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

Transcriptome Analysis Reveals Genes Respond to Chlorophyll Deficiency in Green and Yellow Leaves of Chrysanthemum morifolium Ramat

Chlorophyll is vital for photosynthesis to produce sugars and other useful biochemical products in green plants. However, the molecular effects of chlorophyll deficiency in Chrysanthemum are largely unknown. In this study, we identified a bud sport mutant chrysanthemum belonging to the variety ‘Nannong Binyun’, which has yellow branches. Plant physiological studies have shown that the yellow color is revealed due to chlorophyll loss. RNA extracts of yellow and green tissues were analyzed using high-throughput RNA-sequencing, and a total of 11,649 tissue enriched unigenes that respond to chlorophyll deficiency were identified, including 4803 unigenes upregulated in yellow tissues and 6846 unigenes in green tissues. GO analysis revealed that these tissue-enriched genes may involve in the physiological processes of chlorophyll accumulation and photosynthesis. In addition, many DEGs from the families of AP2-EREBP, bHLH, MYB, and FAR1 that are associated with plant development and stress response were detected. Our study found that most of the genes from the GRAS family were downregulated in yellow leaves, indicating their putative roles in stem cell maintenance and possible contribution to leaf size determination.

The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

Roles of a Cysteine Desulfhydrase LCD1 in Regulating Leaf Senescence in Tomato

Hydrogen sulfide (H2S), a novel gasotransmitter in both mammals and plants, plays important roles in plant development and stress responses. Leaf senescence represents the final stage of leaf development. The role of H2S-producing enzyme L-cysteine desulfhydrase in regulating tomato leaf senescence is still unknown. In the present study, the effect of an L-cysteine desulfhydrase LCD1 on leaf senescence in tomato was explored by physiological analysis. LCD1 mutation caused earlier leaf senescence, whereas LCD1 overexpression significantly delayed leaf senescence compared with the wild type in 10-week tomato seedlings. Moreover, LCD1 overexpression was found to delay dark-induced senescence in detached tomato leaves, and the lcd1 mutant showed accelerated senescence. An increasing trend of H2S production was observed in leaves during storage in darkness, while LCD1 deletion reduced H2S production and LCD1 overexpression produced more H2S compared with the wild-type control. Further investigations showed that LCD1 overexpression delayed dark-triggered chlorophyll degradation and reactive oxygen species (ROS) accumulation in detached tomato leaves, and the increase in the expression of chlorophyll degradation genes NYC1, PAO, PPH, SGR1, and senescence-associated genes (SAGs) during senescence was attenuated by LCD1 overexpression, whereas lcd1 mutants showed enhanced senescence-related parameters. Moreover, a correlation analysis indicated that chlorophyll content was negatively correlated with H2O2 and malondialdehyde (MDA) content, and also negatively correlated with the expression of chlorophyll degradation-related genes and SAGs. Therefore, these findings increase our understanding of the physiological functions of the H2S-generating enzyme LCD1 in regulating leaf senescence in tomato.

Root-to-Shoot Long-Distance Mobile miRNAs Identified from Nicotiana Rootstocks

Root-derived mobile signals play critical roles in coordinating a shoot's response to underground conditions. However, the identification of root-to-shoot long-distance mobile signals has been scant. In this study, we aimed to characterize root-to-shoot endogenous mobile miRNAs by using an Arabidopsis/Nicotiana interfamilial heterograft in which these two taxonomically distant species with clear genetic backgrounds had sufficient diversity in differentiating miRNA sources. Small RNA deep sequencing analysis revealed that 82 miRNAs from the Arabidopsis scion could travel through the graft union to reach the rootstock, whereas only a very small subset of miRNA (6 miRNAs) preferred the root-to-shoot movement. We demonstrated in an ex vivo RNA imaging experiment that the root-to-shoot mobile Nb-miR164, Nb-miR395 and Nb-miR397 were targeted to plasmodesmata using the bacteriophage coat protein MS2 system. Furthermore, the Nb-miR164 was shown to move from the roots to the shoots to induce phenotypic changes when its overexpressing line was used as rootstock, strongly supporting that root-derived Nb-miR164 was able to modify the scion trait via its long-distance movement.

