The prolific ATL family of RING-H2 ubiquitin ligases

Genome-Wide Identification and Functional Analysis of the Genes of the ATL Family in Maize during High-Temperature Stress in Maize

Maize is a significant food and feed product, and abiotic stress significantly impacts its growth and development. Arabidopsis Toxicosa en Levadura (ATL), a member of the RING-H2 E3 subfamily, modulates various physiological processes and stress responses in Arabidopsis. However, the role of ATL in maize remains unexplored. In this study, we systematically identified the genes encoding ATL in the maize genome. The results showed that the maize ATL family consists of 77 members, all predicted to be located in the cell membrane and cytoplasm, with a highly conserved RING domain. Tissue-specific expression analysis revealed that the expression levels of ATL family genes were significantly different in different tissues. Examination of the abiotic stress data revealed that the expression levels of ATL genes fluctuated significantly under different stress conditions. To further understand the biological functions of maize ATL family genes under high-temperature stress, we studied the high-temperature phenotypes of the maize ZmATL family gene ZmATL10 and its homologous gene AtATL27 in Arabidopsis. The results showed that overexpression of the ZmATL10 and AtATL27 genes enhanced resistance to high-temperature stress.

OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5-OsRbohB module to suppress rice immunity

Ubiquitination-mediated protein degradation is integral to plant immunity, with E3 ubiquitin ligases acting as key factors in this process. Here, we report the functions of OsATL32, a plasma membrane-localized Arabidopsis Tóxicos En Levadura (ATL)-type E3 ubiquitin ligase, in rice (Oryza sativa) immunity and its associated regulatory network. We found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe oryzae. The OsATL32 protein level declines in response to infection by a compatible M. oryzae strain or to chitin treatment. OsATL32 negatively regulates rice resistance to blast and bacterial leaf blight diseases, as well as chitin-triggered immunity. Biochemical and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species (ROS) accumulation by mediating ubiquitination and degradation of the ROS-producing OsRac5-OsRbohB module, which enhances rice immunity against M. oryzae. The protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation, preventing its negative effect on rice immunity. This study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.

Potato E3 ubiquitin ligase StRFP1 positively regulates late blight resistance by degrading sugar transporters StSWEET10c and StSWEET11

Potato (Solanum tuberosum) is the fourth largest food crop in the world. Late blight, caused by oomycete Phytophthora infestans, is the most devastating disease threatening potato production. Previous research has shown that StRFP1, a potato Arabidopsis Tóxicos en Levadura (ATL) family protein, positively regulates late blight resistance via its E3 ligase activity. However, the underlying mechanism is unknown. Here, we reveal that StRFP1 is associated with the plasma membrane (PM) and undergoes constitutive endocytic trafficking. Its PM localization is essential for inhibiting P. infestans colonization. Through in vivo and in vitro assays, we investigated that StRFP1 interacts with two sugar transporters StSWEET10c and StSWEET11 at the PM. Overexpression (OE) of StSWEET10c or StSWEET11 enhances P. infestans colonization. Both StSWEET10c and StSWEET11 exhibit sucrose transport ability in yeast, and OE of StSWEET10c leads to an increased sucrose content in the apoplastic fluid of potato leaves. StRFP1 ubiquitinates StSWEET10c and StSWEET11 to promote their degradation. We illustrate a novel mechanism by which a potato ATL protein enhances disease resistance by degrading susceptibility (S) factors, such as Sugars Will Eventually be Exported Transporters (SWEETs). This offers a potential strategy for improving disease resistance by utilizing host positive immune regulators to neutralize S factors.

Overexpression of a TaATL1 encoding RING-type E3 ligase negatively regulates cell division and flowering time in Arabidopsis thaliana

The transition of food crops from the vegetative to reproductive stages is an important process that affects the final yield. Despite extensive characterization of E3 ligases in model plants, their roles in wheat development remain unknown. In this study, we elucidated the molecular function of wheat TaATL1 (Arabidopsis thaliana Toxicos EN Levadura), which acts as a negative regulator of flowering time and cell division. TaATL1 amino acid residues contain a RING domain and exist mainly in a beta-turn form. The expression level of TaATL1 was highly reduced during the transition from vegetative to reproductive stages. TaATL1 is localized in the nucleus and exhibits E3 ligase activity. Transgenic Arabidopsis plants, in which the TaATL1 gene is constitutively overexpressed under the control of the cauliflower mosaic virus 35 S promoter, exhibited regulation of cell numbers, thereby influencing both leaf and root growth. Moreover, TaATL1 overexpression plants showed a late-flowering phenotype compared to wild-type (WT) plants. Following transcriptome analysis, it was discovered that 1661 and 901 differentially expressed genes were down- or up- regulated, respectively, in seedling stages between WT and TaATL1 overexpression. TaATL1 transcripts are involved in cell division, flowering, and signaling. Overall, our findings demonstrated that the regulatory mechanism of wheat TaATL1 gene plays a significant role in cell division-mediated flowering in Arabidopsis.

The Auto-Regulation of ATL2 E3 Ubiquitin Ligase Plays an Important Role in the Immune Response against Alternaria brassicicola in Arabidopsis thaliana

The ubiquitin/26S proteasome system is a crucial regulatory mechanism that governs various cellular processes in plants, including signal transduction, transcriptional regulation, and responses to biotic and abiotic stressors. Our study shows that the RING-H2-type E3 ubiquitin ligase, Arabidopsis Tóxicos en Levadura 2 (ATL2), is involved in response to fungal pathogen infection. Under normal growth conditions, the expression of the ATL2 gene is low, but it is rapidly and significantly induced by exogenous chitin. Additionally, ATL2 protein stability is markedly increased via chitin treatment, and its degradation is prolonged when 26S proteasomal function is inhibited. We found that an atl2 null mutant exhibited higher susceptibility to Alternaria brassicicola, while plants overexpressing ATL2 displayed increased resistance. We also observed that the hyphae of A. brassicicola were strongly stained with trypan blue staining, and the expression of A. brassicicola Cutinase A (AbCutA) was dramatically increased in atl2. In contrast, the hyphae were weakly stained, and AbCutA expression was significantly reduced in ATL2-overexpressing plants. Using bioinformatics, live-cell confocal imaging, and cell fractionation analysis, we revealed that ATL2 is localized to the plasma membrane. Further, it is demonstrated that the ATL2 protein possesses E3 ubiquitin ligase activity and found that cysteine 138 residue is critical for its function. Moreover, ATL2 is necessary to successfully defend against the A. brassicicola fungal pathogen. Altogether, our data suggest that ATL2 is a plasma membrane-integrated protein with RING-H2-type E3 ubiquitin ligase activity and is essential for the defense response against fungal pathogens in Arabidopsis.

