Plant ubiquitin-proteasome pathway and its role in gibberellin signaling

Mapping of resistance genes to powdery mildew based on DNA re-sequencing and bulk segregant analysis in Capsicum

Powdery mildew caused by Leveillula taurica adversely affects the development and growth of pepper plants. However, there have been few reports on the fine mapping and quantitative trait locus (QTLs) gene cloning of resistance genes to powdery mildew in pepper. Herein, an F2 segregating population was constructed using the high resistance material "NuMex Suave Red" and the extremely susceptible material "c89" for bulked segregant analysis and DNA re-sequencing (BSA-seq). Molecular markers were used to achieve fine mapping, followed by expression verification. A major QTL located on chromosome 5 (Chr5, 7.20-11.75 Mb) that is associated with resistance to powdery mildew in pepper was mapped using BSA-seq. A narrow interval of 64.86 kb encompassing five genes was refined using InDel and KSAP molecular markers developed from the QTL region. Among them, the expression of the ubiquitin-conjugating enzyme E2 gene, Capana05g000392, was significantly upregulated in multiple resistant materials. In addition, there was a single nucleotide polymorphism (SNP) of A/G in the 241st position of the CDS sequence of Capana05g000392, which in turn leads to an amino acid polymorphism of M/V between susceptible parent and resistant parent. Overall, these results indicate that the Capana05g000392 gene may serve as a robust potential factor against powdery mildew in pepper. These findings further elucidate the genetic mechanism of resistance to powdery mildew in pepper and facilitate molecular marker-assisted breeding.

The SINA1-BSD1 Module Regulates Vegetative Growth Involving Gibberellin Biosynthesis in Tomato

In plants, vegetative growth is controlled by synergistic and/or antagonistic effects of many regulatory factors. Here, the authors demonstrate that the ubiquitin ligase seven in absentia1 (SINA1) mammalian BTF2-like transcription factors, Drosophila synapse-associated proteins, and yeast DOS2-like proteins (BSD1) function as a regulatory module to control vegetative growth in tomato via regulation of the production of plant growth hormone gibberellin (GA). SINA1 negatively regulates the protein level of BSD1 through ubiquitin-proteasome-mediated degradation, and the transgenic tomato over-expressing SINA1 (SINA1-OX) resembles the dwarfism phenotype of the BSD1-knockout (BSD1-KO) tomato plant. BSD1 directly activates expression of the BSD1-regulated gene 1 (BRG1) via binding to a novel core BBS (standing for BSD1 binding site) binding motif in the BRG1 promoter. Knockout of BRG1 (BRG1-KO) in tomato also results in a dwarfism phenotype, suggesting BRG1 plays a positive role in vegetative growth as BSD1 does. Significantly, GA contents are attenuated in transgenic SINA1-OX, BSD1-KO, and BRG1-KO plants exhibiting dwarfism phenotype and exogenous application of bioactive GA3 restores their vegetative growth. Moreover, BRG1 is required for the expression of multiple GA biosynthesis genes and BSD1 activates three GA biosynthesis genes promoting GA production. Thus, this study suggests that the SINA1-BSD1 module controls vegetative growth via direct and indirect regulation of GA biosynthesis in tomato.

Genomic-wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)

Seven in absentia proteins, which contain a conserved SINA domain, are involved in regulating various aspects of wheat (Triticum aestivum L.) growth and development, especially in response to environmental stresses. However, it is unclear whether TaSINA family members are involved in regulating grain development until now. In this study, the expression pattern, genomic polymorphism, and relationship with grain-related traits were analyzed for all TaSINA members. Most of the TaSINA genes identified showed higher expression levels in young wheat spikes or grains than other organs. The genomic polymorphism analysis revealed that at least 62 TaSINA genes had different haplotypes, where the haplotypes of five genes were significantly correlated with grain-related traits. Kompetitive allele-specific PCR markers were developed to confirm the single nucleotide polymorphisms in TaSINA101 and TaSINA109 among the five selected genes in a set of 292 wheat accessions. The TaSINA101-Hap II and TaSINA109-Hap II haplotypes had higher grain weight and width compared to TaSINA101-Hap I and TaSINA109-Hap I in at least three environments, respectively. The qRT-PCR assays revealed that TaSINA101 was highly expressed in the palea shell, seed coat, and embryo in young wheat grains. The TaSINA101 protein was unevenly distributed in the nucleus when transiently expressed in the protoplast of wheat. Three homozygous TaSINA101 transgenic lines in rice (Oryza sativa L.) showed higher grain weight and size compared to the wild type. These findings provide valuable insight into the biological function and elite haplotype of TaSINA family genes in wheat grain development at a genomic-wide level.

Degradation and mechanism analysis of protein macromolecules by functional bacteria in tobacco leaves

Tobacco, a crop of significant economic importance, was greatly influenced in leaf quality by protein content. However, current processing parameters fail to adequately meet the requirements for protein degradation. Microorganisms possess potential advantages for degrading proteins and enhancing the quality of tobacco leaves, and hold substantial potential in the process of curing. To effectively reduce the protein content in tobacco leaves, thereby improving the quality and safety of the tobacco leaves. In this study, tobacco leaf were used as experimental material. From these, the BSP1 strain capable of effectively degrading proteins was isolated and identified as Bacillus subtilis by 16S rDNA analysis. Furthermore, the mechanisms were analyzed by integrating microbiome, transcriptome, and metabolome. Before curing, BSP1 was applied to the surface of tobacco leaves. The results indicated that BSP1 effectively improves the activity of key enzymes and the content of related substances, thereby enhancing protein degradation. Additionally, protein degradation was achieved by regulating the diversity of the microbial community on the surface of the tobacco leaves and the ubiquitin-proteasome pathway. This study provided new strategies for extracting and utilizing functional strains from tobacco leaves, opening new avenues for enhancing the quality of tobacco leaves.

Comparative Proteomic Analysis of Ridge Gourd Seed (Luffa acutangula (L.) Roxb.) during Artificial Aging

Seed aging is a complicated process influenced by environmental conditions, impacting biochemical processes in seeds and causing deterioration that results in reduced viability and vigor. In this study, we investigated the seed aging process of ridge gourd, which is one of the most exported commercial seeds in Thailand using sequential window acquisition of all theoretical fragment ion spectra mass spectrometry. A total of 855 proteins were identified among the two groups (0 d/15 d and 0 d/30 d). The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of differentially expressed proteins revealed that in ridge gourd seeds, the aging process altered the abundance of proteins related to the oxidative stress response, nutrient reservoir, and metabolism pathway. The most identified DEPs were mitochondrial proteins, ubiquitin-proteasome system proteins, ribosomal proteins, carbohydrate metabolism-related proteins, and stress response-related proteins. This study also presented the involvement of aconitase and glutathione pathway-associated enzymes in seed aging, with aconitase and total glutathione being determined as possible suggestive biomarkers for aged ridge gourd seeds. This acquired knowledge has the potential to considerably improve growing methods and seed preservation techniques, enhancing seed storage and maintenance.

