NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis

Genetic Network between Leaf Senescence and Plant Immunity: Crucial Regulatory Nodes and New Insights

Leaf senescence is an essential physiological process that is accompanied by the remobilization of nutrients from senescent leaves to young leaves or other developing organs. Although leaf senescence is a genetically programmed process, it can be induced by a wide variety of biotic and abiotic factors. Accumulating studies demonstrate that senescence-associated transcription factors (Sen-TFs) play key regulatory roles in controlling the initiation and progression of leaf senescence process. Interestingly, recent functional studies also reveal that a number of Sen-TFs function as positive or negative regulators of plant immunity. Moreover, the plant hormone salicylic acid (SA) and reactive oxygen species (ROS) have been demonstrated to be key signaling molecules in regulating leaf senescence and plant immunity, suggesting that these two processes share similar or common regulatory networks. However, the interactions between leaf senescence and plant immunity did not attract sufficient attention to plant scientists. Here, we review the regulatory roles of SA and ROS in biotic and abiotic stresses, as well as the cross-talks between SA/ROS and other hormones in leaf senescence and plant immunity, summarize the transcriptional controls of Sen-TFs on SA and ROS signal pathways, and analyze the cross-regulation between senescence and immunity through a broad literature survey. In-depth understandings of the cross-regulatory mechanisms between leaf senescence and plant immunity will facilitate the cultivation of high-yield and disease-resistant crops through a molecular breeding strategy.

Regulatory changes in TaSNAC8-6A are associated with drought tolerance in wheat seedlings

Wheat is a staple crop produced in arid and semi-arid areas worldwide, and its production is frequently compromised by water scarcity. Thus, increased drought tolerance is a priority objective for wheat breeding programmes, and among their targets, the NAC transcription factors have been demonstrated to contribute to plant drought response. However, natural sequence variations in these genes have been largely unexplored for their potential roles in drought tolerance. Here, we conducted a candidate gene association analysis of the stress-responsive NAC gene subfamily in a wheat panel consisting of 700 varieties collected worldwide. We identified a drought responsive gene, TaSNAC8-6A, that is tightly associated with drought tolerance in wheat seedlings. Further analysis found that a favourable allele TaSNAC8-6A^In-313 , carrying an insertion in the ABRE promoter motif, is targeted by TaABFs and confers enhanced drought-inducible expression of TaSNAC8-6A in drought-tolerant genotypes. Transgenic wheat and Arabidopsis TaSNAC8-6A overexpression lines exhibited enhanced drought tolerance through induction of auxin- and drought-response pathways, confirmed by transcriptomic analysis, that stimulated lateral root development, subsequently improving water-use efficiency. Taken together, our findings reveal that natural variation in TaSNAC8-6A and specifically the TaSNAC8-6A^In-313 allele strongly contribute to wheat drought tolerance and thus represent a valuable genetic resource for improvement of drought-tolerant germplasm for wheat production.

Lfo-miR164b and LfNAC1 as autumn leaf senescence regulators in Formosan sweet gum (Liquidambar formosana Hance)

In this study, a microRNA microarray was used to investigate the microRNA profiles from young green leaves, and senescent red leaves and yellow leaves of Formosan sweet gum (Liquidambar formosana Hance). The conserved microRNA miR164 was highly expressed in green leaves compared to senescent leaves. The pri-microRNA of miR164 was identified and named lfo-miR164b based on its secondary structure. In Agrobacterium-mediated transient expression experiment, lfo-miR164b was confirmed to regulate the leaf senescence-associated gene LfNAC1 and LfNAC100. Transient overexpression of LfNAC1 induced the expression of leaf senescence genes in Nicotiana benthamiana. In addition, LfNAC1 activated the expression of proLfSGR::YFP, suggesting the regulatory role of LfNAC1 in leaf senescence. In summary, miR164 inhibits the expression of LfNAC1 in spring and summer, later on LfNAC1 actives leaf senescence-associated genes to cause leaf senescence following a gradual decline of miR164 as the seasons change. The "miR164-NAC" regulatory mechanism was confirmed in Formosan sweet gum autumn leaf senescence.

Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis

Plant organ growth is widely accepted to be determined by cell division and cell expansion, but, unlike that in animals, the contribution of cell elimination has rarely been recognized. We investigated this paradigm during Arabidopsis lateral root formation, when the lateral root primordia (LRP) must traverse three overlying cell layers within the parent root. A subset of LRP-overlying cells displayed the induction of marker genes for cell types undergoing developmental cell death, and their cell death was detected by electron, confocal, and light sheet microscopy techniques. LRP growth was delayed in cell-death-deficient mutants lacking the positive cell death regulator ORESARA1/ANAC092 (ORE1). LRP growth was restored in ore1-2 knockout plants by genetically inducing cell elimination in cells overlying the LRP or by physically killing LRP-overlying cells by ablation with optical tweezers. Our results support that, in addition to previously discovered mechanisms, cell elimination contributes to regulating lateral root emergence.

Novel Aspects of Nitrate Regulation in Arabidopsis

Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO₃ ^-), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO₃ ^- regulation and starting to unravel the NO₃ ^- regulatory network. Great reviews have been made recently by scientists on the key regulators in NO₃ ^- signaling, NO₃ ^- effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO₃ ^- regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO₃ ^- signaling, and NO₃ ^- regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO₃ ^- regulation and provide a basis for further exploration of NO₃ ^- regulatory network.