RhWRKY33 Positively Regulates Onset of Floral Senescence by Responding to Wounding- and Ethylene-Signaling in Rose Plants

Rose plants are one of the most important horticultural crops, whose commercial value mainly depends on long-distance transportation, and wounding and ethylene are the main factors leading to their quality decline and accelerated senescence in the process. However, underlying molecular mechanisms of crosstalk between wounding and ethylene in the regulation of flower senescence remain poorly understood. In relation to this, transcriptome analysis was performed on rose flowers subjected to various treatments, including control, wounding, ethylene, and wounding- and ethylene- (EW) dual treatment. A large number of differentially expressed genes (DEGs) were identified, ranging from 2,442 between the ethylene- and control-treated groups to 4,055 between the EW- and control-treated groups. Using weighted gene co-expression network analysis (WGCNA), we identified a hub gene RhWRKY33 (rchiobhmchr5g0071811), accumulated in the nucleus, where it may function as a transcription factor. Moreover, quantitative reverse transcription PCR (RT-qPCR) results showed that the expression of RhWRKY33 was higher in the wounding-, ethylene, and EW-treated petals than in the control-treated petals. We also functionally characterized the RhWRKY33 gene through virus-induced gene silencing (VIGS). The silencing of RhWRKY33 significantly delayed the senescence process in the different treatments (control, wounding, ethylene, and EW). Meanwhile, we found that the effect of RhWRKY33-silenced petals under ethylene and EW dual-treatment were stronger than those under wounding treatment in delaying the petal senescence process, implying that RhWRKY33 is closely involved with ethylene and wounding mediated petal senescence. Overall, the results indicate that RhWRKY33 positively regulates the onset of floral senescence mediated by both ethylene and wounding signaling, but relies heavily on ethylene signaling.

CRISPR/Cas9 mutants of tomato MICRORNA164 genes uncover their functional specialization in development

Plant MICRORNA164 (miR164) plays diverse regulatory functions by post-transcriptional repression of certain NAM/ATAF/CUC-domain transcription factors. However, the involvement of miR164 in fleshy fruit development and ripening remains poorly understood. Here, de novo prediction of tomato (Solanum lycopersicum) MIR164 genes identified four genes (SlMIR164a-d), of which SlMIR164d has an atypically long pre-miRNA. The roles of the fruit expressed SlMIR164a, b, and d were studied by analysis of their Clustered Regularly Interspaced Short Palindromic Repeats mutants. The slmir164bCR mutant plants exhibited shoot and flower abnormalities characteristic of ectopic boundary specification, whereas the shoot and flower development of slmir164aCR and slmir164dCR mutants were indistinguishable from wild-type. Strikingly, the knockout of SlMIR164a practically eliminated sly-miR164 from the developing and ripening fruit pericarp. The sly-miR164-deficient slmir164aCR fruits were smaller than the wild-type, due to reduced pericarp cell division and expansion, and displayed intense red color and matte, instead of glossy appearance, upon ripening. We found that the fruit skin phenotypes were associated with morphologically abnormal outer epidermis and thicker cuticle. Quantitation of sly-miR164 target transcripts in slmir164aCR ripening fruits demonstrated the upregulation of SlNAM3 and SlNAM2. Specific expression of their miR164-resistant versions in the pericarp resulted in the formation of extremely small fruits with abnormal epidermis, highlighting the importance of their negative regulation by sly-miR164a. Taken together, our results demonstrate that SlMIR164a and SlMIR164b play specialized roles in development: SlMIR164b is required for shoot and flower boundary specification, and SlMIR164a is required for fruit growth including the expansion of its outer epidermis, which determines the properties of the fruit skin.

Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis

Leaf senescence, the final stage of leaf development, is influenced by numerous internal and environmental signals. However, how biotic stresses such as pathogen infection regulate leaf senescence remains largely unclear. In this study, we found that the premature leaf senescence in Arabidopsis caused by the soil-borne vascular fungus Verticillium dahliae was impaired by disruption of a protein elicitor from V. dahliae 1 named PevD1. Constitutive or inducible overexpression of PevD1 accelerated Arabidopsis leaf senescence. Interestingly, a senescence-associated NAC transcription factor, ORE1, was targeted by PevD1. PevD1 could interact with and stabilize ORE1 protein by disrupting its interaction with the RING-type ubiquitin E3 ligase NLA. Mutation of ORE1 suppressed the premature senescence caused by overexpressing PevD1, whereas overexpression of ORE1 or PevD1 led to enhanced ethylene production and thereby leaf senescence. We showed that ORE1 directly binds the promoter of ACS6 and promotes its expression for mediating PevD1-induced ethylene biosynthesis. Loss-of-function of ACSs could suppress V. dahliae-induced leaf senescence in ORE1-overexpressing plants. Furthermore, we found thatPevD1 also interacts with Gossypium hirsutum ORE1 (GhORE1) and that virus-induced gene silencing of GhORE1 delays V. dahliae-triggered leaf senescence in cotton, indicating a possibly conserved mechanism in plants. Taken together, these results suggest that V. dahliae induces leaf senescence by secreting the effector PevD1 to manipulate the ORE1-ACS6 cascade, providing new insights into biotic stress-induced senescence in plants.

