the molecular functions of OsGIRP1 as a negative regulator in response to the stress of radiation. The RING (Really Interesting New Gene) finger proteins are known to play crucial roles in various abiotic stresses in plants. Here, we report on RING finger E3 ligase, Oryza sativa gamma rays-induced RING finger protein1 gene (OsGIRP1), which is highly induced by gamma rays (GR) irradiation. In vitro ubiquitination assay demonstrated that a single amino acid substitution (OsGIRP1(C196A)) of the RING domain showed no E3 ligase activity, supporting the notion that the activity of most E3s is specified by a RING domain. We isolated at least 6 substrate proteins of OsGIRP1, including 2 Rubisco subunits, OsrbcL1 and OsrbcSl, via yeast two-hybridization and bimolecular fluorescence complementation assays. OsGIRP1 and its partner proteins were targeted to the cytosol and the cytosol or chloroplasts, respectively; however, florescence signals of the complexes with OsGIPR1 were observed in the cytosol. Protein degradation in cell extracts showed that OsGIRP1 mediates proteolysis of 2 substrates, OsrbcS1 and OsrbcL1, via the 26S proteasome degradation pathway. The Arabidopsis plants overexpressing OsGIRP1 clearly exhibited increased sensitivity to GR irradiation. These results might suggest that OsGIRP1 acts as a negative regulator of GR response to mediate the degradation of photosynthesis-related proteins.

Molecular functions of genes related to grain shape in rice

Because grain shape is an important component of rice grain yield, the discovery of genes related to rice grain shape has attracted much attention of rice breeding programs. In recent years, some of these genes have been cloned and studied. They have been found not only regulate grain shape by changing the shape of the spikelet hull, but also regulate endosperm development through control of cell division using different molecular mechanisms. In this paper, we review the recent research on genes related to rice grain shape and their possible regulatory mechanisms.

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by "top-down" and "guide-gene" approaches. More than 50% of OsMYBs were strongly correlated under 50 experimental conditions with 51 hub genes via "top-down" approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by "guide-gene" approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.

Positive regulation of rice RING E3 ligase OsHIR1 in arsenic and cadmium uptakes

The metalloid arsenic (As) and the heavy metal cadmium (Cd) are ubiquitously found at low concentrations in the earth. High concentrations of these elements in the soil and crops are severely dangerous to human health. We attempted to retrieve the RING E3 ubiquitin ligase gene for regulating As and Cd uptakes via the ubiquitin 26S proteasome system. Semi-quantitative reverse transcription polymerase chain reaction was conducted for a total of 47 Oryza sativa RING finger protein (OsRFP) genes to assess their expression patterns when exposed to As and Cd treatments. We identified one gene Oryza sativa heavy metal induced RING E3 ligase 1 (OsHIR1), which was significantly upregulated with both treatments. A yeast hybrid screen and a bimolecular fluorescence complementation assay showed that OsHIR1 clearly interacts with 5 substrate proteins, including tonoplast intrinsic protein 4;1 (OsTIP4;1) in the plasma membrane. In addition, OsHIR1 strongly degraded the protein level of OsTIP4;1 via the ubiquitin 26S proteasome system. Heterogeneous overexpression of OsHIR1 in Arabidopsis exhibited As- and Cd-insensitive phenotypes and resulted in decreased As and Cd accumulation in the shoots and roots, relative to the control. Herein, we report the novel finding that the OsHIR1 E3 ligase positively regulates OsTIP4;1 related to As and Cd uptakes.

The rice RING E3 ligase, OsCTR1, inhibits trafficking to the chloroplasts of OsCP12 and OsRP1, and its overexpression confers drought tolerance in Arabidopsis

Plant growth under low water availability adversely affects many key processes with morphological, physiological, biochemical and molecular consequences. Here, we found that a rice gene, OsCTR1, encoding the RING Ub E3 ligase plays an important role in drought tolerance. OsCTR1 was highly expressed in response to dehydration treatment and defense-related phytohormones, and its encoded protein was localized in both the chloroplasts and the cytosol. Intriguingly, the OsCTR1 protein was found predominantly targeted to the cytosol when rice protoplasts transfected with OsCTR1 were treated with abscisic acid (ABA). Several interacting partners were identified, which were mainly targeted to the chloroplasts, and interactions with OsCTR1 were confirmed by using biomolecular fluorescence complementation (BiFC). Interestingly, two chloroplast-localized proteins (OsCP12 and OsRP1) interacted with OsCTR1 in the cytosol, and ubiquitination by OsCTR1 led to protein degradation via the Ub 26S proteasome. Heterogeneous overexpression of OsCTR1 in Arabidopsis exhibited hypersensitive phenotypes with respect to ABA-responsive seed germination, seedling growth and stomatal closure. The ABA-sensitive transgenic plants also showed improvement in their tolerance against severe water deficits. Taken together, our findings lend support to the hypothesis that the molecular functions of OsCTR1 are related to tolerance to water-deficit stress via ABA-dependent regulation and related systems.