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach

BACKGROUND

Leaf senescence is a complex process, controlled by multiple genetic and environmental variables. In sunflower, leaf senescence is triggered abruptly following anthesis thereby limiting the capacity of plants to keep their green leaf area during grain filling, which subsequently has a strong impact on crop yield. Recently, we performed a selection of contrasting sunflower inbred lines for the progress of leaf senescence through a physiological, cytological and molecular approach. Here we present a large scale transcriptomic analysis using RNA-seq and its integration with metabolic profiles for two contrasting sunflower inbred lines, R453 and B481-6 (early and delayed senescence respectively), with the aim of identifying metabolic pathways associated to leaf senescence.

RESULTS

Gene expression profiles revealed a higher number of differentially expressed genes, as well as, higher expression levels in R453, providing evidence for early activation of the senescence program in this line. Metabolic pathways associated with sugars and nutrient recycling were differentially regulated between the lines. Additionally, we identified transcription factors acting as hubs in the co-expression networks; some previously reported as senescence-associated genes in model species but many are novel candidate genes.

CONCLUSIONS

Understanding the onset and the progress of the senescence process in crops and the identification of these new candidate genes will likely prove highly useful for different management strategies to mitigate the impact of senescence on crop yield. Functional characterization of candidate genes will help to develop molecular tools for biotechnological applications in breeding crop yield.

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.

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.

Arabidopsis ANAC092 regulates auxin-mediated root development by binding to the ARF8 and PIN4 promoters

Auxin is an important plant hormone that is essential for growth and development due to its effects on organogenesis, morphogenesis, tropisms, and apical dominance. The functional diversity of auxin highlights the importance of its biosynthesis, transport, and associated responses. In this study, we show that a NAC transcription factor, ANAC092 (also named AtNAC2 and ORESARA1), known to positively regulate leaf senescence and contribute to abiotic stress responses, also affects primary root development. Plants overexpressing ANAC092 had altered root meristem lengths and shorter primary roots compared with the wild-type control. Additionally, expression of the proANAC092::GUS was strongly induced by indole-3-acetic acid. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that the YUCCA2, PIN, and ARF expression levels were downregulated in ANAC092-overexpressing plants. Moreover, yeast one-hybrid and chromatin immunoprecipitation assays confirmed that ANAC092 binds to the promoters of AUXIN RESPONSE FACTOR 8 (ARF8) and PIN-FORMED 4 (PIN4). Furthermore, a dual-luciferase assay indicated that ANAC092 decreases ARF8 and PIN4 promoter activities. We also applied a CRISPR/Cas9 system to mutate ANAC092. The roots of three of the analyzed mutants were longer than normal. Collectively, our findings indicate that ANAC092 negatively affects root development by controlling the auxin pathway.

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

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

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.

Organelle DNA degradation contributes to the efficient use of phosphate in seed plants

Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin.

Arabidopsis NITROGEN LIMITATION ADAPTATION regulates ORE1 homeostasis during senescence induced by nitrogen deficiency

Nitrogen is an important macronutrient in plants and its deficiency induces rapid leaf senescence. Two genes, ORE1 and NITROGEN LIMITATION ADAPTATION (NLA), have been implicated in regulating the senescence process but their relationship is unclear^1,2. Here, we show that nla and pho2 (also known as ubc24) plants develop rapid leaf senescence under nitrogen-starvation condition, whereas ore1 and nla/ore1 and pho2 (ubc24)/ore1 plants stay green. These results suggest that ORE1 acts downstream of NLA and PHO2 (UBC24). NLA interacts with ORE1 in the nucleus and regulates its stability through polyubiquitination using PHO2 (UBC24) as the E2 conjugase. Our findings identified ORE1 as a downstream target of NLA/PHO2 (UBC24) and showed that post-translational regulation of ORE1 levels determines leaf senescence during nitrogen deficiency.

Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems

Pith parenchyma cells store water in various plant organs. These cells are especially important for producing sugar and ethanol from the sugar juice of grass stems. In many plants, the death of pith parenchyma cells reduces their stem water content. Previous studies proposed that a hypothetical D gene might be responsible for the death of stem pith parenchyma cells in Sorghum bicolor, a promising energy grass, although its identity and molecular function are unknown. Here, we identify the D gene and note that it is located on chromosome 6 in agreement with previous predictions. Sorghum varieties with a functional D allele had stems enriched with dry, dead pith parenchyma cells, whereas those with each of six independent nonfunctional D alleles had stems enriched with juicy, living pith parenchyma cells. D expression was spatiotemporally coupled with the appearance of dead, air-filled pith parenchyma cells in sorghum stems. Among D homologs that are present in flowering plants, Arabidopsis ANAC074 also is required for the death of stem pith parenchyma cells. D and ANAC074 encode previously uncharacterized NAC transcription factors and are sufficient to ectopically induce programmed death of Arabidopsis culture cells via the activation of autolytic enzymes. Taken together, these results indicate that D and its Arabidopsis ortholog, ANAC074, are master transcriptional switches that induce programmed death of stem pith parenchyma cells. Thus, targeting the D gene will provide an approach to breeding crops for sugar and ethanol production.

GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia

Leaf growth is a complex process that involves the action of diverse transcription factors (TFs) and their downstream gene regulatory networks. In this study, we focus on the functional characterization of the Arabidopsis thaliana TF GROWTH-REGULATING FACTOR9 (GRF9) and demonstrate that it exerts its negative effect on leaf growth by activating expression of the bZIP TF OBP3-RESPONSIVE GENE 3 (ORG3). While grf9 knockout mutants produce bigger incipient leaf primordia at the shoot apex, rosette leaves and petals than the wild type, the sizes of those organs are reduced in plants overexpressing GRF9 (GRF9ox). Cell measurements demonstrate that changes in leaf size result from alterations in cell numbers rather than cell sizes. Kinematic analysis and 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay revealed that GRF9 restricts cell proliferation in the early developing leaf. Performing in vitro binding site selection, we identified the 6-base motif 5'-CTGACA-3' as the core binding site of GRF9. By global transcriptome profiling, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) we identified ORG3 as a direct downstream, and positively regulated target of GRF9. Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf.