A comprehensive overview of miRNA targeting drought stress resistance in plants

MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.

Morphological Characterization and Transcriptional Regulation of Corolla Closure in Ipomoea purpurea

Corolla closure protects pollen from high-temperature stress during pollen germination and fertilization in the ornamental plant morning glory (Ipomoea purpurea). However, the morphological nature of this process and the molecular events underpinning it remain largely unclear. Here, we examined the cellular and gene expression changes that occur during corolla closure in the I. purpurea. We divided the corolla closure process into eight stages (S0-S7) based on corolla morphology. During flower opening, bulliform cells appear papillate, with pigments in the adaxial epidermis of the corolla. These cells have distinct morphology from the smaller, flat cells in the abaxial epidermis in the corolla limb and intermediate of the corolla. During corolla closure, the bulliform cells of the adaxial epidermis severely collapse compared to cells on the abaxial side. Analysis of transparent tissue and cross sections revealed that acuminate veins in the corolla are composed of spiral vessels that begin to curve during corolla closure. When the acuminate veins were compromised, the corolla failed to close normally. We performed transcriptome analysis to obtain a time-course profile of gene expression during the process from the open corolla stage (S0) to semi-closure (S3). Genes that were upregulated from S0 to S1 were enriched in the polysaccharide degradation pathway, which positively regulates cell wall reorganization. Senescence-related transcription factor genes were expressed beginning at S1, leading to the activation of downstream autophagy-related genes at S2. Genes associated with peroxisomes and ubiquitin-mediated proteolysis were upregulated at S3 to enhance reactive oxygen species scavenging and protein degradation. Therefore, bulliform cells and acuminate veins play essential roles in corolla closure. Our findings provide a global understanding of the gene regulatory processes that occur during corolla closure in I. purpurea.

Arabidopsis WRKY71 regulates ethylene-mediated leaf senescence by directly activating EIN2, ORE1 and ACS2 genes

Leaf senescence is a pivotal step in the last stage of the plant life cycle and is influenced by various external and endogenous cues. A series of reports have indicated the involvement of the WRKY transcription factors in regulating leaf senescence, but the molecular mechanisms and signaling pathways remain largely unclear. Here we provide evidence demonstrating that WRKY71 acts as a positive regulator of leaf senescence in Arabidopsis. WRKY71-1D, an overexpressor of WRKY71, exhibited early leaf senescence, while wrky71-1, the WRKY71 loss-of-function mutant, displayed delayed leaf senescence. Accordingly, a set of senescence-associated genes (SAGs) were substantially elevated in WRKY71-1D but markedly decreased in wrky71-1. Chromatin immunoprecipitation assays indicated that WRKY71 can bind directly to the promoters of SAG13 and SAG201. Transcriptome analysis suggested that WRKY71 might mediate multiple cues to accelerate leaf senescence, such as abiotic stresses, dark and ethylene. WRKY71 was ethylene inducible, and treatment with the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid enhanced leaf senescence in WRKY71-1D but caused only a marginal delay in leaf senescence in wrky71-1. In vitro and in vivo assays demonstrated that WRKY71 can directly regulate ETHYLENE INSENSITIVE2 (EIN2) and ORESARA1 (ORE1), genes of the ethylene signaling pathway. Consistently, leaf senescence of WRKY71-1D was obviously retarded in the ein2-5 and nac2-1 mutants. Moreover, WRKY71 was also proved to interact with ACS2 in vitro and in vivo. Treatment with AgNO₃ and aminoethoxyvinylglycine and acs2-1 could greatly arrest the leaf senescence of WRKY71-1D. In conclusion, our data revealed that WRKY71 mediates ethylene signaling and synthesis to hasten leaf senescence in Arabidopsis.

Senescence-Associated Glycine max (Gm)NAC Genes: Integration of Natural and Stress-Induced Leaf Senescence

Leaf senescence is a genetically regulated developmental process that can be triggered by a variety of internal and external signals, including hormones and environmental stimuli. Among the senescence-associated genes controlling leaf senescence, the transcriptional factors (TFs) comprise a functional class that is highly active at the onset and during the progression of leaf senescence. The plant-specific NAC (NAM, ATAF, and CUC) TFs are essential for controlling leaf senescence. Several members of Arabidopsis AtNAC-SAGs are well characterized as players in elucidated regulatory networks. However, only a few soybean members of this class display well-known functions; knowledge about their regulatory circuits is still rudimentary. Here, we describe the expression profile of soybean GmNAC-SAGs upregulated by natural senescence and their functional correlation with putative AtNAC-SAGs orthologs. The mechanisms and the regulatory gene networks underlying GmNAC081- and GmNAC030-positive regulation in leaf senescence are discussed. Furthermore, new insights into the role of GmNAC065 as a negative senescence regulator are presented, demonstrating extraordinary functional conservation with the Arabidopsis counterpart. Finally, we describe a regulatory circuit which integrates a stress-induced cell death program with developmental leaf senescence via the NRP-NAC-VPE signaling module.

