A Tripartite Amplification Loop Involving the Transcription Factor WRKY75, Salicylic Acid, and Reactive Oxygen Species Accelerates Leaf Senescence

Functional characterization of poplar WRKY75 in salt and osmotic tolerance

The WRKY transcription factor family is one of the most important families in plants, playing a significant role in plant growth and development, as well as in stress responses. However, functional studies on the family in response to abiotic stresses are limited in poplar. In the present study, we cloned a WRKY transcription factor gene PagWRKY75, which was down-regulated during early stages of salt and osmotic stresses. The PagWRKY75 protein belongs to the WRKY IIc subfamily. It is located in the nucleus and can bind to the W box. We obtained transgenic poplar lines with PagWRKY75 overexpression or inhibited expression by RNA interference. Stress treatment experiments indicated that the transgenic poplar lines overexpressing PagWRKY75 were more sensitive to salt and osmotic stresses, compared to wild type. The transgenic lines with PagWRKY75 inhibition displayed opposite effects. Furthermore, our results showed that PagWRKY75 can reduce the ability of reactive oxygen species scavenging and the accumulation of proline under stresses, and positively regulate the water loss rate of leaves. These results indicate that the transcription factor PagWRKY75 can negatively regulate salt and osmotic tolerance by modulating various physiological processes.

Leaf Senescence: The Chloroplast Connection Comes of Age

Leaf senescence is a developmental process critical for plant fitness, which involves genetically controlled cell death and ordered disassembly of macromolecules for reallocating nutrients to juvenile and reproductive organs. While natural leaf senescence is primarily associated with aging, it can also be induced by environmental and nutritional inputs including biotic and abiotic stresses, darkness, phytohormones and oxidants. Reactive oxygen species (ROS) are a common thread in stress-dependent cell death and also increase during leaf senescence. Involvement of chloroplast redox chemistry (including ROS propagation) in modulating cell death is well supported, with photosynthesis playing a crucial role in providing redox-based signals to this process. While chloroplast contribution to senescence received less attention, recent findings indicate that changes in the redox poise of these organelles strongly affect senescence timing and progress. In this review, the involvement of chloroplasts in leaf senescence execution is critically assessed in relation to available evidence and the role played by environmental and developmental cues such as stress and phytohormones. The collected results indicate that chloroplasts could cooperate with other redox sources (e.g., mitochondria) and signaling molecules to initiate the committed steps of leaf senescence for a best use of the recycled nutrients in plant reproduction.

Manipulating osa-MIR156f Expression by D18 Promoter to Regulate Plant Architecture and Yield Traits both in Seasonal and Ratooning Rice

Background

Rice (Oryza sativa L.) feeds more than half of the world's population. Ratooning rice is an economical alternative to the second seasonal rice, thus increasing the yield of ratooning rice is highly important.

Results

Here we report an applicable transgenic line constructed through the manipulation of osa-MIR156f expression in rice shoot using the OsGA3ox2 (D18) promoter. In seasonal rice, the D18-11 transgenic line showed moderate height and more effective tillers with normal panicle. In ratooning rice, axillary buds outgrew from the basal node of the D18-11 transgenic line before the harvest of seasonal rice. More effective tillers produced by the outgrowth of axillary buds contributed to the plant architecture improvement and yield increase. Additionally, it was found that osa-miR156f down-regulated the expression of tillering regulators, such as TEOSINTE BRANCHED1 (TB1) and LAX PANICLE 1 (LAX1). The expression of DWARF10, DWARF27 and DWARF53, three genes being involved in the biosynthesis and signaling of strigolactone (SL), decreased in the stem of the D18-11 transgenic line.

Conclusion

Our results indicated that the manipulation of osa-MIR156f expression may have application significance in rice genetic breeding. This study developed a novel strategy to regulate plant architecture and grain yield potential both in the seasonal and ratooning rice.

Deciphering hydrogen peroxide-induced signalling towards stress tolerance in plants

Plants encounter a variety of adverse environmental conditions, such as high salinity, drought, extreme heat/cold and heavy metals contamination (abiotic stress) or attack of various pathogens (biotic stress). These detrimental environmental factors enhanced the ROS production such as singlet oxygen (¹O₂), superoxide (O₂ ^•-), hydrogen peroxide (H₂O₂) and hydroxyl radicals (OH^•). ROS are highly reactive and directly target several cellular molecules and metabolites, which lead to severe cellular dysfunction. Plants respond to oxidative damages by activating antioxidant machinery to trigger signalling cascades for stress tolerance. H₂O₂ signalling balances the plant metabolism through cross-talk with other signals and plant hormones during growth, development and stress responses. H₂O₂ facilitates the regulation of different stress-responsive transcription factors (TFs) including NAC, Zinc finger, WRKY, ERF, MYB, DREB and bZIP as both upstream and downstream events during stress signalling. The present review focuses on the biological synthesis of the H₂O₂ and its effect on the upregulation of kinase genes and stress related TFs for imparting stress tolerance.

