Ethylene-insensitive3 is a senescence-associated gene that accelerates age-dependent leaf senescence by directly repressing miR164 transcription in Arabidopsis

Target of Rapamycin (TOR) Negatively Regulates Ethylene Signals in Arabidopsis

Target of rapamycin (TOR) acts as a master regulator in coordination of cell growth with energy and nutrient availability. Despite the increased appreciation of the essential role of the TOR complex in interaction with phytohormone signaling, little is known about its function on ethylene signaling. Here, through expression analysis, genetic and biochemical approaches, we reveal that TOR functions in the regulation of ethylene signals. Transcriptional analysis indicates that TOR inhibition by AZD8055 upregulated senescence- and ethylene-related genes expression. Furthermore, ethylene insensitive mutants like etr1-1, ein2-5 and ein3 eil1, showed more hyposensitivity to AZD8055 than that of WT in hypocotyl growth inhibition. Similarly, blocking ethylene signals by ethylene action inhibitor Ag+ or biosynthesis inhibitor aminoethoxyvinylglycine (AVG) largely rescued hypocotyl growth even in presence of AZD8055. In addition, we also demonstrated that Type 2A phosphatase-associated protein of 46 kDa (TAP46), a downstream component of TOR signaling, physically interacts with 1-aminocy-clopropane-1-carboxylate (ACC) synthase ACS2 and ACS6. Arabidopsis overexpressing ACS2 or ACS6 showed more hypersensitivity to AZD8055 than WT in hypocotyl growth inhibition. Moreover, ACS2/ACS6 protein was accumulated under TOR suppression, implying TOR modulates ACC synthase protein levels. Taken together, our results indicate that TOR participates in negatively modulating ethylene signals and the molecular mechanism is likely involved in the regulation of ethylene biosynthesis by affecting ACSs in transcription and protein levels.

Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes

In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited. Using soil samples from typical tea plantations spanning c. 2167 km north-east to south-west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient. The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter-module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf-Mandelbrot distribution (niche-based mechanisms), which provided evidence for deterministic-based processes. Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity.

DEAR4, a Member of DREB/CBF Family, Positively Regulates Leaf Senescence and Response to Multiple Stressors in Arabidopsis thaliana

Leaf senescence is a programmed developmental process regulated by various endogenous and exogenous factors. Here we report the characterization of the senescence-regulating role of DEAR4 (AT4G36900) from the DREB1/CBF (dehydration-responsive element binding protein 1/C-repeat binding factor) family in Arabidopsis. The expression of DEAR4 is associated with leaf senescence and can be induced by ABA, JA, darkness, drought and salt stress. Transgenic plants over-expressing DEAR4 showed a dramatically enhanced leaf senescence phenotype under normal and dark conditions while the dear4 knock-down mutant displayed delayed senescence. DEAR4 over-expressing plants showed decreased seed germination rate under ABA and salt stress conditions as well as decreased drought tolerance, indicating that DEAR4 was involved in both senescence and stress response processes. Furthermore, we found that DEAR4 protein displayed transcriptional repressor activities in yeast cells. DEAR4 could directly repress the expression of a subset of COLD-REGULATED (COR) and RESPONSIVE TO DEHYDRATION (RD) genes which have been shown to be involved in leaf longevity and stress response. Also we found that DERA4 could induce the production of Reactive oxygen species (ROS), the common signal of senescence and stress responses, which gives us the clue that DEAR4 may play an integrative role in senescence and stress response via regulating ROS production.

Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

Ethylene insensitive3-like2 (OsEIL2) confers stress sensitivity by regulating OsBURP16, the β subunit of polygalacturonase (PG1β-like) subfamily gene in rice

The transcription factors EIN3 (ETHYLENE-INSENSITIVE 3) and EILs (EIN3-Likes) play important roles in plant development and defense responses; however, their mechanism in these processes remain unclear. Here, we report that OsEIL2, an EIN3-like transcription factor from rice (Oryza sativa), plays important roles in abiotic stress and leaf senescence. OsEIL2 is a nuclear-localized protein with transactivation activity in the C-terminus (amino acids 344-583) and can be induced by NaCl, polyethylene glycol (PEG), dark, and abscisic acid (ABA) treatment. Transgenic plants of overexpressing OsEIL2 (OsEIL2-OX) show reduced tolerance to salt and drought stress compared with the controls. While the transgenic plants of overexpressing OsEIL2-RNA interference (OsEIL2-RNAi) exhibit enhanced tolerance to salt and drought stress compared with the controls. Moreover, seedlings of OsEIL2-overexpressing transgenic plants exhibit delayed leaf development and an accelerated dark-induced senescence phenotype, whereas OsEIL2-RNAi plants display the opposite phenotype. We further found that OsEIL2 functions upstream of OsBURP14 and OsBURP16. OsBURP14 and OsBURP16 are the members of the β subunit of polygalacturonase subfamilies. OsBURP16 overexpression reduced pectin content and cell adhesion and increased abiotic stress sensitivity in rice. OsEIL2 binds directly to the promoter of OsBURP14 and OsBURP16 and activates their transcript levels. We also found that OsEIL2 overexpression decreased the pectin content by increasing polygalacturonase (PG) activity. Taken together, these results revealed a new mechanism of OsEIL2 in abiotic stress responses. These findings provide new insights into plant resistance to abiotic stress.

The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development

The presence of small tooth-like indentations, or serrations, characterizes leaf margins of Arabidopsis thaliana plants. The NAC family member CUP-SHAPED COTYLEDON 2 (CUC2), which undergoes post-transcriptional gene silencing by three micro-RNA genes (MIR164A, B and C), controls the extension of leaf serration. Here, we analyzed the role of AtHB1, a transcription factor (TF) belonging to the homeodomain-leucine zipper subfamily I, in shaping leaf margins. Using mutants with an impaired silencing pathway as background, we obtained transgenic plants expressing AtHB1 over 100 times compared to controls. These plants presented an atypical developmental phenotype characterized by leaves with deep serration. Transcript measurements revealed that CUC2 expression was induced in plants overexpressing AtHB1 and repressed in athb1 mutants, indicating a positive regulation exerted by this TF. Moreover, molecular analyses of AtHB1 overexpressing and mutant plants revealed that AtHB1 represses MIR164 transcription. We found that overexpression of MIR164B was able to reverse the serration phenotype of plants overexpressing AtHB1. Finally, chromatin immunoprecipitation assays revealed that AtHB1 was able to bind in vivo the promoter regions of all three MIR164 encoding loci. Altogether, our results indicate that AtHB1 directly represses MIR164 expression to enhance leaf serration by increasing CUC2 levels.