ATL Protein Family: Novel Regulators in Plant Response to Environmental Stresses

Plants actively develop intricate regulatory mechanisms to counteract the harmful effects of environmental stresses. The ubiquitin-proteasome pathway, a crucial mechanism, employs E3 ligases (E3s) to facilitate the conjugation of ubiquitin to specific target substrates, effectively marking them for proteolytic degradation. E3s play critical roles in many biological processes, including phytohormonal signaling and adaptation to environmental stresses. Arabidopsis Toxicosa en Levadura (ATL) proteins, belonging to a subfamily of RING-H2 E3s, actively modulate diverse physiological processes and plant responses to environmental stresses. Despite studies on the functions of certain ATL family members in rice and Arabidopsis, most ATLs still need more comprehensive study. This review presents an overview of the ubiquitin-proteasome system (UPS), specifically focusing on the pivotal role of E3s and associated enzymes in plant development and environmental adaptation. Our study seeks to unveil the active modulation of plant responses to environmental stresses by E3s and ATLs, emphasizing the significance of ATLs within this intricate process. By emphasizing the importance of studying the roles of E3s and ATLs, our review contributes to developing more resilient plant varieties and promoting sustainable agricultural practices while establishing a research roadmap for the future.

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.

Evolution of the Tóxicos en Levadura 63 (TL63) gene family in plants and functional characterization of Arabidopsis thaliana TL63 under oxidative stress

MAIN CONCLUSION

TL63 orthologs were angiosperm specific and had undergone motifs loss and gain, and increased purifying selection. AtTL63 was involved in the response of yeast and Arabidopsis plants to oxidative stress. The Tóxicos en Levadura (TL) family, a class of E3 ubiquitin ligases with typical RING-H2 type zinc finger structure, plays a pivotal role in mediating physiological processes and responding to stress in plants. However, the evolution and function of TL63 remain unclear. In this study, TL63 homologs were dated roughly back to the origin of land plants and confirmed to have subjected to the gain and loss of motifs and increased purifying selection. Phylogenetic analysis displayed that 279 TL63s could be divided into four main clades (Clade A-D). Notably, the ancestral tandem TL40/41 cluster contributed to the expansion of modern Brassicaceae TL40/41. The substitution rate tests revealed that the TL63 lineage was evidently different from other lineages. The codon usage index exhibited that monocotyledons preferred to use not A3s and T3s, but C3s, G3s, CAI, CBI and Fop. Sequence analysis showed that the TL63 homologs had conserved TM and GLD motifs and RING-H2 domain whose key amino acid residues accounted for the high average abundance. Particularly, Arabidopsis thaliana TL63 (AtTL63) was located in the nuclei, cell membranes and peroxisomes and expressed universally and significantly throughout A. thaliana development. Under H2O2 treatment, low or moderate expression of the AtTL63 held beneficial effects on the growth and viability of yeast cells and the mutation or overexpression of the AtTL63 positively affected the growth of A. thaliana plants. In brief, this study could supply useful insight into the evolution of the plant TL63s and the AtTL63 functions under oxidative stress.

Comprehensive identification and characterization of lncRNAs and circRNAs reveal potential brown planthopper-responsive ceRNA networks in rice

Brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most destructive pests of rice. Non-coding RNA plays an important regulatory role in various biological processes. However, comprehensive identification and characterization of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in BPH-infested rice have not been performed. Here, we performed a genome-wide analysis of lncRNAs and circRNAs in BPH6-transgenic (resistant, BPH6G) and Nipponbare (susceptible, NIP) rice plants before and after BPH feeding (early and late stage) via deep RNA-sequencing. A total of 310 lncRNAs and 129 circRNAs were found to be differentially expressed. To reveal the different responses of resistant and susceptible rice to BPH herbivory, the potential functions of these lncRNAs and circRNAs as competitive endogenous RNAs (ceRNAs) were predicted and investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Dual-luciferase reporter assays revealed that miR1846c and miR530 were targeted by the lncRNAs XLOC_042442 and XLOC_028297, respectively. In responsive to BPH infestation, 39 lncRNAs and 21 circRNAs were predicted to combine with 133 common miRNAs and compete for miRNA binding sites with 834 mRNAs. These mRNAs predictably participated in cell wall organization or biogenesis, developmental growth, single-organism cellular process, and the response to stress. This study comprehensively identified and characterized lncRNAs and circRNAs, and integrated their potential ceRNA functions, to reveal the rice BPH-resistance network. These results lay a foundation for further study on the functions of lncRNAs and circRNAs in the rice-BPH interaction, and enriched our understanding of the BPH-resistance response in rice.

StATL2-like could affect growth and cold tolerance of plant by interacting with StCBFs

Our results confirmed that StATL2-like could interact with StCBFs and regulate plant growth. Meanwhile, StATL2-like acted as a negative regulator on low-temperature tolerance in plants. As important transcription factors for resisting many kinds of stresses, C-repeat-binding factors (CBF) play a key role in plant low-temperature tolerance by increasing COR genes expressions. Here, we report that StATL2-like, a RING-H2 E3 ubiquitin in Solanum tuberosum L., interacted with StCBF1 and StCBF4, respectively. AtATL2 is a highly homologous gene of StATL2-like in Arabidopsis thaliana. Under normal conditions, atl2 Arabidopsis mutant showed a growth inhibition phenotype while overexpressed StATL2-like in wild type Arabidopsis and atl2 mutant promoted plant growth. Besides, atl2 mutant had better low-temperature tolerance compared with wild type and StATL2-like transgenic lines which demonstrated that StATL2-like acted as a negatively regulator on low-temperature tolerance in plant. Moreover, atl2 mutant improved the scavenging capacity of reactive oxygen species (ROS) and alleviate the damage of photosynthetic system II (PSII) compared with StATL2-like transgenic lines under cold conditions. These results suggested a new component in CBF-dependent pathway to regulate plant growth and response to low-temperature stress in potato plants.

ATL8, a RING E3 ligase, modulates root growth and phosphate homeostasis in Arabidopsis

Ubiquitination-mediated post-translational modification of proteins is a pivotal regulatory mechanism involved in the growth and development of the plant. The Arabidopsis Tóxicos en Levadura (ATL) family is a group of RING-type ubiquitin ligases (E3) and ATL8 is a membrane-localized protein. Here, a reverse genetics approach was used to elucidate the role of ATL8 in phosphate (Pi) homeostasis. Deficiencies of Pi and sucrose (Suc) enhanced the relative expression level of ATL8 in different tissues of the wild-type (Wt). The relative expression level of ATL8 was attenuated and augmented in the mutant (atl8) and overexpression lines (Oe1 and Oe2), respectively. There were significant reductions in different root traits, root hairs, root to shoot ratio, and total Pi content in atl8 compared with the Wt under different Pi regimes. On the contrary, Oe1 and Oe2 lines exhibited enhancement in some of these traits. Noticeably, anthocyanin content was significantly reduced in Oe1 and Oe2 compared with the Wt and atl8 under P- condition. Abscisic acid (ABA) treatment led to an increase in the primary root length of atl8 compared with the Wt, suggesting a cross-talk between ABA and ATL8 on root growth. Furthermore, the relative expression levels of the genes involved in the maintenance of Pi homeostasis (WRKY75, RNS1, E3L, and ACP5) were differentially modulated in atl8, Oe1, and Oe2 compared with the Wt under different Pi regimes. The results revealed the pivotal role of ATL8 in mediating morphophysiological and molecular adaptive responses to Pi deficiency.