CpWRKY71, a WRKY Transcription Factor Gene of Wintersweet (Chimonanthus praecox), Promotes Flowering and Leaf Senescence in Arabidopsis

The WRKY transcription factors are one of the most important plant-specific transcription factors and play vital roles in various biological processes. However, the functions of WRKY genes in wintersweet (Chimonanthus praecox) are still unknown. In this report, a group IIc WRKY gene, CpWRKY71, was isolated from wintersweet. CpWRKY71 was localized to the nucleus and possessed transcriptional activation activity. qRT-PCR (quantitative real-time PCR) analysis showed that CpWRKY71 was expressed in all tissues tested, with higher expression in flowers and senescing leaves. During the flower development, the highest expression was detected in the early-withering stage, an obvious expression of CpWRKY71 was also observed in the flower primordia differentiation and the bloom stage. Meanwhile, the expression of CpWRKY71 was influenced by various abiotic stress and hormone treatments. The expression patterns of the CpWRKY71 gene were further confirmed in CpWRKY71pro:GUS (β-glucuronidase) plants. Heterologous overexpression of CpWRKY71 in Arabidopsis caused early flowering. Consistent with the early flowering phenotype, the expression of floral pathway integrators and floral meristem identity (FMI) genes were significantly up-regulated in transgenic plants. In addition, we also observed that the transgenic plants of CpWRKY71 exhibited precocious leaf senescence. In conclusion, our results suggested that CpWRKY71 may be involved in the regulation of flowering and leaf senescence in Arabidopsis. Our study provides a foundation for further characterization of CpWRKY genes function in wintersweet, and also enrich our knowledge of molecular mechanism about flowering and senescence in wintersweet.

Signal Transduction in Leaf Senescence: Progress and Perspective

Leaf senescence is a degenerative process that is genetically controlled and involves nutrient remobilization prior to the death of leaf tissues. Age is a key developmental determinant of the process along with other senescence inducing factors. At the cellular level, different hormones, signaling molecules, and transcription factors contribute to the regulation of senescence. This review summarizes the recent progress in understanding the complexity of the senescence process with primary focuses on perception and transduction of senescence signals as well as downstream regulatory events. Future directions in this field and potential applications of related techniques in crop improvement will be discussed.

The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis

Long noncoding RNAs (lncRNAs) are crucial regulators in many plant biological processes. However, it remains unknown whether lncRNAs can respond to nitrate or function in nitrate regulation. We detected 695 lncRNAs, 480 known and 215 novel, in Arabidopsis seedling roots; six showed altered expression in response to nitrate treatment, among which T5120 showed the highest induction. Overexpression of T5120 in Arabidopsis promoted the response to nitrate, enhanced nitrate assimilation and improved biomass and root development. Biochemical and molecular analyses revealed that NLP7, a master nitrate regulatory transcription factor, directly bound to the nitrate-responsive cis-element (NRE)-like motif of the T5120 promoter and activated T5120 transcription. In addition, T5120 partially restored the nitrate signalling and assimilation phenotypes of nlp7 mutant, suggesting that T5120 is involved in NLP7-mediated nitrate regulation. Interestingly, the expression of T5120 was regulated by the nitrate sensor NRT1.1. Therefore, T5120 is modulated by NLP7 and NRT1.1 to regulate nitrate signalling. Our work reveals a new regulatory mechanism in which lncRNA T5120 functions in nitrate regulation, providing new insights into the nitrate signalling network. Importantly, lncRNA T5120 can promote nitrate assimilation and plant growth to improve nitrogen use efficiency.

OsWRKY5 Promotes Rice Leaf Senescence via Senescence-Associated NAC and Abscisic Acid Biosynthesis Pathway

The onset of leaf senescence is triggered by external cues and internal factors such as phytohormones and signaling pathways involving transcription factors (TFs). Abscisic acid (ABA) strongly induces senescence and endogenous ABA levels are finely tuned by many senescence-associated TFs. Here, we report on the regulatory function of the senescence-induced TF OsWRKY5 TF in rice (Oryza sativa). OsWRKY5 expression was rapidly upregulated in senescing leaves, especially in yellowing sectors initiated by aging or dark treatment. A T-DNA insertion activation-tagged OsWRKY5-overexpressing mutant (termed oswrky5-D) promoted leaf senescence under natural and dark-induced senescence (DIS) conditions. By contrast, a T-DNA insertion oswrky5-knockdown mutant (termed oswrky5) retained leaf greenness during DIS. Reverse-transcription quantitative PCR (RT-qPCR) showed that OsWRKY5 upregulates the expression of genes controlling chlorophyll degradation and leaf senescence. Furthermore, RT-qPCR and yeast one-hybrid analysis demonstrated that OsWRKY5 indirectly upregulates the expression of senescence-associated NAM/ATAF1/2/CUC2 (NAC) genes including OsNAP and OsNAC2. Precocious leaf yellowing in the oswrky5-D mutant might be caused by elevated endogenous ABA concentrations resulting from upregulated expression of ABA biosynthesis genes OsNCED3, OsNCED4, and OsNCED5, indicating that OsWRKY is a positive regulator of ABA biosynthesis during leaf senescence. Furthermore, OsWRKY5 expression was suppressed by ABA treatment. Taken together, OsWRKY5 is a positive regulator of leaf senescence that upregulates senescence-induced NAC, ABA biosynthesis, and chlorophyll degradation genes.