ATBS1-INTERACTING FACTOR 2 negatively regulates dark- and brassinosteroid-induced leaf senescence through interactions with INDUCER OF CBF EXPRESSION 1

ATBS1-INTERACTING FACTOR 2 (AIF2) is a non-DNA-binding basic helix-loop-helix (bHLH) transcription factor. We demonstrated that AIF2 retards dark-triggered and brassinosteroid (BR)-induced leaf senescence in Arabidopsis thaliana. Dark-triggered BR synthesis and the subsequent activation of BRASSINAZOLE RESISTANT 1 (BZR1), a BR signaling positive regulator, result in BZR1 binding to the AIF2 promoter in a dark-dependent manner, reducing AIF2 transcript levels and accelerating senescence. BR-induced down-regulation of AIF2 protein stability partly contributes to the progression of dark-induced leaf senescence. Furthermore, AIF2 interacts with INDUCER OF CBF EXPRESSION 1 (ICE1) via their C-termini. Formation of the AIF2-ICE1 complex and subsequent up-regulation of C-REPEAT BINDING FACTORs (CBFs) negatively regulates dark-triggered, BR-induced leaf senescence. This involves antagonistic down-regulation of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), modulated through AIF2-dependent inhibition of ICE1's binding to the promoter. PIF4-dependent activities respond to dark-induced early senescence and may promote BR synthesis and BZR1 activation to suppress AIF2 and accelerate dark-induced senescence. Taken together, these findings suggest a coordination of AIF2 and ICE1 functions in maintaining stay-green traits.

Diverse and dynamic roles of F-box proteins in plant biology

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.

ZmDREB1A Regulates RAFFINOSE SYNTHASE Controlling Raffinose Accumulation and Plant Chilling Stress Tolerance in Maize

Raffinose accumulation is positively correlated with plant chilling stress tolerance; however, the understanding of the function and regulation of raffinose metabolism under chilling stress remains in its infancy. RAFFINOSE SYNTHASE (RAFS) is the key enzyme for raffinose biosynthesis. In this study, we report that two independent maize (Zea mays) zmrafs mutant lines, in which raffinose was completely abolished, were more sensitive to chilling stress and their net photosynthetic product (total soluble sugars and starch) accumulation was significantly decreased compared with controls after chilling stress. A similar characterization of the maize dehydration responsive element (DRE)-binding protein 1A mutant (zmdreb1a) showed that ZmRAFS expression and raffinose content were significantly decreased compared with its control under chilling stress. Overexpression of maize ZmDREB1A in maize leaf protoplasts increased ZmDREB1A amounts, which consequently upregulated the expression of maize ZmRAFS and the Renilla LUCIFERASE (Rluc), which was controlled by the ZmRAFS promoter. Deletion of the single dehydration-responsive element (DRE) in the ZmRAFS promoter abolished ZmDREB1A's influence on Rluc expression, while addition of three copies of the DRE in the ZmRAFS promoter dramatically increased Rluc expression when ZmDREB1A was simultaneously overexpressed. Electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative PCR demonstrated that ZmDREB1A directly binds to the DRE motif in the promoter of ZmRAFS both in vitro and in vivo. These data demonstrate that ZmRAFS, which was directly regulated by ZmDREB1A, enhances both raffinose biosynthesis and plant chilling stress tolerance.

Genetic Interaction Among Phytochrome, Ethylene and Abscisic Acid Signaling During Dark-Induced Senescence in Arabidopsis thaliana

Leaf senescence is induced by various internal and external stimuli. Dark-induced senescence has been extensively investigated, but the detailed mechanism underlying it is not well understood. The red light/far-red light receptor phytochrome B and its downstream transcription factors, PYHTOCHROME INTERACTING FACTORs (PIFs) 4 and 5, are known to play an important role in dark-induced senescence. Furthermore, the senescence-inducing phytohormones, ethylene and abscisic acid (ABA) are reported to be involved in dark-induced senescence. In this study, we analyzed the relationship between ethylene, ABA and PIFs in dark-induced leaf senescence. A triple mutant of the core ABA signaling components; SNF1-related protein kinases 2D (SRK2D), SRK2E, and SRK2I, displayed an ABA insensitive phenotype in ABA-induced senescence, whilst the ethylene insensitive mutant ein2 demonstrated low sensitivity to ABA, suggesting that ethylene signaling is involved in ABA-induced senescence. However, the pif4 pif5 mutant did not display low sensitivity to ABA, suggesting that PIF4 and PIF5 act upstream of ABA signaling. Although PIF4 and PIF5 reportedly regulate ethylene production, the triple mutant ein2 pif4 pif5 showed a stronger delayed senescence phenotype than ein2 or pif4 pif5, suggesting that EIN2 and PIF4/PIF5 partially regulate leaf senescence independently of each other. While direct target genes for PIF4 and PIF5, such as LONG HYPOCOTYL IN FAR-RED1 (HFR1) and PHYTOCHROME INTERACTING FACTOR 3-LIKE 1 (PIL1), showed transient upregulation under dark conditions (as is seen in the shade avoidance response), expression of STAY GREEN1 (SGR1), ORESARA1 (ORE1) and other direct target genes of PIF5, continued to increase during dark incubation. It is possible that transcription factors other than PIF4 and PIF5 are involved in the upregulation of SGR1 and ORE1 at a later stage of dark-induced senescence. Possible candidates are senescence-induced senescence regulators (SIRs), which include the NAC transcription factors ORE1 and AtNAP. In fact, ORE1 is known to bind to the SGR1 promoter and promotes its expression. It is therefore inferred that the phytochrome-PIF pathway regulates initial activation of senescence and subsequently, induced SIRs reinforce leaf senescence during dark-induced senescence.

BES1 directly binds to the promoter of the ACC oxidase 1 gene to regulate gravitropic response in the roots of Arabidopsis thaliana

Brassinosteroids (BRs) are known to be endogenous regulators of ethylene production, suggesting that some BR activity in plant growth and development is associated with ethylene. Here, we demonstrated that ethylene production in Arabidopsis thaliana roots is increased by BR signaling via the ethylene biosynthetic gene for ACC oxidase 1 (ACO1). Electrophoretic mobility shift and chromatin immune-precipitation assays showed that the BR transcription factor BES1 directly binds to two E-box sequences located in the intergenic region of ACO1. GUS expression using site mutations of the E-box sequences verified that ACO1 is normally expressed only when BES1 binds to the E-boxes in the putative promoter of ACO1, indicating that this binding is essential for ACO1 expression and the subsequent production of ethylene in A. thaliana roots. BR exogenously applied to A. thaliana roots enhanced the gravitropic response. Additionally, bes1-D exhibited a greater gravitropic response than did the wild-type specimens, proving that BR is a positive regulator of the gravitropic response in A. thaliana roots. The knock-down mutant aco1-1 showed a slightly lower gravitropic response than did the wild-type specimens, while bes1-D X aco1-1 exhibited a lower gravitropic response than did bes1-D. Therefore, ACO1 is a direct downstream target for BR transcription factor BES1, which controls ethylene production for gravitropism in A. thaliana roots.