RNA-seq analysis reveals the genes/pathways responsible for genetic plasticity of rice to varying environmental conditions on direct-sowing and transplanting

Rice cultivation by transplanting requires plenty of water. It might become a challenging task in future to grow rice by transplanting due to the climatic change, water and labor scarcities. Direct-sown rice (DSR) is emerging as a resource-conserving and climate-smart alternative to transplanted rice (TPR). However, no specific variety has been bred for dry/direct-sown conditions. The present study was undertaken to decipher the molecular basis of genetic plasticity of rice under different planting methods. Comparative RNA-seq analysis revealed a number (6133) of genes exclusively up-regulated in Nagina-22 (N-22) leaf under DSR conditions, compared to that (3538) in IR64 leaf. Several genes up-regulated in N-22 were down-regulated in IR64. Genes for growth-regulation and nutrient-reservoir activities, transcription factors, translational machinery, carbohydrate metabolism, cell cycle/division, and chromatin organization/epigenetic modifications were considerably up-regulated in the leaf of N-22 under DSR conditions. Complementary effects of these factors in rendering genetic plasticity were confirmed by the agronomic/physiological performance of rice cultivar. Thus, growth-regulation/nutrient-reservoir activities, transcription factors, and translational machinery are important molecular factors responsible for the observed genetic plasticity/adaptability of Nagina-22 to different planting methods. This might help to develop molecular markers for DSR breeding, replacing TPR with DSR for better water-productivity, and minimizing greenhouse-gas emission necessary for negative emission agriculture.

OsATL38 mediates mono-ubiquitination of the 14-3-3 protein OsGF14d and negatively regulates the cold stress response in rice

One of the major regulatory pathways that permits plants to convert an external stimulus into an internal cellular response within a short period of time is the ubiquitination pathway. In this study, OsATL38 was identified as a low temperature-induced gene that encodes a rice homolog of Arabidopsis Tóxicos en Levadura RING-type E3 ubiquitin (Ub) ligase, which was predominantly localized to the plasma membrane. OsATL38-overexpressing transgenic rice plants exhibited decreased tolerance to cold stress as compared with wild-type rice plants. In contrast, RNAi-mediated OsATL38 knockdown transgenic progeny exhibited markedly increased tolerance to cold stress relative to that of wild-type plants, which indicated a negative role of OsATL38 in response to cold stress. Yeast two-hybrid, in vitro pull-down, and co-immunoprecipitation assays revealed that OsATL38 physically interacted with OsGF14d, a rice 14-3-3 protein. An in vivo target ubiquitination assay indicated that OsGF14d was mono-ubiquitinated by OsATL38. osgf14d knockout mutant plants were more sensitive to cold stress than wild-type rice plants, indicating that OsGF14d is a positive factor in the response to cold stress. These results provide evidence that the RING E3 Ub ligase OsATL38 negatively regulates the cold stress response in rice via mono-ubiquitination of OsGF14d 14-3-3 protein.

The molecular events underpinning cultivar differences in melatonin counteracting salt damage in Phaseolus vulgaris

Melatonin (N -acetyl-5-methoxytryptamine) plays important roles in multiple stress responses, especially under salt stress. However, cultivar differences in melatonin mediated salt stress tolerance are unclear. Phaseolus vulgaris L. (common bean) cultivars Jiyin 1 (JY, salt-tolerant) and Xuliyabai (XL, salt-sensitive) were used in this study. Exogenous melatonin significantly improved root growth under salt stress in JY, but had little effect on XL. Physiology analysis showed significant differences in activities of antioxidant enzymes (superoxide, SOD; and catalase, CAT) and malondialdehyde content between JY and XL. Meanwhile, the change of ABA content in JY and XL root was opposite in salt plus melatonin treatment. Comparative root transcriptomes of JY and XL revealed 3505 and 668 differentially expressed genes (DEGs) regulated by salt stress and melatonin. The most enriched melatonin-responsive genes under salt stress are mainly involved in regulation of transcription, oxidation-reduction process, transcription factor activity, oxidoreductase activity. In addition, melatonin induced more obvious changes of DEGs in JY than that in XL under salt condition. Melatonin also significantly induced 41 DEGs only in JY, including signal transduction genes, transcription factors, ubiquitin protein ligases, ion homeostasis and osmotic adjustment genes etc. This study uncovered the molecular mechanism of cultivar difference of melatonin response under salt stress in common bean.

Salt responsive alternative splicing of a RING finger E3 ligase modulates the salt stress tolerance by fine-tuning the balance of COP9 signalosome subunit 5A

Increasing evidence points to the tight relationship between alternative splicing (AS) and the salt stress response in plants. However, the mechanisms linking these two phenomena remain unclear. In this study, we have found that Salt-Responsive Alternatively Spliced gene 1 (SRAS1), encoding a RING-Type E3 ligase, generates two splicing variants: SRAS1.1 and SRAS1.2, which exhibit opposing responses to salt stress. The salt stress-responsive AS event resulted in greater accumulation of SRAS1.1 and a lower level of SRAS1.2. Comprehensive phenotype analysis showed that overexpression of SRAS1.1 made the plants more tolerant to salt stress, whereas overexpression of SRAS1.2 made them more sensitive. In addition, we successfully identified the COP9 signalosome 5A (CSN5A) as the target of SRAS1. CSN5A is an essential player in the regulation of plant development and stress. The full-length SRAS1.1 promoted degradation of CSN5A by the 26S proteasome. By contrast, SRAS1.2 protected CSN5A by competing with SRAS1.1 on the same binding site. Thus, the salt stress-triggered AS controls the ratio of SRAS1.1/SRAS1.2 and switches on and off the degradation of CSN5A to balance the plant development and salt tolerance. Together, these results provide insights that salt-responsive AS acts as post-transcriptional regulation in mediating the function of E3 ligase.

High salinity severely affects plant growth and development, impairing crop production worldwide. E3 ligase is a stress-responsive regulator through ubiquitin-proteasome system for selective protein degradation. The E3s are regulated by transcriptional regulation and post-translational modifications. Here, we have discovered that stress-responsive AS acts as a post-transcriptional regulation modulating the function of E3 ligases. Intriguingly, the truncated proteins generated by salt-responsive AS play opposite roles compared with the full-length E3 ligase. The truncated isoform losing key domain could not degrade the target protein, instead, it interacts and competes with the E3 ligase through binding the same domain of the targets. This finding contributes significantly to a deeper mechanistic understanding of how AS regulates the function of E3 ligase in response to salt stress.

Endoplasmic reticulum-related E3 ubiquitin ligases: Key regulators of plant growth and stress responses

Accumulating evidence has revealed that the ubiquitin proteasome system plays fundamental roles in the regulation of diverse cellular activities in eukaryotes. The ubiquitin protein ligases (E3s) are central to the proteasome system because of their ability to determine its substrate specificity. Several studies have demonstrated the essential role of a group of ER (endoplasmic reticulum)-localized E3s in the positive or negative regulation of cell homeostasis. Most ER-related E3s are conserved between plants and mammals, and a few plant-specific components have been reported. In this review, we summarize the functions of ER-related E3s in plant growth, ER-associated protein degradation and ER-phagy, abiotic and biotic stress responses, and hormone signaling. Furthermore, we highlight several questions that remain to be addressed and suggest directions for further research on ER-related E3 ubiquitin ligases.

