Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation

Search for Expression Marker Genes That Reflect the Physiological Conditions of Blossom End Enlargement Occurrence in Cucumber

Blossom end enlargement (BEE) is a postharvest deformation that may be related to the influx of photosynthetic assimilates before harvest. To elucidate the mechanism by which BEE occurs, expression marker genes that indicate the physiological condition of BEE-symptomatic fruit are necessary. First, we discovered that preharvest treatment with a synthetic cytokinin, N-(2-Chloro-4-pyridyl)-N'-phenylurea (CPPU), promoted fruit growth and suppressed BEE occurrence. This suggests that excessive assimilate influx is not a main cause of BEE occurrence. Subsequently, the expression levels of seven sugar-starvation marker genes, CsSEF1, AS, CsFDI1, CsPID, CsFUL1, CsETR1, and CsERF1B, were compared among symptomatic and asymptomatic fruits, combined with and without CPPU treatment. Only CsSEF1 showed a higher expression level in asymptomatic fruits than in symptomatic fruits, regardless of CPPU treatment. This was then tested using fruits stored via the modified-atmosphere packaging technique, which resulted in a lower occurrence of BEE, and the asymptomatic fruits showed a higher CsSEF1 expression level than symptomatic fruits, regardless of the packaging method. CsSEF1 codes a CCCH-type zinc finger protein, and an increase in the expression of CsSEF1 was correlated with a decrease in the fruit respiration rate. Thus, CsSEF1 may be usable as a BEE expression marker gene.

Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

Oxygen is essential for plant growth and development. Hypoxia occurs in plants due to limited oxygen availability following adverse environmental conditions as well in hypoxic niches in otherwise normoxic environments. However, the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains unknown. In animal systems dynamic fluctuations in oxygen availability are known as cyclic hypoxia. In this study, we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis plants. Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE FACTORS type VII (ERFVII) that are central components of the oxygen-sensing machinery in plants. The ERFVII-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant cells. This study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

Review: Structural-functional relationship of WRKY transcription factors: Unfolding the role of WRKY in plants

WRKY as the name suggests, are the transcription factors (TFs) that contain the signature WRKY domains, hence named after it. Since their discovery in 1994, they have been well studied in plants with exploration of approximately 74 WRKY genes in the model plant, Arabidopsis alone. However, the study of these transcription factors (TFs) is not just limited to model plant now. They have been studied widely in crop plants as well, because of their tremendous contribution in stress as well as in growth and development. Here, in this review, we describe the story of WRKY TFs from their identification to their origin, the binding mechanisms, structure and their contribution in regulating plant development and stress physiology. High throughput transcriptomics-based data also opened a doorway to understand the comprehensive and detailed functioning of WRKY TFs in plants. Indeed, the detailed functional role of each and every WRKY member in regulating the gene expression is required to pave the path to develop holistic understanding of their role in stress physiology and developmental processes in plants.

Enhanced use of chemical fertilizers and mitigation of heavy metal toxicity using biochar and the soil fungus Bipolaris maydis AF7 in rice: Genomic and metabolomic perspectives

Chemical fertilizers are the primary source of crop nutrition; however, their increasing rate of application has created environmental hazards, such as heavy metal toxicity and eutrophication. The synchronized use of chemical fertilizers and eco-friendly biological tools, such as microorganisms and biochar, may provide an efficient foundation to promote sustainable agriculture. Therefore, the current study aimed to optimize the nutrient uptake using an inorganic fertilizer, sulfate of potash (SOP) from the plant growth-promoting fungus Bipolaris maydis AF7, and biochar under heavy metal toxicity conditions in rice. Bioassay analysis showed that AF7 has high resistance to heavy metals and a tendency to produce gibberellin, colonize the fertilizer, and increase the intake of free amino acids. In the plant experiment, the co-application of AF7 +Biochar+MNF+SOP significantly lowered the heavy metal toxicity, enhanced the nutrient uptake in the rice shoots, and improved the morphological attributes (total biomass). Moreover, the co-application augmented the glucose and sucrose levels, whereas it significantly lowered the endogenous phytohormone levels (salicylic acid and jasmonic acid) in the rice shoots. The increase in nutrient content aligns with the higher expression of the OsLSi6, PHT1, and OsHKT1 genes. The plant growth traits and heavy metal tolerance of AF7 were validated by whole-genome sequencing that showed the presence of the heavy metal tolerance and detoxification protein, siderophore iron transporter, Gibberellin cluster GA4 desaturase, and DES_1 genes, as well as others that regulate glucose, antioxidants, and amino acids. Because the AF7 +biochar+inorganic fertilizer works synergistically, nutrient availability to the crops could be improved, and heavy metal toxicity and environmental hazards could be minimized.

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

Metabolome profiling of arbuscular mycorrhizal fungus treated Ocimum tenuiflorum L. provides insights into deviation in allocation of carbon compounds to secondary metabolism

Arbuscular mycorrhiza (AM) has been reported to influence secondary metabolism of Ocimum tenuiflorum L., thereby improving its therapeutic and commercial importance. To explain changes in the secondary metabolite profile, the study reports effects of AM on leaf metabolome of two high yielding genotypes of O. tenuiflorum inoculated with Rhizophagus intraradices. NMR-based non-targeted metabolic fingerprinting was related to changes at physiological, biochemical, and molecular levels in mycorrhizal (M) plants. AM resulted in higher accumulation of sucrose, which could be related with enhanced photosynthesis by virtue of increased uptake of mineral nutrients. A strong positive correlation between sucrose and net photosynthetic rate and sucrose and mineral nutrients supported that AM-mediated increase in uptake of mineral nutrients is associated with enhanced photosynthetic rate and accumulation of sucrose. Further, higher sucrose synthase activity resulted in increased glucose. Hexokinase activity was also higher in M plants resulting in higher pyruvate accumulation. On the contrary, Krebs cycle was compromised in M plants as evident by lower activities of its enzymes and concentrations of organic and amino acids. Nevertheless, AM increased activities and expressions of enzymes of terpenoid biosynthesis, shikimate, and phenylpropanoid pathways, thereby resulting in augmented production of terpenoids, phenylalanine, and phenols, respectively. Thus, metabolic reprogramming downstream of glycolysis was apparent wherein AMF resulted in more allocation of carbon resources to secondary metabolism as opposed to primary metabolism, which was supported by Pearson's correlation analysis. Higher C:N ratio in M plants explains the provision of more carbon resources to secondary metabolism as against primary metabolism.