Molecular and functional characterization of ShNAC1, an NAC transcription factor from Solanum habrochaites

NAC transcription factors (TFs) are important regulators of plant adaptation to abiotic stress. In this study, we functionally characterized an NAC TF, ShNAC1, from Solanum habrochaites. ShNAC1 was up-regulated by drought, cold, and salt stresses, and it displayed lower expression at the late stage of stress treatments than its orthologous gene in S. lycopersicum. Overexpression of ShNAC1 in tomato resulted in reduced cold, drought, and salt tolerance. Additionally, ShNAC1 displayed the highest expression in senescent leaf, and overexpressing ShNAC1 accelerated salt- and dark-induced leaf senescence. ShNAC1 was located in the nucleus without transactivation activity. RNA-seq analysis revealed that 81% (190 out of 234) differentially-expressed genes (DEGs) showed down-regulation in the transgenic line L2 compared with wild-type, suggesting that ShNAC1 may function as a transcriptional repressor. Among these down-regulated DEGs, many were involved in stress responses, such as SlHKT1;1, SlMAPKKK59, SlJA2, SlTIL, SlALDH2B1, etc. Noticeably, one ACS gene and three ACO genes involved in ethylene biosynthesis were up-regulated, while seven ERF genes in the ethylene signal transduction pathway were down-regulated in the transgenic lines, respectively. Our results suggested that ShNAC1 negatively regulates tolerance to abiotic stress in tomato probably by modulating the ethylene biosynthesis and signal transduction pathways.

KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis

Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.

OsNAC2 positively affects salt-induced cell death and binds to the OsAP37 and OsCOX11 promoters

Plant development and adaptation to environmental stresses are intimately associated with programmed cell death (PCD). Although some of the mechanisms regulating PCD [e.g., accumulation of reactive oxygen species (ROS)] are common among responses to different abiotic stresses, the pathways mediating salt-induced PCD remain largely uncharacterized. Here we report that overexpression of OsNAC2, which encodes a plant-specific transcription factor, promotes salt-induced cell death accompanied by the loss of plasma membrane integrity, nuclear DNA fragmentation, and changes to caspase-like activity. In OsNAC2-knockdown lines, cell death was markedly decreased in response to severe salt stress. Additionally, OsNAC2 expression was enhanced in rice seedlings exposed to a high NaCl concentration. Moreover, the results of quantitative real-time PCR, chromatin immunoprecipitation, dual-luciferase, and yeast one-hybrid assays indicated that OsNAC2 targeted genes that encoded an ROS scavenger (OsCOX11) and a caspase-like protease (OsAP37). Furthermore, K⁺ -efflux channels (OsGORK and OsSKOR) were clearly activated by OsNAC2. Overall, our results suggested that OsNAC2 accelerates NaCl-induced PCD and provide new insights into the mechanisms that affect ROS accumulation, plant caspase-like activity, and K⁺ efflux.

Plant organ senescence - regulation by manifold pathways

Senescence is the final stage of plant ontogeny before death. Senescence may occur naturally because of age or may be induced by various endogenous and exogenous factors. Despite its destructive character, senescence is a precisely controlled process that follows a well-defined order. It is often inseparable from programmed cell death (PCD), and a correlation between these processes has been confirmed during the senescence of leaves and petals. Despite suggestions that senescence and PCD are two separate processes, with PCD occurring after senescence, cell death responsible for senescence is accompanied by numerous changes at the cytological, physiological and molecular levels, similar to other types of PCD. Independent of the plant organ analysed, these changes are focused on initiating the processes of cellular structural degradation via fluctuations in phytohormone levels and the activation of specific genes. Cellular structural degradation is genetically programmed and dependent on autophagy. Phytohormones/plant regulators are heavily involved in regulating the senescence of plant organs and can either promote [ethylene, abscisic acid (ABA), jasmonic acid (JA), and polyamines (PAs)] or inhibit [cytokinins (CKs)] this process. Auxins and carbohydrates have been assigned a dual role in the regulation of senescence, and can both inhibit and stimulate the senescence process. In this review, we introduce the basic pathways that regulate senescence in plants and identify mechanisms involved in controlling senescence in ephemeral plant organs. Moreover, we demonstrate a universal nature of this process in different plant organs; despite this process occurring in organs that have completely different functions, it is very similar. Progress in this area is providing opportunities to revisit how, when and which way senescence is coordinated or decoupled by plant regulators in different organs and will provide a powerful tool for plant physiology research.

Small but powerful: function of microRNAs in plant development

MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs. We will summarize the regulatory networks of miRNAs in a series of developmental processes, including meristem development, establishment of lateral organ polarity and boundaries, vegetative and reproductive organ growth, etc. We will also conclude the conserved and species-specific roles of plant miRNAs in evolution and discuss the strategies for further elucidating the functional mechanisms of miRNAs during plant development.