AtWRKY75 positively regulates age-triggered leaf senescence through gibberellin pathway

WRKY transcription factors play essential roles during leaf senescence. However, the mechanisms by which they regulate this process remains largely unknown. Here, we identified the transcription factor WRKY75 as a positive regulator during leaf senescence. Mutations of WRKY75 caused a delay in age-triggered leaf senescence, whereas overexpression of WRKY75 markedly accelerated this process. Expression of senescence-associated genes (SAGs) was suppressed in WRKY75 mutants but increased in WRKY75-overexpressing plants. Further analysis demonstrated that WRKY75 directly associates with the promoters of SAG12 and SAG29, to activate their expression. Conversely, GAI and RGL1, two DELLA proteins, can suppress the WRKY75-mediated activation, thereby attenuating SAG expression during leaf senescence. Genetic analyses showed that GAI gain-of-function or RGL1 overexpression can partially rescue the accelerated senescence phenotype caused by WRKY75 overexpression. Furthermore, WRKY75 can positively regulate WRKY45 expression during leaf senescence. Our data thus imply that WRKY75 may positively modulate age-triggered leaf senescence through the gibberellin-mediated signaling pathway.

Transcriptional Regulation and Signaling of Developmental Programmed Cell Death in Plants

Developmental programmed cell death (dPCD) has multiple functions in plant growth and development, and is of great value for industrial production. Among them, wood formed by xylem dPCD is one of the most widely used natural materials. Therefore, it is crucial to explore the molecular mechanism of plant dPCD. The dPCD process is tightly regulated by genetic networks and is involved in the transduction of signaling molecules. Several key regulators have been identified in diverse organisms and individual PCD events. However, complex molecular networks controlling plant dPCD remain highly elusive, and the original triggers of this process are still unknown. This review summarizes the recent progress on the transcriptional regulation and signaling of dPCD during vegetative and reproductive development. It is hoped that this review will provide an overall view of the molecular regulation of dPCD in different developmental processes in plants and identify specific mechanisms for regulating these dPCD events. In addition, the application of plants in industrial production can be improved by manipulating dPCD in specific processes, such as xylogenesis.

Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters

Comparative analysis of miRNAs and their gene targets between the evergreen and yellowish-brown Cryptomeria fortunei phenotypes in cold winters suggests a possible role of miRNA-regulated pathways in needle color. Cryptomeria fortunei (Chinese cedar) is a conifer tree of considerable economic, ornamental and ecological importance. Despite the evergreen nature of C. fortunei, most needles turn yellowish- or reddish-brown in winter. The roles of microRNAs (miRNAs) in regulating pigment biosynthesis in color-leafed plants have been widely investigated. However, whether or not an miRNA-mediated staged discoloration mechanism exists in evergreen C. fortunei is currently unknown. In this study, we deciphered the microRNAs landscape in overwintering C. fortunei needles using high-throughput sequencing. A total of 517 known and 212 novel miRNA mature/star sequences, including 233 differentially expressed miRNAs, were identified. Based on integrated transcriptome and miRNA analysis, 2702 target unigenes of the miRNAs were predicted and these targets were significantly enriched in pigment-related biosynthesis pathways. A miRNA-target pigment biosynthesis regulatory network was then constructed, and its module miRNA (ath-miR858b, aly-miR858-3p, cme-miR828 and novel33_mature)-MYBs (v-myb avian myeloblastosis viral oncogene homolog) appeared to be a key factor regulating needle discoloration in C. fortunei. These miRNA-MYBs were further confirmed by degradome sequencing. Overall, these findings provide new insight into the posttranscriptional regulatory mechanism of leaf/needle discoloration in gymnosperms and may contribute to the miRNA-mediated genetic improvement of evergreen C. fortunei needles.