ATLs and BTLs, plant-specific and general eukaryotic structurally-related E3 ubiquitin ligases

Major components of the ubiquitin proteasome system are the enzymes that operate on the transfer of ubiquitin to selected target substrate, known as ubiquitin ligases. The RING finger is a domain that is present in key classes of ubiquitin ligases. This domain coordinates the interaction with a suitable E2 conjugase and the transfer of ubiquitin from the E2 to protein targets. Additional domains coupled to the same polypeptide are important for modulating the function of these ubiquitin ligases. Plants contain several types of E3 ubiquitin ligases that in many cases have expanded as multigene families. Some families are specific to the plant lineage, whereas others may have a common ancestor among plants and other eukaryotic lineages. Arabidopsis Tóxicos en Levadura (ATLs) and BCA2 zinc finger ATLs (BTLs) are two families of ubiquitin ligases that share some common structural features. These are intronless genes that encode a highly related RING finger domain, and yet during evolutionary history, their mode of gene expansion and function is rather different. In each of these two families, the co-occurrence of transmembrane helices or C2/C2 (BZF finger) domains with a selected variation on the RING finger has been subjected to strong selection pressure in order to preserve their unique domain architectures during evolution.

Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant

In order to develop a rice population with improved important traits such as flowering time, we developed 2,911 M2 targeting-induced local lesions in genomes (TILLING) lines by irradiating rice seeds with γ-rays. In all, 15 M3 lines were obtained from 3 different M2 lines that exhibited an early-maturing phenotype: these plants matured approximately 25 days faster than wild-type (WT) plants. To identify genome-wide DNA polymorphisms, we performed whole-genome resequencing of both the plant types, i.e., WT and early-maturing TILLING 1 (EMT1), and obtained mapped reads of 118,488,245 bp (99.53 %) and 128,489,860 bp (99.72 %), respectively; Nipponbare was used as the reference genome. We obtained 63,648 and 147,728 single nucleotide polymorphisms (SNPs) and 33,474 and 31,082 insertions and deletions (InDels) for the WT and EMT1, respectively. Interestingly, there was a higher number of SNPs (2.6-fold) and slightly lower number of InDels (0.9-fold) in EMT1 than in WT. The expression of at least 202 structurally altered genes was changed in EMT1, and functional enrichment analysis of these genes revealed that their molecular functions were related to flower development. These results might provide a critical insight into the regulatory pathways of rice flowering.

Overexpression of a maize E3 ubiquitin ligase gene enhances drought tolerance through regulating stomatal aperture and antioxidant system in transgenic tobacco

Drought is one of the most important limiting factors in crop production. In our previous study, a putative Arabidopsis thaliana SALT- AND DROUGHT-INDUCED RING FINGER1 (AtSDIR1) homolog encoding a RING-finger protein from Zea mays (ZmRFP1) was cloned and its expression pattern and Ub E3 ligase activity were characterized. However, it is uncertain that ZmRFP1 acts as a positive regulator during drought stress. In this study, we further characterized ZmRFP1 in transgenic tobacco to investigate drought tolerance and possible function mechanisms. Overexpression of ZmRFP1 enhanced drought tolerance in tobacco. The transgenic tobacco lines had more closed stomatal pores, higher proline accumulation, but lower levels of malondialdehyde (MDA) when compared with the wild type (WT) under drought stress. Further investigation showed that ZmRFP1 transgenic plants displayed higher SOD and CAT activities, increased NtSOD and NtCAT transcript levels, and decreased reactive oxygen species (ROS) accumulation under drought stress. Taken together, our results demonstrate that ZmRFP1 confers drought stress tolerance in transgenic tobacco not only by increasing the ability to retain water, but also by reducing ROS accumulation and membrane damage through enhancing the antioxidant system. ZmRFP1 might serve as a candidate gene in genetic improvement for drought tolerance engineering in cereal crop plants.

