Nitrate Reductases Are Relocalized to the Nucleus by AtSIZ1 and Their Levels Are Negatively Regulated by COP1 and Ammonium

Highly sensitive site-specific SUMOylation proteomics in Arabidopsis

SUMOylation-the attachment of a small ubiquitin-like modifier (SUMO) to target proteins-plays roles in controlling plant growth, nutrient signalling and stress responses. SUMOylation studies in plants are scarce because identifying SUMOylated proteins and their sites is challenging. To date, only around 80 SUMOylation sites have been identified. Here we introduce lysine-null SUMO1 into the Arabidopsis sumo1 sumo2 mutant and establish a two-step lysine-null SUMO enrichment method. We identified a site-specific SUMOylome comprising over 2,200 SUMOylation sites from 1,300 putative acceptors that function in numerous nuclear processes. SUMOylation marks occur on several motifs, differing from the canonical ψKxE motif in distant eukaryotes. Quantitative comparisons demonstrate that SUMOylation predominantly enhances the stability of SUMO1 acceptors. Our study delivers a highly sensitive and efficient method for site-specific SUMOylome studies and provides a comprehensive catalogue of Arabidopsis SUMOylation, serving as a valuable resource with which to further explore how SUMOylation regulates protein function.

PYRIDOX(AM)INE 5'-PHOSPHATE OXIDASE3 of Arabidopsis thaliana maintains carbon/nitrogen balance in distinct environmental conditions

The identification of factors that regulate C/N utilization in plants can make a substantial contribution to optimization of plant health. Here, we explored the contribution of pyridox(am)ine 5'-phosphate oxidase3 (PDX3), which regulates vitamin B6 homeostasis, in Arabidopsis (Arabidopsis thaliana). Firstly, N fertilization regimes showed that ammonium application rescues the leaf morphological phenotype of pdx3 mutant lines but masks the metabolite perturbance resulting from impairment in utilizing soil nitrate as a source of N. Without fertilization, pdx3 lines suffered a C/N imbalance and accumulated nitrogenous compounds. Surprisingly, exploration of photorespiration as a source of endogenous N driving this metabolic imbalance, by incubation under high CO2, further exacerbated the pdx3 growth phenotype. Interestingly, the amino acid serine, critical for growth and N management, alleviated the growth phenotype of pdx3 plants under high CO2, likely due to the requirement of pyridoxal 5'-phosphate for the phosphorylated pathway of serine biosynthesis under this condition. Triggering of thermomorphogenesis by growth of plants at 28 °C (instead of 22 °C) did not appear to require PDX3 function, and we observed that the consequent drive toward C metabolism counters the C/N imbalance in pdx3. Further, pdx3 lines suffered a salicylic acid-induced defense response, probing of which unraveled that it is a protective strategy mediated by nonexpressor of pathogenesis related1 (NPR1) and improves fitness. Overall, the study demonstrates the importance of vitamin B6 homeostasis as managed by the salvage pathway enzyme PDX3 to growth in diverse environments with varying nutrient availability and insight into how plants reprogram their metabolism under such conditions.

Current perspectives of ubiquitination and SUMOylation in abiotic stress tolerance in plants

Post-translational modification (PTM) is a critical and rapid mechanism to regulate all the major cellular processes through the modification of diverse protein substrates. Substrate-specific covalent attachment of ubiquitin and Small Ubiquitin-Like Modifier (SUMO) with the target proteins, known as ubiquitination and SUMOylation, respectively, are crucial PTMs that regulate almost every process in the cell by modulating the stability and fidelity of the proteins. Ubiquitination and SUMOylation play a very significant role to provide tolerance to the plants in adverse environmental conditions by activating/deactivating the pre-existing proteins to a great extent. We reviewed the importance of ubiquitination and SUMOylation in plants, implicating its prospects in various abiotic stress regulations. An exhaustive study of molecular mechanisms of ubiquitination and SUMOylation of plant proteins and their role will contribute to the understanding of physiology underlying mitigation of the abiotic stresses and survival in plants. It will be helpful to strategize the improvement of crops for abiotic stress tolerance.