Effect of Nitrogen Reactive Compounds on Aging in Seed

Reactive nitrogen species (RNS) are universal compounds that are constantly present in plant cells. RNS function depends on their actual level (the "nitrosative door" concept), duration of plant exposure to RNS and the context of the exposure. RNS are involved in the nitration of nucleic acids and fatty acids, posttranslational protein modifications (nitration and S-nitrosylation), and modulation of reactive oxygen species metabolism. RNS are regulatory molecules of various physiological processes in plants, including seed formation, maturation, dormancy and germination. The free radical theory of aging, well documented for animals, indicated that RNS participate in the regulation of the life span. Some data point to RNS contribution in preservation of seed vigor and/or regulation of seed longevity. Seed aging is a problem for biologists and agriculture, which could be solved by application of RNS, as a factor that may potentially expand seed vitality resulting in increased germination rate. The review is focused on RNS, particularly nitric oxide contribution to regulation of seed aging.

Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon)

Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5' end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5' ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3' fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.

RhMYB108, an R2R3-MYB transcription factor, is involved in ethylene- and JA-induced petal senescence in rose plants

Rose (Rosa hybrida) plants are major ornamental species worldwide, and their commercial value greatly depends on their open flowers, as both the quality of fully open petals and long vase life are important. Petal senescence can be started and accelerated by various hormone signals, and ethylene is considered an accelerator of petal senescence in rose. To date, however, the underlying mechanism of signaling crosstalk between ethylene and other hormones such as JA in petal senescence remains largely unknown. Here, we isolated RhMYB108, an R2R3-MYB transcription factor, which is highly expressed in senescing petals as well as in petals treated with exogenous ethylene and JA. Applications of exogenous ethylene and JA markedly accelerated petal senescence, while the process was delayed in response to applications of 1-MCP, an ethylene action inhibitor. In addition, silencing of RhMYB108 alter the expression of SAGs such as RhNAC029, RhNAC053, RhNAC092, RhSAG12, and RhSAG113, and finally block ethylene- and JA-induced petal senescence. Furthermore, RhMYB108 was identified to target the promoters of RhNAC053, RhNAC092, and RhSAG113. Our results reveal a model in which RhMYB108 functions as a receptor of ethylene and JA signals to modulate the onset of petal senescence by targeting and enhancing senescence-associated gene expression.

Transgenic expression of rice MYB102 (OsMYB102) delays leaf senescence and decreases abiotic stress tolerance in Arabidopsis thaliana

MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the rapid responses to unfavorable environmental conditions. We recently reported the isolation and characterization of a rice (Oryza sativa) MYB TF, OsMYB102, which is involved in the regulation of leaf senescence by downregulating abscisic acid (ABA) biosynthesis and the downstream signaling response. Based on the similarities of their sequences and expression patterns, OsMYB102 appears to be a homolog of the Arabidopsis thaliana AtMYB44 TF. Since AtMYB44 is a key regulator of leaf senescence and abiotic stress responses, it is important to examine whether AtMYB44 homologs in other plants also act similarly. Here, we generated transgenic Arabidopsis plants expressing OsMYB102 (OsMYB102-OX). The OsMYB102-OX plants showed a delayed senescence phenotype during dark incubation and were more susceptible to salt and drought stresses, considerably similar to Arabidopsis plants overexpressing AtMYB44. Real-time quantitative PCR (RT-qPCR) revealed that, in addition to known senescence-associated genes, genes encoding the ABA catabolic enzymes AtCYP707A3 and AtCYP707A4 were also significantly upregulated in OsMYB102-OX, leading to a significant decrease in ABA accumulation. Furthermore, protoplast transient expression and chromatin immunoprecipitation assays revealed that OsMYB102 directly activated AtCYP707A3 expression. Based on our findings, it is probable that the regulatory functions of AtMYB44 homologs in plants are highly conserved and they have vital roles in leaf senescence and the abiotic stress responses.

Transcription Factors Associated with Leaf Senescence in Crops

Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables. Different crops present a delay in leaf senescence with an important impact on grain yield trough the maintenance of the photosynthetic leaf area during the reproductive stage. Additionally, because of the temporal gap between the onset and phenotypic detection of the senescence process, candidate genes are key tools to enable the early detection of this process. In this sense and given the importance of some transcription factors as hub genes in senescence pathways, we present a comprehensive review on senescence-associated transcription factors, in model plant species and in agronomic relevant crops. This review will contribute to the knowledge of leaf senescence process in crops, thus providing a valuable tool to assist molecular crop breeding.

Negative Regulation of Age-Related Developmental Leaf Senescence by the IAOx Pathway, PEN1, and PEN3

Early age-related developmental senescence was observed in Arabidopsis cyp79B2/cyp79B3 double mutants that cannot produce indole-3-acetaldoxime (IAOx), the precursor to indole glucosinolates (IGs), camalexin and auxin. The early senescence phenotype was not observed when senescence was induced by darkness. The cyp79B2/cyp79B3 mutants had lower auxin levels, but did not display auxin-deficient phenotypes. Camalexin biosynthesis mutants senesced normally; however, IG transport and exosome-related pen1/pen3 double mutants displayed early senescence. The early senescence in pen1/pen3 mutants depended on salicylic acid and was not observed in pen1 or pen3 single mutants. Quantitation of IGs showed reduced levels in cyp79B2/cyp79B3 mutants, but unchanged levels in pen1/pen3, even though both of these double mutants display early senescence. We discuss how these genetic data provide evidence that IAOx metabolites are playing a protective role in leaf senescence that is dependent on proper trafficking by PEN1 and PEN3, perhaps via the formation of exosomes.

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.

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra)

INTRODUCTION

The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response.

OBJECTIVES

We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant Brassica nigra and monitored the herbivore-induced responses in relation to leaf ontogeny.

METHODS

As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites.

RESULTS

Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance.

CONCLUSIONS

The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.