An alternative splicing variant of PtRD26 delays leaf senescence by regulating multiple NAC transcription factors in Populus

During leaf senescence, the final stage of leaf development, nutrients are recycled from leaves to other organs, and therefore proper control of senescence is thus critical for plant fitness. Although substantial progress has been achieved in understanding leaf senescence in annual plants, the molecular factors that control leaf senescence in perennial woody plants are largely unknown. Using RNA sequencing, we obtained a high-resolution temporal profile of gene expression during autumn leaf senescence in poplar (Populus tomentosa). Identification of hub transcription factors (TFs) by co-expression network analysis of genes revealed that senescence-associated NAC family TFs (Sen-NAC TFs) regulate autumn leaf senescence. Age-dependent alternative splicing (AS) caused an intron retention (IR) event in the pre-mRNA encoding PtRD26, a NAC-TF. This produced a truncated protein PtRD26IR, which functions as a dominant-negative regulator of senescence by interacting with multiple hub Sen-NAC TFs, thereby repressing their DNA-binding activities. Functional analysis of senescence-associated splicing factors identified two U2 auxiliary factors that are involved in AS of PtRD26IR. Correspondingly, silencing of these factors decreased PtRD26IR transcript abundance and induced early senescence. We propose that an age-dependent increase of IR splice variants derived from Sen-NAC TFs is a regulatory program to fine tune the molecular mechanisms that regulate leaf senescence in trees.

Glucose- and sucrose-signaling modules regulate the Arabidopsis juvenile-to-adult phase transition

CINV1, converting sucrose into glucose and fructose, is a key entry of carbon into cellular metabolism, and HXK1 functions as a pivotal sensor for glucose. Exogenous sugars trigger the Arabidopsis juvenile-to-adult phase transition via a miR156A/SPL module. However, the endogenous factors that regulate this process remain unclear. In this study, we show that sucrose specifically induced the PAP1 transcription factor directly and positively controls CINV1 activity. Furthermore, we identify a glucose feed-forward loop (sucrose-CINV1-glucose-HXK1-miR156-SPL9-PAP1-CINV1-glucose) that controls CINV1 activity to convert sucrose into glucose signaling to dynamically control the juvenile-to-adult phase transition. Moreover, PAP1 directly binds to the SPL9 promoter, activating SPL9 expression and triggering the sucrose-signaling-mediated juvenile-to-adult phase transition. Therefore, a glucose-signaling feed-forward loop and a sucrose-signaling pathway synergistically regulate the Arabidopsis juvenile-to-adult phase transition. Collectively, we identify a molecular link between the major photosynthate sucrose, the entry point of carbon into cellular metabolism, and the plant juvenile-to-adult phase transition.

Age-Dependent Abiotic Stress Resilience in Plants

Developmental age is a strong determinant of stress responses in plants. Differential susceptibility to various environmental stresses is widely observed at both the organ and whole-plant level. While it is clear that age determines stress susceptibility, the causes, regulatory mechanisms, and functions are only now beginning to emerge. Compared with concepts on age-related biotic stress resilience, advancements in the abiotic stress field are relatively limited. In this review, we focus on current knowledge of ontogenic resistance to abiotic stresses, highlighting examples at the organ (leaf) and plant level, preceded by an overview of the relevant concepts in plant aging. We also discuss age-related abiotic stress resilience mechanisms, speculate on their functional relevance, and outline outstanding questions.

Identification and Expression Profiling Analysis of the Cation/Ca2+ Exchanger (CCX) Gene Family: Overexpression of SlCCX1-LIKE Regulates the Leaf Senescence in Tomato Flowering Phase

Cation gradients in plant cellular compartments are maintained by the synergistic actions of various ion exchangers, pumps, and channels. Cation/Ca2+ exchanger (CCX) is one of the clades of the Ca2+/cation antiporter super family. Here, five SlCCX genes were identified in tomato. Sequence analysis indicated that SlCCXs have the conserved motifs as the CCX domain. Analysis of the expression level of each member of tomato CCX gene family under cation (Mg2+, Mn2+, Na+, and Ca2+) treatment was determined by qRT-PCR. Tomato CCX demonstrated different degrees of responding to cation treatment. Changes in SlCCX1-LIKE expression was induced by Mg2+ and Mn2+ treatment. Analysis of the expression of SlCCX genes in different tissues demonstrated that constitutive high expression of a few genes, including SlCCX1-LIKE and SlCCX5, indicated their role in tomato organ growth and development. Overexpression of SlCCX1-LIKE dramatically induced leaf senescence. Transcriptome analysis showed that genes related to ROS and several IAA signaling pathways were significantly downregulated, whereas ETH and ABA signaling pathway-related genes were upregulated in overexpression of SlCCX1-LIKE (OE-SlCCX1-LIKE) plants, compared with the wild type (WT). Moreover, overexpression of SlCCX1-LIKE plants accumulated more ROS content but less Mg2+ content. Collectively, the findings of this study provide insights into the base mechanism through which CCXs regulate leaf senescence in tomato.