Geminiviral C2 proteins inhibit active autophagy to facilitate virus infection by impairing the interaction of ATG7 and ATG8

Autophagy is a conserved intracellular degradation process that plays an active role in plant response to virus infections. Here we report that geminiviruses counteract activated autophagy-mediated antiviral defense in plant cells through the C2 proteins they encode. We found that, in Nicotiana benthamiana plants, tomato leaf curl Yunnan virus (TLCYnV) infection upregulated the transcription levels of autophagy-related genes (ATGs). Overexpression of NbATG5, NbATG7, or NbATG8a in N. benthamiana plants decreased TLCYnV accumulation and attenuated viral symptoms. Interestingly, transgenic overexpression of NbATG7 promoted the growth of N. benthamiana plants and enhanced plant resistance to TLCYnV. We further revealed that the C2 protein encoded by TLCYnV directly interacted with the ubiquitin-activating domain of ATG7. This interaction competitively disrupted the ATG7-ATG8 binding in N. benthamiana and Solanum lycopersicum plants, thereby inhibiting autophagy activity. Furthermore, we uncovered that the C2-mediated autophagy inhibition mechanism was conserved in three other geminiviruses. In summary, we discovered a novel counter-defensive strategy employed by geminiviruses that enlists their C2 proteins as disrupters of ATG7-ATG8 interactions to defeat antiviral autophagy.

Phosphoinositides in plant-pathogen interaction: trends and perspectives

Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.

GABA shunt pathway is stimulated in response to early defoliation-induced carbohydrate limitation in Mandarin fruits

The regulation of sugar and organic acid metabolism during fruit development has a major effect on high-quality fruit production. The reduction of leaf area is a common feature in plant growth, induced by abiotic and biotic stresses and disturbing source/sink ratio, thus impacting fruit quality. Here, we induced carbohydrate limitation by partial leaf defoliation at the beginning of the second stage of mandarin development (before the citrate peak). Resulting changes were monitored in the short-term (48 h and 1 week) and long-term (7 weeks) after the defoliation. Short-term response to early defoliation implied metabolic settings to re-feed TCA for sustaining respiration rate. These features involved (i) vacuolar sucrose degradation (high acid invertase activity and mRNA expression level) and enhanced glycolytic flux (high ATP-phosphofructokinase activity), (ii) malic and citric acid utilization (increased phosphoenolpyruvate kinase and NADP-Isocitrate dehydrogenase) associated with vacuolar citric acid release (high mRNA expression of the transporter CsCit1) and (iii) stimulation of GABA shunt pathway (low GABA content and increased mRNA expression of succinate semialdehyde dehydrogenase). A steady-state proline level was found in ED fruits although an increase in P5CS mRNA expression level. These results contribute to a better knowledge of the molecular basis of the relationship between defoliation and sugar and organic acid metabolism in mandarin fruit.

Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis

Macroautophagy/autophagy is a conserved recycling process that maintains cellular homeostasis during environmental stress. Autophagy is negatively regulated by TOR (target of rapamycin), a nutrient-regulated protein kinase that in plants is activated by several phytohormones, leading to increased growth. However, the detailed molecular mechanisms by which TOR integrates autophagy and hormone signaling are poorly understood. Here, we show that TOR modulates brassinosteroid (BR)-regulated plant growth and stress-response pathways. Active TOR was required for full BR-mediated growth in Arabidopsis thaliana. Autophagy was constitutively up-regulated upon blocking BR biosynthesis or signaling, and down-regulated by increasing the activity of the BR pathway. BIN2 (brassinosteroid-insensitive 2) kinase, a GSK3-like kinase functioning as a negative regulator in BR signaling, directly phosphorylated RAPTOR1B (regulatory-associated protein of TOR 1B), a substrate-recruiting subunit in the TOR complex, at a conserved serine residue within a typical BIN2 phosphorylation motif. Mutation of RAPTOR1B serine 916 to alanine, to block phosphorylation by BIN2, repressed autophagy and increased phosphorylation of the TOR substrate ATG13a (autophagy-related protein 13a). By contrast, this mutation had only a limited effect on growth. We present a model in which RAPTOR1B is phosphorylated and inhibited by BIN2 when BRs are absent, activating the autophagy pathway. When BRs signal and inhibit BIN2, RAPTOR1B is thus less inhibited by BIN2 phosphorylation. This leads to increased TOR activity and ATG13a phosphorylation, and decreased autophagy activity. Our studies define a new mechanism by which coordination between BR and TOR signaling pathways helps to maintain the balance between plant growth and stress responses.

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) in transgenic wheat confers tolerance to phosphorus starvation

In plants, autophagy plays an important role in regulating intracellular degradation and amino acid recycling in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) shows strong resistance to various abiotic stresses; however, current understanding of the regulation network of abiotic stress resistance in foxtail millet remains limited. In this study, we aimed to determine the autophagy-related gene SiATG8a in foxtail millet. We found that SiATG8a was mainly expressed in the stem and was induced by low-phosphorus (LP) stress. Overexpression of SiATG8a in wheat (Triticum aestivum) significantly increased the grain yield and spike number per m² under LP treatment compared to those in the WT varieties S366 and S4056. There was no significant difference in the grain P content between SiATG8a-overexpressing wheat and WT wheat under normal phosphorus (NP) and LP treatments. However, the phosphorus (P) content in the roots, stems, and leaves of transgenic plants was significantly higher than that in WT plants under NP and LP conditions. Furthermore, the expression of P transporter genes, such as TaPHR1, TaPHR3, TaIPS1, and TaPT9, in SiATG8a-transgenic wheat was higher than that in WT under LP. Collectively, overexpression of SiATG8a increases the P content of roots, stems, and leaves of transgenic wheat under LP conditions by modulating the expression of P-related transporter gene, which may result in increased grain yield; thus, SiATG8a is a candidate gene for generating transgenic wheat with improved tolerance to LP stress in the field.

Regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses

Selective autophagy functions as a regulatory mechanism by targeting native and functional proteins to ensure their proper levels and activities in plant adaptive responses. Autophagy is a cellular degradation and recycling pathway with a key role in cellular homeostasis and metabolism. Autophagy is initiated with the biogenesis of autophagosomes, which fuse with the lysosomes or vacuoles to release their contents for degradation. Under nutrient starvation or other adverse environmental conditions, autophagy usually targets unwanted or damaged proteins, organelles and other cellular components for degradation and recycling to promote cell survival. Over the past decade, however, a substantial number of studies have reported that autophagy in plants also functions as a regulatory mechanism by targeting enzymes, structural and regulatory proteins that are not necessarily damaged or dysfunctional to ensure their proper abundance and function to facilitate cellular changes required for response to endogenous and environmental conditions. During plant-pathogen interactions in particular, selective autophagy targets specific pathogen components as a defense mechanism and pathogens also utilize autophagy to target functional host factors to suppress defense mechanisms. Autophagy also targets native and functional protein regulators of plant heat stress memory, hormone signaling, and vesicle trafficking associated with plant responses to abiotic and other conditions. In this review, we discuss advances in the regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses, what questions remain and how further progress in the analysis of these special regulatory roles of autophagy can help understand biological processes important to plants.

Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator

Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A. halleri to predict the related scale-free organ specific co-expression networks, for the first time. A total of 19,653 genes of root and 18,081 genes of shoot were grouped into 14 modules and subjected to GO and KEGG enrichment analysis. "Photosynthesis" and "photosynthesis-antenna proteins" were identified as the most enriched and common pathway to both root and shoot. Whereas "glucosinolate biosynthesis," "autophagy," and "SNARE interactions in vesicular transport" were specific to root, and "circadian rhythm" was found to be enriched only in shoot. Later, hub and bottleneck genes were identified in each module by using cytoHubba plugin based on Cytoscape and scoring the relevance of each gene to the topology of the network. The modules with the most significant differential expression pattern across control and treatment (Cd-Zn treatment) were selected and their hub and bottleneck genes were screened to validate their possible involvement in heavy metal stress. Moreover, we combined the analysis of co-expression modules together with protein-protein interactions (PPIs), confirming some genes as potential candidates in plant heavy metal stress and as biomarkers. The results from this analysis shed the light on the pivotal functions to the hyperaccumulative trait of A. halleri, giving perspective to new paths for future research on this species.

The significance of WRKY45 transcription factor in metabolic adjustments during dark-induced leaf senescence

Plants are constantly exposed to environmental changes that affect their performance. Metabolic adjustments are crucial to controlling energy homoeostasis and plant survival, particularly during stress. Under carbon starvation, coordinated reprogramming is initiated to adjust metabolic processes, which culminate in premature senescence. Notwithstanding, the regulatory networks that modulate transcriptional control during low energy remain poorly understood. Here, we show that the WRKY45 transcription factor is highly induced during both developmental and dark-induced senescence. The overexpression of Arabidopsis WRKY45 resulted in an early senescence phenotype characterized by a reduction of maximum photochemical efficiency of photosystem II and chlorophyll levels in the later stages of darkness. The detailed metabolic characterization showed significant changes in amino acids coupled with the accumulation of organic acids in WRKY45 overexpression lines during dark-induced senescence. Furthermore, the markedly upregulation of alternative oxidase (AOX1a, AOX1d) and electron transfer flavoprotein/ubiquinone oxidoreductase (ETFQO) genes suggested that WRKY45 is associated with a dysregulation of mitochondrial signalling and the activation of alternative respiration rather than amino acids catabolism regulation. Collectively our results provided evidence that WRKY45 is involved in the plant metabolic reprogramming following carbon starvation and highlight the potential role of WRKY45 in the modulation of mitochondrial signalling pathways.

Role of sugar and auxin crosstalk in plant growth and development

Under the natural environment, nutrient signals interact with phytohormones to coordinate and reprogram plant growth and survival. Sugars are important molecules that control almost all morphological and physiological processes in plants, ranging from seed germination to senescence. In addition to their functions as energy resources, osmoregulation, storage molecules, and structural components, sugars function as signaling molecules and interact with various plant signaling pathways, such as hormones, stress, and light to modulate growth and development according to fluctuating environmental conditions. Auxin, being an important phytohormone, is associated with almost all stages of the plant's life cycle and also plays a vital role in response to the dynamic environment for better growth and survival. In the previous years, substantial progress has been made that showed a range of common responses mediated by sugars and auxin signaling. This review discusses how sugar signaling affects auxin at various levels from its biosynthesis to perception and downstream gene activation. On the same note, the review also highlights the role of auxin signaling in fine-tuning sugar metabolism and carbon partitioning. Furthermore, we discussed the crosstalk between the two signaling machineries in the regulation of various biological processes, such as gene expression, cell cycle, development, root system architecture, and shoot growth. In conclusion, the review emphasized the role of sugar and auxin crosstalk in the regulation of several agriculturally important traits. Thus, engineering of sugar and auxin signaling pathways could potentially provide new avenues to manipulate for agricultural purposes.

Proteomic and metabolomic analysis of Nicotiana benthamiana under dark stress

Exposure to extended periods of darkness is a common source of abiotic stress that significantly affects plant growth and development. To understand how Nicotiana benthamiana responds to dark stress, the proteomes and metabolomes of leaves treated with darkness were studied. In total, 5763 proteins and 165 primary metabolites were identified following dark treatment. Additionally, the expression of autophagy-related gene (ATG) proteins was transiently upregulated. Weighted gene coexpression network analysis (WGCNA) was utilized to find the protein modules associated with the response to dark stress. A total of four coexpression modules were obtained. The results indicated that heat-shock protein (HSP70), SnRK1-interacting protein 1, 2A phosphatase-associated protein of 46 kDa (Tap46), and glutamate dehydrogenase (GDH) might play crucial roles in N. benthamiana's response to dark stress. Furthermore, a protein-protein interaction (PPI) network was constructed and top-degreed proteins were predicted to identify potential key factors in the response to dark stress. These proteins include isopropylmalate isomerase (IPMI), eukaryotic elongation factor 5A (ELF5A), and ribosomal protein 5A (RPS5A). Finally, metabolic analysis suggested that some amino acids and sugars were involved in the dark-responsive pathways. Thus, these results provide a new avenue for understanding the defensive mechanism against dark stress at the protein and metabolic levels in N. benthamiana.

Hexokinase gene OsHXK1 positively regulates leaf senescence in rice

BACKGROUND

Leaf senescence is a highly complex and meticulous regulatory process, and the disruption of any factor involved in leaf senescence might lead to premature or delayed leaf senescence and thus result in reduced or increased crop yields. Despite sincere efforts by scientists, there remain many unsolved problems related to the regulatory factors and molecular mechanisms of leaf senescence.

RESULTS

This study successfully revealed that OsHXK1 was highly expressed in senescent leaves of rice. The upregulation of OsHXK1 led to premature senescence of rice leaves, a decreased level of chlorophyll, and damage to the chloroplast structure. The overexpression of OsHXK1 resulted in increases in glucose and ROS levels and produced programmed cell death (PCD) signals earlier at the booting stage. Further analysis showed that expression level of the respiratory burst oxidase homolog (RBOH) genes and OsGLO1 were increased in OsHXK1-overexpressing plants at the booting stage.

CONCLUSIONS

Overall, the outcomes of this study suggested that OsHXK1 could act as a positive regulator of rice leaf senescence by mediating glucose accumulation and inducing an increase in ROS.

Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions

The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.

Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos

During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, likely affecting the global RNA profile of rice genes. Most genes that exhibit sugar-regulation in rice embryos under aerobic conditions are responsive to low energy and anaerobic conditions, indicating that sugar regulation is strongly associated with energy and anaerobic signaling. The interference pattern of sugar regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for altering the expression of sugar-regulated genes. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar regulated gene expression. Anaerobically responsive genes substantially overlap with low energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those provoked by low energy conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It has been noted that abscisic acid (ABA) responsive genes are over representative of genes upregulated under low energy conditions, in contrast to downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.