Genetic redundancy of senescence-associated transcription factors in Arabidopsis

Leaf senescence is a genetically programmed process that constitutes the last stage of leaf development, and involves massive changes in gene expression. As a result of the intensive efforts that have been made to elucidate the molecular genetic mechanisms underlying leaf senescence, 184 genes that alter leaf senescence phenotypes when mutated or overexpressed have been identified in Arabidopsis thaliana over the past two decades. Concurrently, experimental evidence on functional redundancy within senescence-associated genes (SAGs) has increased. In this review, we focus on transcription factors that play regulatory roles in Arabidopsis leaf senescence, and describe the relationships among gene duplication, gene expression level, and senescence phenotypes. Previous findings and our re-analysis demonstrate the widespread existence of duplicate SAG pairs and a correlation between gene expression levels in duplicate genes and senescence-related phenotypic severity of the corresponding mutants. We also highlight effective and powerful tools that are available for functional analyses of redundant SAGs. We propose that the study of duplicate SAG pairs offers a unique opportunity to understand the regulation of leaf senescence and can guide the investigation of the functions of redundant SAGs via reverse genetic approaches.

Petal senescence: a hormone view

Flowers are highly complex organs that have evolved to enhance the reproductive success of angiosperms. As a key component of flowers, petals play a vital role in attracting pollinators and ensuring successful pollination. Having fulfilled this function, petals senesce through a process that involves many physiological and biochemical changes that also occur during leaf senescence. However, petal senescence is distinct, due to the abundance of secondary metabolites in petals and the fact that petal senescence is irreversible. Various phytohormones are involved in regulating petal senescence, and are thought to act both synergistically and antagonistically. In this regard, there appears to be developmental point during which such regulatory signals are sensed and senescence is initiated. Here, we review current understanding of petal senescence, and discuss associated regulatory mechanisms involving hormone interactions and epigenetic regulation.

Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

BACKGROUND

Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms.

RESULTS

We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter. We showed that they were tolerant to drought stress with reduced loss of grain yield under drought conditions compared with wild type plants. To understand the molecular mechanisms underlying this tolerance, we here performed chromatin immunoprecipitation (ChIP)-Seq and RNA-Seq analyses to identify the direct target genes of the OsNAC proteins using the RCc3:6MYC-OsNAC expressing roots. A total of 475 binding loci for the 4 OsNAC proteins were identified by cross-referencing their binding to promoter regions and the expression levels of the corresponding genes. The binding loci were distributed among the promoter regions of 391 target genes that were directly up-regulated by one of the OsNAC proteins in four RCc3:6MYC-OsNAC transgenic lines. Based on gene ontology (GO) analysis, the direct target genes were related to transmembrane/transporter activity, vesicle, plant hormones, carbohydrate metabolism, and TFs. The direct targets of each OsNAC range from 4.0-8.7% of the total number of up-regulated genes found in the RNA-Seq data sets. Thus, each OsNAC up-regulates a set of direct target genes that alter root system architecture in the RCc3:OsNAC plants to confer drought tolerance. Our results provide a valuable resource for functional dissection of the molecular mechanisms of drought tolerance.

CONCLUSIONS

Many of the target genes, including transmembrane/transporter, vesicle related, auxin/hormone related, carbohydrate metabolic processes, and transcription factor genes, that are up-regulated by OsNACs act as the cellular components which would alter the root architectures of RCc3:OsNACs for drought tolerance.

WRKY70 prevents axenic activation of plant immunity by direct repression of SARD1

SARD1 is an activator of plant immunity that promotes production of the hormone salicylic acid (SA) and activation of defense gene expression. SARD1 itself is strongly inducible by infection. Here, we investigated the transcriptional control of SARD1. We used yeast one-hybrid assays to identify WRKY70. The WRKY70 binding site was defined using electrophoretic mobility shift assays, and its importance was investigated using an Arabidopsis thaliana protoplast system. The effect of wrky70 mutations was studied by measurements of pathogen growth, SA concentrations, and gene expression by RNA-seq. WRKY70 binds to a GACTTTT motif in the SARD1 promoter in yeast and Arabidopsis protoplasts. Plants with wrky70 mutations have elevated expression of SARD1 in the absence of pathogens, but not when infected. Expression profiling revealed that WRKY70 represses many pathogen-inducible genes in the absence of pathogens, yet is required for activation of many other pathogen-inducible genes in infected plants. The GACTTTT motif is enriched in the promoters of both these gene sets, and conserved in SARD1 orthologs within the Brassicaceae. WRKY70 represses SARD1 by binding the motif GACTTTT in the absence of pathogens. Conservation of the WRKY70 binding among the Brassicaceae suggests that WRKY70 repression of SARD1 is important for fitness.

Arabidopsis EARLY FLOWERING3 increases salt tolerance by suppressing salt stress response pathways

Arabidopsis EARLY FLOWERING3 (ELF3) functions in modulating light input to the circadian clock, as a component of ELF3-ELF4-LUX ARRHYTHMO (LUX) evening complex. However, the role of ELF3 in stress responses remains largely unknown. In this study, we show that ELF3 enhances plants' resilience to salt stress: ELF3-overexpressing (ELF3-OX) plants are salt-tolerant, while elf3 mutants are more sensitive to salt stress. The expressions of many salt stress- and senescence-associated genes are altered in elf3-1 and ELF3-OX plants compared with wild-type. During salt stress, ELF3 suppresses factors that promote salt stress response pathways, mainly GIGANTEA (GI), at the post-translational level, and PHYTOCHROME INTERACTING FACTOR4 (PIF4), at the transcriptional level. To enhance the salt stress response, PIF4 directly downregulates the transcription of JUNGBRUNNEN1 (JUB1/ANAC042), encoding a transcription factor that upregulates the expression of stress tolerance genes, DREB2A and DELLA. Furthermore, PIF4 directly upregulates the transcription of ORESARA1 (ORE1/ANAC092) and SAG29, positive regulators of salt stress response pathways. Based on our results, we propose that ELF3 modulates key regulatory components in salt stress response pathways at the transcriptional and post-translational levels.