Overexpression of the maize transcription factor ZmVQ52 accelerates leaf senescence in Arabidopsis

Leaf senescence plays an important role in the improvement of maize kernel yields. However, the underlying regulatory mechanisms of leaf senescence in maize are largely unknown. We isolated ZmVQ52 and studied the function of ZmVQ52 which encoded, a VQ family transcription factor. ZmVQ52 is constitutively expressed in maize tissues, and mainly expressed in the leaf; it is located in the nucleus of maize protoplasts. Four WRKY family proteins-ZmWRKY20, ZmWRKY36, ZmWRKY50, and ZmWRKY71-were identified as interacting with ZmVQ52. The overexpression of ZmVQ52 in Arabidopsis accelerated premature leaf senescence. The leaf of the ZmVQ52-overexpression line showed a lower chlorophyll content and higher senescence rate than the WT. A number of leaf senescence regulating genes were up-regulated in the ZmVQ52-overexpression line. Additionally, hormone treatments revealed that the leaf of the ZmVQ52-overexpressed line was more sensitive to salicylic acid (SA) and jasmonic acid (JA), and had an enhanced tolerance to abscisic acid (ABA). Moreover, a transcriptome analysis of the ZmVQ52-overexpression line revealed that ZmVQ52 is mainly involved in the circadian pathway and photosynthetic pathways.

AtWDS1 negatively regulates age-dependent and dark-induced leaf senescence in Arabidopsis

Although the involvement of ROS (reactive oxygen species) in leaf senescence is well known, the factors governing this accumulation of ROS are not fully characterized. In this study, analysis of transgenic overexpressing and knock out lines of AtWDS1 (encoding a WD repeat protein), indicates that AtWDS1 negatively regulates age-dependent and dark-induced leaf senescence. Furthermore, we observed ROS accumulation and altered tolerance of oxidative stress in atwds1 plants, as well as upregulated expression of oxidative stress-responsive genes. The location of an EGFP-AtWDS1 fusion protein in the nucleus of transformed cells and plants indicates that AtWDS1 is a nuclear protein, and, using a Dual-Luciferase assay, we showed that AtWDS1 can act as a transcription activator. However, the lack of a nuclear localization sequence in AtWDS1 suggests that its presence in the nucleus must depend on interactions with other proteins. Indeed, we found that AtWDS1 interacts directly with AtRanBPM, and that mutation of the AtRanBPM gene results in partial mislocalization of AtWDS1 in the cytoplasm. Together, these results suggest a role for AtWDS1 as a novel modulator of redox homeostasis, which responds to developmental and stress signals to regulate leaf senescence.

MdUGT88F1-Mediated Phloridzin Biosynthesis Regulates Apple Development and Valsa Canker Resistance

In apple (Malus domestica), the polyphenol profile is dominated by phloridzin, but its physiological role remains largely elusive. Here, we used MdUGT88F1 (a key UDP-glucose:phloretin 2'-O-glucosyltransferase gene) transgenic apple lines and Malus spp. germplasm to gain more insight into the physiological role of phloridzin in apple. Decreasing phloridzin biosynthesis in apple lines by RNA silencing of MdUGT88F1 led to a series of severe phenotypic changes that included severe stunting, reduced internode length, spindly leaf shape, increased stem numbers, and weak adventitious roots. These changes were associated directly with reduced lignin levels and disorders in cell wall polysaccharides. Moreover, compact organization of tissues and thickened bark enhanced resistance to Valsa canker (caused by the fungus Valsa mali), which was associated with lignin- and cell wall polysaccharide-mediated increases of salicylic acid and reactive oxygen species. Phloridzin was also assumed to be utilized directly as a sugar alternative and a toxin accelerator by V. mali in apple. Therefore, after infection with V. mali, a higher level of phloridzin slightly compromised resistance to Valsa canker in MdUGT88F1-overexpressing apple lines. Taken together, our results shed light on the importance of MdUGT88F1-mediated biosynthesis of phloridzin in the interplay between plant development and pathogen resistance in apple trees.