The sugar-responsive circadian clock regulator bZIP63 modulates plant growth

Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

Protein Carbonylation: Emerging Roles in Plant Redox Biology and Future Prospects

Plants are sessile in nature and they perceive and react to environmental stresses such as abiotic and biotic factors. These induce a change in the cellular homeostasis of reactive oxygen species (ROS). ROS are known to react with cellular components, including DNA, lipids, and proteins, and to interfere with hormone signaling via several post-translational modifications (PTMs). Protein carbonylation (PC) is a non-enzymatic and irreversible PTM induced by ROS. The non-enzymatic feature of the carbonylation reaction has slowed the efforts to identify functions regulated by PC in plants. Yet, in prokaryotic and animal cells, studies have shown the relevance of protein carbonylation as a signal transduction mechanism in physiological processes including hydrogen peroxide sensing, cell proliferation and survival, ferroptosis, and antioxidant response. In this review, we provide a detailed update on the most recent findings pertaining to the role of PC and its implications in various physiological processes in plants. By leveraging the progress made in bacteria and animals, we highlight the main challenges in studying the impacts of carbonylation on protein functions in vivo and the knowledge gap in plants. Inspired by the success stories in animal sciences, we then suggest a few approaches that could be undertaken to overcome these challenges in plant research. Overall, this review describes the state of protein carbonylation research in plants and proposes new research avenues on the link between protein carbonylation and plant redox biology.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

Metabolomics Analysis in Different Development Stages on SP0 Generation of Rice Seeds After Spaceflight

Spaceflight is a special abiotic stress condition. In recent years, it has been confirmed that the spaceflight caused the stress response of rice seeds, and the protein level, transcription level, and methylation level will change during the planting process after returning to the ground. However, the changes at the metabolome level are not very clear. In this study, two kinds of rice seeds, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the ShiJian-10 retractable satellite (SJ-10) for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the spaceflight caused the stress response of rice. The TLP and TS of DN3 identified 110 and 57 different metabolites, respectively, while the TLP and TS of DN6 identified 104 and 74 different metabolites, respectively. These metabolites included amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the tricarboxylic acid cycle (TCA) and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggested that the response mechanisms of the two different rice strains to spaceflight stress are different, and these differences may be reflected in energy consumption and compound biosynthesis of rice in different growth and development stages. This study provided new insights for further exploring the effects of spaceflight.

Restriction of cytosolic sucrose hydrolysis profoundly alters development, metabolism, and gene expression in Arabidopsis roots

Plant roots depend on sucrose imported from leaves as the substrate for metabolism and growth. Sucrose and hexoses derived from it are also signalling molecules that modulate growth and development, but the importance for signalling of endogenous changes in sugar levels is poorly understood. We report that reduced activity of cytosolic invertase, which converts sucrose to hexoses, leads to pronounced metabolic, growth, and developmental defects in roots of Arabidopsis (Arabidopsis thaliana) seedlings. In addition to altered sugar and downstream metabolite levels, roots of cinv1 cinv2 mutants have reduced elongation rates, cell and meristem size, abnormal meristematic cell division patterns, and altered expression of thousands of genes of diverse functions. Provision of exogenous glucose to mutant roots repairs relatively few of the defects. The extensive transcriptional differences between mutant and wild-type roots have hallmarks of both high sucrose and low hexose signalling. We conclude that the mutant phenotype reflects both low carbon availability for metabolism and growth and complex sugar signals derived from elevated sucrose and depressed hexose levels in the cytosol of mutant roots. Such reciprocal changes in endogenous sucrose and hexose levels potentially provide rich information about sugar status that translates into flexible adjustments of growth and development.

Whether Gametophytes are Reduced or Unreduced in Angiosperms Might Be Determined Metabolically

In angiosperms, meiotic failure coupled with the formation of genetically unreduced gametophytes in ovules (apomeiosis) constitute major components of gametophytic apomixis. These aberrant developmental events are generally thought to be caused by mutation. However, efforts to locate the responsible mutations have failed. Herein, we tested a fundamentally different hypothesis: apomeiosis is a polyphenism of meiosis, with meiosis and apomeiosis being maintained by different states of metabolic homeostasis. Microarray analyses of ovules and pistils were used to differentiate meiotic from apomeiotic processes in Boechera (Brassicaceae). Genes associated with translation, cell division, epigenetic silencing, flowering, and meiosis characterized sexual Boechera (meiotic). In contrast, genes associated with stress responses, abscisic acid signaling, reactive oxygen species production, and stress attenuation mechanisms characterized apomictic Boechera (apomeiotic). We next tested whether these metabolic differences regulate reproductive mode. Apomeiosis switched to meiosis when premeiotic ovules of apomicts were cultured on media that increased oxidative stress. These treatments included drought, starvation, and H₂O₂ applications. In contrast, meiosis switched to apomeiosis when premeiotic pistils of sexual plants were cultured on media that relieved oxidative stress. These treatments included antioxidants, glucose, abscisic acid, fluridone, and 5-azacytidine. High-frequency apomeiosis was initiated in all sexual species tested: Brassicaceae, Boechera stricta, Boechera exilis, and Arabidopsis thaliana; Fabaceae, Vigna unguiculata; Asteraceae, Antennaria dioica. Unreduced gametophytes formed from ameiotic female and male sporocytes, first division restitution dyads, and nucellar cells. These results are consistent with modes of reproduction and types of apomixis, in natural apomicts, being regulated metabolically.

AUTOPHAGY-RELATED14 and Its Associated Phosphatidylinositol 3-Kinase Complex Promote Autophagy in Arabidopsis

Phosphatidylinositol 3-phosphate (PI3P) is an essential membrane signature for both autophagy and endosomal sorting that is synthesized in plants by the class III phosphatidylinositol 3-kinase (PI3K) complex, consisting of the VPS34 kinase, together with ATG6, VPS15, and either VPS38 or ATG14 as the fourth subunit. Although Arabidopsis (Arabidopsis thaliana) plants missing the three core subunits are infertile, vps38 mutants are viable but have aberrant leaf, root, and seed development, Suc sensing, and endosomal trafficking, suggesting that VPS38 and ATG14 are nonredundant. Here, we evaluated the role of ATG14 through a collection of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and T-DNA insertion mutants disrupting the two Arabidopsis paralogs. atg14a atg14b double mutants were relatively normal phenotypically but displayed pronounced autophagy defects, including reduced accumulation of autophagic bodies and cargo delivery during nutrient stress. Unexpectedly, homozygous atg14a atg14b vps38 triple mutants were viable but showed severely compromised rosette development and reduced fecundity, pollen germination, and autophagy, consistent with a need for both ATG14 and VPS38 to fully actuate PI3P biology. However, the triple mutants still accumulated PI3P, but they were hypersensitive to the PI3K inhibitor wortmannin, indicating that the ATG14/VPS38 component is not essential for PI3P synthesis. Collectively, the ATG14/VPS38 mutant collection now permits the study of plants altered in specific aspects of PI3P biology.