A novel sweetpotato RING-H2 type E3 ubiquitin ligase gene IbATL38 enhances salt tolerance in transgenic Arabidopsis

Arabidopsis Toxicos en Levadura (ATL) proteins compose a subfamily of E3 ubiquitin ligases and play major roles in regulating plant growth, cold, drought, oxidative stresses response and pathogen defense in plants. However, the role in enhancing salt tolerance has not been reported to date. Here, we cloned a novel RING-H2 type E3 ubiquitin ligase gene, named IbATL38, from sweetpotato cultivar Lushu 3. This gene was highly expressed in the leaves of sweetpotato and strongly induced by NaCl and abscisic acid (ABA). This IbATL38 was localized to nucleus and plasm membrane and possessed E3 ubiquitin ligase activity. Overexpression of IbATL38 in Arabidopsis significantly enhanced salt tolerance, along with inducible expression of a series of stress-responsive genes and prominently decrease of H₂O₂ content. These results suggest that IbATL38 as a novel E3 ubiquitin ligase may play an important role in salt stress response.

The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew Pathogen Plasmopara viticola

Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine (Vitis vinifera L.). Genetic resistance is an effective and sustainable control strategy, but major resistance genes (encoding receptors for specific pathogen effectors) introgressed from wild Vitis species, although effective, may be non-durable because the pathogen can evolve to avoid specific recognition. Previous transcriptomic studies in the resistant species Vitis riparia highlighted the activation of signal transduction components during infection. The transfer of such components to V. vinifera might confer less specific and therefore more durable resistance. Here, we describe the generation of transgenic V. vinifera lines constitutively expressing the V. riparia E3 ubiquitin ligase gene VriATL156. Phenotypic and molecular analysis revealed that the transgenic plants were less susceptible to P. viticola than vector-only controls, confirming the role of this E3 ubiquitin ligase in the innate immune response. Two independent transgenic lines were selected for detailed analysis of the resistance phenotype by RNA-Seq and microscopy, revealing the profound reprogramming of transcription to achieve resistance that operates from the earliest stages of pathogen infection. The introduction of VriATL156 into elite grapevine cultivars could therefore provide an effective and sustainable control measure against downy mildew.

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.

Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana

Multigene families in plants expanded from ancestral genes via gene duplication mechanisms constitute a significant fraction of the coding genome. Although most duplicated genes are lost over time, many are retained in the genome. Clusters of tandemly arrayed genes are commonly found in the plant genome where they can promote expansion of gene families. In the present study, promoter fusion to the GUS reporter gene was used to examine the promoter architecture of duplicated E3 ligase genes that are part of group C in the Arabidopsis thaliana ATL family. Acquisition of gene expression by AtATL78, possibly generated from defective AtATL81 expression, is described. AtATL78 expression was purportedly enhanced by insertion of a TATA box within the core promoter region after a short tandem duplication that occurred during evolution of Brassicaceae lineages. This gene is associated with an adaptation to drought tolerance of A. thaliana. These findings also suggest duplicated genes could serve as a reservoir of tacit genetic information, and expression of these duplicated genes is activated upon acquisition of core promoter sequences. Remarkably, drought transcriptome profiling in response to rehydration suggests that ATL78-dependent gene expression predominantly affects genes with root-specific activities.

E3 ubiquitin ligase ATL61 acts as a positive regulator in abscisic acid mediated drought response in Arabidopsis

Abscisic acid (ABA) is an important plant hormone that mediates abiotic stresses in plant growth and development. A number of E3 ligases have been reported to be involved in ABA signaling pathway. In this study, we identified a C3H2C3 RING-type E3 ligase, Arabidopsis thaliana Tόxicos en Levadura 61 (ATL61), which regulated drought stress in planta. Enzyme assay in vitro demonstrated that ATL61 had E3 ubiquitin ligase activity, while point mutation of ATL61^{H109A, H122A} (mATL61) abolished its E3 ubiquitin ligase activity. ATL61 overexpression plants exhibited ABA hypersensitivity and were more tolerant to drought, while the atl61 mutant plants were insensitive to ABA. Moreover, mATL61 overexpression lines exhibited similar ABA-related phenotypes with wild type (WT) plants. The transcript abundances of ABA-mediated drought stress-related genes RD20 and RD22 were higher in ATL61 overexpression plants than those in WT, atl61, and mATL61 plants. Our results indicated that ATL61 acted as a positive regulator in the ABA-mediated drought stress response.

Role and mechanisms of callose priming in mycorrhiza-induced resistance

Mycorrhizal plants display enhanced resistance to several pathogens. However, the molecular mechanisms regulating mycorrhiza-induced resistance (MIR) are still elusive. We aim to study the mechanisms underlying MIR against Botrytis cinerea and the role of callose accumulation during this process. Mycorrhizal tomato plants inoculated with Rhizoglomus irregularis displayed callose priming upon B. cinerea infection. The callose inhibitor 2-deoxy-d-glucose abolished MIR, confirming the relevance of callose in the bioprotection phenomena. While studying the mechanisms underlying mycorrhiza-induced callose priming, we found that mycorrhizal plants display an enhanced starch degradation rate that is correlated with increased levels of β-amylase1 transcripts following pathogen infection. Starch mobilization in mycorrhizal plants seems coordinated with the increased transcription of sugar transporter and invertase genes. Moreover, the expression levels of genes encoding the vesicular trafficking proteins ATL31 and SYP121 and callose synthase PMR4 were higher in the mycorrhizal plants and further boosted by subsequent pathogen infection. All these proteins play a key role in the priming of callose accumulation in Arabidopsis, suggesting that callose priming is an induced resistance mechanism conserved in different plant species. This evidence highlights the importance of sugar mobilization and vesicular trafficking in the priming of callose as a defence mechanism in mycorrhiza-induced resistance.

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.

An E3 ubiquitin ligase from Nicotiana benthamiana targets the replicase of Bamboo mosaic virus and restricts its replication

One up-regulated host gene identified previously was found involved in the infection process of Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. The full length cDNA of this gene was cloned by 5' and 3'-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved really interesting new gene (RING) domain and a transmembrane domain. The gene might function as an ubiquitin E3 ligase. We designated this protein in Nicotiana benthamiana as ubiquitin E3 ligase containing RING domain 1 (NbUbE3R1). Further characterization by using Tobacco rattle virus-based virus-induced gene silencing (loss-of-function) revealed that increased BaMV accumulation was in both knockdown plants and protoplasts. The gene might have a defensive role in the replication step of BaMV infection. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed in N. benthamiana plants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/△TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting the accumulation of BaMV. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an up-regulated gene, NbUbE3R1 that plays a role in BaMV replication.