Enhanced Senescence Process is the Major Factor Stopping Spike Differentiation of Wheat Mutant ptsd1

Complete differentiation of the spikes guarantees the final wheat (Triticum aestivum L.) grain yield. A unique wheat mutant that prematurely terminated spike differentiation (ptsd1) was obtained from cultivar Guomai 301 treated with ethyl methane sulfonate (EMS). The molecular mechanism study on ptsd1 showed that the senescence-associated genes (SAGs) were highly expressed, and spike differentiation related homeotic genes were depressed. Cytokinin signal transduction was weakened and ethylene signal transduction was enhanced. The enhanced expression of Ca²⁺ signal transduction related genes and the accumulation of reactive oxygen species (ROS) caused the upper spikelet cell death. Many genes in the WRKY, NAC and ethylene response factor (ERF) transcription factor (TF) families were highly expressed. Senescence related metabolisms, including macromolecule degradation, nutrient recycling, as well as anthocyanin and lignin biosynthesis, were activated. A conserved tae-miR164 and a novel-miR49 and their target genes were extensively involved in the senescence related biological processes in ptsd1. Overall, the abnormal phytohormone homeostasis, enhanced Ca²⁺ signaling and activated senescence related metabolisms led to the spikelet primordia absent their typical meristem characteristics, and ultimately resulted in the phenotype of ptsd1.

Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis

Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism.

Transcriptome analysis reveals novel insights into the continuous cropping induced response in Codonopsis tangshen, a medicinal herb

Codonopsis tangshen Oliv. (C. tangshen Oliv.), a famous medicinal herb in China, is seriously affected by continuous cropping (C-cro). The physiological and biochemical results indicated that C-cro significantly affected the malonaldehyde (MDA) and chlorophyll content, as well as activities of catalase (CAT) and superoxide dismutase (SOD) when compared with the non-continuous cropping (NC-cro) group. Transcriptome profiling found 762 differentially expressed genes, including 430 up-regulated and 332 down-regulated genes by C-cro. In addition, pathway enrichment analysis revealed that genes related to 'Tyrosine degradation I', 'Glycogen synthesis' and 'Phenylalanine and tyrosine catabolism' were up-regulated, and genes associated with 'Signal transduction', 'Immune system', etc. were down-regulated by C-cro. The expression of target genes was further validated by Q-PCR. In this study, we demonstrated the effects of C-cro on C. tangshen at the transcriptome level, and found possible C-cro responsive candidate genes. These findings could be further beneficial for improving the continuous cropping tolerance.

Expression and Regulation of PpEIN3b during Fruit Ripening and Senescence via Integrating SA, Glucose, and ACC Signaling in Pear (Pyrus pyrifolia Nakai. Whangkeumbae)

The economic value of fruit is reduced by having a short shelf life. Whangkeumbae is a type of sand pear (Pyrus pyrifolia) considered a climacteric fruit. The pear is famous for its smooth surface and good flavor. However, its shelf life is very short because of senescence and disease after harvest and a burst of ethylene (ET) production prompting the onset of fruit ripening. In plants, ETHYLENE INSENSITIVE3 (EIN3) and EIN3like (EIL), located in the nucleus, are important components of the ET signaling pathway and act as transcription factors. EIN3s and EILs belong to a small family involved in regulating the expression of ethylene response factor gene (ERF), whose encoding protein is the final component in the ET signaling pathway. The mutation of these components will cause defects in the ethylene pathway. In this study, one gene encoding an EIN3 was cloned and identified from Whangkeumbae and designated PpEIN3b. The deduced PpEIN3b contained a conserved EIN3 domain, a bipartite nuclear localization signal profile (NLS_BP), and an N-6 adenine-specific DNA methylase signature (N6_MTASE). PpEIN3b belongs to the EIN3 super-family by phylogenetic analysis. Quantitative RT-PCR (qRT-PCR) analysis revealed that PpEIN3b was preferentially expressed in fruit. Additionally, its expression was developmentally regulated during fruit ripening and senescence. Furthermore, PpEIN3b transcripts were obviously repressed by salicylic acid (SA) and glucose treatment in pear fruit and in diseased fruit, while it was significantly induced by 1-aminocyclopropane-1-carboxylic acid (ACC) treatment. Taken together, our results reveal the expression and regulation profiles of PpEIN3b and suggest that PpEIN3b might integrate SA, glucose, and ACC signaling to regulate fruit ripening and senescence in pear, which would provide a candidate gene for this regulation to obtain fruit with a long shelf life and improved economic value.

Characterization and Cloning of Grape Circular RNAs Identified the Cold Resistance-Related Vv-circATS1

Circular RNAs (circRNAs) are widely distributed and play essential roles in a series of developmental processes, although none have been identified or characterized in grapevines (Vitis vinifera). In this study, we characterized the function of grape circRNA and uncovered thousands of putative back-splicing sites by global transcriptome analysis. Our results indicated that several reported circRNA prediction algorithms should be used simultaneously to obtain comprehensive and reliable circRNA predictions in plants. Furthermore, the length of introns flanking grape circRNAs was closely related to exon circularization. Although the longer introns flanking grape circRNAs appeared to circularize more efficiently, a 20- to 50-nt region seemed large enough to drive grape circRNA biogenesis. In addition, the endogenous introns flanking circularized exon(s) in conjunction with reverse complementary sequences could support the accurate and efficient circularization of various exons in grape, which constitutes a new tool for exploring the functional consequences caused by circRNA expression. Finally, we identified 475 differentially expressed circRNAs in grape leaves under cold stress. Overexpression of Vv-circATS1, a circRNA derived from glycerol-3-P acyltransferase, improved cold tolerance in Arabidopsis (Arabidopsis thaliana), while the linear RNA derived from the same sequence cannot. These results indicate the functional difference between circRNA and linear RNA, and provide new insight into plant abiotic stress resistance.

Expression profiling of CTR1-like and EIN2-like genes in buds and leaves of Populus tremula, and in vitro study of the interaction between their polypeptides

In Arabidopsis, the serine/threonine protein kinase Constitutive Triple Response 1 (CTR1) and Ethylene Insensitive 2 polypeptide (EIN2) functions are key negative and positive components, respectively, in the ethylene signalling route. Here, we report on an in silico study of members of the CTR1-like and EIN2-like polypeptide families from poplars. The expression of CTR1-like and EIN2-like genes such as Ptre-CTR1, Ptre-CTR3 and Ptre-EIN2a was studied in Populus tremula buds and leaves in response to dehydration, various light conditions and under senescence. In buds under dehydration, the maximal fold-change of the Ptre-CTR1, Ptre-CTR3 and Ptre-EIN2a expression level recorded almost identical values. This suggests that maintenance of a constant ratio between the transcript levels of genes encoding positive and negative ethylene signalling components is required under stress. The expression of the studied genes was 1.4-to 3-fold higher in response to darkness, but 4.5- to 51.2-fold and 21.6- to 51.2-fold higher under the early and moderate leaf senescence, respectively. It is worth noting that the senescence-related Ptre-EIN2a and Ptre-CTR3a expression profiles were very similar. Using in vitro assays, we demonstrated the ability of the catalytic domain of Ptre-CTR1 to phosphorylate the Ptre-EIN2a-like polypeptide, which is similar to that in Arabidopsis. The target substrate, the Ptre-CEND2a polypeptide (C-terminal part of Ptre-EIN2a), was only phosphorylated by the protein kinase Ptre-CTR1 and not by Ptre-CTR3. Moreover, the addition of Ptre-CTR3 polypeptides (-CTR3a or -CTR3b forms) to the reaction mixture had an inhibitory effect on Ptre-CTR1 auto- and trans-phosphorylation. In contrast to Ptre-CTR1, Ptre-CTR3 may act as a positive regulator in ethylene signalling in poplar; however, this hypothesis requires in vivo confirmation. Thus, the ethylene signalling route in poplar seems to be under the control of certain additional mechanisms which have not been reported in Arabidopsis.