COP1-ERF1-SCE1 regulatory module fine-tunes stress response under light-dark cycle in Arabidopsis

ETHYLENE RESPONSE FACTOR 1 (ERF1) plays an important role in integrating hormone crosstalk and stress responses. Previous studies have shown that ERF1 is unstable in the dark and its degradation is mediated by UBIQUITIN-CONJUGATING ENZYME 18. However, whether there are other enzymes regulating ERF1's stability remains unclear. Here, we use various in vitro and in vivo biochemical, genetic and stress-tolerance tests to demonstrate that both CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUMO-CONJUGATING ENZYME 1 (SCE1) regulate the stability of ERF1. We also performed transcriptomic analyses to understand their common regulatory pathways. We show that COP1 mediates ERF1 ubiquitination in the dark while SCE1 mediates ERF1 sumoylation in the light. ERF1 stability is positively regulated by SCE1 and negatively regulated by COP1. Upon abiotic stress, SCE1 plays a positive role in stress defence by regulating the expression of ERF1's downstream stress-responsive genes, whereas COP1 plays a negative role in stress response. Moreover, ERF1 also promotes photomorphogenesis and the expression of light-responsive genes. Our study reveals the molecular mechanism of how COP1 and SCE1 counteract to regulate ERF1's stability and light-stress signalling crosstalk.

Function of hormone signaling in regulating nitrogen-use efficiency in plants

Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice

We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL groups; next, we focused on OsCUL3c, the third CUL3 of the CUL3 family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the OsCUL3c region, representing 79 haplotypes (haps), were found. Haplotyping revealed that group I (hap A and hap C) and group II (hap B1 and hap D) were different mutated variants, which showed their association with phenotypes under salt stress. These results were supported by cis-regulatory elements (CREs) and transcription factor binding sites (TFBSs) analyses. We found that LTR, MYC, [AP2; ERF], and NF-YB, which are related to salt stress, drought stress, and the response to abscisic acid (ABA), have distinct positions and numbers in the haplotypes of group I and group II. An RNA Seq analysis of the two predominant haplotypes from each group showed that the OsCUL3c expression of the group I representative was upregulated and that of group II was downregulated, which was confirmed by RT-qPCR. Promoter changes might affect the transcriptional responses to salt stress, leading to different regulatory mechanisms for the expression of different haplotypes. We speculate that OsCUL3c influences the regulation of salt-related responses, and haplotype variations play a role in this regulation.

Multi-omics insights into the mechanism of the high-temperature tolerance in a thermotolerant Chlorella sorokiniana

Improving high-temperature tolerance of microalgae is crucial to enhance the robustness and economy of microalgae industrial production. Herein, a continuous adaptive laboratory evolution (ALE) system was developed to generate the thermotolerant strain of Chlorella sorokiniana. The resulting thermotolerant strain TR42 exhibited excellent cell growth and biomass production at 42 °C, the temperature that the original strain (OS) could not survive. The high-temperature resistant mechanism of TR42 was investigated by integrating the physiology, transcriptome, proteome and metabolome analyses, which involved enhancing antioxidant capacity, maintaining protein homeostasis, remodeling photosynthetic metabolism, and regulating the synthesis of heat-stress related metabolites. The proof-of-concept high-temperature outdoor cultivation demonstrated that TR42 exhibited 1.15- to 5.72-fold increases in biomass production and 1.62- to 7.04-fold increases in lipid productivity compared to those of OS, respectively, which provided a promising platform for microalgae industrial production. Thus, the multi-system thermotolerant mechanism of TR42 offered potential targets for enhancing high-temperature tolerance of microalgae.

Transcriptomic and Metabolomic Analyses Reveal the Importance of Lipid Metabolism and Photosynthesis Regulation in High Salinity Tolerance in Barley (Hordeum vulgare L.) Leaves Derived from Mutagenesis Combined with Microspore Culture

Barley is the most salt-tolerant cereal crop. However, little attention has been paid to the salt-tolerant doubled haploids of barley derived from mutagenesis combined with isolated microspore culture. In the present study, barley doubled haploid (DH) line 20, which was produced by mutagenesis combined with isolated microspore culture, showed stably and heritably better salt tolerance than the wild type H30 in terms of fresh shoot weight, dry shoot weight, K+/Na+ ratio and photosynthetic characteristics. Transcriptome and metabolome analyses were performed to compare the changes in gene expression and metabolites between DH20 and H30. A total of 462 differentially expressed genes (DEGs) and 152 differentially accumulated metabolites (DAMs) were identified in DH20 compared to H30 under salt stress. Among the DAMs, fatty acids were the most accumulated in DH20 under salt stress. The integration of transcriptome and metabolome analyses revealed that nine key biomarkers, including two metabolites and seven genes, could distinguish DH20 and H30 when exposed to high salt. The pathways of linoleic acid metabolism, alpha-linolenic acid metabolism, glycerolipid metabolism, photosynthesis, and alanine, aspartate and glutamate metabolism were significantly enriched in DH20 with DEGs and DAMs in response to salt stress. These results suggest that DH20 may enhance resilience by promoting lipid metabolism, maintaining energy metabolism and decreasing amino acids metabolism. The study provided novel insights for the rapid generation of homozygous mutant plants by mutagenesis combined with microspore culture technology and also identified candidate genes and metabolites that may enable the mutant plants to cope with salt stress.

The amino acid residue E96 of Ghd8 is crucial for the formation of the flowering repression complex Ghd7-Ghd8-OsHAP5C in rice

Ghd7 is an important gene involved in the photoperiod flowering pathway in rice. A Ghd7-involved transcriptional regulatory network has been established, but its translational regulatory pathway is poorly understood. The mutant suppressor of overexpression of Ghd7 (sog7) was identified from EMS-induced mutagenesis on the background of ZH11 overexpressing Ghd7. MutMap analysis revealed that SOG7 is allelic to Ghd8 and delayed flowering under long-day (LD) conditions. Biochemical assays showed that Ghd8 interacts with OsHAP5C and Ghd7 both in vivo and in vitro. Surprisingly, a point mutation E96K in the α2 helix of the Ghd8 histone fold domain (HFD) destroyed its ability to interact with Ghd7. The prediction of the structure shows that mutated amino acid is located in the interaction region of CCT/NF-YB/YC complexes, which alter the structure of α4 of Ghd8. This structural difference prevents the formation of complex NF-YB/YC. The triple complex of Ghd8-OsHAP5C-Ghd7 directly bound to the promotor of Hd3a and downregulated the expression of Ehd1, Hd3a and RFT1, and finally resulted in a delayed heading. These findings are helpful in deeply understanding the Ghd7-involved photoperiod flowering pathway and promote the elucidation of rice heading.