The SUMO E3 Ligase MdSIZ1 Sumoylates a Cell Number Regulator MdCNR8 to Control Organ Size

Plant growth and organ size putatively associated with crop yield are regulated by a complex network of genes including ones for controlling cell proliferation. The gene fw2.2 was first identified in tomatoes and reported to govern fruit size variation through controlling cell division. In this study, we isolated a putative ortholog of the tomato fw2.2 gene from apple, Cell Number Regulator 8 (MdCNR8). Our functional analysis showed that MdCNR8 may control fruit size and root growth. MdCNR8 was mediated by the SUMO E3 ligase MdSIZ1, and SUMOylation of MdCNR8 at residue-Lys39 promoted the translocation of MdCNR8 from plasma membrane to the nucleus. The effect of MdCNR8 in inhibiting root elongation could be completely counteracted by the coexpression of MdSIZ1. Moreover, the lower cell proliferation of apple calli due to silencing MdSIZ1 could be rescued by silencing MdCNR8. Collectively, our results showed that the MdSIZ1-mediated SUMOylation is required for the fulfillment of MdCNR8 in regulating cell proliferation to control plant organ size. This regulatory interaction between MdSIZ1 and MdCNR8 will facilitate understanding the mechanism underlying the regulation of organ size.

The Regulation of Nitrate Reductases in Response to Abiotic Stress in Arabidopsis

The two homologous genes, NIA1 and NIA2, encode nitrate reductases in Arabidopsis, which govern the reduction of nitrate to nitrite. This step is the rate-limiting step of the nitrate assimilation and utilization. Therefore, the regulation of NIA1 and NIA2 is important for plant development and growth. Although they are similar in sequence and structure, their regulations are different. Genetic analysis uncovers that NIA1, rather than NIA2, plays a predominant role in adopting to ABA stress. Although both long-term stress conditions can cause an improvement in NIA1 levels, a decrease in NIA1 levels under short-term treatments seems to be necessary for plants to switch from the growth status into the adopting status. Interestingly, the downregulation of the NR is distinct under different stress conditions. Under ABA treatment, the NR proteins are degraded via a 26S-proteasome dependent manner, while the transcriptional regulation is the main manner to rapidly reduce the NIA1 levels under nitrogen deficiency and NaCl stress conditions. These results indicate that under stress conditions, the regulation of NIA1 is complex, and it plays a key role in regulating the balance between growth and adaptation.

Protein Tyrosine Nitration in Plant Nitric Oxide Signaling

Nitric oxide (NO), which is ubiquitously present in living organisms, regulates many developmental and stress-activated processes in plants. Regulatory effects exerted by NO lies mostly in its chemical reactivity as a free radical. Proteins are main targets of NO action as several amino acids can undergo NO-related post-translational modifications (PTMs) that include mainly S-nitrosylation of cysteine, and nitration of tyrosine and tryptophan. This review is focused on the role of protein tyrosine nitration on NO signaling, making emphasis on the production of NO and peroxynitrite, which is the main physiological nitrating agent; the main metabolic and signaling pathways targeted by protein nitration; and the past, present, and future of methodological and strategic approaches to study this PTM. Available information on identification of nitrated plant proteins, the corresponding nitration sites, and the functional effects on the modified proteins will be summarized. However, due to the low proportion of in vivo nitrated peptides and their inherent instability, the identification of nitration sites by proteomic analyses is a difficult task. Artificial nitration procedures are likely not the best strategy for nitration site identification due to the lack of specificity. An alternative to get artificial site-specific nitration comes from the application of genetic code expansion technologies based on the use of orthogonal aminoacyl-tRNA synthetase/tRNA pairs engineered for specific noncanonical amino acids. This strategy permits the programmable site-specific installation of genetically encoded 3-nitrotyrosine sites in proteins expressed in Escherichia coli, thus allowing the study of the effects of specific site nitration on protein structure and function.