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.

Rice transcription factor OsMYB102 delays leaf senescence by down-regulating abscisic acid accumulation and signaling

MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the responses to several abiotic stresses. In rice (Oryza sativa), the roles of MYB-related TFs in leaf senescence are not well documented. Here, we examined rice MYB TF gene OsMYB102 and found that an OsMYB102 T-DNA activation-tagged line (termed osmyb102-D), which constitutively expresses OsMYB102 under the control of four tandem repeats of the 35S promoter, and OsMYB102-overexpressing transgenic lines (35S:OsMYB102 and 35S:GFP-OsMYB102) maintain green leaves much longer than the wild-type under natural, dark-induced, and abscisic acid (ABA)-induced senescence conditions. Moreover, an osmyb102 knockout mutant showed an accelerated senescence phenotype under dark-induced and ABA-induced leaf senescence conditions. Microarray analysis showed that a variety of senescence-associated genes (SAGs) were down-regulated in the osmyb102-D line. Further studies demonstrated that overexpression of OsMYB102 controls the expression of SAGs, including genes associated with ABA degradation and ABA signaling (OsABF4, OsNAP, and OsCYP707A6), under dark-induced senescence conditions. OsMYB102 inhibits ABA accumulation by directly activating the transcription of OsCYP707A6, which encodes the ABA catabolic enzyme ABSCISIC ACID 8'-HYDROXYLASE. OsMYB102 also indirectly represses ABA-responsive genes, such as OsABF4 and OsNAP. Collectively, these results demonstrate that OsMYB102 plays a critical role in leaf senescence by down-regulating ABA accumulation and ABA signaling responses.

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.

The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis

The roles of histone demethylation in the regulation of plant flowering, disease resistance, rhythmical response, and seed germination have been elucidated recently; however, how histone demethylation affects leaf senescence remains largely unclear. In this study, we exploited yeast one-hybrid (Y1H) to screen for the upstream regulators of NONYELLOWING1 (NYE1), and identified RELATIVE OF EARLY FLOWERING6 (REF6), a histone H3 lysine 27 tri-methylation (H3K27me3) demethylase, as a putative binding protein of NYE1 promoter. By in vivo and in vitro analyses, we demonstrated that REF6 directly binds to the motif CTCGYTY in NYE1/2 promoters through its zinc finger domain and positively regulates their expression. Loss-of-function of REF6 delayed chlorophyll (Chl) degradation, whereas overexpression of REF6 accelerated Chl degradation. Subsequently, we revealed that REF6 positively regulates the general senescence process by directly up-regulating ETHYLENE INSENSITIVE 2 (EIN2), ORESARA1 (ORE1), NAC-LIKE, ACTIVATED BY AP3/PI (NAP), PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK), PHYTOALEXIN DEFICIENT 4 (PAD4), LIPOXYGENASE 1 (LOX1), NAC DOMAIN CONTAINING PROTEIN 3 (AtNAC3), and NAC TRANSCRIPTION FACTOR-LIKE 9 (NTL9), the key regulatory and functional genes predominantly involved in the regulation of developmental leaf senescence. Importantly, loss-of-function of REF6 increased H3K27me3 levels at all the target Senescence associated genes (SAGs). We therefore conclusively demonstrate that H3K27me3 methylation represents an epigenetic mechanism prohibiting the premature transcriptional activation of key developmentally up-regulated senescence regulatory as well as functional genes in Arabidopsis.

Leaves of higher plants start yellowing and subsequently die (senescence) at particular developmental stages as a result of both internal and external regulations. Leaf senescence is evolved to facilitate nutrient remobilization to young/important organs to meet their rapid development, and a large number of genes (Senescence associated genes, SAGs) are activated to regulate/facilitate the process. It has been intriguing how these genes are kept transcriptionally inactive to ensure an effective photosynthesis before the initiation of leaf senescence. Here, we reveal an epigenetic mechanism responsible for the prohibition of their premature transcription. We found that an H3K27me3 demethylase, RELATIVE OF EARLY FLOWERING 6 (REF6), directly promotes the expression of its ten target senescence regulatory and functional genes (EIN2, ORE1, NAP, AtNAC3, NTL9, NYE1/2, LOX1, PAD4, and PPDK), which are involved in major phytohormones’ signaling, biosynthesis, and chlorophyll degradation. Crucially, REF6 is substantially involved in promoting the H3K27me3 demethylation of both their promoter and/or coding regions during the aging process of leaves. We therefore provide conclusive evidence that H3K27me3 methylation is an epigenetic mechanism hindering the premature transcriptional activation of key SAGs, which helps to explain the “aging effect” of senescence initiation.

The Role and Regulation of Autophagy and the Proteasome During Aging and Senescence in Plants

Aging and senescence in plants has a major impact on agriculture, such as in crop yield, the value of ornamental crops, and the shelf life of vegetables and fruits. Senescence represents the final developmental phase of the leaf and inevitably results in the death of the organ. Still, the process is completely under the control of the plant. Plants use their protein degradation systems to maintain proteostasis and transport or salvage nutrients from senescing organs to develop reproductive parts. Herein, we present an overview of current knowledge about the main protein degradation pathways in plants during senescence: The proteasome and autophagy. Although both pathways degrade proteins, autophagy appears to prevent aging, while the proteasome functions as a positive regulator of senescence.

Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs

MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.