Leaf senescence: progression, regulation, and application

Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.

PHYTOCHROME INTERACTING FACTORS PIF4 and PIF5 promote heat stress induced leaf senescence in Arabidopsis

Leaf senescence can be triggered by multiple abiotic stresses including darkness, nutrient limitation, salinity, and drought. Recently, heatwaves have been occurring more frequently, and they dramatically affect plant growth and development. However, the underlying molecular networks of heat stress-induced leaf senescence remain largely uncharacterized. Here we showed that PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 proteins could efficiently promote heat stress-induced leaf senescence in Arabidopsis. Transcriptomic profiling analysis revealed that PIF4 and PIF5 are likely to function through multiple biological processes including hormone signaling pathways. Further, we characterized NAC019, SAG113, and IAA29 as direct transcriptional targets of PIF4 and PIF5. The transcription of NAC019, SAG113, and IAA29 changes significantly in daytime after heat treatment. In addition, we demonstrated that PIF4 and PIF5 proteins were accumulated during the recovery after heat treatment. Moreover, we showed that heat stress-induced leaf senescence is gated by the circadian clock, and plants might be more actively responsive to heat stress-induced senescence during the day. Taken together, our findings proposed important roles for PIF4 and PIF5 in mediating heat stress-induced leaf senescence, which may help to fully illustrate the molecular network of heat stress-induced leaf senescence in higher plants and facilitate the generation of heat stress-tolerant crops.

The phytotoxin COR induces transcriptional reprogramming of photosynthetic, hormonal and defence networks in tomato

Coronatine (COR) is a non-host specific phytotoxin secreted by Pseudomonas syringae pv. tomato that can induce leaf chlorosis and increase the virulence of pathogens during plant-pathogen interactions. Studies have shown that COR can regulate multiple physiological processes in plants, but its involvement in bacterial pathogenesis and plant growth regulation is not well understood. In this study, transcriptome sequencing was carried out on 4-week-old tomato leaves that were either mock-treated or treated with COR. Transcriptome sequencing led to the identification of 6144 differentially expressed genes (DEGs), of which 4361 genes were downregulated and 1783 genes were upregulated upon COR treatment. To obtain functional information on the DEGs, we annotated these genes using GO and KEGG databases. Functional classification analysis showed that the DEGs were primarily involved in photosynthesis, chlorophyll and carotenoid biosynthesis, jasmonic acid (JA) synthesis and phenylpropane metabolism. A total of 23 genes related to chlorophyll biosynthesis had significant changes, of which 22 genes were downregulated and one gene was upregulated, indicating that chlorophyll biosynthesis was inhibited upon COR treatment. A total of 17 photosystem I related genes and 22 photosystem II related genes involving 20 protein subunits were also downregulated. In the JA synthesis pathway, 25 genes were up regulated, and six genes were downregulated in COR treated samples. COR was also involved in the regulation of multiple secondary metabolites. The identified DEGs will help us better understand the virulence effects and physiological functions of COR and provide a theoretical basis for breeding resistance into economically important crops.

Salicylic acid and ethylene coordinately promote leaf senescence

Leaf senescence is an intrinsic biological process of plants. The phytohormones salicylic acid (SA) and ethylene (ET) are known to promote senescence. However, their relationship in this process is still unclear. We found that EIN3 and EIL1, two key transcription factors in ET signaling, are required for SA-induced leaf senescence in Arabidopsis. Furthermore, ET enhances the effect of SA in promoting senescence. Biochemical studies revealed that NPR1, the master regulator of SA signaling, interacts with EIN3 to promote its transcriptional activity. Our study suggests that SA and ET function coordinately in senescence, which is in contrast to their antagonistic crosstalk in other biological processes.

Ethylene and salicylic acid synergistically accelerate leaf senescence in Arabidopsis

The phytohormones ethylene and salicylic acid (SA) have long been known to promote senescence, but their interplay during this process remains elusive. Here we report the synergistic effects of ethylene and SA on promoting leaf senescence in Arabidopsis. EIN3, a key transcription factor of ethylene signaling, physically interacted with the core SA signaling regulator NPR1 in senescing leaves. EIN3 and NPR1 synergistically promoted the expression of the senescence-associated genes ORE1 and SAG29. The senescence phenotype was more delayed for the ein3eil1npr1 triple mutant than ein3eil1 or npr1 with ethylene or/and SA treatment. NPR1-promoted leaf senescence may depend on functional EIN3/EIL1.