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (Sorghum bicolor L.). In the present study, 59 SbPUB genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 SbPUB genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. SbPUB genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most PUB genes (16) were found on chromosome 4, but there were no PUB genes on chromosome 5. Analysis of cis-acting elements showed that SbPUB genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several SbPUB genes had diverse expressions under different salt treatments. To verify the expression of SbPUBs, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 SbPUB genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that PUB genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.

Transcriptome alterations of radish shoots exposed to cadmium can be interpreted in the context of leaf senescence

Till now few transcriptome studies have described shoot responses of heavy metal (HM)-sensitive plants to excess Cd and still a unifying model of Cd action is lacking. Using RNA-seq technique, the transcriptome responses of radish (Raphanus sativus L.) leaves to Cd stress were investigated in plants raised hydroponically under control and 5.0 mg L^-1 Cd. The element was mainly accumulated in roots and led to declined biomass and photosynthetic pigments, increased H₂O₂ and lipid peroxidation, and the accumulation of sugars, protein thiols, and phytochelatins. Out of 524 differentially expressed genes (DEGs), 244 and 280 upregulated and downregulated ones were assigned to 82 and 115 GO terms, respectively. The upregulated DEGs were involved in osmotic regulation, protein metabolism, chelators, and carbohydrate metabolisms, whereas downregulated DEGs were related to photosynthesis, response to oxidative stress, glucosinolate, and secondary metabolite biosynthesis. Our transcriptome data suggest that Cd triggers ROS production and photosynthesis decline associated with increased proteolysis through ubiquitin-proteasome system (UPS)- and chloroplast-proteases and in this way brings about re-mobilization of N and C stores into amino acids and sugars. Meanwhile, declined glucosinolate metabolism in favor of chelator synthesis and upregulation of dehydrins as inferred from transcriptome analysis confers shoots some tolerance to the HM-derived ionic/osmotic imbalances. Thus, the induction of leaf senescence might be a major long-term response of HM-sensitive plants to Cd toxicity.

Calcium/calmodulin-mediated microbial symbiotic interactions in plants

Cytoplasmic calcium (Ca²⁺) transients and nuclear Ca²⁺ oscillations act as hubs during root nodulation and arbuscular mycorrhizal symbioses. Plants perceive bacterial Nod factors or fungal signals to induce the Ca²⁺ oscillation in the nucleus of root hair cells, and subsequently activate calmodulin (CaM) and Ca²⁺/CaM-dependent protein kinase (CCaMK). Ca²⁺ and CaM-bound CCaMK phosphorylate transcription factors then initiate down-stream signaling events. In addition, distinct Ca²⁺ signatures are activated at different symbiotic stages: microbial colonization and infection; nodule formation; and mycorrhizal development. Ca²⁺ acts as a key signal that regulates a complex interplay of downstream responses in many biological processes. This short review focuses on advances in Ca²⁺ signaling-regulated symbiotic events. It is meant to be an introduction to readers in and outside the field of bacterial and fungal symbioses. We summarize the molecular mechanisms underlying Ca²⁺/CaM-mediated signaling in fine-tuning both local and systemic symbiotic events.

Dark secrets of phytomelatonin

Phytomelatonin is a newly identified plant hormone, and its primary functions in plant growth and development remain relatively poorly appraised. Phytomelatonin is a master regulator of reactive oxygen species (ROS) signaling and acts as a darkness signal in circadian stomatal closure. Plants exhibit at least three interrelated patterns of interaction between phytomelatonin and ROS production. Exogenous melatonin can induce flavonoid biosynthesis, which might be required for maintenance of antioxidant capacity under stress, after harvest, and in leaf senescence conditions. However, several genetic studies have provided direct evidence that phytomelatonin plays a negative role in the biosynthesis of flavonoids under non-stress conditions. Phytomelatonin delays flowering time in both dicot and monocot plants, probably via its receptor PMTR1 and interactions with the gibberellin, strigolactone, and ROS signaling pathways. Furthermore, phytomelatonin signaling also functions in hypocotyl and shoot growth in skotomorphogenesis and ultraviolet B (UV-B) exposure; the G protein α-subunit (Arabidopsis GPA1 and rice RGA1) and constitutive photomorphogenic1 (COP1) are important signal components during this process. Taken together, these findings indicate that phytomelatonin acts as a darkness signal with important regulatory roles in circadian stomatal closure, flavonoid biosynthesis, flowering, and hypocotyl and shoot growth.

Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth

As a key transcription factor in the brassinosteroid (BR) signaling pathway, the activity and expression of BES1 (BRI1-EMS-SUPPRESSOR 1) are stringently regulated. BES1 degradation is mediated by ubiquitin-related 26S proteasomal and autophagy pathways, which attenuate and terminate BR signaling; however, the opposing deubiquitinases (DUBs) are still unknown. Here, we showed that the ubp12-2w/13-3 double mutant phenocopies the BR-deficient dwarf mutant, suggesting that the two DUBs UBP12/UBP13 antagonize ubiquitin-mediated degradation to stabilize BES1. These two DUBs can trim tetraubiquitin with K46 and K63 linkages in vitro. UBP12/BES1 and UBP13/BES1 complexes are localized in both cytosol and nuclei. UBP12/13 can deubiquitinate polyubiquitinated BES1 in vitro and in planta, and UBP12 interacts with and deubiquitinates both inactive, phosphorylated BES1 and active, dephosphorylated BES1 in vivo. UBP12 overexpression in BES1^OE plants significantly enhances cell elongation in hypocotyls and petioles and increases the ratio of leaf length to width compared with BES1^OE or UBP12^OE plants. Hypocotyl elongation and etiolation result from elevated BES1 levels because BES1 degradation is retarded by UBP12 in darkness or in light with BR. Protein degradation inhibitor experiments show that the majority of BES1 can be degraded by either the proteasomal or the autophagy pathway, but a minor BES1 fraction remains pathway specific. In conclusion, UBP12/UBP13 deubiquitinate BES1 to stabilize the latter as a positive regulator for BR responses.