NIN-like protein7 and PROTEOLYSIS6 functional interaction enhances tolerance to sucrose, ABA, and submergence

Nitrate (NO3) assimilation and signaling regulate plant growth through the relevant function of the transcription factor NIN-like Protein7 (NLP7). NO3 is also the main source for plants to produce nitric oxide (NO), which regulates growth and stress responses. NO-mediated regulation requires efficient sensing via the PROTEOLYSIS6 (PRT6)-mediated proteasome-triggered degradation of group VII of ethylene response transcription factors through the Cys/Arg N-degron pathway. The convergence of NO3 signaling and N-degron proteolysis on NO-mediated regulation remains largely unknown. Here, we investigated the functional interaction between NLP7 and PRT6 using Arabidopsis (Arabidopsis thaliana) double prt6 nlp7 mutant plants as well as complementation lines overexpressing NLP7 in different mutant genetic backgrounds. prt6 nlp7 mutant plants displayed several potentiated prt6 characteristic phenotypes, including slower vegetative growth, increased NO content, and diminished tolerance to abiotic stresses such as high-sucrose concentration, abscisic acid, and hypoxia-reoxygenation. Although NLP7 has an N-terminus that could be targeted by the N-degron proteolytic pathway, it was not a PRT6 substrate. The potential PRT6- and NO-regulated nucleocytoplasmic translocation of NLP7, which is likely modulated by posttranslational modifications, is proposed to act as a regulatory loop to control NO homeostasis and action.

Phytosulfokine α (PSKα) delays senescence and reinforces SUMO1/SUMO E3 ligase SIZ1 signaling pathway in cut rose flowers (Rosa hybrida cv. Angelina)

Roses are widely used as cut flowers worldwide. Petal senescence confines the decorative quality of cut rose flowers, an impressively considerable economic loss. Herein, we investigated the SUMO1/SUMO E3 ligase SIZ1 signaling pathway during bud opening, and petal senescence of cut rose flowers. Our results exhibited that the higher expression of SUMO1 and SUMO E3 ligase SIZ1 during bud opening was accompanied by lower endogenous H2O2 accumulation arising from higher expression and activities of SOD, CAT, APX, and GR, promoting proline accumulation by increasing P5CS expression and activity and enhancing GABA accumulation by increasing GAD expression and activity. In harvested flowers, lower expressions of SUMO1 and SUMO E3 ligase SIZ1 during petal senescence were associated with higher endogenous H2O2 accumulation due to lower expression and activities of SOD, CAT, APX, and GR. Therefore, promoting the activity of the GABA shunt pathway as realized by higher expression and activities of GABA-T and SSADH accompanied by increasing OAT expression and activity for sufficiently supply proline in rose flowers during petal senescence might serve as an endogenous antisenescence mechanism for slowing down petals senescence by avoiding endogenous H2O2 accumulation. Following phytosulfokine α (PSKα) application, postponing petal senescence in cut rose flowers could be ascribed to higher expression of SUMO1 and SUMO E3 ligase SIZ1 accompanied by higher expression and activities of SOD, CAT, APX, and GR, higher activity of GABA shunt pathway as realized by higher expression and activities of GAD, GABA-T, and SSADH, higher expression and activities of P5CS and OAT for supplying proline and higher expression of HSP70 and HSP90. Therefore, our results highlight the potential of the PSKα as a promising antisenescence signaling peptide in the floriculture industry for postponing senescence and extending the vase life of cut rose flowers.