N-hydroxypipecolic acid and salicylic acid: a metabolic duo for systemic acquired resistance

Recent research has established that the pipecolate pathway, a three-step biochemical sequence from l-lysine to N-hydroxypipecolic acid (NHP), is central for plant systemic acquired resistance (SAR). NHP orchestrates SAR establishment in concert with the immune signal salicylic acid (SA). Here, we outline the biochemistry of NHP formation from l-Lys and address novel progress on SA biosynthesis in Arabidopsis and other plant species. In Arabidopsis, the pathogen-inducible pipecolate and salicylate pathways are activated by common and distinct regulatory elements and mutual interactions between both metabolic branches exist. The mode of action of NHP in SAR involves direct induction of SAR gene expression, signal amplification, priming for enhanced defense activation and positive interplay with SA signaling to ensure elevated plant immunity.

OsZIP1 functions as a metal efflux transporter limiting excess zinc, copper and cadmium accumulation in rice

BACKGROUND

Metal homeostasis is critical for plant growth, development and adaptation to environmental stresses and largely governed by a variety of metal transporters. The plant ZIP (Zn-regulated transporter, Iron-regulated transporter-like Protein) family proteins belong to the integral membrane transporters responsible for uptake and allocation of essential and non-essential metals. However, whether the ZIP family members mediate metal efflux and its regulatory mechanism remains unknown.

RESULTS

In this report, we provided evidence that OsZIP1 is a metal-detoxified transporter through preventing excess Zn, Cu and Cd accumulation in rice. OsZIP1 is abundantly expressed in roots throughout the life span and sufficiently induced by excess Zn, Cu and Cd but not by Mn and Fe at transcriptional and translational levels. Expression of OsZIP-GFP fusion in rice protoplasts and tobacco leaves shows that OsZIP1 resides in the endoplasmic reticulum (ER) and plasma membrane (PM). The yeast (Saccharomyces cerevisiae) complementation test shows that expression of OsZIP1 reduced Zn accumulation. Transgenic rice overexpressing OsZIP1 grew better under excess metal stress but accumulated less of the metals in plants. In contrast, both oszip1 mutant and RNA interference (RNAi) lines accumulated more metal in roots and contributed to metal sensitive phenotypes. These results suggest OsZIP1 is able to function as a metal exporter in rice when Zn, Cu and Cd are excess in environment. We further identified the DNA methylation of histone H3K9me2 of OsZIP1 and found that OsZIP1 locus, whose transcribed regions imbed a 242 bp sequence, is demethylated, suggesting that epigenetic modification is likely associated with OsZIP1 function under Cd stress.

CONCLUSION

OsZIP1 is a transporter that is required for detoxification of excess Zn, Cu and Cd in rice.

AtSPX1-mediated transcriptional regulation during leaf senescence in Arabidopsis thaliana

Leaf senescence is the final stage of leaf growth, a highly coordinated and complicated process. Phosphorus as an essential macronutrient for plant growth is remobilized from senescing leaves to other vigorous parts of the plant. In this study, through data mining, we found some phosphate starvation induced genes such as AtSPX1, were significantly induced in aging leaves in Arabidopsis. We applied a reverse genetics approach to investigate the phenotypes of transgenic plants and mutant plants, and the results showed that the overexpression of AtSPX1 accelerated leaf senescence, suppressed Pi accumulation, promoted SA production and H₂O₂ levels in leaves, while the mutant lines of AtSPX1 showed slightly delayed leaf senescence. We conducted RNA-seq-based transcriptome analysis together with GO and GSEA enrichment analyses for transgenic vs. wild-type plants to elucidate the possible underlying regulatory mechanism. The 558 genes that were up-regulated in the overexpression plants 35S::AtSPX1/WT, were significantly enriched in the process of leaf senescence, Pi starvation responses and SA signaling pathways, as were the target genes of some transcription factors such as WRKYs and NACs. In a word, we characterized AtSPX1 as a key regulator, which mediated the crosstalks among leaf senescence, Pi starvation and SA signaling pathways in Arabidopsis thaliana.

DRL1, Encoding A NAC Transcription Factor, Is Involved in Leaf Senescence in Grapevine

The NAC (for NAM, ATAF1,2, and CUC2) proteins family are plant-specific transcription factors, which play important roles in leaf development and response to environmental stresses. In this study, an NAC gene, DRL1, isolated from grapevine Vitis vinifera L. "Yatomi Rose", was shown to be involved in leaf senescence. The quantity of DRL1 transcripts decreased with advancing leaf senescence in grapevine. Overexpressing the DRL1 gene in tobacco plants significantly delayed leaf senescence with respect to chlorophyll concentration, potential quantum efficiency of photosystem II (Fv/Fm), and ion leakage. Moreover, exogenous abscisic acid (ABA) markedly reduced the expression of DRL1, and the ABA and salicylic acid (SA) concentration was lower in the DRL1-overexpressing transgenic plants than in the wild-type plants. The DRL1 transgenic plants exhibited reduced sensitivity to ABA-induced senescence but no significant change in the sensitivity to jasmonic acid-, SA- or ethylene-induced senescence. Transcriptomic analysis and RNA expression studies also indicated that the transcript abundance of genes associated with ABA biosynthesis and regulation, including 9-cis-epoxycarotenoid dioxygenase (NCED1), NCED5, zeaxanthin epoxidase1 (ZEP1), ABA DEFICIENT2 (ABA2), ABA4, and ABA INSENSITIVE 2 (ABI2), was markedly reduced in the DRL1-overexpressing plants. These results suggested that DRL1 plays a role as a negative regulator of leaf senescence by regulating ABA synthesis.