Geminivirus C4 proteins inhibit GA signaling via prevention of NbGAI degradation, to promote viral infection and symptom development in N. benthamiana

The phytohormone gibberellin (GA) is a vital plant signaling molecule that regulates plant growth and defense against abiotic and biotic stresses. To date, the molecular mechanism of the plant responses to viral infection mediated by GA is still undetermined. DELLA is a repressor of GA signaling and is recognized by the F-box protein, a component of the SCF^SLY1/GID2 complex. The recognized DELLA is degraded by the ubiquitin-26S proteasome, leading to the activation of GA signaling. Here, we report that ageratum leaf curl Sichuan virus (ALCScV)-infected N. benthamiana plants showed dwarfing symptoms and abnormal flower development. The infection by ALCScV significantly altered the expression of GA pathway-related genes and decreased the content of endogenous GA in N. benthamiana. Furthermore, ALCScV-encoded C4 protein interacts with the DELLA protein NbGAI and interferes with the interaction between NbGAI and NbGID2 to prevent the degradation of NbGAI, leading to inhibition of the GA signaling pathway. Silencing of NbGAI or exogenous GA₃ treatment significantly reduces viral accumulation and disease symptoms in N. benthamiana plants. The same results were obtained from experiments with the C4 protein encoded by tobacco curly shoot virus (TbCSV). Therefore, we propose a novel mechanism by which geminivirus C4 proteins control viral infection and disease symptom development by interfering with the GA signaling pathway.

Gibberellins (GAs) are plant hormones essential for many developmental processes in plants. Plant virus infection can induce abnormal flower development and influence the GA pathway, resulting in plant dwarfing symptoms, but the underlying mechanisms are still not well described. Here, we demonstrate that the geminivirus-encoded C4 protein regulates the GA signaling pathway to promote viral accumulation and disease symptom development. By directly interacting with NbGAI, the C4 protein interferes with the interaction between NbGAI and NbGID2, which inhibits the degradation of NbGAI. As a result, the GA signaling pathway is blocked, and the infected plants display symptoms of typical dwarfing and delayed flowering. Our results reveal a novel mechanism by which geminivirus C4 proteins influence viral pathogenicity by interfering with the GA signaling pathway and provide new insights into the interaction between the virus and host.

Expression Patterns and Functional Analysis of 11 E3 Ubiquitin Ligase Genes in Rice

E3 ubiquitin ligases are involved in many processes, regulating the response to biotic and abiotic stresses. In this study, 11 E3 ubiquitin ligase genes from Arabidopsis, which were hypothesized to function in response to biotic or abiotic stresses were selected, and the homologous genes in rice were found. Their functions were analyzed in rice. These 11 E3 ubiquitin ligase genes showed different patterns of expression under different treatments. The BMV:OsPUB39-infiltrated seedlings showed decreased resistance to Magnaporthe grisea (M. grisea) when compared with BMV:00-infiltrated seedlings, whereas the BMV:OsPUB34- and BMV:OsPUB33-infiltrated seedlings showed increased resistance. The involvement of these genes in the resistance against M. grisea may be attributed to the regulation of the accumulation of reactive oxygen species (ROS) and expression levels of defense-related genes. Seedlings infiltrated by BMV:OsATL69 showed decreased tolerance to drought stress, whereas BMV:OsPUB33-infiltraed seedlings showed increased tolerance, possibly through the regulation of proline content, sugar content, and expression of drought-responsive genes. BMV:OsATL32-infiltrated seedlings showed decreased tolerance to cold stress by regulating malondialdehyde (MDA) content and the expression of cold-responsive genes.

Genetic Perturbation of the Starch Biosynthesis in Maize Endosperm Reveals Sugar-Responsive Gene Networks

In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such as large subunit of AGPase Shrunken2 (Sh2) and isoamylase type DBE Sugary1 (Su1). While many starch biosynthesis enzymes have been characterized, the mechanisms of certain genes (including Sugary enhancer1) are yet undefined, and very little is understood about the regulation of starch biosynthesis. As a model, we utilize commercially important sweet corn mutations, sh2 and su1, to genetically perturb starch production in the endosperm. To characterize the transcriptomic response to starch mutations and identify potential regulators of this pathway, differential expression and coexpression network analysis was performed on near-isogenic lines (NILs) (wildtype, sh2, and su1) in six genetic backgrounds. Lines were grown in field conditions and kernels were sampled in consecutive developmental stages (blister stage at 14 days after pollination (DAP), milk stage at 21 DAP, and dent stage at 28 DAP). Kernels were dissected to separate embryo and pericarp from the endosperm tissue and 3' RNA-seq libraries were prepared. Mutation of the Su1 gene led to minimal changes in the endosperm transcriptome. Responses to loss of sh2 function include increased expression of sugar (SWEET) transporters and of genes for ABA signaling. Key regulators of starch biosynthesis and grain filling were identified. Notably, this includes Class II trehalose 6-phosphate synthases, Hexokinase1, and Apetala2 transcription factor-like (AP2/ERF) transcription factors. Additionally, our results provide insight into the mechanism of Sugary enhancer1, suggesting a potential role in regulating GA signaling via GRAS transcription factor Scarecrow-like1.

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.

Bacterial effectors mimicking ubiquitin-proteasome pathway tweak plant immunity

Plant pathogenic Gram-negative bacteria evade the host plant immune system by secreting Type III (T3E) and Type IV effector (T4E) proteins into the plant cytoplasm. Mostly T3Es are secreted into the plant cells to establish pathogenicity by affecting the vital plant process viz. metabolic pathways, signal transduction and hormonal regulation. Ubiquitin-26S proteasome system (UPS) exists as one of the important pathways in plants to control plant immunity and various cellular processes by employing several enzymes and enzyme components. Pathogenic and non-pathogenic bacteria are found to secrete effectors into plants with structural and/or functional similarity to UPS pathway components like ubiquitin E3 ligases, F-box domains, cysteine proteases, inhibitor of host UPS or its components, etc. The bacterial effectors mimic UPS components and target plant resistance proteins for degradation by proteasomes, thereby taking control over the host cellular activities as a strategy to exert virulence. Thus, the bacterial effectors circumvent plant cellular pathways leading to infection and disease development. This review highlights known bacterial T3E and T4E proteins that function and interfere with the ubiquitination pathway to regulate the immune system of plants.

Repression of barley cathepsins, HvPap-19 and HvPap-1, differentially alters grain composition and delays germination

During barley germination, cysteine proteases are essential in the mobilization of storage compounds providing peptides and amino acids to sustain embryo growth until photosynthesis is completely established. Knockdown barley plants, generated by artificial miRNA, for the cathepsins B- and F-like HvPap-19 and HvPap-1 genes, respectively, showed less cysteine protease activities and consequently lower protein degradation. The functional redundancy between proteases triggered an enzymatic compensation associated with an increase in serine protease activities in both knockdown lines, which was not sufficient to maintain germination rates and behaviour. Concomitantly, these transgenic lines showed alterations in the accumulation of protein and carbohydrates in the grain. While the total amount of protein increased in both transgenic lines, the starch content decreased in HvPap-1 knockdown lines and the sucrose concentration was reduced in silenced HvPap-19 grains. Consequently, phenotypes of HvPap-1 and HvPap-19 artificial miRNA lines showed a delay in the grain germination process. These data demonstrate the potential of exploring the properties of barley proteases for selective modification and use in brewing or in the livestock feeding industry.