Fine mapping of a dominant gene conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in barley

We fine-mapped and physically anchored a dominant gene (Rbs7) conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in a genomic interval of 304 kb on barley chromosome 6H. Spot blotch, caused by Bipolaris sorokiniana, is an economically important disease on barley in the Upper Midwest region of the USA and Prairie Provinces of Canada. A new pathotype (pathotype 7, represented by isolate ND4008) of B. sorokiniana has been identified, which is highly virulent on barley cultivars with resistance to other pathotypes of the fungus. In this study, we fine-mapped a dominant gene conferring resistance to pathotype 7 in the barley line PI 235186. Genetic analysis of the F₁ and F₂ plants from a cross between PI 356741 (highly susceptible to ND4008) and PI 235186 (highly resistant to ND4008) indicated that a single dominant gene (Rbs7) controls the resistance in PI 235186. This result was confirmed by genetic analysis of the F_2:3 families and a recombinant inbred line (RIL) population derived from the same cross. Bulked segregant analysis using simple sequence repeat markers localized Rbs7 on the short arm of chromosome 6H. Additional DNA markers were developed from the 6H pseudomolecule sequence of barley cv. Morex and mapped to the genomic region carrying Rbs7 using the RIL population and F₂ recombinants derived from the PI 356741 × PI 235186 cross. Rbs7 was fine-mapped between two markers (M13.06 and M13.37), which spans a physical distance of 304 kb on Morex chromosome 6H. These results provide a foundation for future cloning of the resistance gene and development of user-friendly molecular markers that can be used for development of spot-blotch-resistant cultivars in barley breeding programs.

Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

BACKGROUND

Gray leaf spot (GLS), which is caused by the necrotrophic fungi Cercospora zeae-maydis and Cercospora zeina, is one of the most impactful diseases in maize worldwide. The aim of the present study is to identify the resistance genes and understand the molecular mechanisms for GLS resistance.

RESULTS

Two cultivars, 'Yayu889' and 'Zhenghong532,' which are distinguished as resistant and susceptible cultivars, respectively, were challenged with the GLS disease and a RNA-seq experiment was conducted on infected plants at 81, 89, 91, and 93 days post planting (dap). Compared with the beginning stage at 81 dap, 4666, 1733, and 1166 differentially expressed genes (DEGs) were identified at 89, 91, and 93 dap, respectively, in 'Yayu889,' while relatively fewer, i.e., 4713, 881, and 722 DEGs, were identified in 'Zhenghong532.' Multiple pathways involved in the response of maize to GLS, including 'response to salicylic acid,' 'protein phosphorylation,' 'oxidation-reduction process,' and 'carotenoid biosynthetic process,' were enriched by combining differential expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). The expression of 12 candidate resistance proteins in these pathways were quantified by the multiple reaction monitoring (MRM) method. This approach identified two candidate resistance proteins, a calmodulin-like protein and a leucine-rich repeat receptor-like protein kinase with SNPs that were located in QTL regions for GLS resistance. Metabolic analysis showed that, compared with 'Zhenghong532,' the amount of salicylic acid (SA) and total carotenoids in 'Yayu889' increased, while peroxidase activity decreased during the early infection stages, suggesting that increased levels of SA, carotenoids, and reactive oxygen species (ROS) may enhance the defense response of 'Yayu889' to GLS.

CONCLUSION

By combining transcriptome and proteome analyses with comparisons of resistance QTL regions, calmodulin-like protein and leucine-rich repeat receptor-like protein kinase were identified as candidate GLS resistance proteins. Moreover, we found that the metabolic pathways for ROS, SA, and carotenoids are especially active in the resistant cultivar. These findings could lead to a better understanding of the GLS resistance mechanisms and facilitate the breeding of GLS-resistant maize cultivars.

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.

PAMP-responsive ATL gene StRFP1 and its orthologue NbATL60 positively regulate Phytophthora infestans resistance in potato and Nicotiana benthamiana

Ubiquitination is a post-translational modification that plays a crucial role during the regulation of plant immune signalling. The plant ATL family consists of a large number of putative RING type ubiquitin ligases. We show that potato ATL family gene StRFP1 and its orthologue NbATL60 from N. benthamiana both respond to Phytophthora infestans culture filtrate (CF) and flg22 induction. StRFP1 positively regulates immunity against P. infestans in potato. Ectopic transient expression of StRFP1 or expression of NbATL60 in N. benthamiana also enhances late blight resistance. By contrast, silencing NbATL60 in N. benthamiana reduces late blight resistance and leads to plant growth inhibition. Both StRFP1 and NbATL60 localize to the plasma membrane and intracellular puncta and possess E3 Ligase activity in vitro. Furthermore we demonstrate that the RING finger domain mutants of StRFP1 and NbATL60 lost E3 ligase activity and fail to suppress P. infestans colonization in N. benthamiana, indicating that E3 ligase activity is critical for StRFP1 and NbATL60 to regulate immunity. Overexpression or RNA interference of StRFP1 in transgenic potato led to increased or decreased expression of PTI maker genes (WRKY7, WRKY8, ACRE31 and Pti5) respectively. Similarly silencing of NbATL60 in N. benthamiana decreases expression of these PTI marker genes. Moreover, VIGS of NbATL60 in N. benthamiana did not compromise P. infestans PAMP INF1 or R2/Avr2, R3a/AVR3a, Rx/Cp and Pto/AvrPto triggered cell death. These results indicate that ATL genes StRFP1 and NbATL60 contribute to basal immunity (PTI) in Solanaceous plants.

The Cuticle Mutant eca2 Modifies Plant Defense Responses to Biotrophic and Necrotrophic Pathogens and Herbivory Insects

We isolated previously several Arabidopsis thaliana mutants with constitutive expression of the early microbe-associated molecular pattern-induced gene ATL2, named eca (expresión constitutiva de ATL2). Here, we further explored the interaction of eca mutants with pest and pathogens. Of all eca mutants, eca2 was more resistant to a fungal pathogen (Botrytis cinerea) and a bacterial pathogen (Pseudomonas syringae) as well as to a generalist herbivorous insect (Spodoptera littoralis). Permeability of the cuticle is increased in eca2; chemical characterization shows that eca2 has a significant reduction of both cuticular wax and cutin. Additionally, we determined that eca2 did not display a similar compensatory transcriptional response, compared with a previously characterized cuticular mutant, and that resistance to B. cinerea is mediated by the priming of the early and late induced defense responses, including salicylic acid- and jasmonic acid-induced genes. These results suggest that ECA2-dependent responses are involved in the nonhost defense mechanism against biotrophic and necrotrophic pathogens and against a generalist insect by modulation and priming of innate immunity and late defense responses. Making eca2 an interesting model to characterize the molecular basis for plant defenses against different biotic interactions and to study the initial events that take place in the cuticle surface of the aerial organs.

Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases

Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset. This revealed strong correlations between ATL proteins and diverse signal transduction components and transcriptional regulators, in particular those involved in immunity. An enrichment analysis of cis-regulatory elements in ATL gene promoters and related co-expressed genes highlighted the importance of hormones in the regulation of ATL gene expression. Our work identified several ATL proteins as candidates for further studies aiming to decipher specific grapevine resistance mechanisms activated in response to pathogens.

Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines

Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the prediction of family functions based on several features, such as the presence of sequence motifs or of particular sites for post-translational modification and the expression profile of family members in different conditions. This work describes a detailed protocol for gene family characterization. Here, the procedure is applied to the characterization of the Arabidopsis Tóxicos in Levadura (ATL) E3 ubiquitin ligase family in grapevine. The methods include the genome-wide identification of family members, the characterization of gene localization, structure, and duplication, the analysis of conserved protein motifs, the prediction of protein localization and phosphorylation sites as well as gene expression profiling across the family in different datasets. Such procedure, which could be extended to further analyses depending on experimental purposes, could be applied to any gene family in any plant species for which genomic data are available, and it provides valuable information to identify interesting candidates for functional studies, giving insights into the molecular mechanisms of plant adaptation to their environment.

Ubiquitin related enzymes and plant-specific ubiquitin ligase ATL family in tomato plants

Ubiquitination is one of the fundamental post-translational modifications of proteins with ubiquitin, a conserved 76-amino acid protein present in eukaryotes, which is catalyzed by ubiquitin ligase. Compared with humans, the number of ubiquitin ligase genes is nearly double in plant species such as Arabidopsis and rice, suggesting that this enzyme plays critical roles in many aspects of plant growth, including development and abiotic and biotic environmental stress responses. In addition to its fundamental activities in eukaryotic cells, ubiquitin signaling mediates plant specific cellular functions, including phytohormone response, seed and fruit development, and biotic and abiotic stress responses. The ATL family is a RING-H2 type ubiquitin ligase widely conserved in plant species. We previously showed that the plant specific ubiquitin ligase ATL31 regulates the carbon/nitrogen-nutrient response and pathogen resistance in Arabidopsis, and we identified and characterized the basic biochemical function of an ATL31 homologue in tomato plants (Solanum lycopersicum L.). This protein, called SlATL31, may act as a ubiquitin ligase in tomato fruit. The tomato is a major crop plant and a model system for fleshy fruit development. This review provides an overview of the ubiquitin ligases and related enzymes, and highlights the ubiquitin ligase ATL family in tomato plants.

RING-H2-type E3 gene VpRH2 from Vitis pseudoreticulata improves resistance to powdery mildew by interacting with VpGRP2A

Grapevine is one of the world's most important fruit crops. European cultivated grape species have the best fruit quality but show almost no resistance to powdery mildew (PM). PM caused by Uncinula necator is a harmful disease that has a significant impact on the economic value of the grape crop. In this study, we examined a RING-H2-type ubiquitin ligase gene VpRH2 that is associated with significant PM-resistance of Chinese wild-growing grape Vitis pseudoreticulata accession Baihe-35-1. The expression of VpRH2 was clearly induced by U. necator inoculation compared with its homologous gene VvRH2 in a PM-susceptible grapevine V. vinifera cv. Thompson Seedless. Using a yeast two-hybrid assay we confirmed that VpRH2 interacted with VpGRP2A, a glycine-rich RNA-binding protein. The degradation of VpGRP2A was inhibited by treatment with the proteasome inhibitor MG132 while VpRH2 did not promote the degradation of VpGRP2A. Instead, the transcripts of VpRH2 were increased by over-expressing VpGRP2A while VpRH2 suppressed the expression of VpGRP2A. Furthermore, VpGRP2A was down-regulated in both Baihe-35-1 and Thompson Seedless after U. necator inoculation. Specifically, we generated VpRH2 overexpression transgenic lines in Thompson Seedless and found that the transgenic plants showed enhanced resistance to powdery mildew compared with the wild-type. In summary, our results indicate that VpRH2 interacts with VpGRP2A and plays a positive role in resistance to powdery mildew.

AhDGR2, an amaranth abiotic stress-induced DUF642 protein gene, modifies cell wall structure and composition and causes salt and ABA hyper-sensibility in transgenic Arabidopsis

An amaranth DGR gene, induced under abiotic stress, modifies cell wall structure and causes hypersensitivity to ABA and salt when overexpressed in Arabidopsis. DUF642 is a highly conserved plant-specific family of unknown cell wall-associated proteins. The AhDGR2 gene, coding for a DUF642 protein, was significantly induced in grain amaranth (Amaranthus hypochondriacus) plants subjected to water-deficit and salinity stress, thereby suggesting its participation in abiotic stress tolerance in this plant. A role in development was also inferred from the higher AhDGR2 expression rates detected in young tissues. Subsequent overexpression of AhDGR2 in transgenic Arabidopsis plants (OE-AhDGR2) supported its possible role in development processes. Thus, OE-AhDGR2 plants generated significantly longer roots when grown in normal MS medium. However, they showed a hypersensitivity to increasing concentrations of abscisic acid or NaCl in the medium, as manifested by shorter root length, smaller and slightly chlorotic rosettes, as well as highly reduced germination rates. Contrary to expectations, OE-AhDGR2 plants were intolerant to abiotic stress. Moreover, cell walls in transgenic plants were thinner, in leaves, and more disorganized, in roots, and had significantly modified pectin levels. Lower pectin methylesterase activity detected in leaves of OE-AhDGR2 plants, but not in roots, was contrary to previous reports associating DUF642 proteins and decreased pectin esterification levels in cell walls. Nonetheless, microarray data identified candidate genes whose expression levels explained the phenotypes observed in leaves of OE-AhDGR2 plants, including several involved in cell wall integrity and extension, growth and development, and resistance to abiotic stress. These results support the role of DUF642 proteins in cell wall-related processes and offer novel insights into their possible role(s) in plants.

Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members

The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.

Extensive transcriptomic studies on the roles played by abscisic acid and auxins in the development and ripening of strawberry fruits

Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. Hormonal regulation of gene expression along all these processes in strawberries is still to be fully elucidated. Although auxins and ABA have been pointed out as the major regulatory hormones, few high-throughput analyses have been carried out to date. The role for ethylene and gibberellins as regulatory hormones during the development and ripening of the strawberry fruit remain still elusive. By using a custom-made and high-quality oligo microarray platform done with over 32,000 probes including all of the genes actually described in the strawberry genome, we have analysed the expression of genes during the development and ripening in the receptacles of these fruits. We classify these genes into two major groups depending upon their temporal and developmental expression. First group are genes induced during the initial development stages. The second group encompasses genes induced during the final maturation and ripening processes. Each of these two groups has been also divided into four sub-groups according their pattern of hormonal regulation. By analyzing gene expression, we clearly show that auxins and ABA are the main and key hormones that combined or independently are responsible of the development and ripening process. Auxins are responsible for the receptacle fruit development and, at the same time¸ prevent ripening by repressing crucial genes. ABA regulates the expression of the vast majority of genes involved in the ripening. The main genes expressed under the control of these hormones are presented and their physiological rule discussed. We also conclude that ethylene and gibberellins do not seem to play a prominent role during these processes.

PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development

REALLY INTERESTING NEW GENE (RING) proteins play important roles in the regulation of many processes by recognizing target proteins for ubiquitination. Previously, we have shown that the expression of PtaRHE1, encoding a Populus tremula × Populus alba RING-H2 protein with E3 ubiquitin ligase activity, is associated with tissues undergoing secondary growth. To further elucidate the role of PtaRHE1 in vascular tissues, we have undertaken a reverse genetic analysis in poplar. Within stem secondary vascular tissues, PtaRHE1 and its corresponding protein are expressed predominantly in the phloem. The downregulation of PtaRHE1 in poplar by artificial miRNA triggers alterations in phloem fibre patterning, characterized by an increased portion of secondary phloem fibres that have a reduced cell wall thickness and a change in lignin composition, with lower levels of syringyl units as compared with wild-type plants. Following an RNA-seq analysis, a biological network involving hormone stress signalling, as well as developmental processes, could be delineated. Several candidate genes possibly associated with the altered phloem fibre phenotype observed in amiRPtaRHE1 poplar were identified. Altogether, our data suggest a regulatory role for PtaRHE1 in secondary phloem fibre development.

Pale-green phenotype of atl31atl6 double mutant leaves is caused by disruption of 5-aminolevulinic acid biosynthesis in Arabidopsis thaliana

Arabidopsis ubiquitin ligases ATL31 and homologue ATL6 control the carbon/nitrogen nutrient and pathogen responses. A mutant with the loss-of-function of both atl31 and atl6 developed light intensity-dependent pale-green true leaves, whereas the single knockout mutants did not. Plastid ultrastructure and Blue Native-PAGE analyses revealed that pale-green leaves contain abnormal plastid structure with highly reduced levels of thylakoid proteins. In contrast, the pale-green leaves of the atl31/atl6 mutant showed normal Fv/Fm. In the pale-green leaves of the atl31/atl6, the expression of HEMA1, which encodes the key enzyme for 5-aminolevulinic acid synthesis, the rate-limiting step in chlorophyll biosynthesis, was markedly down-regulated. The expression of key transcription factor GLK1, which directly promotes HEMA1 transcription, was also significantly decreased in atl31/atl6 mutant. Finally, application of 5-aminolevulinic acid to the atl31/atl6 mutants resulted in recovery to a green phenotype. Taken together, these findings indicate that the 5-aminolevulinic acid biosynthesis step was inhibited through the down-regulation of chlorophyll biosynthesis-related genes in the pale-green leaves of atl31/atl6 mutant.

Rice ubiquitin ligase EL5 prevents root meristematic cell death under high nitrogen conditions and interacts with a cytosolic GAPDH

Root formation in rice transformants overexpressing mutated EL5 (mEL5) was severely inhibited because of meristematic cell death. Cell death was caused by nitrogen sources, particularly nitrate forms, in the culture medium. Nitrite treatment increased the cytokinin contents in roots, but mEL5 contained more cytokinins than non-transformants. Transcriptome profiling showed overlaps between nitrite-responsive genes in non-transformants and genes with altered expression in untreated mEL5. These results indicate that impairment of EL5 function activates nitrogen signaling despite the absence of a nitrogen source. Physical interaction between the EL5 C-terminal region and a cytosolic glyceraldehyde-3-phosphate dehydrogenase, OsGapC2, was demonstrated in vitro and in vivo. Elucidation of the role of glyceraldehyde-3-phosphate dehydrogenase in oxidative cell death in plants is expected in future.

The Arabidopsis EDR1 protein kinase negatively regulates the ATL1 E3 ubiquitin ligase to suppress cell death

Loss-of-function mutations in the Arabidopsis thaliana ENHANCED DISEASE RESISTANCE1 (EDR1) gene confer enhanced programmed cell death under a variety of abiotic and biotic stress conditions. All edr1 mutant phenotypes can be suppressed by missense mutations in the KEEP ON GOING gene, which encodes a trans-Golgi network/early endosome (TGN/EE)-localized E3 ubiquitin ligase. Here, we report that EDR1 interacts with a second E3 ubiquitin ligase, ARABIDOPSIS TOXICOS EN LEVADURA1 (ATL1), and negatively regulates its activity. Overexpression of ATL1 in transgenic Arabidopsis induced severe growth inhibition and patches of cell death, while transient overexpression in Nicotiana benthamiana leaves induced cell death and tissue collapse. The E3 ligase activity of ATL1 was required for both of these processes. Importantly, we found that ATL1 interacts with EDR1 on TGN/EE vesicles and that EDR1 suppresses ATL1-mediated cell death in N. benthamiana and Arabidopsis. Lastly, knockdown of ATL1 expression suppressed cell death phenotypes associated with the edr1 mutant and made Arabidopsis hypersusceptible to powdery mildew infection. Taken together, our data indicate that ATL1 is a positive regulator of programmed cell death and EDR1 negatively regulates ATL1 activity at the TGN/EE and thus controls stress responses initiated by ATL1-mediated ubiquitination events.

The ubiquitination machinery of the ubiquitin system

The protein ubiquitin is a covalent modifier of proteins, including itself. The ubiquitin system encompasses the enzymes required for catalysing attachment of ubiquitin to substrates as well as proteins that bind to ubiquitinated proteins leading them to their final fate. Also included are activities that remove ubiquitin independent of, or in concert with, proteolysis of the substrate, either by the proteasome or proteases in the vacuole. In addition to ubiquitin encoded by a family of fusion proteins, there are proteins with ubiquitin-like domains, likely forming ubiquitin's β-grasp fold, but incapable of covalent modification. However, they serve as protein-protein interaction platforms within the ubiquitin system. Multi-gene families encode all of these types of activities. Within the ubiquitination machinery "half" of the ubiquitin system are redundant, partially redundant, and unique components affecting diverse developmental and environmental responses in plants. Notably, multiple aspects of biotic and abiotic stress responses require, or are modulated by, ubiquitination. Finally, aspects of the ubiquitin system have broad utility: as components to enhance gene expression or to regulate protein abundance. This review focuses on the ubiquitination machinery: ubiquitin, unique aspects about the synthesis of ubiquitin and organization of its gene family, ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases, or E3s. Given the large number of E3s in Arabidopsis this review covers the U box, HECT and RING type E3s, with the exception of the cullin-based E3s.

Phosphorylation of Arabidopsis ubiquitin ligase ATL31 is critical for plant carbon/nitrogen nutrient balance response and controls the stability of 14-3-3 proteins

Ubiquitin ligase plays a fundamental role in regulating multiple cellular events in eukaryotes by fine-tuning the stability and activity of specific target proteins. We have previously shown that ubiquitin ligase ATL31 regulates plant growth in response to nutrient balance between carbon and nitrogen (C/N) in Arabidopsis. Subsequent study demonstrated that ATL31 targets 14-3-3 proteins for ubiquitination and modulates the protein abundance in response to C/N-nutrient status. However, the underlying mechanism for the targeting of ATL31 to 14-3-3 proteins remains unclear. Here, we show that ATL31 interacts with 14-3-3 proteins in a phosphorylation-dependent manner. We identified Thr(209), Ser(247), Ser(270), and Ser(303) as putative 14-3-3 binding sites on ATL31 by motif analysis. Mutation of these Ser/Thr residues to Ala in ATL31 inhibited the interaction with 14-3-3 proteins, as demonstrated by yeast two-hybrid and co-immunoprecipitation analyses. Additionally, we identified in vivo phosphorylation of Thr(209) and Ser(247) on ATL31 by MS analysis. A peptide competition assay showed that the application of synthetic phospho-Thr(209) peptide, but not the corresponding unphosphorylated peptide, suppresses the interaction between ATL31 and 14-3-3 proteins. Moreover, Arabidopsis plants overexpressing mutated ATL31, which could not bind to 14-3-3 proteins, showed accumulation of 14-3-3 proteins and growth arrest in disrupted C/N-nutrient conditions similar to wild-type plants, although overexpression of intact ATL31 resulted in repression of 14-3-3 accumulation and tolerance to the conditions. Together, these results demonstrate that the physiological role of phosphorylation at 14-3-3 binding sites on ATL31 is to modulate the binding ability and stability of 14-3-3 proteins to control plant C/N-nutrient response.