Water stress-induced flag leaf senescence may be accelerated by rehydration

The aim of the study was to determine molecular, biochemical and physiological responses of non-fully recovered DH line of triticale exposed to water stress during generative stage. The study involved two DH lines of winter triticale that produce different number of shoots with ears during rehydration. We analyzed the content of proteins associated with the photosynthetic apparatus and plant senescence. We also determined the content of hydrogen peroxide and assimilation pigments and assessed stomatal conductance and activity of the photosynthetic apparatus. Water stress-initiated senescence did not slow down during rehydration in the not fully recovered DH line. This line showed an increase in pheophorbide a oxygenase (PaO), a protein associated with chlorophyll degradation, and a decrease in the proteins related to its synthesis (chlorophyll synthase - ChS, protochlorophilide oxidoreductase - POR). Pheophorbide a oxygenase is a marker of accelerated cell death as it catalyzes opening of the porphyrin ring in the chlorophyll degradation pathway. The level of hydrogen peroxide remained high during rehydration with the photosynthetic apparatus being one of its sources. Lower content of Rieske protein reduced the quantum yield of electron transport (ϕR_o) from the primary acceptors Q_A/Q_B to the final acceptors in PSI. Intensification of metabolic processes during rehydration resulted in overloading the electron transport chain in PSII and transfer of electrons from the primary acceptors to oxygen molecule. Overproduction of hydrogen peroxide accelerated senescence during rehydration and significantly reduced plant yield.

Leaf Senescence: Systems and Dynamics Aspects

Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants' fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.

Hydrogen sulfide, a novel small molecule signalling agent, participates in the regulation of ganoderic acids biosynthesis induced by heat stress in Ganoderma lucidum

Hydrogen sulfide (H₂S), an emerging small-molecule signalling agent, was recently shown to play a significant role in many physiological processes, but relatively few studies have been conducted on microorganisms compared with mammals and plants. By studying the pretreatment of H₂S donor sodium hydrosulfide (NaHS) and the scavenger hypotaurine (HT) and Cystathionine β-synthase silenced strains, we found that H₂S could alleviate the HS-induced ganoderic acids (GAs) biosynthesis. Our transcriptome results also showed that many signaling pathways and metabolic pathways, such as the glycolysis, TCA, oxidative phosphorylation and pentose phosphate pathway, are influenced by H₂S. Further experimental results indicated that H₂S could affect the physiological process of Ganoderma lucidum by interacting with multiple signals, including ROS, NO, AMPK, sphingolipid, mTOR, phospholipase D and MAPK, and physiological and pharmacological analyses showed that H₂S might alleviate the biosynthesis of GAs by inhibiting the intracellular calcium in G. lucidum.

Multi-omic and physiologic approach to understand Lotus japonicus response upon exposure to 3,4 dimethylpyrazole phosphate nitrification inhibitor

Nitrogen fertilization is a major force in global greenhouse gases emissions and causes environmental contamination through nitrate leaching. The use of nitrification inhibitors has been proven successful to mitigate these effects. However, there is an increasing concern about the undesired effects that their potential persistence in the soil or accumulation in plants may provoke. In this study, we first exposed Lotus japonicus plants to high amounts of 3,4 dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA) nitrification inhibitors. Exposure to doses higher than 1 mg·L^-1 provoked DMPP accumulation mostly in the aerial part, while DMPSA was only detected from 10 mg·L^-1 and nearly no translocation. To evaluate the effect that DMPP accumulation in leaves may provoke on plant performance we combined a transcriptome, proteome, and physiological analysis in plants treated with 10 mg/ L of DMPP. This treatment provoked changes in the expression of 229 genes and 59 proteins. Overall, we evidence that when DMPP accumulates in leaves it induces stress responses, notably provoking changes in cell redox balance, hormone signaling, protein synthesis and turnover and carbon and nitrogen metabolism.

Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress

Light is essential to plant growth and development. Extended darkness causes dramatic gene expression changes, leading to leaf senescence, hypocotyl growth, petiole elongation, reduced leaf area, and early flowering, etc. However, the underlying mechanism of response to darkness at epigenetic levels remains largely unknown. In this study, we conducted ChIP-seq to generate global epigenomic profiles of H3K4me3 under 3-day extended darkness and normal light conditions in Arabidopsis. We applied chromatin state analysis together with self-organization mapping (SOM) to study the combination of epigenetic regulation under dark stress. The SOM map clusters the segments on the genome according to multiple diverse epigenomic datasets, which breaks the limit of dispersed distribution of epigenetic marks on the genome. Through SOM analysis, we also found that the signals of H3K4me3 were mainly increased after darkness. Analysis of H3K4me3-changed genes together with differentially expressed genes indicated that the genes showing dark-increased H3K4me3 were most involved in senescence and autophagy, and cross-talk existed between dark-induced and natural senescence. In summary, we studied the regulation of the epigenetic H3K4me3 marks of Arabidopsis in response to dark stress using chromatin state and SOM analyses. Our study revealed the regulatory mechanisms of the epigenome in response to dark stress, and SOM analysis based on chromatin states used in our study will also be helpful for other studies on dynamic changes of multiple epigenetic marks.