Genome-wide identification and evolution of HECT genes in wheat

Background

As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops.

Methods

Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana.

Results

The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

Stalk architecture, cell wall composition, and QTL underlying high stalk flexibility for improved lodging resistance in maize

BACKGROUND

Stalk fracture caused by strong wind can severely reduce yields in maize. Stalks with higher stiffness and flexibility will exhibit stronger lodging resistance. However, stalk flexibility is rarely studied in maize. Stalk fracture of the internode above the ear before tasseling will result in the lack of tassel and pollen, which is devastating for pollination in seed production. In this study, we focused on stalk lodging before tasseling in two maize inbred lines, JING724 and its improved line JING724A1 and their F_2:3 population.

RESULTS

JING724A1 showed a larger stalk fracture angle than JING724, indicating higher flexibility. In addition, compared to JING724, JING724A1 also had longer and thicker stalks, with a conical, frustum-shaped internode above the ear. Microscopy and X-ray microcomputed tomography of the internal stalk architecture revealed that JING724A1 had more vascular bundles and thicker sclerenchyma tissue. Furthermore, total soluble sugar content of JING724A1, especially the glucose component, was substantially higher than in JING724. Using an F_2:3 population derived from a JING724 and JING724A1 cross, we performed bulk segregant analysis for stalk fracture angle and detected one QTL located on Chr3: 14.00-19.28 Mb. Through transcriptome data analysis and ∆ (SNP-index), we identified two candidate genes significantly associated with high stalk fracture angle, which encode a RING/U-box superfamily protein (Zm00001d039769) and a MADS-box transcription factor 54 (Zm00001d039913), respectively. Two KASP markers designed from these two candidate genes also showed significant correlations with stalk fracture angle.

CONCLUSIONS

The internode shape and glucose content are possibly correlated with stalk flexibility in maize. Two genes in the detected QTL are potentially associated with stalk fracture angle. These novel phenotypes and associated loci will provide a theoretical foundation for understanding the genetic mechanisms of lodging, and facilitate the selection of maize varieties with improved flexibility and robust lodging resistance.

The Ubiquitin-Specific Protease TNI/UBP14 Functions in Ubiquitin Recycling and Affects Auxin Response

The ubiquitin-mediated proteasomal pathway regulates diverse cellular processes in plants by rapidly degrading target proteins, including the repressors of hormone signaling. Though ubiquitin proteases play a key role in this process by cleaving polyubiquitin chains to monomers, their function has not been studied in detail by mutational analysis. Here, we show that mutation in TARANI/UBIQUITIN-SPECIFIC PROTEASE14 (TNI/UBP14) leads to reduced auxin response and widespread auxin-related phenotypic defects in Arabidopsis (Arabidopsis thaliana). In a tni partial loss-of-function mutant that was originally isolated based on altered leaf shape, activity of the auxin-responsive reporters DR5::GUS, DR5::nYFP, and IAA2::GUS was reduced. Genetic interaction studies suggest that TNI is involved in auxin signaling and acts alongside TIR1, ARF7, and AUX1 Map-based cloning identified TNI as UBP14 Inefficient splicing of the mutant TNI transcript resulted in the formation of an inactive UBP14 protein, which led to accumulation of polyubiquitin chains and excess polyubiquitinated proteins in the mutant. In addition to the reduced auxin response, increased levels of DII:VENUS, IAA18:GUS, and HS::AXR3-NT:GUS were also observed in tni, perhaps due to inefficient polyubiquitin hydrolysis and proteasome-mediated degradation. Together, our study identifies a function for TNI/UBP14 in the auxin response through ubiquitin recycling.

Associations between phytohormones and cellulose biosynthesis in land plants

BACKGROUND

Phytohormones are small molecules that regulate virtually every aspect of plant growth and development, from basic cellular processes, such as cell expansion and division, to whole plant environmental responses. While the phytohormone levels and distribution thus tell the plant how to adjust itself, the corresponding growth alterations are actuated by cell wall modification/synthesis and internal turgor. Plant cell walls are complex polysaccharide-rich extracellular matrixes that surround all plant cells. Among the cell wall components, cellulose is typically the major polysaccharide, and is the load-bearing structure of the walls. Hence, the cell wall distribution of cellulose, which is synthesized by large Cellulose Synthase protein complexes at the cell surface, directs plant growth.

SCOPE

Here, we review the relationships between key phytohormone classes and cellulose deposition in plant systems. We present the core signalling pathways associated with each phytohormone and discuss the current understanding of how these signalling pathways impact cellulose biosynthesis with a particular focus on transcriptional and post-translational regulation. Because cortical microtubules underlying the plasma membrane significantly impact the trajectories of Cellulose Synthase Complexes, we also discuss the current understanding of how phytohormone signalling impacts the cortical microtubule array.

CONCLUSION

Given the importance of cellulose deposition and phytohormone signalling in plant growth and development, one would expect that there is substantial cross-talk between these processes; however, mechanisms for many of these relationships remain unclear and should be considered as the target of future studies.

Wheat RING E3 ubiquitin ligase TaDIS1 degrade TaSTP via the 26S proteasome pathway

Drought stress has a great impact on wheat yields. The ubiquitin/26S proteasome system is one of the most important mechanisms employed by plants for responding to stress. E3 ubiquitin ligase is an important part of the ubiquitin/26S proteasome system. In wheat, the mechanism of E3 ubiquitin ligase TaDIS1 has not been investigated in great detail. In this study, TaSTP was identified as an interacting partner using yeast two-hybrid screening. The results obtained from bimolecular fluorescence complementation, pull-down, and co-immunoprecipitation assays also demonstrated that TaDIS1 interacts with TaSTP. In vitro ubiquitination assays showed that TaDIS1 has an E3 ubiquitin ligase activity and the results based on two TaDIS1 mutants suggested that the RING domain is essential for its E3 ubiquitin ligase activity. In addition, we used MG132 to show that TaSTP can be degraded by TaDIS1 via the 26S proteasome pathway. The transcript levels of TaSTP showed that it can also respond to different abiotic stresses, such as drought, salt, and abscisic acid treatment. RING E3 ubiquitin ligase TaDIS1 may through the posttranslational regulation of TaSTP to play an important role in drought tolerance.

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

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

UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2

Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. In Arabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive growth regulators. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression of UBP12 or UBP13 strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in which UBP12 and UBP13 were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.