Involvement of ethylene receptors in the salt tolerance response of Cucurbita pepo

Abiotic stresses have a negative effect on crop production, affecting both vegetative and reproductive development. Ethylene plays a relevant role in plant response to environmental stresses, but the specific contribution of ethylene biosynthesis and signalling components in the salt stress response differs between Arabidopsis and rice, the two most studied model plants. In this paper, we study the effect of three gain-of-function mutations affecting the ethylene receptors CpETR1B, CpETR1A, and CpETR2B of Cucurbita pepo on salt stress response during germination, seedling establishment, and subsequent vegetative growth of plants. The mutations all reduced ethylene sensitivity, but enhanced salt tolerance, during both germination and vegetative growth, demonstrating that the three ethylene receptors play a positive role in salt tolerance. Under salt stress, etr1b, etr1a, and etr2b germinate earlier than WT, and the root and shoot growth rates of both seedlings and plants were less affected in mutant than in WT. The enhanced salt tolerance response of the etr2b plants was associated with a reduced accumulation of Na⁺ in shoots and leaves, as well as with a higher accumulation of compatible solutes, including proline and total carbohydrates, and antioxidant compounds, such as anthocyanin. Many membrane monovalent cation transporters, including Na⁺/H⁺ and K⁺/H⁺ exchangers (NHXs), K⁺ efflux antiporters (KEAs), high-affinity K⁺ transporters (HKTs), and K⁺ uptake transporters (KUPs) were also highly upregulated by salt in etr2b in comparison with WT. In aggregate, these data indicate that the enhanced salt tolerance of the mutant is led by the induction of genes that exclude Na⁺ in photosynthetic organs, while maintaining K⁺/Na⁺ homoeostasis and osmotic adjustment. If the salt response of etr mutants occurs via the ethylene signalling pathway, our data show that ethylene is a negative regulator of salt tolerance during germination and vegetative growth. Nevertheless, the higher upregulation of genes involved in Ca²⁺ signalling (CpCRCK2A and CpCRCK2B) and ABA biosynthesis (CpNCED3A and CpNCED3B) in etr2b leaves under salt stress likely indicates that the function of ethylene receptors in salt stress response in C. pepo can be mediated by Ca²⁺ and ABA signalling pathways.

The Molecular Basis of Age-Modulated Plant De Novo Root Regeneration Decline in Arabidopsis thaliana

Plants possess a regeneration capacity that enables them to survive after wounding. For example, detached Arabidopsis thaliana leaves are able to form adventitious roots from their cutting sites even in the absence of exogenous hormone supplements, as process termed de novo root regeneration (DNRR). Wounding rapidly induces auxin biosynthesis at the cutting sites and then elicits a signaling cascade to promote cell fate transitions and finally generate the adventitious roots. However, rooting rates in older plants are much lower than in younger leaf explants. In this review, we highlight the recent breakthroughs in the understanding of DNRR decay in older plants from at least two independent signaling routes: (i) via the accumulation of EIN3 protein in older plants, which directly suppresses expression of WUSCHEL RELATED HOMEOBOX (WOX) genes to inhibit rooting; (ii) the miR156-SPLs-AP2/ERFs pathway, which modulates root regeneration by reducing auxin biosynthesis.

ASCORBATE PEROXIDASE6 delays the onset of age-dependent leaf senescence

Age-dependent changes in reactive oxygen species (ROS) levels are critical in leaf senescence. While H2O2-reducing enzymes such as catalases and cytosolic ASCORBATE PEROXIDASE1 (APX1) tightly control the oxidative load during senescence, their regulation and function are not specific to senescence. Previously, we identified the role of ASCORBATE PEROXIDASE6 (APX6) during seed maturation in Arabidopsis (Arabidopsis thaliana). Here, we show that APX6 is a bona fide senescence-associated gene. APX6 expression is specifically induced in aging leaves and in response to senescence-promoting stimuli such as abscisic acid (ABA), extended darkness, and osmotic stress. apx6 mutants showed early developmental senescence and increased sensitivity to dark stress. Reduced APX activity, increased H2O2 level, and altered redox state of the ascorbate pool in mature pre-senescing green leaves of the apx6 mutants correlated with the early onset of senescence. Using transient expression assays in Nicotiana benthamiana leaves, we unraveled the age-dependent post-transcriptional regulation of APX6. We then identified the coding sequence of APX6 as a potential target of miR398, which is a key regulator of copper redistribution. Furthermore, we showed that mutants of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7), the master regulator of copper homeostasis and miR398 expression, have a higher APX6 level compared with the wild type, which further increased under copper deficiency. Our study suggests that APX6 is a modulator of ROS/redox homeostasis and signaling in aging leaves that plays an important role in developmental- and stress-induced senescence programs.