Suppression of tryptophan synthase activates cotton immunity by triggering cell death via promoting SA synthesis

Primary metabolism plays an important role in plant growth and development, however the relationship between primary metabolism and the adaptive immune response is largely unknown. Here, we employed RNA interference (RNAi), virus-induced gene silencing (VIGS) technology, phytohormone profiling, genetic studies, and transcriptome and metabolome analysis to investigate the function of the tryptophan synthesis pathway in the resistance of cotton to V. dahliae. We found that knock-down of GbTSA1 (Tryptophan Synthase α) and GbTSB1 (tryptophan synthase β) induced a spontaneous cell death phenotype in a salicylic acid (SA)-dependent manner and enhanced resistance to V. dahliae in cotton plants. Metabolome analysis showed that indole and indolic metabolites were highly accumulated in GbTSA1- or GbTSB1-silenced plants. Transcriptomic analysis showed that exogenous indole promotes the expression levels of genes involved in SA synthesis and the defense response. Similarly, indole application strongly enhanced cotton resistance to V. dahliae. These results suggested that metabolic intermediates in the Trp synthesis pathway may be a signal to activate SA synthesis. These results also provided a strategy to elicit plant defense responses by the application of indole.

GOLDEN2-LIKE Transcription Factors Regulate WRKY40 Expression in Response to Abscisic Acid

Arabidopsis (Arabidopsis thaliana) GARP (Golden2, ARR-B, Psr1) family transcription factors, GOLDEN2-LIKE1 and -2 (GLK1/2), function in different biological processes; however, whether and how these transcription factors modulate the response to abscisic acid (ABA) remain unknown. In this study, we used a glk1 glk2 double mutant to examine the role of GLK1/2 in the ABA response. The glk1 glk2 double mutant displayed ABA-hypersensitive phenotypes during seed germination and seedling development and an osmotic stress-resistant phenotype during seedling development. Genome-wide RNA sequencing analysis of the glk1 glk2 double mutant revealed that GLK1/2 regulate several ABA-responsive genes, including WRKY40, in the presence of ABA. Chromatin immunoprecipitation and gel retardation assays showed that GLK1/2 directly associate with the WRKY40 promoter via the recognition of a consensus sequence. Additionally, RNA sequencing analysis of the glk1 glk2 double mutant and wrky40 single mutant revealed that GLK1/2 and WRKY40 control a common set of downstream target genes in response to ABA. Furthermore, results of a genetic interaction test showed that the glk1 glk2 wrky40 triple mutant displayed similar ABA hypersensitivity to the wrky40 single mutant and the glk1 glk2 double mutant, while the glk1 glk2 wrky40 abi5-c (ABI5 CRISPR/Cas9 mutant) quadruple mutant displayed similar ABA hyposensitivity to the abi5-7 single mutant. Based on these results, we propose that the GLK1/2-WRKY40 transcription module plays a negative regulatory role in the ABA response.

The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton.

RESULTS

In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2.

CONCLUSIONS

Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.

A feedback loop between CaWRKY41 and H2O2 coordinates the response to Ralstonia solanacearum and excess cadmium in pepper

WRKY transcription factors have been implicated in both plant immunity and plant responses to cadmium (Cd); however, the mechanism underlying the crosstalk between these processes is unclear. Here, we characterized the roles of CaWRKY41, a group III WRKY transcription factor, in immunity against the pathogenic bacterium Ralstonia solanacearum and Cd stress responses in pepper (Capsicum annuum). CaWRKY41 was transcriptionally up-regulated in response to Cd exposure, R. solanacearum inoculation, and H2O2 treatment. Virus-induced silencing of CaWRKY41 increased Cd tolerance and R. solanacearum susceptibility, while heterologous overexpression of CaWRKY41 in Arabidopsis impaired Cd tolerance, and enhanced Cd and zinc (Zn) uptake and H2O2 accumulation. Genes encoding reactive oxygen species-scavenging enzymes were down-regulated in CaWRKY41-overexpressing Arabidopsis plants, whereas genes encoding Zn transporters and enzymes involved in H2O2 production were up-regulated. Consistent with these findings, the ocp3 (overexpressor of cationic peroxidase 3) mutant, which has elevated H2O2 levels, displayed enhanced sensitivity to Cd stress. These results suggest that a positive feedback loop between H2O2 accumulation and CaWRKY41 up-regulation coordinates the responses of pepper to R. solanacearum inoculation and Cd exposure. This mechanism might reduce Cd tolerance by increasing Cd uptake via Zn transporters, while enhancing resistance to R. solanacearum.