Natural allelic variation of GVS1 confers diversity in the regulation of leaf senescence in Arabidopsis

Leaf senescence affects plant fitness. Plants that evolve in different environments are expected to acquire distinct regulations of leaf senescence. However, the adaptive and evolutionary roles of leaf senescence are largely unknown. We investigated leaf senescence in 259 natural accessions of Arabidopsis by quantitatively assaying dark-induced senescence responses using a high-throughput chlorophyll fluorescence imaging system. A meta-analysis of our data with phenotypic and climatic information demonstrated biological and environmental links with leaf senescence. We further performed genome-wide association mapping to identify the genetic loci underlying the diversity of leaf senescence responses. We uncovered a new locus, Genetic Variants in leaf Senescence (GVS1), with high similarity to reductase, where a single nonsynonymous nucleotide substitution at GVS1 mediates the diversity of the senescence trait. Loss-of-function mutations of GVS1 in Columbia-0 delayed leaf senescence and increased sensitivity to oxidative stress, suggesting that this GVS1 variant promotes optimal responses to developmental and environmental signals. Intriguingly, gvs1 loss-of-function mutants display allele- and accession-dependent phenotypes, revealing the functional diversity of GVS1 alleles not only in leaf senescence, but also oxidative stress. Our discovery of GVS1 as the genetic basis of natural variation in senescence programs reinforces its adaptive potential in modulating life histories across diverse environments.

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.

Transcriptomic profiling identifies differentially expressed genes associated with programmed cell death of nucellar cells in Ginkgo biloba L

BACKGROUND

Previously, we demonstrated that pollen chamber formation (PCF) in G. biloba ovules was a process of programmed cell death (PCD) within the nucellar cells at the micropylar end. However, the signal triggering the cascades of the programmed events in these nucellar cells remains unexplored.

RESULTS

A transcriptomic strategy was employed to unravel the mechanism underlying the nucellar PCD via the comparative profiles of RNA-seq between pre-PCF and post-PCF ovules. A total of 5599 differentially expressed genes (DEGs) with significance was identified from G. biloba ovules and classified into three main categories of GO annotation, including 17 biological processes, 15 cellular components and 17 molecular functions. KEGG analysis showed that 72 DEGs were enriched in "Plant hormone signal transduction". Furthermore, 99 DEGs were found to be associated with the PCD process, including the genes involved in ethylene signaling pathway, PCD initiation, and PCD execution. Moreover, calcium-cytochemical localization indicated that calcium could play a role in regulating PCD events within the nucellar cells during pollen chamber formation in G. biloba ovules.

CONCLUSIONS

A putative working model, consisting of three overlapping processes, is proposed for the nucellar PCD: at the stage of PCD preparation, ethylene signaling pathway is activated for transcriptional regulation of the downstream targets; subsequently, at the stage of PCD initiation, the upregulated expression of several transcription factors, i.e., NAC, bHLH, MADS-box, and MYB, further promotes the corresponding transcript levels of CYTOCHROME C and CALMODULINs, thereby, leads to the PCD initiation via the calcium-dependent signaling cascade; finally, at the stage of PCD execution, some proteases like metacaspases and vacuolar processing enzyme for hydrolysis, together with the process of autophagy, play roles in the clearance of cellular components. Afterwards, a pollen chamber is generated from the removal of specific nucellar cells in the developing ovule.

The Arabidopsis AMOT1/EIN3 gene plays an important role in the amelioration of ammonium toxicity

Ammonium (NH4+) toxicity inhibits shoot growth in Arabidopsis, but the underlying mechanisms remain poorly characterized. Here, we show that a novel Arabidopsis mutant, ammonium tolerance 1 (amot1), exhibits enhanced shoot growth tolerance to NH4+. Molecular cloning revealed that amot1 is a new allele of EIN3, a key regulator of ethylene responses. The amot1 mutant and the allelic ein3-1 mutants show greater NH4+ tolerance than the wild type. Moreover, transgenic plants overexpressing EIN3 (EIN3ox) are more sensitive to NH4+ toxicity The ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) increases shoot sensitivity to NH4+, whereas the ethylene perception inhibitor Ag+ decreases sensitivity. NH4+ induces ACC and ethylene accumulation. Furthermore, ethylene-insensitive mutants such as etr1-3 and ein3eil1 display enhanced NH4+ tolerance. In contrast, the ethylene overproduction mutant eto1-1 exhibits decreased ammonium tolerance. AMOT1/EIN3 positively regulates shoot ROS accumulation, leading to oxidative stress under NH4+ stress, a trait that may be related to increased expression of peroxidase-encoding genes. These findings demonstrate the role of AMOT1/EIN3 in NH4+ tolerance and confirm the strong link between NH4+ toxicity symptoms and the accumulation of hydrogen peroxide.

Impaired Function of the Calcium-Dependent Protein Kinase, OsCPK12, Leads to Early Senescence in Rice (Oryza sativa L.)

Premature leaf senescence affects plant yield and quality, and numerous researches about it have been conducted until now. In this study, we identified an early senescent mutant es4 in rice (Oryza sativa L.); early senescence appeared approximately at 60 dps and became increasingly senescent with the growth of es4 mutant. We detected that content of reactive oxygen species (ROS) and malondialdehyde (MDA), as well as activity of superoxide dismutase (SOD) were elevated, while chlorophyll content, soluble protein content, activity of catalase (CAT), activity of peroxidase (POD) and photosynthetic rate were reduced in the es4 mutant leaves. We mapped es4 in a 33.5 Kb physical distance on chromosome 4 by map-based cloning. Sequencing analysis in target interval indicated there was an eight bases deletion mutation in OsCPK12 which encoded a calcium-dependent protein kinase. Functional complementation of OsCPK12 in es4 completely restored the normal phenotype. We used CRISPR/Cas9 for targeted disruption of OsCPK12 in ZH8015 and all the mutants exhibited the premature senescence. All the results indicated that the phenotype of es4 was caused by the mutation of OsCPK12. Overexpression of OsCPK12 in ZH8015 enhanced the net photosynthetic rate (P n) and chlorophyll content. OsCPK12 was mainly expressed in green organs. The results of qRT-PCR analysis showed that the expression levels of some key genes involved in senescence, chlorophyll biosynthesis, and photosynthesis were significantly altered in the es4 mutant. Our results demonstrate that the mutant of OsCPK12 triggers the premature leaf senescence; however, the overexpression of OsCPK12 may delay its growth period and provide the potentially positive effect on productivity in rice.

Ethylene Treatment in Studying Leaf Senescence in Arabidopsis

Plant leaf senescence is the final process of leaf development that involves the mobilization of nutrients from old leaves to newly growing tissues. Leaf senescence involves a coordinated action at the cellular and organism levels under the control of a highly regulated genetic program. However, leaf senescence is also influenced by multiple internal and environmental signals that are integrated into the age information. Among these internal factors, the simple gaseous phytohormone ethylene is well-known to be an important endogenous modulator of plant leaf senescence and fruit ripening. Ethylene and its biosynthetic precursor ACC (1-aminocyclopropane-l-carboxylic acid) as well as inhibitors of ethylene biosynthesis aminoethoxyvinylglycine (AVG) and action (AgNO₃) or the inhibitor of ethylene perception 1-MCP (1-methylcyclopropene) have been widely used by the research community of plant leaf senescence. However, until now, no systemically experimental method about the usage of ethylene in studying the molecular mechanisms of leaf senescence in Arabidopsis is available. Here, we provide detailed methods for exogenous application of ethylene and its inhibitors in studying Arabidopsis leaf senescence, which has been successfully used in our laboratory.