The Ubiquitin-Binding Protein OsDSK2a Mediates Seedling Growth and Salt Responses by Regulating Gibberellin Metabolism in Rice

UBL-UBA (ubiquitin-like-ubiquitin-associated) proteins are ubiquitin receptors and transporters in the ubiquitin-proteasome system that play key roles in plant growth and development. High salinity restricts plant growth by disrupting cellular metabolism, but whether UBL-UBA proteins are involved in this process is unclear. Here, we demonstrate that the UBL-UBA protein OsDSK2a (DOMINANT SUPPRESSOR of KAR2) mediates seedling growth and salt responses in rice (Oryza sativa). Through analysis of osdsk2a, a mutant with retarded seedling growth, as well as in vitro and in vivo assays, we demonstrate that OsDSK2a combines with polyubiquitin chains and interacts with the gibberellin (GA)-deactivating enzyme ELONGATED UPPERMOST INTERNODE (EUI), resulting in its degradation through the ubiquitin-proteasome system. Bioactive GA levels were reduced, and plant growth was retarded in the osdsk2a mutant. By contrast, eui mutants displayed increased seedling growth and bioactive GA levels. OsDSK2a levels decreased in plants under salt stress. Moreover, EUI accumulated under salt stress more rapidly in osdsk2a than in wild-type plants. Thus, OsDSK2a and EUI play opposite roles in regulating plant growth under salt stress by affecting GA metabolism. Under salt stress, OsDSK2a levels decrease, thereby increasing EUI accumulation, which promotes GA metabolism and reduces plant growth.

CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants

CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.

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

Background

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

Results

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

Conclusions

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

Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency

Nitrogen deficiency (-N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1. Little is known about post-translational regulation of ORE1 in this process. Here, we show that UBP12/UBP13 (ubiquitin-specific protease 12/13) antagonize the action of NLA (nitrogen limitation adaptation) E3 ligase to maintain ORE1 homeostasis. In vitro pull-down and in vivo co-immunoprecipitation assays demonstrated specific binding between UBP12/UBP13 and ORE1. We further analyzed in various genotypes total Chl content and expression levels of senescence-related genes under -N conditions. We found that UBP12/UBP13 can deubiquitinate polyubiquitinated ORE1 in vitro and increase the stability of ORE1 in vivo in MG132/cycloheximide-chase experiments. Plants overexpressing UBP12/UBP13 display accelerated leaf senescence which is reversed by the ore1 mutation. By contrast, the senescence phenotype of plants overexpressing ORE1 is exacerbated by UBP12/UBP13 overexpression. The expression of senescence-related genes tracks the senescence phenotype. ORE1 protein levels can be elevated by UBP12/UBP13 overexpression but decreased in ubp12-2w/13-3. In conclusion, UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under -N conditions. Our study shows that UBP12/UBP13 counteracts the effect of NLA E3 ligase to accelerate leaf senescence under nitrogen starvation.

Comprehensive transcriptome profiling and phenotyping of rootstock and scion in a tomato/potato heterografting system

Tomato/potato heterografting-triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting-induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self-grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St-R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA₃ content of stolon and tuber, compared with self-grafted potato (St-WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA-Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St-WT and St-R; some of these genes are involved in plant hormone signal transduction, with GID1-like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA-based interactions between rootstocks and scions after tomato/potato heterografting.

The Scope, Functions, and Dynamics of Posttranslational Protein Modifications

Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.

Protein Language: Post-Translational Modifications Talking to Each Other

Post-translational modifications (PTMs) are at the heart of many cellular signaling events. Apart from a single regulatory PTM, there are also PTMs that function in orchestrated manners. Such PTM crosstalk usually serves as a fine-tuning mechanism to adjust cellular responses to the slightest changes in the environment. While PTM crosstalk has been studied in depth in various species; in plants, this field is just emerging. In this review, we discuss recent studies on crosstalk between three of the most common protein PTMs in plant cells, being phosphorylation, ubiquitination, and sumoylation, and we highlight the diverse underlying mechanisms as well as signaling outputs of such crosstalk.

Revisiting the Role of Ethylene and N-End Rule Pathway on Chilling-Induced Dormancy Release in Arabidopsis Seeds

Dormant Arabidopsis (Arabidopsis thaliana) seeds do not germinate easily at temperatures higher than 10–15 °C. Using mutants affected in ethylene signaling (etr1, ein2 and ein4) and in the N-end-rule pathway of the proteolysis (prt6 and ate1-ate2) we have investigated the effects of cold and ethylene on dormancy alleviation. Ethylene (10–100 ppm) and 2–4 days chilling (4 °C) strongly stimulate the germination of wild type (Col-0) seeds at 25 °C. Two to four days of chilling promote the germination at 25 °C of all the mutants suggesting that release of dormancy by cold did not require ethylene and did not require the N-end-rule pathway. One mutant (etr1) that did not respond to ethylene did not respond to GA₃ either. Mutants affected in the N-end rule (prt6 and ate1-ate2) did not respond to ethylene indicating that also this pathway is required for dormancy alleviation by ethylene; they germinated after chilling and in the presence of GA₃. Cold can activate the ethylene signaling pathway since it induced an accumulation of ETR1, EINI4, and EIN2 transcripts, the expression of which was not affected by ethylene and GA₃. Both cold followed by 10 h at 25 °C and ethylene downregulated the expression of PRT6, ATE1, ATE2, and of ABI5 involved in ABA signaling as compared to dormant seeds incubated at 25 °C. In opposite, the expression of RGA, GAI, and RGL2 encoding three DELLAs was induced at 4 °C but downregulated in the presence of ethylene.

Positive and negative regulation of seed germination by the Arabidopsis GA hormone receptors, GID1a, b, and c

Epistasis analysis of gid1 single and double mutants revealed that GID1c is a key positive regulator of seed germination, whereas the GID1b receptor can negatively regulate germination in dormant seeds and in the dark. The GID1 GA receptors were expected to positively regulate germination because the plant hormone gibberellin (GA) is required for seed germination in Arabidopsis thaliana. The three GA hormone receptors, GID1a, GID1b, and GID1c, positively regulate GA responses via GA/GID1-stimulated destruction of DELLA (Asp-Glu-Leu-Leu-Ala) repressors of GA responses. The fact that the gid1abc triple mutant but not gid1 double mutants fail to germinate indicates that all three GA receptors can positively regulate non-dormant seed germination in the light. It was known that the gid1abc triple mutant fails to lose dormancy through the dormancy breaking treatments of cold stratification (moist chilling of seeds) and dry after-ripening (a period of dry storage). Previous work suggested that there may be some specialization of GID1 gene function during germination because GID1b mRNA expression was more highly induced by after-ripening, whereas GID1a and GID1c mRNA levels were more highly induced by cold stratification. In light-germinated dormant seeds, the gid1b mutation can partly rescue the germination efficiency of gid1a but not of gid1c seeds. Thus, GID1b can function as an upstream negative regulator GID1c, a positive regulator of dormant seed germination. Further experiments showed that GID1b can negatively regulate dark germination. Wild-type Arabidopsis seeds do not germinate well in the dark. The gid1b and gid1ab double mutants germinated much more efficiently than wild type, gid1c, or gid1ac mutants in the dark. The observation that the gid1ab double mutant also shows increased dark germination suggests that GID1b, and to some extent GID1a, can act as upstream negative regulators of GID1c. Since the gid1abc triple mutant failed to germinate in the dark, it appears that GID1c is a key downstream positive regulator of dark germination. This genetic analysis indicates that the three GID1 receptors have partially specialized functions in GA signaling.