Vacuolar processing enzyme translocates to the vacuole through the autophagy pathway to induce programmed cell death

The caspase-like vacuolar processing enzyme (VPE) is a key factor in programmed cell death (PCD) associated with plant stress responses. Growth medium lacking a carbon source and dark conditions caused punctate labeling of 35S::VPE1-GFP (StVPE1-GFP) in potato leaves. Under conditions of carbon starvation, VPE activity and PCD symptoms strongly increased in BY-2 cells, but to a much lesser extent in VPE-RNAi BY-2 cells. During extended exposure to carbon starvation, VPE expression and activity levels peaked, with a gradual increase in BY-2 cell death. Histological analysis of StVPE1-GFP in BY-2 cells showed that carbon starvation induces its translocation from the endoplasmic reticulum to the central vacuole through tonoplast engulfment. Exposure of BY-2 culture to the macroautophagy/autophagy inhibitor concanamycin A led to, along with an accumulation of autophagic bodies, accumulation of StVPE1-GFP in the cell vacuole. This accumulation did not occur in the presence of 3-methyladenine, an inhibitor of early-stage autophagy. BY-2 cells constitutively expressing RFP-StATG8IL, an autophagosome marker, showed colocalization with the StVPE1-GFP protein in the cytoplasm and vacuole. RNAi silencing of the core autophagy component ATG4 in BY-2 cells reduced VPE activity and cell death. These results are the first to suggest that VPE translocates to the cell vacuole through the autophagy pathway, leading to PCD.Abbreviations: ATG: autophagy related; CLP: caspase-like protease; HR: hypersensitive response; PCD: programmed cell death; St: Solanum tuberosum; VPE: vacuolar processing enzyme.

Transcriptional networks regulating root vascular development

Vascular development involves multiple processes, including the establishment of vascular stem cells (e.g. procambium/cambium cells), stem cell divisions, and cell specification. A number of key transcription factors regulating vascular development have been identified, and the molecular mechanisms underlying these regulators have been keenly investigated. These studies uncovered that transcriptional regulation and phytohormone signaling have central roles in proceeding vascular developmental processes. Recent research approaches contributed to identify key transcription factors and their downstream genes, which enhanced our understanding of vascular development. This review discusses some research approaches and emerging molecular mechanisms that mediate the activation of transcriptional networks regulating root vascular development.

Transcriptome Analysis of Pistacia vera Inflorescence Buds in Bearing and Non-Bearing Shoots Reveals the Molecular Mechanism Causing Premature Flower Bud Abscission

The alteration of heavy ("ON/bearing") and light ("OFF/non-bearing") yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The analysis provides insights into the transcript changes between inflorescence buds on bearing and non-bearing shoots, that we indicated as "ON" and "OFF", and shed light on the molecular mechanisms causing premature inflorescence bud abscission in the pistachio cultivar "Bianca" which can be related to the alternate bearing behavior. In this study, a transcriptome analysis was performed in inflorescence buds of "ON" and "OFF" shoots. A total of 14,330 differentially expressed genes (DEGs), most of which are involved in sugar metabolism, plant hormone pathways, secondary metabolism and oxidative stress pathway, were identified. Our results shed light on the molecular mechanisms underlying inflorescence bud abscission in pistachio and we proposed a hypothetical model behind the molecular mechanism causing this abscission in "ON" shoots. Results highlighted how changes in genes expressed in nutrient pathways (carbohydrates and mineral elements) in pistachio "ON" vs. "OFF" inflorescence buds triggers a cascade of events involving trehalose-6-phosphate and target of rapamycin (TOR) signaling, SnRK1 complex, hormones, polyamines and ROS which end, through programmed cell death and autophagy phenomena, with the abscission of inflorescence buds. This is the first study reporting gene expression profiling of the fate of "ON" and "OFF" inflorescence buds associated with the alternate bearing in the pistachio.

Drought stress-induced autophagy gene expression is correlated with carbohydrate concentrations in Caragana korshinskii

Autophagy has been reported to be an adapt function of plant cells under various stresses. In this report, autophagy-related gene expressions and carbohydrate concentrations in Caragana korshinskii leaf cells under drought stress were investigated. Leaf samples of C. korshinskii plants of an estimated 15-year-old were collected from three sites with different drought stress (annual precipitation range, 325.8 to 440.8 mm) at the Loess Plateau in northwestern China. Autophagy was observed in C. korshinskii samples from all three sites and was revealed by autophagosomes in the cytoplasm of mesophyll cells and increased chloroplasts degradation observed by transmission electron microscopy. Furthermore, with the drought stress increase, autophagy-related gene expressions were upregulated and leaf concentration of sucrose was increased, while concentrations of monosaccharide sugars such as glucose, fructose and galactose were decreased. The results suggested that drought stress induced autophagy gene expression, which may serve as a survival mechanism for nutrient remobilisation.

Two Nucleoporin98 homologous genes jointly participate in the regulation of starch degradation to repress senescence in Arabidopsis

BACKGROUND

Starch is synthesized during daylight for temporary storage in leaves and then degraded during the subsequent night to support plant growth and development. Impairment of starch degradation leads to stunted growth, even senescence and death. The nuclear pore complex is involved in many cellular processes, but its relationship with starch degradation has been unclear until now. We previously identified that two Nucleoporin98 genes (Nup98a and Nup98b) redundantly regulate flowering via the CONSTANS (CO)-independent pathway in Arabidopsis thaliana. The double mutant also shows severe senescence phenotypes.

RESULTS

We find that Nucleoporin 98 participates in the regulation of sugar metabolism in leaves and is also involved in senescence regulation in Arabidopsis. We show that Nup98a and Nup98b function redundantly at different stages of starch degradation. The nup98a-1 nup98b-1 double mutant accumulates more starch, showing a severe early senescence phenotype compared to wild type plants. The expression of marker genes related to starch degradation is impaired in the nup98a-1 nup98b-1 double mutant, and marker genes of carbon starvation and senescence express their products earlier and in higher abundance than in wild type plants, suggesting that abnormalities in energy metabolism are the main cause of senescence in the double mutant. Addition of sucrose to the growth medium rescues early senescence phenotypes of the nup98a-1 nup98b-1 mutant.

CONCLUSIONS

Our results provide evidence for a novel role of the nuclear pore complex in energy metabolism related to growth and development, in which Nup98 functions in starch degradation to control growth regulation in Arabidopsis.

Tolerant mechanisms to O2 deficiency under submergence conditions in plants

Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.

Target of Rapamycin Signaling in Plant Stress Responses

Target of Rapamycin (TOR) is an atypical Ser/Thr protein kinase that is evolutionally conserved among yeasts, plants, and mammals. In plants, TOR signaling functions as a central hub to integrate different kinds of nutrient, energy, hormone, and environmental signals. TOR thereby orchestrates every stage of plant life, from embryogenesis, meristem activation, root, and leaf growth to flowering, senescence, and life span determination. Besides its essential role in the control of plant growth and development, recent research has also shed light on its multifaceted roles in plant environmental stress responses. Here, we review recent findings on the involvement of TOR signaling in plant adaptation to nutrient deficiency and various abiotic stresses. We also discuss the mechanisms underlying how plants cope with such unfavorable conditions via TOR-abscisic acid crosstalk and TOR-mediated autophagy, both of which play crucial roles in plant stress responses. Until now, little was known about the upstream regulators and downstream effectors of TOR in plant stress responses. We propose that the Snf1-related protein kinase-TOR axis plays a role in sensing various stress signals, and predict the key downstream effectors based on recent high-throughput proteomic analyses.