Crosstalk between cytokinin and ethylene signaling pathways regulates leaf abscission in cotton in response to chemical defoliants

Abscission is a process that allows plants to shed tissues or organs via cell separation, and occurs throughout the life cycle. Removal of leaves through the use of chemical defoliants is very important for mechanical harvesting of cotton (Gossypium hirsutum). However, our knowledge of the molecular mechanisms of the defoliation response involved is limited. In this study, RNA-seq was conducted in order to profile the differentially expressed genes (DEGs) between cultivars X50 (sensitive to chemical defoliants) and X33 (relatively insensitive) at different time points after treatment with thidiazuron and ethephon (TE). A total of 2434 DEGs were identified between the two cultivars across the different time-points. Functional categories according to GO and KEGG analyses revealed that plant hormone signal transduction and zeatin biosynthesis were involved in the response to TE. Cytokinin oxidase/dehydrogenase (CKX) genes and ethylene-related genes were up-regulated following TE treatment, and were associated with increased level of ethylene, especially in cultivar X50. Down-regulation of GhCKX3 resulted in delayed defoliation and a reduced ethylene response. The results show that crosstalk between cytokinin and ethylene regulates cotton defoliation, and provide new insights into the molecular mechanisms underlying the mode of action of defoliants in cotton.

Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance

Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.

The Catalase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

Catalases (CATs), which were coded by the catalase gene family, were a type notably distinguished ROS-metabolizing proteins implicated to perform various physiological functions in plant growth, development and stress responses. However, no systematical study has been performed in cotton. In the present study, we identified 7 and 7 CAT genes in the genome of Gossypium hirsutum L. Additionally, G. barbadense L., respectively. The results of the phylogenetic and synteny analysis showed that the CAT genes were divided into two groups, and whole-genome duplication (WGD) or polyploidy events contributed to the expansion of the GossypiumCAT gene family. Expression patterns analysis showed that the CAT gene family possessed temporal and spatial specificity and was induced by the Verticillium dahliae infection. In addition, we predicted the putative molecular regulatory mechanisms of the CAT gene family. Based on the analysis and preliminary verification results, we hypothesized that the CAT gene family, which might be regulated by transcription factors (TFs), alternative splicing (AS) events and miRNAs at different levels, played roles in cotton development and stress tolerance through modulating the reactive oxygen species (ROS) metabolism. This is the first report on the genome-scale analysis of the cotton CAT gene family, and these data will help further study the roles of CAT genes during stress responses, leading to crop improvement.

The Strawberry FaWRKY1 Transcription Factor Negatively Regulates Resistance to Colletotrichum acutatum in Fruit Upon Infection

Strawberry (Fragaria ×ananassa) is a major food crop worldwide, due to the flavor, aroma and health benefits of the fruit, but its productivity and quality are seriously limited by a large variety of phytopathogens, including Colletotrichum spp. So far, key factors regulating strawberry immune response remain unknown. The FaWRKY1 gene has been previously proposed as an important element mediating defense responses in strawberry to Colletotrichum acutatum. To get further insight into the functional role that FaWRKY1 plays in the defense mechanism, Agrobacterium-mediated transient transformation was used both to silence and overexpress the FaWRKY1 gene in strawberry fruits (Fragaria ×ananassa cv. Primoris), which were later analyzed upon C. acutatum inoculation. Susceptibility tests were performed after pathogen infection comparing the severity of disease between the two agroinfiltrated opposite halves of the same fruit, one half bearing a construct either for FaWRKY1 overexpression or RNAi-mediated silencing and the other half bearing the empty vector, as control. The severity of tissue damage was monitored and found to be visibly reduced at five days after pathogen inoculation in the fruit half where FaWRKY1 was transiently silenced compared to that of the opposite control half and statistical analysis corroborated a significant reduction in disease susceptibility. Contrarily, a similar level of susceptibility was found when FaWRKY1 overexpression and control fruit samples, was compared. These results unravel a negative regulatory role of FaWRKY1 in resistance to the phytopathogenic fungus C. acutatum in strawberry fruit and contrast with the previous role described for this gene in Arabidopsis as positive regulator of resistance against the bacteria Pseudomonas syringae. Based on previous results, a tentative working model for WRKY75 like genes after pathogen infection is proposed and the expression pattern of potential downstream FaWRKY1 target genes was also analyzed in strawberry fruit upon C. acutatum infection. Our results highlight that FaWRKY1 might display different function according to species, plant tissue and/or type of pathogen and underline the intricate FaWRKY1 responsive defense regulatory mechanism taking place in strawberry against this important crop pathogen.