Plant-Derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae

Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis-regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver/reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC-EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF-DNA binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast.

A Conserved Carbon Starvation Response Underlies Bud Dormancy in Woody and Herbaceous Species

Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence. Although some key genes involved in the onset of bud latency have been identified, the gene regulatory networks (GRNs) controlled by these genes are not well defined. Moreover, it has not been determined whether bud dormancy induced by environmental cues, such as a low red-to-far-red light ratio, shares genetic mechanisms with bud latency induced by other causes, such as apical dominance or a short-day photoperiod. Furthermore, the evolution and conservation of these GRNs throughout angiosperms is not well established. We have reanalyzed public transcriptomic datasets that compare quiescent and active axillary buds of Arabidopsis, with datasets of axillary buds of the woody species Vitis vinifera (grapevine) and apical buds of Populus tremula x Populus alba (poplar) during the bud growth-to-dormancy transition. Our aim was to identify potentially common GRNs induced during the process that leads to bud para-, eco- and endodormancy. In Arabidopsis buds that are entering eco- or paradormancy, we have identified four induced interrelated GRNs that correspond to a carbon (C) starvation syndrome, typical of tissues undergoing low C supply. This response is also detectable in poplar and grapevine buds before and during the transition to dormancy. In all eukaryotes, C-limiting conditions are coupled to growth arrest and latency like that observed in dormant axillary buds. Bud dormancy might thus be partly a consequence of the underlying C starvation syndrome triggered by environmental and endogenous cues that anticipate or signal conditions unfavorable for sustained shoot growth.

Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops

As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.

Arabidopsis ANAC069 binds to C[A/G]CG[T/G] sequences to negatively regulate salt and osmotic stress tolerance

ANAC069 binds to the DNA sequence of C[A/G]CG[T/G] to regulate the expression of genes, resulting in decreased ROS scavenging capability and proline biosynthesis, which contribute to increased sensitivity to salt and osmotic stress. NAM-ATAF1/2 and CUC2 (NAC) proteins are plant-specific transcription factors that play important roles in abiotic stress responses. In the present study, we characterized the physiological and regulatory roles of Arabidopsis thaliana ANAC069 in response to abiotic stresses. Arabidopsis plants overexpressing ANAC069 displayed increased sensitivity to abscisic acid, salt, and osmotic stress. Conversely, ANAC069 knockdown plants showed enhanced tolerance to salt and osmotic stress, but no change in ABA sensitivity. Further studies showed that ANAC069 inhibits the expression of SOD, POD, GST, and P5CS genes. Consequently, the transcript level of ANAC069 correlated negatively with the reactive oxygen species (ROS) scavenging ability and the proline level. The genes regulated by ANAC069 were further studied using a gene chip on a genome-wide scale, and 339 and 226 genes up- and downregulated by ANAC069 were identified. Analysis of the promoters of the genes affected by ANAC069 suggested that ANAC069 regulates the expression of genes mainly through interacting with the DNA sequence C[A/G]CG[T/G] in response to abiotic stresses. Collectively, our data suggest that ANAC069 could recognize C[A/G]CG[T/G] sequences to regulate the expression of genes that negatively regulates salt and osmotic stress tolerance by decreasing ROS scavenging capability and proline biosynthesis.

An NAM Domain Gene, GhNAC79, Improves Resistance to Drought Stress in Upland Cotton

Plant-specific NAC proteins comprise one of the largest transcription factor families in plants and play important roles in plant development and the stress response. Gossypium hirsutum L. is a major source of fiber, but its growth and productivity are limited by many biotic and abiotic stresses. In this study, the NAC domain gene GhNAC79 was functionally characterized in detail, and according to information about the cotton genome sequences, it was located on scaffold42.1, containing three exons and two introns. Promoter analysis indicated that the GhNAC79 promoter contained both basic and stress-related elements, and it was especially expressed in the cotyledon of Arabidopsis. A transactivation assay in yeast demonstrated that GhNAC79 was a transcription activator, and its activation domain was located at its C-terminus. The results of qRT-PCR proved that GhNAC79 was preferentially expressed at later stages of cotyledon and fiber development, and it showed high sensitivity to ethylene and meJA treatments. Overexpression of GhNAC79 resulted in an early flowering phenotype in Arabidopsis, and it also improved drought tolerance in both Arabidopsis and cotton. Furthermore, VIGS-induced silencing of GhNAC79 in cotton led to a drought-sensitive phenotype. In summary, GhNAC79 positively regulates drought stress, and it also responds to ethylene and meJA treatments, making it a candidate gene for stress studies in cotton.

Dark-induced leaf senescence: new insights into a complex light-dependent regulatory pathway

563 I. 563 II. 564 III. 564 IV. 565 V. 565 VI. 567 VII. 567 568 References 568 SUMMARY: Leaf senescence - the coordinated, active process leading to the organized dismantling of cellular components to remobilize resources - is a fundamental aspect of plant life. Its tight regulation is essential for plant fitness and has crucial implications for the optimization of plant productivity and storage properties. Various investigations have shown light deprivation and light perception via phytochromes as key elements modulating senescence. However, the signalling pathways linking light deprivation and actual senescence processes have long remained obscure. Recent analyses have demonstrated that PHYTOCHROME-INTERACTING FACTORS (PIFs) are major transcription factors orchestrating dark-induced senescence (DIS) by targeting chloroplast maintenance, chlorophyll metabolism, hormone signalling and production, and the expression of senescence master regulators, uncovering potential molecular links to the energy deprivation signalling pathway. PIF-dependent feed-forward regulatory modules might be of critical importance for the highly complex and initially light-reversible DIS induction.