Over-expression of SINAL7 increases biomass and drought tolerance, and also delays senescence in Arabidopsis

The seven in absentia like 7 gene (At5g37890, SINAL7) from Arabidopsis thaliana encodes a RING finger protein belonging to the SINA superfamily that possesses E3 ubiquitin-ligase activity. SINAL7 has the ability to self-ubiquitinate and to mono-ubiquitinate glyceraldehyde-3-P dehydrogenase 1 (GAPC1), suggesting a role for both proteins in a hypothetical signaling pathway in Arabidopsis. In this study, the in vivo effects of SINAL7 on plant physiology were examined by over-expressing SINAL7 in transgenic Arabidopsis plants. Phenotypic and gene expression analyses suggest the involvement of SINAL7 in the regulation of several vegetative parameters, essentially those that affect the aerial parts of the plants. Over-expression of SINAL7 resulted in an increase in the concentrations of hexoses and sucrose, with a concommitant increase in plant biomass, particularly in the number of rosette leaves and stem thickness. Interestingly, using the CAB1 (chlorophyll ab binding protein 1) gene as a marker revealed a delay in the onset of senescence. Transgenic plants also displayed a remarkable level of drought resistance, indicating the complexity of the response to SINAL7 over-expression.

Arabidopsis Aspartic Protease ASPG1 Affects Seed Dormancy, Seed Longevity and Seed Germination

Seed storage proteins (SSPs) provide free amino acids and energy for the process of seed germination. Although degradation of SSPs by the aspartic proteases isolated from seeds has been documented in vitro, there is still no genetic evidence for involvement of aspartic proteases in seed germination. Here we report that the aspartic protease ASPG1 (ASPARTIC PROTEASE IN GUARD CELL 1) plays an important role in the process of dormancy, viability and germination of Arabidopsis seeds. We show that aspg1-1 mutants have enhanced seed dormancy and reduced seed viability. A significant increase in expression of DELLA genes which act as repressors in the gibberellic acid signal transduction pathway were detected in aspg1-1 during seed germination. Seed germination of aspg1-1 mutants was more sensitive to treatment with paclobutrazol (PAC; a gibberellic acid biosynthesis inhibitor). In contrast, seed germination of ASPG1 overexpression (OE) transgenic lines showed resistant to PAC. The degradation of SSPs in germinating seeds was severely impaired in aspg1-1 mutants. Moreover, the development of aspg1-1 young seedlings was arrested when grown on the nutrient-free medium. Thus ASPG1 is important for seed dormancy, seed longevity and seed germination, and its function is associated with degradation of SSPs and regulation of gibberellic acid signaling in Arabidopsis.

Differential expression of gibberellin- and abscisic acid-related genes implies their roles in the bud activity-dormancy transition of tea plants

Thirty genes involved in GA and ABA metabolism and signalling were identified, and the expression profiles indicated that they play crucial roles in the bud activity-dormancy transition in tea plants. Gibberellin (GA) and abscisic acid (ABA) are fundamental phytohormones that extensively regulate plant growth and development, especially bud dormancy and sprouting transition in perennial plants. However, there is little information on GA- and ABA-related genes and their expression profiles during the activity-dormancy transition in tea plants. In the present study, 30 genes involved in the metabolism and signalling pathways of GA and ABA were first identified, and their expression patterns in different tissues were assessed. Further evaluation of the expression patterns of selected genes in response to GA₃ and ABA application showed that CsGA3ox, CsGA20ox, CsGA2ox, CsZEP and CsNCED transcripts were differentially expressed after exogenous treatment. The expression profiles of the studied genes during winter dormancy and spring sprouting were investigated, and somewhat diverse expression patterns were found for GA- and ABA-related genes. This diversity was associated with the bud activity-dormancy cycle of tea plants. These results indicate that the genes involved in the metabolism and signalling of GA and ABA are important for regulating the bud activity-dormancy transition in tea plants.

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.

Regulation of the stability of RGF1 receptor by the ubiquitin-specific proteases UBP12/UBP13 is critical for root meristem maintenance

ROOT MERISTEM GROWTH FACTOR (RGF) 1 is an important peptide hormone that regulates root growth. Upon binding to its receptor, RGFR1, RGF1 regulates the expression of two transcription factors, PLETHORA 1 and 2 (PLT1/2), to influence root meristem development. Here, we show that the ubiquitin-specific proteases UBP12 and UBP13 are positive regulators of root meristem development and that UBP13 interacts directly with RGF1 receptor (RGFR1) and its close homolog RGFR2. The ubp12,13 double-mutant root is completely insensitive to exogenous applied RGF1. Consistent with this result, RGF1-induced ubiquitination and turnover of RGFR1 protein were accelerated in ubp12,13-mutant plants but were delayed in transgenic plants overexpressing UBP13 Genetic analysis showed that PLT2 or RGFR1 overexpression partially rescued the short-root phenotype and the reduced cortical root meristem cell number in ubp12,13 plants. Together, our results demonstrate that UBP12/13 are regulators of the RGF1-RGFR1-PLT1/2 signaling pathway and that UBP12/13 can counteract RGF1-induced RGFR1 ubiquitination, stabilize RGFR1, and maintain root cell sensitivity to RGF1.

Molecular networks orchestrating plant cell growth

Plant cell growth can broadly be categorized into either diffuse or tip growth. Here we compare gene regulatory networks (GRNs) controlling growth of hypocotyls and root hairs as examples for diffuse and tip growth, respectively. Accumulating evidence shows that GRNs in both cell types are multi-layered in structure and fine-tuned by transcriptional and post-translational mechanisms. We discuss how these GRNs regulate the expression of proteins controlling cell wall remodeling or other growth regulatory processes. Finally, we highlight how specific regulators within GRNs adjust plant cell growth in response to variable environmental conditions.