The Cotton GhWRKY91 Transcription Factor Mediates Leaf Senescence and Responses to Drought Stress in Transgenic Arabidopsis thaliana

WRKY transcription factors (TFs) play essential roles in the plant response to leaf senescence and abiotic stress. However, the WRKY TFs involved in leaf senescence and stress tolerance in cotton (Gossypium hirsutum L.) are still largely unknown. In this study, a WRKY gene, GhWRKY91, was isolated and thoroughly characterized. Transcriptional activity assays showed that GhWRKY91 could activate transcription in yeast. The expression pattern of GhWRKY91 during leaf senescence, and in response to abscisic acid (ABA) and drought stress was evaluated. β-Glucuronidase (GUS) activity driven by the GhWRKY91 promoter in transgenic Arabidopsis was reduced upon exposure to ABA and drought treatments. Constitutive expression of GhWRKY91 in Arabidopsis delayed natural leaf senescence. GhWRKY91 transgenic plants exhibited increased drought tolerance and presented delayed drought-induced leaf senescence, as accompanied by reinforced expression of stress-related genes and attenuated expression of senescence-associated genes (SAGs). Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) revealed that GhWRKY91 directly targets GhWRKY17, a gene associated with ABA signals and reactive oxygen species (ROS) production. A transient dual-luciferase reporter assay demonstrated that GhWRKY91 activated the expression of GhWRKY17. Our results suggest that GhWRKY91 might negatively regulate natural and stress-induced leaf senescence and provide a foundation for further functional studies on leaf senescence and the stress response in cotton.

Genome editing using CRISPR/Cas9-targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses

Developing more crops able to sustainably produce high yields when grown under biotic/abiotic stresses is an important goal, if crop production and food security are to be guaranteed in the face of ever-increasing human population and unpredictable global climatic conditions. However, conventional crop improvement, through random mutagenesis or genetic recombination, is time-consuming and cannot keep pace with increasing food demands. Targeted genome editing (GE) technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR)/(CRISPR)-associated protein 9 (Cas9), have great potential to aid in the breeding of crops that are able to produce high yields under conditions of biotic/abiotic stress. This is due to their high efficiency, accuracy and low risk of off-target effects, compared with conventional random mutagenesis methods. The use of CRISPR/Cas9 system has grown very rapidly in recent years with numerous examples of targeted mutagenesis in crop plants, including gene knockouts, modifications, and the activation and repression of target genes. The potential of the GE approach for crop improvement has been clearly demonstrated. However, the regulation and social acceptance of GE crops still remain a challenge. In this review, we evaluate the recent applications of the CRISPR/Cas9-mediated GE, as a means to produce crop plants with greater resilience to the stressors they encounter when grown under increasing stressful environmental conditions.

Knockout of SlMAPK3 Reduced Disease Resistance to Botrytis cinerea in Tomato Plants

Mitogen-activated protein kinases (MAPKs) play an important role in defense responses to biotic and abiotic stresses. In order to investigate the role of SlMAPK3 in tomato plant resistance to Botrytis cinerea, two lines of slmapk3 mutants and wild-type (WT) tomato plants were used. The results showed that slmapk3 mutants were more susceptible to B. cinerea and that knockout of SlMAPK3 reduced the activities of defense enzymes and enhanced the accumulation of reactive oxygen species (ROS). Furthermore, we detected the expressions of salicylic acid (SA) and jasmonic acid (JA) signaling-related genes and found that knockout of SlMAPK3 enhanced the expressions of SlPR1, SlPAD4 and SlEDS1, whereas reduced the expressions of SlLoxC, SlPI I and SlPI II and enhanced the expressions of SlJAZ1 and SlMYC2. We postulate that SlMAPK3 plays a positive role in tomato plant resistance to B. cinerea through regulating ROS accumulation and SA and JA defense signaling pathways.

Reactive oxygen species in plant development

Reactive oxygen species (ROS) are produced by metabolic pathways in almost all cells. As signaling components, ROS are best known for their roles in abiotic and biotic stress-related events. However, recent studies have revealed that they are also involved in numerous processes throughout the plant life cycle, from seed development and germination, through to root, shoot and flower development. Here, we provide an overview of ROS production and signaling in the context of plant growth and development, highlighting the key functions of ROS and their interactions with plant phytohormonal networks.

Redox-dependent control of nuclear transcription in plants

Redox-dependent regulatory networks are affected by altered cellular or extracellular levels of reactive oxygen species (ROS). Perturbations of ROS production and scavenging homeostasis have a considerable impact on the nuclear transcriptome. While the regulatory mechanisms by which ROS modulate gene transcription in prokaryotes, lower eukaryotes, and mammalian cells are well established, new insights into the mechanism underlying redox control of gene expression in plants have only recently been known. In this review, we aim to provide an overview of the current knowledge on how ROS and thiol-dependent transcriptional regulatory networks are controlled. We assess the impact of redox perturbations and oxidative stress on transcriptome adjustments using cat2 mutants as a model system and discuss how redox homeostasis can modify the various parts of the transcriptional machinery.