The rice RING finger E3 ligase, OsHCI1, drives nuclear export of multiple substrate proteins and its heterogeneous overexpression enhances acquired thermotolerance

Thermotolerance is very important for plant survival when plants are subjected to lethally high temperature. However, thus far little is known about the functions of RING E3 ligase in response to heat shock in plants. This study found that one rice gene encoding the RING finger protein was specifically induced by heat and cold stress treatments but not by salinity or dehydration and named it OsHCI1 (Oryza sativa heat and cold induced 1). Subcellular localization results showed that OsHCI1 was mainly associated with the Golgi apparatus and moved rapidly and extensively along the cytoskeleton. In contrast, OsHCI1 may have accumulated in the nucleus under high temperatures. OsHCI1 physically interacted with nuclear substrate proteins including a basic helix-loop-helix transcription factor. Transient co-overexpression of OsHCI1 and each of three nuclear proteins showed that their fluorescent signals moved into the cytoplasm as punctuate formations. Heterogeneous overexpression of OsHCI1 in Arabidopsis highly increased survival rate through acquired thermotolerance. It is proposed that OsHCI1 mediates nuclear-cytoplasmic trafficking of nuclear substrate proteins via monoubiquitination and drives an inactivation device for the nuclear proteins under heat shock.

Comprehensive analysis of the rice RING E3 ligase family reveals their functional diversity in response to abiotic stress

A large number of really interesting new gene (RING) E3 ligases contribute to the post-translational modification of target proteins during plant responses to environmental stresses. However, the physical interactome of RING E3 ligases in rice remains largely unknown. Here, we evaluated the expression patterns of 47 Oryza sativa RING finger protein (OsRFP) genes in response to abiotic stresses via semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) and in silico analysis. Subsequently, molecular dissection of nine OsRFPs was performed by the examination of their E3 ubiquitin ligase activity, subcellular localization, and physical interaction with target proteins. Most of the OsRFPs examined possessed E3 ligase activity and showed diverse subcellular localization. Yeast two-hybrid analysis was then employed to construct a physical interaction map of seven OsRFPs with their 120 interacting proteins. The results indicated that these OsRFPs required dynamic translocation and partitioning for their cellular activation. Heterogeneous overexpression of each of the OsRFP genes in Arabidopsis suggested that they have functionally diverse responses to abiotic stresses, which may have been acquired during evolution. This comprehensive study provides insights into the biological functions of OsRFPs, which may be useful in understanding how rice plants adapt to unfavourable environmental conditions.

Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening

BACKGROUND

Pine wilt disease (PWD), caused by the pinewood nematode (PWN; Bursaphelenchus xylophilus), damages and kills pine trees and is causing serious economic damage worldwide. Although the ecological mechanism of infestation is well described, the plant's molecular response to the pathogen is not well known. This is due mainly to the lack of genomic information and the complexity of the disease. High throughput sequencing is now an efficient approach for detecting the expression of genes in non-model organisms, thus providing valuable information in spite of the lack of the genome sequence. In an attempt to unravel genes potentially involved in the pine defense against the pathogen, we hereby report the high throughput comparative sequence analysis of infested and non-infested stems of Pinus pinaster (very susceptible to PWN) and Pinus pinea (less susceptible to PWN).

RESULTS

Four cDNA libraries from infested and non-infested stems of P. pinaster and P. pinea were sequenced in a full 454 GS FLX run, producing a total of 2,083,698 reads. The putative amino acid sequences encoded by the assembled transcripts were annotated according to Gene Ontology, to assign Pinus contigs into Biological Processes, Cellular Components and Molecular Functions categories. Most of the annotated transcripts corresponded to Picea genes-25.4-39.7%, whereas a smaller percentage, matched Pinus genes, 1.8-12.8%, probably a consequence of more public genomic information available for Picea than for Pinus. The comparative transcriptome analysis showed that when P. pinaster was infested with PWN, the genes malate dehydrogenase, ABA, water deficit stress related genes and PAR1 were highly expressed, while in PWN-infested P. pinea, the highly expressed genes were ricin B-related lectin, and genes belonging to the SNARE and high mobility group families. Quantitative PCR experiments confirmed the differential gene expression between the two pine species.

CONCLUSIONS

Defense-related genes triggered by nematode infestation were detected in both P. pinaster and P. pinea transcriptomes utilizing 454 pyrosequencing technology. P. pinaster showed higher abundance of genes related to transcriptional regulation, terpenoid secondary metabolism (including some with nematicidal activity) and pathogen attack. P. pinea showed higher abundance of genes related to oxidative stress and higher levels of expression in general of stress responsive genes. This study provides essential information about the molecular defense mechanisms utilized by P. pinaster and P. pinea against PWN infestation and contributes to a better understanding of PWD.