A hidden link between leaf development and senescence

Leaf senescence is the final step of leaf development and is usually accompanied by visible color changes from green to yellow or brown. Unlike the senescence of the whole body of animals and unicellular organisms, which is often associated with death, leaf senescence in plants requires highly integrative processes towards cell death with nutrient recycling and storage. Since leaf senescence plays pivotal roles in the production of plant biomass and grain yield, the mechanisms of degradation and relocation of macromolecules as well as the regulation of signaling and biosynthetic pathways have received much attention. The importance of the plant hormone ethylene in the onset of leaf senescence has been clearly documented. However, research has increasingly demonstrated that the function of ethylene in the regulation of leaf senescence is dependent on leaf development. This review raises the issue of how ethylene requires developmental regulators and focuses on the developmental aspect of leaf senescence. It also emphasizes the remarkable impact that developmental regulators have on regulating the onset of leaf senescence.

HOMEOBOX PROTEIN52 Mediates the Crosstalk between Ethylene and Auxin Signaling during Primary Root Elongation by Modulating Auxin Transport-Related Gene Expression

The gaseous hormone ethylene participates in many physiological processes in plants. Ethylene-inhibited root elongation involves PIN-FORMED2 (PIN2)-mediated basipetal auxin transport, but the molecular mechanisms underlying the regulation of PIN2 function by ethylene (and therefore auxin distribution) are poorly understood. Here, we report that the plant-specific and ethylene-responsive HD-Zip gene HB52 is involved in ethylene-mediated inhibition of primary root elongation in Arabidopsis thaliana Biochemical and genetic analyses demonstrated that HB52 is ethylene responsive and acts downstream of ETHYLENE-INSENSITIVE3 (EIN3). HB52 knockdown mutants displayed an ethylene-insensitive phenotype during primary root elongation, while its overexpression resulted in short roots, as observed in ethylene-treated plants. In addition, root auxin distribution and gravitropism were impaired in HB52 knockdown and overexpression lines. Consistent with these findings, in vitro and in vivo binding experiments showed that HB52 regulates the expression of auxin transport-related genes, including PIN2, WAVY ROOT GROWTH1 (WAG1), and WAG2 by physically binding to their promoter regions. These findings suggest that HB52 functions in the ethylene-mediated inhibition of root elongation by modulating the expression of auxin transport components downstream of EIN3, revealing a mechanism in which HB52 acts as an important node in the crosstalk between ethylene and auxin signaling during plant growth and development.

Arabidopsis ACC Oxidase 1 Coordinated by Multiple Signals Mediates Ethylene Biosynthesis and Is Involved in Root Development

Ethylene regulates numerous aspects of plant growth and development. Multiple external and internal factors coordinate ethylene production in plant tissues. Transcriptional and post-translational regulations of ACC synthases (ACSs), which are key enzymes mediating a rate-limiting step in ethylene biosynthesis have been well characterized. However, the regulation and physiological roles of ACC oxidases (ACOs) that catalyze the final step of ethylene biosynthesis are largely unknown in Arabidopsis. Here, we show that Arabidopsis ACO1 exhibits a tissue-specific expression pattern that is regulated by multiple signals, and plays roles in the lateral root development in Arabidopsis. Histochemical analysis of the ACO1 promoter indicated that ACO1 expression was largely modulated by light and plant hormones in a tissue-specific manner. We demonstrated that point mutations in two E-box motifs on the ACO1 promoter reduce the light-regulated expression patterns of ACO1. The aco1-1 mutant showed reduced ethylene production in root tips compared to wild-type. In addition, aco1-1 displayed altered lateral root formation. Our results suggest that Arabidopsis ACO1 integrates various signals into the ethylene biosynthesis that is required for ACO1's intrinsic roles in root physiology.

Ethylene signaling is critical for synergid cell functional specification and pollen tube attraction

ETHYLENE INSENSITIVE 3 (EIN3) is a key regulator of ethylene signaling, and EIN3-BINDING F-BOX1 (EBF1) and EBF2 are responsible for EIN3 degradation. Previous reports have shown that the ebf1 ebf2 double homozygous mutant cannot be identified. In this study, the genetic analysis revealed that the ebf1 ebf2 female gametophyte is defective. The pollination experiment showed that ebf1 ebf2 ovules failed to attract pollen tubes. In female gametophyte/ovule, the synergid cell is responsible for pollen tube attraction. Observation of the pEIN3::EIN3-GFP transgenic lines showed that EIN3 signal was over-accumulated at the micropylar end of ebf1 ebf2 female gametophyte. The overexpression of stabilized EIN3 in synergid cell led to the defect of pollen tube guidance. These results suggested that the over-accumulated EIN3 in ebf1 ebf2 synergid cell blocks its pollen tube attraction which leads to the failure of ebf1 ebf2 homozygous plant. We identified that EIN3 directly activated the expression of a sugar transporter, SENESCENCE-ASSOCIATED GENE29 (SAG29/SWEET15). Overexpression of SAG29 in synergid cells blocked pollen tube attraction, suggesting that SAG29 might play a role in ethylene signaling to repel pollen tube entry. Taken together, our study reveals that strict control of ethylene signaling is critical for the synergid cell function during plant reproduction.

Sucrose Signaling Regulates Anthocyanin Biosynthesis Through a MAPK Cascade in Arabidopsis thaliana

Anthocyanin accumulation specifically depends on sucrose (Suc) signaling. However, the molecular basis of this process remains unknown. In this study, in vitro pull-down assays identified ETHYLENE-INSENSITIVE3 (EIN3), a component of both sugar signaling or/and metabolism. This protein interacted with YDA, and the physiological relevance of this interaction was confirmed by in planta co-immunoprecipitation, yeast two-hybrid (Y2H) assay, and bimolecular fluorescence complementation. Ethylene insensitive3-like 1 (eil1) ein3 double-mutant seedlings, but not ein3-1 seedlings, showed anthocyanin accumulation. Furthermore, ein3-1 suppressed anthocyanin accumulation in yda-1 plants. Thus, EMB71/YDA-EIN3-EIL1 may form a sugar-mediated gene cascade integral to the regulation of anthocyanin accumulation. Moreover, the EMB71/YDA-EIN3-EIL1 gene cascade module directly targeted the promoter of Transparent Testa 8 (TT8) by direct EIN3 binding. Collectively, our data inferred a molecular model where the signaling cascade of the YDA-EIN3-TT8 appeared to target TT8 via EIN3, thereby modulating Suc signaling-mediated anthocyanin accumulation.