Genetic Analyses of the Arabidopsis ATG1 Kinase Complex Reveal Both Kinase-Dependent and Independent Autophagic Routes during Fixed-Carbon Starvation

Under nutrient and energy-limiting conditions, plants up-regulate sophisticated catabolic pathways such as autophagy to remobilize nutrients and restore energy homeostasis. Autophagic flux is tightly regulated under these circumstances through the AuTophaGy-related1 (ATG1) kinase complex, which relays upstream nutrient and energy signals to the downstream components that drive autophagy. Here, we investigated the role(s) of the Arabidopsis (Arabidopsis thaliana) ATG1 kinase during autophagy through an analysis of a quadruple mutant deficient in all four ATG1 isoforms. These isoforms appear to act redundantly, including the plant-specific, truncated ATG1t variant, and like other well-characterized atg mutants, homozygous atg1abct quadruple mutants display early leaf senescence and hypersensitivity to nitrogen and fixed-carbon starvations. Although ATG1 kinase is essential for up-regulating autophagy under nitrogen deprivation and short-term carbon starvation, it did not stimulate autophagy under prolonged carbon starvation. Instead, an ATG1-independent response arose requiring phosphatidylinositol-3-phosphate kinase (PI3K) and SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), possibly through phosphorylation of the ATG6 subunit within the PI3K complex by the catalytic KIN10 subunit of SnRK1. Together, our data connect ATG1 kinase to autophagy and reveal that plants engage multiple pathways to activate autophagy during nutrient stress, which include the ATG1 route as well as an alternative route requiring SnRK1 and ATG6 signaling.plantcell;31/12/2973/FX1F1fx1.

WRKY1 Mediates Transcriptional Regulation of Light and Nitrogen Signaling Pathways

Plant responses to multiple environmental stimuli must be integrated to enable them to adapt their metabolism and development. Light and nitrogen (N) are two such stimuli whose downstream signaling pathways must be intimately connected to each other to control plant energy status. Here, we describe the functional role of the WRKY1 transcription factor in controlling genome-wide transcriptional reprogramming of Arabidopsis (Arabidopsis thaliana) leaves in response to individual and combined light and N signals. This includes a cross-regulatory network consisting of 724 genes regulated by WRKY1 and involved in both N and light signaling pathways. The loss of WRKY1 gene function has marked effects on the light and N response of genes involved in N uptake and assimilation (primary metabolism) as well as stress response pathways (secondary metabolism). Our results at the transcriptome and at the metabolite analysis level support a model in which WRKY1 enables plants to activate genes involved in the recycling of cellular carbon resources when light is limiting but N is abundant and upregulate amino acid metabolism when both light and N are limiting. In this potential energy conservation mechanism, WRKY1 integrates information about cellular N and light energy resources to trigger changes in plant metabolism.

The effect of plant stress on phosphoinositides

Phosphoinositides are very versatile molecules with a plethora of functions such as cytokinesis, chemotaxis, cell survival, and cell death. Their functions depend on the proteins with which they interact. Thus, when interacting with phospholipases, phosphatases, or kinases, they can be precursors of second messengers in different signalling pathways. They could be second messengers themselves and interact directly with other proteins to modulate their functions trough changing its localization and activity or enhancing its synthesis rate. Because they are more abundant in animal cells and their importance in diseases such as cancer has taken priority, the study of the phosphoinositides in plants has not evolved to the same extent. Nevertheless, several studies have shown the significance of these lipids in plant cells viability and environmental response. This review focuses on phosphoinositides response to abiotic and biotic stress, showing their implication in plant survival during different stages of development. SIGNIFICANCE OF THE STUDY: This review is focused on plant PIPs functions in stress, highlighting in the main differences between plant and mammal PIPs and the novel interactions that could be extrapolated to animal models to contribute in a better understanding of these pivotal molecules.

In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi

Mycoheterotrophic plants have lost photosynthesis and obtain carbon through mycorrhizal fungi colonizing their roots. They are likely to have evolved from mixotrophic ancestors, which rely on both photosynthesis and fungal carbon for their development. Whereas our understanding of the ecological and genomic changes associated with the evolutionary shift to mycoheterotrophy is deepening, little information is known about the specific metabolic and physiological features driving this evolution. We investigated this issue in naturally occurring achlorophyllous variants of temperate mixotrophic orchids. We carried out an integrated transcriptomic and metabolomic analysis of the response to achlorophylly in the leaves of three mixotrophic species sampled in natura. Achlorophyllous leaves showed major impairment of their photosynthetic and mineral nutrition functions, strong accumulation of free amino acids, overexpression of enzymes and transporters related to sugars, amino acids and fatty acid catabolism, as well as induction of some autophagy-related and biotic stress genes. Such changes were reminiscent of these reported for variegated leaves and appeared to be symptomatic of a carbon starvation response. Rather than decisive metabolic innovations, we suggest that the evolution towards mycoheterotrophy in orchids is more likely to be reliant on the versatility of plant metabolism and an ability to exploit fungal organic resources, especially amino acids, to replace missing photosynthates.

Response of the Circadian Clock and Diel Starch Turnover to One Day of Low Light or Low CO2

Diel starch turnover responds rapidly to changes in the light regime. We investigated if these responses require changes in the temporal dynamics of the circadian clock. Arabidopsis (Arabidopsis thaliana) was grown in a 12-h photoperiod for 19 d, shifted to three different reduced light levels or to low CO₂ for one light period, and returned to growth conditions. The treatments produced widespread changes in clock transcript abundance. However, almost all of the changes were restricted to extreme treatments that led to carbon starvation and were small compared to the magnitude of the circadian oscillation. Changes included repression of EARLY FLOWERNG 4, slower decay of dusk components, and a slight phase delay at the next dawn, possibly due to abrogated Evening Complex function and sustained expression of PHYTOCHROME INTERACTING FACTORs and REVEILLEs during the night. Mobilization of starch in the night occurred in a linear manner and was paced to dawn, both in moderate treatments that did not alter clock transcripts and in extreme treatments that led to severe carbon starvation. We conclude that pacing of starch mobilization to dawn does not require retrograde carbon signaling to the transcriptional clock. On the following day, growth decreased, sugars rose, and starch accumulation was stimulated in low-light-treated plants compared to controls. This adaptive response was marked after moderate treatments and occurred independently of changes in the transcriptional clock. It is probably a time-delayed response to low-C signaling in the preceding 24-h cycle, possibly including changes in PHYTOCHROME INTERACTING FACTOR and REVEILLE expression.

Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering

The phloem plays essential roles in the source-to-sink relationship and in long-distance communication, and thereby coordinates growth and development throughout the plant. Here we employed isolation of nuclei tagged in specific cell types coupled with low-input, high-throughput sequencing approaches to analyze the changes of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with gene expression in the phloem companion cells (PCCs) of Arabidopsis(Arabidopsis thaliana) shoots in response to changes in photoperiod. We observed a positive correlation between changes in expression and H3K4me3 levels of genes that are involved in essential PCC functions, including regulation of metabolism, circadian rhythm, development, and epigenetic modifications. By contrast, changes in H3K27me3 signal appeared to contribute little to gene expression changes. These genomic data illustrate the complex gene-regulatory networks that integrate plant developmental and physiological processes in the PCCs. Emphasizing the importance of cell-specific analyses, we identified a previously uncharacterized MORN-motif repeat protein, MORN-MOTIF REPEAT PROTEIN REGULATING FLOWERING1 (MRF1), that was strongly up-regulated in the PCCs in response to inductive photoperiod. The mrf1 mutation delayed flowering, whereas MRF1 overexpression had the opposite effect, indicating that MRF1 acts as a floral promoter.

Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar

Plants have evolved a sophisticated system to respond to various stresses. Fungal attack or infection is one of the most important biotic stresses for most plants. During the defense response to fungal infection, the plant hormones jasmonic acid (JA) and salicylic acid (SA) play critical roles. Here, gene expression data on JA/SA treatments and Melampsora larici-populina (MLP) infection were generated. Integrated transcriptome analyses of these data were performed, and 943 genes in total were identified as common responsive genes (CRG). Gene ontology (GO) term analysis revealed that the genes from CRG are generally involved in the processes of stress responses, metabolism, and growth and development. The further cluster analysis of the CRG identified a set of core genes that are involved in the JA/SA-mediated response to fungal defense with distinct gene expression profiles upon JA/SA treatment, which highlighted the different effects of these two hormones on plant fungal defenses. The modifications of several pathways relative to metabolism, biotic stress, and plant hormone signal pathways suggest the possible roles of JA/SA on the regulation of growth and defense responses. Co-expression modules (CMs) were also constructed using the poplar expression data on JA, SA, M. larici-populina, Septoria musiva, and Marssonina brunnea treatment or infection. A total of 23 CMs were constructed, and different CMs clearly exhibited distinct biological functions, which conformably regulated the concerted processes in response to fungal defense. Furthermore, the GO term analysis of different CMs confirmed the roles of JA and SA in regulating growth and defense responses, and their expression profiles suggested that the growth ability was reduced when poplar deployed defense responses. Several transcription factors (TFs) among the CRG in the co-expression network were proposed as hub genes in regulating these processes. According to this study, our data finely uncovered the possible roles of JA/SA in regulating the balance between growth and defense responses by integrating multiple hormone signaling pathways. We were also able to provide more knowledge on how the plant hormones JA/SA are involved in the regulation of the balance between growth and plant defense.

Responses of seed germination and shoot metabolic profiles of maize (Zea maysL.) to Y2O3nanoparticle stress

The potential risks of rare-earth nanoparticles (RENPs) to plants in the environment are attracting increasing attention due to their wide-spread application. In this regard, little is known about the effects of Y₂O₃ NPs as an important member of RENPs on crop plants. Seed germination is vulnerable to environmental stress, which determines the growth and yield of crops. Here, maize seeds were exposed to a Y₂O₃ NP suspension (0–500 mg L⁻¹) in the dark for 6 days. It was found that the Y₂O₃ NPs had no significant effect on the germination rates (>93%) in all treatments, but they could reduce seed vitality, delay germination, and inhibit seedling growth in a dose-dependent manner. Further, the inhibition effect of Y₂O₃ NPs on root elongation was much stronger than that on shoot elongation. Meanwhile, the activities of peroxidase (POD) and catalase (CAT) in shoots were enhanced with the increase in the Y₂O₃ NP concentration. A high-concentration (≥300 mg L⁻¹) of Y₂O₃ NPs induced a significant increase in the malondialdehyde (MDA) level in shoots compared to the control, indicating that the membrane lipid peroxidation and permeability were enhanced. ¹H NMR-based analysis showed that the polar metabolic profiles were altered significantly after treatment with 0, 10, and 500 mg L⁻¹ of Y₂O₃ NPs, but there was no marked alteration observed for the non-polar metabolic profiles. The polar metabolites (e.g., sugars, amino acids, and most organic acids) showed a dose-dependent increase to Y₂O₃ NP stress, indicating that the metabolic pathways of carbohydrate metabolism, the tricarboxylic acid cycle (TCA), and amino acid synthesis were disturbed. There were significantly positive correlations found among the metabolites related with the antioxidant response and osmotic adjustment. The simultaneous accumulation of these metabolites possibly indicated the adaptation of the seedlings to stress at the cost of retarding glycolysis, TCA, and protein synthesis. The retarded effects finally inhibited the apparent growth of the seedlings. These findings reveal the phytotoxicity of Y₂O₃ NPs and provide physiological and biochemical and molecular-scale perspectives on the response of seedlings to stress.

A hypothetic model for the adaptation of maize to Y₂O₃ NPs stress during seed germination.

Plant autophagy: new flavors on the menu

Autophagy mediates the delivery of cytoplasmic content to vacuoles or lysosomes for degradation or storage. The best characterized autophagy route called macroautophagy involves the sequestration of cargo in double-membrane autophagosomes and is conserved in eukaryotes, including plants. Recently, several new receptors, some of them plant-specific, that select cargo for macroautophagy have been identified. Some of these receptors appear to participate in regulation of competing catabolic pathways, for example proteasome-mediated versus autophagic degradation under specific stress conditions. Vacuolar microautophagy, a process by which the vacuole directly engulf cytoplasmic material, also occurs in plants but its underlying molecular mechanisms are yet to be elucidated.

Understanding and exploiting the roles of autophagy in plants through multi-omics approaches

Autophagy is a highly conserved pathway in eukaryotes that promotes nutrient recycling and cellular homeostasis through the degradation of excess or damaged cytoplasmic constituents. In plants, autophagy is increasingly recognized as a key contributor to development, reproduction, metabolism, leaf senescence, endosperm and grain development, pathogen defense, and tolerance to abiotic and biotic stresses. Characterizing the functional transcriptomic, proteomic, and metabolomic networks relating to autophagy in plants subjected to various extra- and intra-cellular stimuli may help to identify components associated with the pathway. As such, the integration of multi-omics approaches (i.e., transcriptomics, proteomics and metabolomics), along with cellular, genetic and functional analyses, could provide a global perspective regarding the effects of autophagy on plant metabolism, development and stress responses. In this mini-review, recent research progress in plant autophagy is discussed, highlighting the importance of high-throughput omics approaches for defining the underpinning molecular mechanisms of autophagy and understanding its associated regulatory network.