Drought-Up-Regulated TaNAC69-1 is a Transcriptional Repressor of TaSHY2 and TaIAA7, and Enhances Root Length and Biomass in Wheat

A well-known physiological adaptation process of plants encountering drying soil is to achieve water balance by reducing shoot growth and maintaining or promoting root elongation, but little is known about the molecular basis of this process. This study investigated the role of a drought-up-regulated Triticum aestivum NAC69-1 (TaNAC69-1) in the modulation of root growth in wheat. TaNAC69-1 was predominantly expressed in wheat roots at the early vegetative stage. Overexpression of TaNAC69-1 in wheat roots using OsRSP3 (essentially root-specific) and OsPIP2;3 (root-predominant) promoters resulted in enhanced primary seminal root length and a marked increase in maturity root biomass. Competitive growth analysis under water-limited conditions showed that OsRSP3 promoter-driven TaNAC69-1 transgenic lines produced 32% and 35% more above-ground biomass and grains than wild-type plants, respectively. TaNAC69-1 overexpression in the roots down-regulated the expression of TaSHY2 and TaIAA7, which are from the auxin/IAA (Aux/IAA) transcriptional repressor gene family and are the homologs of negative root growth regulators SHY2/IAA3 and IAA7 in Arabidopsis. The expression of TaSHY2 and TaIAA7 in roots was down-regulated by drought stress and up-regulated by cytokinin treatment, which inhibited root growth. DNA binding and transient expression analyses revealed that TaNAC69-1 bound to the promoters of TaSHY2 and TaIAA7, acted as a transcriptional repressor and repressed the expression of reporter genes driven by the TaSHY2 or TaIAA7 promoter. These data suggest that TaNAC69-1 is a transcriptional repressor of TaSHY2 and TaIAA7 homologous to Arabidopsis negative root growth regulators and is likely to be involved in promoting root elongation in drying soil.

Morphological changes in senescing petal cells and the regulatory mechanism of petal senescence

Petal senescence, or programmed cell death (PCD) in petals, is a developmentally regulated and genetically programmed process. During petal senescence, petal cells show morphological changes associated with PCD: tonoplast rupture and rapid destruction of the cytoplasm. This type of PCD is classified as vacuolar cell death or autolytic PCD based on morphological criteria. In PCD of petal cells, characteristic morphological features including an autophagy-like process, chromatin condensation, and nuclear fragmentation are also observed. While the phytohormone ethylene is known to play a crucial role in petal senescence in some plant species, little is known about the early regulation of ethylene-independent petal senescence. Recently, a NAC (NAM/ATAF1,2/CUC2) transcription factor was reported to control the progression of PCD during petal senescence in Japanese morning glory, which shows ethylene-independent petal senescence. In ethylene-dependent petal senescence, functional analyses of transcription factor genes have revealed the involvement of a basic helix-loop-helix protein and a homeodomain-leucine zipper protein in the transcriptional regulation of the ethylene biosynthesis pathway. Here we review the recent advances in our knowledge of petal senescence, mostly focusing on the morphology of senescing petal cells and the regulatory mechanisms of PCD by senescence-associated transcription factors during petal senescence.

Functions and Regulation of Programmed Cell Death in Plant Development

Programmed cell death (PCD) is a collective term for diverse processes causing an actively induced, tightly controlled cellular suicide. PCD has a multitude of functions in the development and health of multicellular organisms. In comparison to intensively studied forms of animal PCD such as apoptosis, our knowledge of the regulation of PCD in plants remains limited. Despite the importance of PCD in plant development and as a response to biotic and abiotic stresses, the complex molecular networks controlling different forms of plant PCD are only just beginning to emerge. With this review, we provide an update on the considerable progress that has been made over the last decade in our understanding of PCD as an inherent part of plant development. We highlight both functions of developmental PCD and central aspects of its molecular regulation.

Molecular Mechanisms of Phosphorus Metabolism and Transport during Leaf Senescence

Leaf senescence, being the final developmental stage of the leaf, signifies the transition from a mature, photosynthetically active organ to the attenuation of said function and eventual death of the leaf. During senescence, essential nutrients sequestered in the leaf, such as phosphorus (P), are mobilized and transported to sink tissues, particularly expanding leaves and developing seeds. Phosphorus recycling is crucial, as it helps to ensure that previously acquired P is not lost to the environment, particularly under the naturally occurring condition where most unfertilized soils contain low levels of soluble orthophosphate (Pi), the only form of P that roots can directly assimilate from the soil. Piecing together the molecular mechanisms that underpin the highly variable efficiencies of P remobilization from senescing leaves by different plant species may be critical for devising effective strategies for improving overall crop P-use efficiency. Maximizing Pi remobilization from senescing leaves using selective breeding and/or biotechnological strategies will help to generate P-efficient crops that would minimize the use of unsustainable and polluting Pi-containing fertilizers in agriculture. This review focuses on the molecular mechanisms whereby P is remobilized from senescing leaves and transported to sink tissues, which encompasses the action of hormones, transcription factors, Pi-scavenging enzymes, and Pi transporters.