Ammonium-mediated reduction in salicylic acid content and recovery of plant growth in Arabidopsis siz1 mutants is modulated by NDR1 and NPR1

The siz1 mutants exhibit high SA accumulation and consequently severe dwarfism. Although siz1 mutants exhibit growth recovery upon exogenous ammonium supply, the underlying mechanism remains unknown. Here, we investigated the effect of ammonium on SA level and plant growth in SA-accumulating mutants. The growth of siz1-2 and siz1-3 mutants was recovered to wild-type (WT) levels upon exogenous ammonium supply, but that of siz1-3 ndr1 (non-race-specific disease resistance 1) and siz1-3 npr1 (non-expressor of pathogenesis related gene 1) double mutants was unaffected. The SA level was decreased by exogenous ammonium application in siz1-3 ndr1, siz1-3 npr1, and siz1-3 mutants. The level of nitrate reductase (NR) was almost the same in all genotypes (WT, siz1-3, ndr1, npr1, siz1-3 ndr1, and siz1-3 npr1), regardless of the ammonium treatment, suggesting that exogenous ammonium supply to ndr1 siz1-3 and npr1 siz1-3 double mutants does not have any effect on their growth and NR levels, but decreases the SA level. Taken together, these results indicate that ammonium acts as a signaling molecule to regulate the SA amount, and NDR1 and NPR1 play a positive role in the ammonium-mediated growth recovery of siz1 mutants.

Lessons from Comparison of Hypoxia Signaling in Plants and Mammals

Hypoxia is an important stress for organisms, including plants and mammals. In plants, hypoxia can be the consequence of flooding and causes important crop losses worldwide. In mammals, hypoxia stress may be the result of pathological conditions. Understanding the regulation of responses to hypoxia offers insights into novel approaches for crop improvement, particularly for the development of flooding-tolerant crops and for producing better therapeutics for hypoxia-related diseases such as inflammation and cancer. Despite their evolutionary distance, plants and mammals deploy strikingly similar mechanisms to sense and respond to the different aspects of hypoxia-related stress, including low oxygen levels and the resulting energy crisis, nutrient depletion, and oxidative stress. Over the last two decades, the ubiquitin/proteasome system and the ubiquitin-like protein SUMO have been identified as key regulators that act in concert to regulate core aspects of responses to hypoxia in plants and mammals. Here, we review ubiquitin and SUMO-dependent mechanisms underlying the regulation of hypoxia response in plants and mammals. By comparing and contrasting these mechanisms in plants and mammals, this review seeks to pinpoint conceptually similar mechanisms but also highlight future avenues of research at the junction between different fields of research.

Nitrogen and Stem Development: A Puzzle Still to Be Solved

High crop yields are generally associated with high nitrogen (N) fertilizer rates. A growing tendency that is urgently demanding the adoption of precision technologies that manage N more efficiently, combined with the advances of crop genetics to meet the needs of sustainable farm systems. Among the plant traits, stem architecture has been of paramount importance to enhance harvest index in the cereal crops. Nonetheless, the reduced stature also brought undesirable effect, such as poor N-uptake, which has led to the overuse of N fertilizer. Therefore, a better understanding of how N signals modulate the initial and late stages of stem development might uncover novel semi-dwarf alleles without pleiotropic effects. Our attempt here is to review the most recent advances on this topic.

COP1 mediates light-dependent regulation of flavonol biosynthesis through HY5 in Arabidopsis

Flavonols, a class of flavonoids, accumulate as protective agents in response to various stresses. Among various environmental stimuli, light is one of the factors regulating flavonol production. MYB12/11/111, members of the R2R3 MYBs family, regulates spatio-temporal flavonol accumulation in Arabidopsis. Although various studies indicate at the involvement of an E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) in flavonoid biosynthesis in response to UV-B, the regulatory roles of these components under visible light are yet to be investigated. Here, we demonstrate that flavonol accumulation in Arabidopsis is light-regulated. Furthermore, our analysis suggests that MYB12 is a HY5-dependent light-inducible gene and plays a key role in the activation of the flavonol biosynthesis in response to light. Our results indicate the involvement of COP1 in the dark-dependent repression of MYB12 expression and flavonol accumulation. In addition, results also suggest that the effect of COP1 on MYB12 is indirect and is mediated through HY5, a direct transcriptional activator of the MYB12. Together these findings indicate that COP1 acts as a master negative regulator of flavonol biosynthesis in the dark.