DELLA proteins negatively regulate dark-induced senescence and chlorophyll degradation in Arabidopsis through interaction with the transcription factor WRKY6

DELLA proteins' negative regulation of dark-induced senescence and chlorophyll degradation in Arabidopsis is through interaction with WRKY6 and thus repression of its transcriptional activities on senescence-related genes. Senescence is an intricate and highly orchestrated process regulated by numerous endogenous and environmental signals. Gibberellins (GAs) and their signaling components DELLA proteins have been known to participate in the regulation of senescence. However, the mechanism of the GA-DELLA system involved in the senescence process remains largely unclear. Darkness is a known environmental factor that induces plant senescence. In this study, exogenous GA₃ (an active form of GA) accelerated but paclobutrazol (a specific GA biosynthesis inhibitor) retarded dark-induced leaf yellowing in Arabidopsis. Moreover, the dark-triggered decrease in chlorophyll content, increase in cell membrane leakage, and upregulation of senescence-associated genes were notably impaired in both endogenous GA-decreased mutants ga3ox1/ga3ox2 and ga20ox1/ga20ox2 compared with those in wild-type Col-0. These effects of darkness were enhanced in the quintuple mutant of DELLA genes gai-t6/rga-t2/rgl1-1/rgl2-1/rgl3-1 and conversely attenuated in the gain-of-function mutant gai and transgenic plant 35S::TAP-RGAd17 compared with wild-type Ler. Subsequently, RGA interacted with the transcription factor WRKY6 in a yeast two-hybrid assay, as confirmed by bimolecular fluorescence complementation and pull-down analyses. In addition, mutation and overexpression of WRKY6 retarded and accelerated dark-induced senescence, respectively. Furthermore, transient expression assays in Arabidopsis protoplasts indicated that RGA and GAI weakened the transcriptional activities of WRKY6 on its downstream senescence-related genes, including SAG13 and SGR. Taken together, these results suggest that GAs positively and DELLAs negatively regulate dark-induced senescence and chlorophyll degradation in Arabidopsis. DELLAs function in this process, at least in part, by interacting with WRKY6.

Ectopic expression of VpSTS29, a stilbene synthase gene from Vitis pseudoreticulata, indicates STS presence in cytosolic oil bodies

Stilbene synthase (STS) and its metabolic products are accumulated in senescing grapevine leaves. Ectopic expression of VpSTS29 in Arabidopsis shows the presence of VpSTS29 in oil bodies and increases trans-piceid in developing leaves. Stilbenes are the natural antimicrobial phytoalexins that are synthesised via the phenylpropanoid pathway. STS is the key enzyme catalysing the production of stilbenes. We have previously reported that the VpSTS29 gene plays an important role in powdery mildew resistance in Vitis pseudoreticulata. However, the synthesis and accumulation of these stilbene products in plant cells remain unclear. Here, we demonstrate that VpSTS29 is present in cytosolic oil bodies and can be transported into the vacuole at particular plant-developmental stages. Western blot and high-performance liquid chromatography showed that STS and trans-piceid accumulated in senescent grape leaves and in pVpSTS29::VpSTS29-expressing Arabidopsis during age-dependent leaf senescence. Subcellular localisation analyses indicated VpSTS29-GFP was present in the cytoplasm and in STS-containing bodies in Arabidopsis. Nile red staining, co-localisation and immunohistochemistry analyses of leaves confirmed that the STS-containing bodies were oil bodies and that these moved randomly in the cytoplasm and vacuole. Detection of protein profiles revealed that no free GFP was detected in the pVpSTS29::VpSTS29-GFP-expressing protoplasts or in Arabidopsis during the dark-light cycle, demonstrating that GFP fluorescence distributed in the STS-containing bodies and vacuole was the VpSTS29-GFP fusion protein. Intriguingly, in comparison to the controls, over-expression of VpSTS29 in Arabidopsis resulted in relatively high levels of trans-piceid, chlorophyll content and of photochemical efficiency accompanied by delayed leaf senescence. These results provide exciting new insights into the subcellular localisation of STS in plant cells and information about stilbene synthesis and storage.

Comparative transcriptome analysis in Arabidopsis ein2/ore3 and ahk3/ore12 mutants during dark-induced leaf senescence

Leaf senescence involves degenerative but active biological processes that require balanced regulation of pro- and anti-senescing activities. Ethylene and cytokinin are major antagonistic regulatory hormones that control the timing and progression rate of leaf senescence. To identify the roles of these hormones in the regulation of leaf senescence in Arabidopsis, global gene expression profiles in detached leaves of the wild type, an ethylene-insensitive mutant (ein2/ore3), and a constitutive cytokinin response mutant (ahk3/ore12) were investigated during dark-induced leaf senescence. Comparative transcriptome analyses revealed that genes involved in oxidative or salt stress response were preferentially altered in the ein2/ore3 mutant, whereas genes involved in ribosome biogenesis were affected in the ahk3/ore12 mutant during dark-induced leaf senescence. Similar results were also obtained for developmental senescence. Through extensive molecular and physiological analyses in ein2/ore3 and ahk3/ore12 during dark-induced leaf senescence, together with responses when treated with cytokinin and ethylene inhibitor, we conclude that ethylene acts as a senescence-promoting factor via the transcriptional regulation of stress-related responses, whereas cytokinin acts as an anti-senescing agent by maintaining cellular activities and preserving the translational machinery. These findings provide new insights into how plants utilize two antagonistic hormones, ethylene and cytokinin, to regulate the molecular programming of leaf senescence.

Cross Regulatory Network Between Circadian Clock and Leaf Senescence Is Emerging in Higher Plants

Circadian clock and senescence have been shown to tightly intertwined with each other in numerous eukaryotes, but the regulation of circadian oscillator on triggering leaf senescence, and vice versa, remains largely unknown in higher plants. Very recently, circadian system and leaf senescence were found to be highly interconnected in higher plants. Circadian clock was shown to regulate leaf senescence through a few cross signaling pathways including age-dependent, plant hormone mediated, and dark induced manners to trigger the onset of leaf senescence. By contrast, circadian clock itself also can be affected by the leaves senescing process. The eventually delineating cross networks between circadian clock and leaf senescence will lay the foundation for understanding the fitness of developmental dynamics of plants with aging.

Ethylene Exerts Species-Specific and Age-Dependent Control of Photosynthesis

Ethylene regulates many different aspects of photosynthesis in an age-dependent and species-specific manner.