Rice ONAC106 Inhibits Leaf Senescence and Increases Salt Tolerance and Tiller Angle

NAM/ATAF1/ATAF2/CUC2 (NAC) is a plant-specific transcription factor (TF) family, and NACs participate in many diverse processes during the plant life cycle. Several Arabidopsis thaliana NACs have important roles in positively or negatively regulating leaf senescence, but in other plant species, including rice, the senescence-associated NACs (senNACs) remain largely unknown. Here we show that the rice senNAC TF ONAC106 negatively regulates leaf senescence. Leaves of onac106-1D (insertion of the 35S enhancer in the promoter region of the ONAC106 gene) mutants retained their green color under natural senescence and dark-induced senescence conditions. Genome-wide transcriptome analysis revealed that key senescence-associated genes (SGR, NYC1, OsNAC5, OsNAP, OsEIN3 and OsS3H) were differentially expressed in onac106-1D during dark-induced senescence. In addition to delayed senescence, onac106-1D also showed a salt stress-tolerant phenotype; key genes that down-regulate salt response signaling (OsNAC5, OsDREB2A, OsLEA3 and OsbZIP23) were rapidly up-regulated in onac106-1D under salt stress. Interestingly, onac106-1D also exhibited a wide tiller angle phenotype throughout development, and the tiller angle-related gene LPA1 was down-regulated in onac106-1D. Using yeast one-hybrid assays, we found that ONAC106 binds to the promoter regions of SGR, NYC1, OsNAC5 and LPA1. Taking these results together, we propose that ONAC106 functions in leaf senescence, salt stress tolerance and plant architecture by modulating the expression of its target genes that function in each signaling pathway.

Strigolactone Regulates Leaf Senescence in Concert with Ethylene in Arabidopsis

Leaf senescence is not a passive degenerative process; it represents a process of nutrient relocation, in which materials are salvaged for growth at a later stage or to produce the next generation. Leaf senescence is regulated by various factors, such as darkness, stress, aging, and phytohormones. Strigolactone is a recently identified phytohormone, and it has multiple functions in plant development, including repression of branching. Although strigolactone is implicated in the regulation of leaf senescence, little is known about its molecular mechanism of action. In this study, strigolactone biosynthesis mutant strains of Arabidopsis (Arabidopsis thaliana) showed a delayed senescence phenotype during dark incubation. The strigolactone biosynthesis genes MORE AXIALLY GROWTH3 (MAX3) and MAX4 were drastically induced during dark incubation and treatment with the senescence-promoting phytohormone ethylene, suggesting that strigolactone is synthesized in the leaf during leaf senescence. This hypothesis was confirmed by a grafting experiment using max4 as the stock and Columbia-0 as the scion, in which the leaves from the Columbia-0 scion senesced earlier than max4 stock leaves. Dark incubation induced the synthesis of ethylene independent of strigolactone. Strigolactone biosynthesis mutants showed a delayed senescence phenotype during ethylene treatment in the light. Furthermore, leaf senescence was strongly accelerated by the application of strigolactone in the presence of ethylene and not by strigolactone alone. These observations suggest that strigolactone promotes leaf senescence by enhancing the action of ethylene. Thus, dark-induced senescence is regulated by a two-step mechanism: induction of ethylene synthesis and consequent induction of strigolactone synthesis in the leaf.

A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence

The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac (both associated with actively expressed genes), was monitored in Arabidopsis (Arabidopsis thaliana) leaves at different time points during developmental senescence along with expression in the form of RNA sequencing data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly 2 times the gene area as H3K9ac marks. Genes with the greatest fold change in expression displayed the largest positively correlated percentage change in coverage for both marks. Most senescence up-regulated genes were premarked by H3K4me3 and H3K9ac but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks was found to closely match the temporal changes in mRNA abundance; 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.

EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis

Degreening, caused by chlorophyll degradation, is the most obvious symptom of senescing leaves. Chlorophyll degradation can be triggered by endogenous and environmental cues, and ethylene is one of the major inducers. ETHYLENE INSENSITIVE3 (EIN3) is a key transcription factor in the ethylene signaling pathway. It was previously reported that EIN3, miR164, and a NAC (NAM, ATAF, and CUC) transcription factor ORE1/NAC2 constitute a regulatory network mediating leaf senescence. However, how this network regulates chlorophyll degradation at molecular level is not yet elucidated. Here we report a feed-forward regulation of chlorophyll degradation that involves EIN3, ORE1, and chlorophyll catabolic genes (CCGs). Gene expression analysis showed that the induction of three major CCGs, NYE1, NYC1 and PAO, by ethylene was largely repressed in ein3 eil1 double mutant. Dual-luciferase assay revealed that EIN3 significantly enhanced the promoter activity of NYE1, NYC1 and PAO in Arabidopsis protoplasts. Furthermore, Electrophoretic mobility shift assay (EMSA) indicated that EIN3 could directly bind to NYE1, NYC1 and PAO promoters. These results reveal that EIN3 functions as a positive regulator of CCG expression during ethylene-mediated chlorophyll degradation. Interestingly, ORE1, a senescence regulator which is a downstream target of EIN3, could also activate the expression of NYE1, NYC1 and PAO by directly binding to their promoters in EMSA and chromatin immunoprecipitation (ChIP) assays. In addition, EIN3 and ORE1 promoted NYE1 and NYC1 transcriptions in an additive manner. These results suggest that ORE1 is also involved in the direct regulation of CCG transcription. Moreover, ORE1 activated the expression of ACS2, a major ethylene biosynthesis gene, and subsequently promoted ethylene production. Collectively, our work reveals that EIN3, ORE1 and CCGs constitute a coherent feed-forward loop involving in the robust regulation of ethylene-mediated chlorophyll degradation during leaf senescence in Arabidopsis.