IRE1B degrades RNAs encoding proteins that interfere with the induction of autophagy by ER stress in Arabidopsis thaliana

Macroautophagy/autophagy is a conserved process in eukaryotes that contributes to cell survival in response to stress. Previously, we found that endoplasmic reticulum (ER) stress induces autophagy in plants via a pathway dependent upon AT5G24360/IRE1B (INOSITOL REQUIRING 1-1), an ER membrane-anchored factor involved in the splicing of AT1G42990/BZIP60 (basic leucine zipper protein 60) mRNA. IRE1B is a dual protein kinase and ribonuclease, and here we determined the involvement of the protein kinase catalytic domain, nucleotide binding and RNase domains of IRE1B in activating autophagy. We found that the nucleotide binding and RNase activity of IRE1B, but not its protein kinase activity or splicing target BZIP60, are required for ER stress-mediated autophagy. Upon ER stress, the RNase activity of IRE1B engages in regulated IRE1-dependent decay of messenger RNA (RIDD), in which mRNAs of secreted proteins are degraded by IRE1 upon ER stress. Twelve genes most highly targeted by RIDD were tested for their role in inhibiting ER stress-induced autophagy, and 3 of their encoded proteins, AT1G66270/BGLU21 (β-glucosidase 21), AT2G16005/ROSY1/ML (MD2-related lipid recognition protein) and AT5G01870/PR-14 (pathogenesis-related protein 14), were found to inhibit autophagy upon overexpression. From these findings, IRE1B is posited to be a 'licensing factor' linking ER stress to autophagy by degrading the RNA transcripts of factors that interfere with the induction of autophagy.

ABBREVIATIONS

ACT2: actin 2; ATG: autophagy-related; BGLU21: β-glucosidase 21; BIP3: binding protein 3; BZIP: basic leucine zipper; DAPI: 4', 6-diamidino-2-phenylindole; DTT: dithiothreitol; ER: endoplasmic reticulum; ERN1: endoplasmic reticulum to nucleus signaling 1; IRE1: inositol requiring 1; GFP: green fluorescent protein; MAP3K5/ASK1: mitogen-activated protein kinase kinase kinase 5; MAPK8/JNK1: mitogen-activated protein kinase 8/c-Jun N-terminal kinase 1; MDC: monodansylcadaverine; PR-14: pathogenesis-related protein 14; RIDD: Regulated IRE1-Dependent Decay of Messenger RNA; ROSY1/ML: interactor of synaptotagmin1/MD2-related lipid recognition protein; Tm: tunicamycin; UPR: unfolded protein response; WT: wild-type.

S-Nitrosylation Targets GSNO Reductase for Selective Autophagy during Hypoxia Responses in Plants

Nitric oxide (NO) regulates diverse cellular signaling through S-nitrosylation of specific Cys residues of target proteins. The intracellular level of S-nitrosoglutathione (GSNO), a major bioactive NO species, is regulated by GSNO reductase (GSNOR), a highly conserved master regulator of NO signaling. However, little is known about how the activity of GSNOR is regulated. Here, we show that S-nitrosylation induces selective autophagy of Arabidopsis GSNOR1 during hypoxia responses. S-nitrosylation of GSNOR1 at Cys-10 induces conformational changes, exposing its AUTOPHAGY-RELATED8 (ATG8)-interacting motif (AIM) accessible by autophagy machinery. Upon binding by ATG8, GSNOR1 is recruited into the autophagosome and degraded in an AIM-dependent manner. Physiologically, the S-nitrosylation-induced selective autophagy of GSNOR1 is relevant to hypoxia responses. Our discovery reveals a unique mechanism by which S-nitrosylation mediates selective autophagy of GSNOR1, thereby establishing a molecular link between NO signaling and autophagy.

Cytosolic invertases contribute to cellulose biosynthesis and influence carbon partitioning in seedlings of Arabidopsis thaliana

In plants, UDP-glucose is the direct precursor for cellulose biosynthesis, and can be converted into other NDP-sugars required for the biosynthesis of wall matrix polysaccharides. UDP-glucose is generated from sucrose by two distinct metabolic pathways. The first pathway is the direct conversion of sucrose to UDP-glucose and fructose by sucrose synthase. The second pathway involves sucrose hydrolysis by cytosolic invertase (CINV), conversion of glucose to glucose-6-phosphate and glucose-1-phosphate, and UDP-glucose generation by UDP-glucose pyrophosphorylase (UGP). Previously, Barratt et al. (Proc. Natl Acad. Sci. USA, 106, 2009 and 13124) have found that an Arabidopsis double mutant lacking CINV1 and CINV2 displayed drastically reduced growth. Whether this reduced growth is due to deficient cell wall production caused by limited UDP-glucose supply, pleiotropic effects, or both, remained unresolved. Here, we present results indicating that the CINV/UGP pathway contributes to anisotropic growth and cellulose biosynthesis in Arabidopsis. Biochemical and imaging data demonstrate that cinv1 cinv2 seedlings are deficient in UDP-glucose production, exhibit abnormal cellulose biosynthesis and microtubule properties, and have altered cellulose organization without substantial changes to matrix polysaccharide composition, suggesting that the CINV/UGP pathway is a key metabolic route to UDP-glucose synthesis in Arabidopsis. Furthermore, differential responses of cinv1 cinv2 seedlings to exogenous sugar supplementation support a function of CINVs in influencing carbon partitioning in Arabidopsis. From these data and those of previous studies, we conclude that CINVs serve central roles in cellulose biosynthesis and carbon allocation in Arabidopsis.

Autophagy: The Master of Bulk and Selective Recycling

Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.

γ-Tubulin has a conserved intrinsic property of self-polymerization into double stranded filaments and fibrillar networks

γ-Tubulin is essential for microtubule nucleation and also plays less understood roles in nuclear and cell-cycle-related functions. High abundancy of γ-tubulin in acentrosomal Arabidopsis cells facilitated purification and biochemical characterization of large molecular species of γ-tubulin. TEM, fluorescence, and atomic force microscopy of purified high molecular γ-tubulin forms revealed the presence of linear filaments with a double protofilament substructure, filament bundles and aggregates. Filament formation from highly purified γ-tubulin free of γ-tubulin complex proteins (GCPs) was demonstrated for both plant and human γ-tubulin. Moreover, γ-tubulin associated with porcine brain microtubules formed oligomers. Experimental evidence on the intrinsic ability of γ-tubulin to oligomerize/polymerize was supported by conservation of α- and β-tubulin interfaces for longitudinal and lateral interactions for γ-tubulins. STED (stimulated emission depletion) microscopy of Arabidopsis cells revealed fine, short γ-tubulin fibrillar structures enriched on mitotic microtubular arrays that accumulated at polar regions of acentrosomal spindles and the outer nuclear envelope before mitosis, and were also present in nuclei. Fine fibrillar structures of γ-tubulin representing assemblies of higher order were localized in cell-cycle-dependent manner at sites of dispersed γ-tubulin location in acentrosomal plant cells as well as at sites of local γ-tubulin enrichment after drug treatment. Our findings that γ-tubulin preserves the capability of prokaryotic tubulins to self-organize into filaments assembling by lateral interaction into bundles/clusters help understanding of the relationship between structure and multiple cellular functions of this protein species and suggest that besides microtubule nucleation and organization, γ-tubulin may also have scaffolding or sequestration functions.