The fate of tandemly duplicated genes assessed by the expression analysis of a group of Arabidopsis thaliana RING-H2 ubiquitin ligase genes of the ATL family

Gene duplication events exert key functions on gene innovations during the evolution of the eukaryotic genomes. A large portion of the total gene content in plants arose from tandem duplications events, which often result in paralog genes with high sequence identity. Ubiquitin ligases or E3 enzymes are components of the ubiquitin proteasome system that function during the transfer of the ubiquitin molecule to the substrate. In plants, several E3s have expanded in their genomes as multigene families. To gain insight into the consequences of gene duplications on the expansion and diversification of E3s, we examined the evolutionary basis of a cluster of six genes, duplC-ATLs, which arose from segmental and tandem duplication events in Brassicaceae. The assessment of the expression suggested two patterns that are supported by lineage. While retention of expression domains was observed, an apparent absence or reduction of expression was also inferred. We found that two duplC-ATL genes underwent pseudogenization and that, in one case, gene expression is probably regained. Our findings provide insights into the evolution of gene families in plants, defining key events on the expansion of the Arabidopsis Tóxicos en Levadura family of E3 ligases.

The carbon/nitrogen regulator ARABIDOPSIS TOXICOS EN LEVADURA31 controls papilla formation in response to powdery mildew fungi penetration by interacting with SYNTAXIN OF PLANTS121 in Arabidopsis

The carbon/nitrogen (C/N) balance of plants is not only required for growth and development but also plays an important role in basal immunity. However, the mechanisms that link C/N regulation and basal immunity are poorly understood. We previously demonstrated that the Arabidopsis (Arabidopsis thaliana) Arabidopsis Tóxicos en Levadura31 (ATL31) ubiquitin ligase, a regulator of the C/N response, positively regulates the defense response against bacterial pathogens. In this study, we identified the plasma membrane-localized soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor SYNTAXIN OF PLANTS121 (SYP121) as a novel ATL31 interactor. The syp121-1 loss-of-function mutant showed similar hypersensitivity to C/N stress conditions as the atl31 atl6 double mutant. SYP121 is essential for resistance to penetration by powdery mildew fungus and positively regulates the formation of cell wall appositions (papillae) at fungal entry sites. Microscopic analysis demonstrated that ATL31 was specifically localized around papillae. In addition, ATL31 overexpressors showed accelerated papilla formation, enhancing their resistance to penetration by powdery mildew fungus. Together, these data indicate that ATL31 plays an important role in connecting the C/N response with basal immunity by promoting papilla formation through its association with SYP121.

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.

Regulation of senescence under elevated atmospheric CO₂ via ubiquitin modification

Elevated atmospheric CO₂ concentration is a serious global environmental problem. Elevated CO₂ affects plant growth by changing primary metabolism, closely related to carbon (C) and nitrogen (N) availability. Under sufficient N conditions, plant growth is dramatically promoted by elevated CO₂. When N availability is limited, however, elevated CO₂ disrupts the balance between cellular C and N (C/N). Disruption of the C/N balance is regarded as an important factor in plant growth defects. Here we highlight the regulation of senescence in higher plants by atmospheric CO₂ and N, and the physiological function of C/N-related ubiquitin ligase ATL31 under condition of elevated CO₂. We also provide an overview of the ubiquitin ligases and related enzymes involved in regulating senescence in plants.

Spliceosomal introns in the 5' untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression

BACKGROUND

Introns located close to the 5' end of a gene or in the 5' untranslated region often exert positive effects on gene expression. This effect, known as intron-mediated enhancement (IME), has been observed in diverse eukaryotic organisms, including plants. The sequences involved in IME seem to be spread across the intron and function in an additive manner. The IMEter algorithm was developed to predict plant introns that may enhance gene expression. We have identified several plant members of the BTL class of E3s, which may have orthologs across eukaryotes, that contain a 5'UTR intron. The RING finger E3 ligases are key enzymes of the ubiquitination system that mediate the transfer of ubiquitin to substrates.

RESULTS

In this study, we retrieved BTL sequences from several angiosperm species and found that 5'UTR introns showing a strong IMEter score were predicted, suggesting that they may be conserved by lineage. Promoter-GUS fusion lines were used to confirm the IME effect of these 5'UTR introns on gene expression. IMEter scores of BTLs were compared with the 5'UTR introns of two gene families MHX and polyubiquitin genes.

CONCLUSIONS

Analysis performed in two Arabidopsis BTL E3 ligases genes indicated that the 5'UTR introns were essential for gene expression in all the tissues tested. Comparison of the average 5'UTR intron size on three gene families in ten angiosperm species suggests that a prevalent size for a 5'UTR intron is in the range of 600 nucleotides, and that the overall IMEter score within a gene family is preserved across several angiosperms. Our results indicated that gene expression dependent on a 5'UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution.

Expansion and diversification of BTL ring-H2 ubiquitin ligases in angiosperms: putative Rabring7/BCA2 orthologs

RING finger E3 ligases are components of the ubiquitin proteasome system (UPS) that mediate the transfer of ubiquitin to substrates. Single-subunit RING finger E3s binds the E2 ubiquitin-conjugating enzyme and contains recognition sequences for the substrate within the same polypeptide. Here we describe the characterization of a class of RING finger E3 ligases that is conserved among eukaryotes. This class encodes a RING-H2 domain related in sequence to the ATL RING-H2 domain, another class of E3 ligases, and a C2/C2 zing finger at the amino-terminus, formerly described as BZF. In viridiplantae (green algae and land plants), we designed this family as BTL for BZF ATLs. BTLs are putative orthologs of the mammalian Rabring7/BCA2 RING-H2 E3s that have expanded in angiosperms. They are found in numbers ranging from three to thirty-one, which is in contrast to the one to three members normally found in animals, fungi, and protists. Furthermore, the number of sequence LOGOs generated in angiosperms is four times greater than that in other eukaryotes. In contrast to ATLs, which show expansion by tandem duplication, tandemly duplicated BTLs are scarce. The mode of action of Rabring7/BCA2 and BTLs may be similar since both the Rabring7/BCA2 BZF and the ath|BTL4 BZF are likely to mediate the binding of ubiquitin. This study introduces valuable information on the evolution and domain structure of the Rabring7/BCA2/BTL class of E3 ligases which may be important for core eukaryotic genes.