Post-Translational Modifications of Nitrate Reductases Autoregulates Nitric Oxide Biosynthesis in Arabidopsis

Nitric oxide (NO) is a regulator of growth, development, and stress responses in living organisms. Plant nitrate reductases (NR) catalyze the reduction of nitrate to nitrite or, alternatively, to NO. In plants, NO action and its targets remain incompletely understood, and the way NO regulates its own homeostasis remains to be elucidated. A significant transcriptome overlapping between NO-deficient mutant and NO-treated wild type plants suggests that NO could negatively regulate its biosynthesis. A significant increase in NO content was detected in transgenic plants overexpressing NR1 and NR2 proteins. In turn, NR protein and activity as well as NO content, decreased in wild-type plants exposed to a pulse of NO gas. Tag-aided immunopurification procedures followed by tandem mass spectrometry allowed identifying NO-triggered post-translational modifications (PTMs) and ubiquitylation sites in NRs. Nitration of tyrosine residues and S-nitrosation of cysteine residues affected key amino acids involved in binding the essential FAD and molybdenum cofactors. NO-related PTMs were accompanied by ubiquitylation of lysine residues flanking the nitration and S-nitrosation sites. NO-induced PTMs of NRs potentially inhibit their activities and promote their proteasome-mediated degradation. This auto-regulatory feedback loop may control nitrate assimilation to ammonium and nitrite-derived production of NO under complex environmental conditions.

E3 SUMO ligase AtSIZ1 regulates the cruciferin content of Arabidopsis seeds

Arabidopsis thaliana E3 SUMO ligase SIZ1 (AtSIZ1) controls vegetative growth and development, including responses to nutrient deficiency and environmental stresses. Here, we analyzed the effect of AtSIZ1 and its E3 SUMO ligase activity on the amount of seed proteins. Proteomic analysis showed that the level of three major nutrient reservoir proteins, CRUCIFERIN1 (CRU1), CRU2, and CRU3, was reduced in the siz1-2 mutant compared with the wild type. However, quantitative real-time PCR (qRT-PCR) analysis showed that transcript levels of CRU1, CRU2, and CRU3 genes were significantly higher in the siz1-2 mutant than in the wild type. Yeast two-hybrid analysis revealed direct interaction of AtSIZ1 with CRU1, CRU2, and CRU3. The sumoylation assay revealed that CRU2, and CRU3 proteins were modified with a small ubiquitin-related modifier (SUMO) by the E3 SUMO ligase activity of AtSIZ1. Additionally, high-performance liquid chromatography (HPLC) analysis showed that the amino acid content was slightly higher in siz1-2 mutant seeds than in wild type seeds. Taken together, our data indicate that AtSIZ1 plays an important role in the accumulation and stability of seed storage proteins through its E3 ligase activity.

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.

Protein Phosphatase (PP2C9) Induces Protein Expression Differentially to Mediate Nitrogen Utilization Efficiency in Rice under Nitrogen-Deficient Condition

Nitrogen (N) is an essential element usually limiting in plant growth and a basic factor for increasing the input cost in agriculture. To ensure the food security and environmental sustainability it is urgently required to manage the N fertilizer. The identification or development of genotypes with high nitrogen utilization efficiency (NUE) which can grow efficiently and sustain yield in low N conditions is a possible solution. In this study, two isogenic rice genotypes i.e., wild-type rice kitaake and its transgenic line PP2C9TL overexpressed protein phosphatase gene (PP2C9) were used for comparative proteomics analysis at control and low level of N to identify specific proteins and encoding genes related to high NUE. 2D gel electrophoresis was used to perform the differential proteome analysis. In the leaf proteome, 30 protein spots were differentially expressed between the two isogenic lines under low N level which were involved in the process of energy, photosynthesis, N metabolism, signaling, and defense mechanisms. In addition, we have found that protein phosphatase enhances nitrate reductase activation by downregulation of SnRK1 and 14-3-3 proteins. Furthermore, we showed that PP2C9TL exhibits higher NUE than WT due to higher activity of nitrate reductase. This study provides new insights on the rice proteome which would be useful in the development of new strategies to increase NUE in cereal crops.