Mutation of Oryza sativa CORONATINE INSENSITIVE 1b (OsCOI1b) delays leaf senescence

Jasmonic acid (JA) functions in plant development, including senescence and immunity. Arabidopsis thaliana CORONATINE INSENSITIVE 1 encodes a JA receptor and functions in the JA-responsive signaling pathway. The Arabidopsis genome harbors a single COI gene, but the rice (Oryza sativa) genome harbors three COI homologs, OsCOI1a, OsCOI1b, and OsCOI2. Thus, it remains unclear whether each OsCOI has distinct, additive, synergistic, or redundant functions in development. Here, we use the oscoi1b-1 knockout mutants to show that OsCOI1b mainly affects leaf senescence under senescence-promoting conditions. oscoi1b-1 mutants stayed green during dark-induced and natural senescence, with substantial retention of chlorophylls and photosynthetic capacity. Furthermore, several senescence-associated genes were downregulated in oscoi1b-1 mutants, including homologs of Arabidopsis thaliana ETHYLENE INSENSITIVE 3 and ORESARA 1, important regulators of leaf senescence. These results suggest that crosstalk between JA signaling and ethylene signaling affects leaf senescence. The Arabidopsis coi1-1 plants containing 35S:OsCOI1a or 35S:OsCOI1b rescued the delayed leaf senescence during dark incubation, suggesting that both OsCOI1a and OsCOI1b are required for promoting leaf senescence in rice. oscoi1b-1 mutants showed significant decreases in spikelet fertility and grain weight, leading to severe reduction of grain yield, indicating that OsCOI1-mediated JA signaling affects spikelet fertility and grain filling.

Crop yield: challenges from a metabolic perspective

Considering the dual use of plants, as bio-factories for foods and feedstock for bio-refining, along with a rising world population, the plant biotechnology field is currently facing a dramatic challenge to develop crops with higher yield. Furthermore, convergent studies predict that global changes in climate will influence crop productivity by modifying most yield-associated traits. Here, we review recent advances in the understanding of plant metabolism directly or indirectly impacting on yield and provide an update of the different pathways proposed as targets for metabolic engineering aiming to optimize source-sink relationships.

Only in dying, life: programmed cell death during plant development

Programmed cell death (PCD) is a fundamental process of life. During the evolution of multicellular organisms, the actively controlled demise of cells has been recruited to fulfil a multitude of functions in development, differentiation, tissue homeostasis, and immune systems. In this review we discuss some of the multiple cases of PCD that occur as integral parts of plant development in a remarkable variety of cell types, tissues, and organs. Although research in the last decade has discovered a number of PCD regulators, mediators, and executers, we are still only beginning to understand the mechanistic complexity that tightly controls preparation, initiation, and execution of PCD as a process that is indispensable for successful vegetative and reproductive development of plants.

Transcriptional analyses of natural leaf senescence in maize

Leaf senescence is an important biological process that contributes to grain yield in crops. To study the molecular mechanisms underlying natural leaf senescence, we harvested three different developmental ear leaves of maize, mature leaves (ML), early senescent leaves (ESL), and later senescent leaves (LSL), and analyzed transcriptional changes using RNA-sequencing. Three sets of data, ESL vs. ML, LSL vs. ML, and LSL vs. ESL, were compared, respectively. In total, 4,552 genes were identified as differentially expressed. Functional classification placed these genes into 18 categories including protein metabolism, transporters, and signal transduction. At the early stage of leaf senescence, genes involved in aromatic amino acids (AAAs) biosynthetic process and transport, cellular polysaccharide biosynthetic process, and the cell wall macromolecule catabolic process, were up-regulated. Whereas, genes involved in amino acid metabolism, transport, apoptosis, and response to stimulus were up-regulated at the late stage of leaf senescence. Further analyses reveals that the transport-related genes at the early stage of leaf senescence potentially take part in enzyme and amino acid transport and the genes upregulated at the late stage are involved in sugar transport, indicating nutrient recycling mainly takes place at the late stage of leaf senescence. Comparison between the data of natural leaf senescence in this study and previously reported data for Arabidopsis implies that the mechanisms of leaf senescence in maize are basically similar to those in Arabidopsis. A comparison of natural and induced leaf senescence in maize was performed. Athough many basic biological processes involved in senescence occur in both types of leaf senescence, 78.07% of differentially expressed genes in natural leaf senescence were not identifiable in induced leaf senescence, suggesting that differences in gene regulatory network may exist between these two leaf senescence programs. Thus, this study provides important information for understanding the mechanism of leaf senescence in maize.

Phytochrome-interacting transcription factors PIF4 and PIF5 induce leaf senescence in Arabidopsis

Plants initiate senescence to shed photosynthetically inefficient leaves. Light deprivation induces leaf senescence, which involves massive transcriptional reprogramming to dismantle cellular components and remobilize nutrients. In darkness, intermittent pulses of red light can inhibit senescence, likely via phytochromes. However, the precise molecular mechanisms transducing the signals from light perception to the inhibition of senescence remain elusive. Here, we show that in Arabidopsis, dark-induced senescence requires phytochrome-interacting transcription factors PIF4 and PIF5 (PIF4/PIF5). ELF3 and phytochrome B inhibit senescence by repressing PIF4/PIF5 at the transcriptional and post-translational levels, respectively. PIF4/PIF5 act in the signalling pathways of two senescence-promoting hormones, ethylene and abscisic acid, by directly activating expression of EIN3, ABI5 and EEL. In turn, PIF4, PIF5, EIN3, ABI5 and EEL directly activate the expression of the major senescence-promoting NAC transcription factor ORESARA1, thus forming multiple, coherent feed-forward loops. Our results reveal how classical light signalling connects to senescence in Arabidopsis.