UBC18 mediates ERF1 degradation under light-dark cycles

Ethylene Response Factor 1 (ERF1) plays a crucial role in biotic and abiotic stress responses. Previous studies have shown that ERF1 regulates stress-responsive gene expression by binding to different cis-acting elements in response to various stress signals. ERF1 was also reported to be unstable in the dark, and it regulates hypocotyl elongation. Here, we elucidated the mechanism underlying degradation of ERF1. Yeast two-hybrid screening showed that UBIQUITIN-CONJUGATING ENZYME 18 (UBC18) interacted with ERF1. The interaction between ERF1 and UBC18 was verified using pull-down assays and coimmunoprecipitation analyses. We then compared the ERF1 protein abundance in the UBC18 mutant and overexpression plants. Based on the results of protein degradation and in vivo ubiquitination assays, we proposed that UBC18 mediates ERF1 ubiquitination and degradation. ERF1 was more stable in UBC18 mutants and less stable in UBC18 overexpression lines compared with that in wild-type plants. ERF1 was degraded by the 26S proteasome system via regulation of UBC18 and promotes dark-repression of downstream genes and proline accumulation. UBC18 negatively regulated drought and salt stress responses by altering the abundance of ERF1 and the expression of genes downstream of ERF1.

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.

Cellular Recycling of Proteins in Seed Dormancy Alleviation and Germination

Each step of the seed-to-seed cycle of plant development including seed germination is characterized by a specific set of proteins. The continual renewal and/or replacement of these biomolecules are crucial for optimal plant adaptation. As proteins are the main effectors inside the cells, their levels need to be tightly regulated. This is partially achieved by specific proteolytic pathways via multicatalytic protease complexes defined as 20S and 26S proteasomes. In plants, the 20S proteasome is responsible for degradation of carbonylated proteins, while the 26S being a part of ubiquitin-proteasome pathway is known to be involved in proteolysis of phytohormone signaling regulators. On the other hand, the role of translational control of plant development is also well-documented, especially in the context of pollen tube growth and light signaling. Despite the current progress that has been made in seed biology, the sequence of cellular events that determine if the seed can germinate or not are still far from complete understanding. The role and mechanisms of regulation of proteome composition during processes occurring in the plant's photosynthetic tissues have been well-characterized since many years, but in non-photosynthetic seeds it has emerged as a tempting research task only since the last decade. This review discusses the recent discoveries providing insights into the role of protein turnover in seed dormancy alleviation, and germination, with a focus on the control of translation and proteasomal proteolysis. The presented novel data of translatome profiling in seeds highlighted that post-transcriptional regulation of germination results from a timely regulated initiation of translation. In addition, the importance of 26S proteasome in the degradation of regulatory elements of cellular signaling and that of the 20S complex in proteolysis of specific carbonylated proteins in hormonal- and light-dependent processes occurring in seeds is discussed. Based on the current knowledge the model of cellular recycling of proteins in germinating seeds is also proposed.

Strigolactone versus gibberellin signaling: reemerging concepts?

MAIN CONCLUSION

In this review, we compare knowledge about the recently discovered strigolactone signaling pathway and the well established gibberellin signaling pathway to identify gaps of knowledge and putative research directions in strigolactone biology. Communication between and inside cells is integral for the vitality of living organisms. Hormonal signaling cascades form a large part of this communication and an understanding of both their complexity and interactive nature is only beginning to emerge. In plants, the strigolactone (SL) signaling pathway is the most recent addition to the classically acting group of hormones and, although fundamental insights have been made, knowledge about the nature and impact of SL signaling is still cursory. This narrow understanding is in spite of the fact that SLs influence a specific spectrum of processes, which includes shoot branching and root system architecture in response, partly, to environmental stimuli. This makes these hormones ideal tools for understanding the coordination of plant growth processes, mechanisms of long-distance communication and developmental plasticity. Here, we summarize current knowledge about SL signaling and employ the well-characterized gibberellin (GA) signaling pathway as a scaffold to highlight emerging features as well as gaps in our knowledge in this context. GA signaling is particularly suitable for this comparison because both signaling cascades share key features of hormone perception and of immediate downstream events. Therefore, our comparative view demonstrates the possible level of complexity and regulatory interfaces of SL signaling.

Bacillus cereus AR156 primes induced systemic resistance by suppressing miR825/825* and activating defense-related genes in Arabidopsis

Small RNAs play an important role in plant immune responses. However, their regulatory function in induced systemic resistance (ISR) is nascent. Bacillus cereus AR156 is a plant growth-promoting rhizobacterium that induces ISR in Arabidopsis against bacterial infection. Here, by comparing small RNA profiles of Pseudomonas syringae pv. tomato (Pst) DC3000-infected Arabidopsis with and without AR156 pretreatment, we identified a group of Arabidopsis microRNAs (miRNAs) that are differentially regulated by AR156 pretreatment. miR825 and miR825* are two miRNA generated from a single miRNA gene. Northern blot analysis indicated that they were significantly downregulated in Pst DC3000-infected plants pretreated with AR156, in contrast to the plants without AR156 pretreatment. miR825 targets two ubiquitin-protein ligases, while miR825* targets toll-interleukin-like receptor (TIR)-nucleotide binding site (NBS) and leucine-rich repeat (LRR) type resistance (R) genes. The expression of these target genes negatively correlated with the expression of miR825 and miR825*. Moreover, transgenic plants showing reduced expression of miR825 and miR825* displayed enhanced resistance to Pst DC3000 infection, whereas transgenic plants overexpressing miR825 and miR825* were more susceptible. Taken together, our data indicates that Bacillus cereus AR156 pretreatment primes ISR to Pst infection by suppressing miR825 and miR825* and activating the defense related genes they targeted.

Silicon Mitigates Salinity Stress by Regulating the Physiology, Antioxidant Enzyme Activities, and Protein Expression in Capsicum annuum 'Bugwang'

Silicon- (Si-) induced salinity stress resistance was demonstrated at physiological and proteomic levels in Capsicum annuum for the first time. Seedlings of C. annuum were hydroponically treated with NaCl (50 mM) with or without Si (1.8 mM) for 15 days. The results illustrated that saline conditions significantly reduced plant growth and biomass and photosynthetic parameters and increased the electrolyte leakage potential, lipid peroxidation, and hydrogen peroxide level. However, supplementation of Si allowed the plants to recover from salinity stress by improving their physiology and photosynthesis. During salinity stress, Si prevented oxidative damage by increasing the activities of antioxidant enzymes. Furthermore, Si supplementation recovered the nutrient imbalance that had occurred during salinity stress. Additionally, proteomic analysis by two-dimensional gel electrophoresis (2DE) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) revealed that Si treatment upregulated the accumulation of proteins involved in several metabolic processes, particularly those associated with nucleotide binding and transferase activity. Moreover, Si modulated the expression of vital proteins involved in ubiquitin-mediated nucleosome pathway and carbohydrate metabolism. Overall, the results illustrate that Si application induced resistance against salinity stress in C. annuum by regulating the physiology, antioxidant metabolism, and protein expression.