PbEIL1 acts upstream of PbCysp1 to regulate ovule senescence in seedless pear

Numerous environmental and endogenous signals control the highly orchestrated and intricate process of plant senescence. Ethylene, a well-known inducer of senescence, has long been considered a key endogenous regulator of leaf and flower senescence, but the molecular mechanism of ethylene-induced ovule senescence has not yet been elucidated. In this study, we found that blockage of fertilization caused ovule abortion in the pear cultivar '1913'. According to transcriptome and phytohormone content data, ethylene biosynthesis was activated by pollination. At the same time, ethylene overaccumulated in ovules, where cells were sensitive to ethylene signals in the absence of fertilization. We identified a transcription factor in the ethylene signal response, ethylene-insensitive 3-like (EIL1), as a likely participant in ovule senescence. Overexpression of PbEIL1 in tomato caused precocious onset of ovule senescence. We further found that EIL1 could directly bind to the promoter of the SENESCENCE-ASSOCIATED CYSTEINE PROTEINASE 1 (PbCysp1) gene and act upstream of senescence. Yeast one-hybrid and dual-luciferase assays revealed the interaction of the transcription factor and the promoter DNA sequence and demonstrated that PbEIL1 enhanced the action of PbCysp1. Collectively, our results provide new insights into how ethylene promotes the progression of unfertilized ovule senescence.

NtMYB12a acts downstream of sucrose to inhibit fatty acid accumulation by targeting lipoxygenase and SFAR genes in tobacco

MYB12 promotes flavonol biosynthesis in plants by targeting several early biosynthesis genes (EBGs) of this pathway. The transcriptions of these EBGs are also induced by sucrose signal. However, whether MYB12 is activated by sucrose signal and what the other roles MYB12 has in regulating plant metabolism are poorly understood. In this study, two NtMYB12 genes were cloned from Nicotiana tabacum. Both NtMYB12a and NtMYB12b are involved in regulating flavonoids biosynthesis in tobacco. NtMYB12a is further shown to inhibit the accumulation of fatty acid (FA) in tobacco leaves and seeds. Post-translational activation and chromatin immunoprecipitation assays demonstrate that NtMYB12a directly promotes the transcriptions of NtLOX6, NtLOX5, NtSFAR4 and NtGDSL2, which encode lipoxygenase (LOX) or SFAR enzymes catalyzing the degradation of FA. NtLOX6 and NtLOX5 are shown to prevent the accumulation of FA in the mature seeds and significantly reduced the percentage of polyunsaturated fatty acids (PUFAs) in tobacco. Sucrose stimulates the transcription of NtMYB12a, and loss function of NtMYB12a partially suppresses the decrease of FA content in tobacco seedlings caused by sucrose treatment. The regulation of sucrose on the expression of NtLOX6 and NtGDSL2 genes is mediated by NtMYB12a, whereas those of NtLOX5 and NtSFAR4 genes are independent of sucrose.

Ethephon Activates the Transcription of Senescence-Associated Genes and Nitrogen Mobilization in Grapevine Leaves (Vitis vinifera cv. Riesling)

Nitrogen (N) remobilization in the context of leaf senescence is of considerable importance for the viability of perennial plants. In late-ripening crops, such as Vitis vinifera, it may also affect berry ripening and fruit quality. Numerous studies on the model plant Arabidopsis thaliana have confirmed an involvement of the plant hormone ethylene in the regulation of senescence. However, ethylene research on grapevine was mostly focused on its involvement in berry ripening and stress tolerance until now. To investigate the effect of ethylene on the initiation, regulation, and progress of senescence-dependent N mobilization in grapevine leaves, we treated field-grown Vitis vinifera cv. Riesling vines with 25 mM ethephon at the end of berry ripening. Ethephon induced premature chlorophyll degradation and caused a shift of the leaf transcriptome equivalent to developmental leaf senescence. The upregulated metabolic processes covered the entire N remobilization process chain, altered the amino acid composition in the leaves, and resulted in an average 60% decrease in leaf N. Our findings increase the fundamental knowledge about the initiation and manipulation of leaf N remobilization in perennial woody plants by ethephon. This offers a methodological approach to the targeted induction of senescence and thus to an improvement in the N supply of grapes.

Ethylene, not ABA, is closely linked to the recovery of gas exchange after drought in four Caragana species

Drought is a cyclical phenomenon in natural environments. During dehydration, stomatal closure is mainly regulated by abscisic acid (ABA) dynamics that limit transpiration in seed plants, but following rehydration, the mechanism of gas exchange recovery is still not clear. In this study, leaf water potential (ψ_leaf ), stomatal conductance (g_s ), leaf hydraulic conductance (K_leaf ), foliar ABA level, ethylene emission rate in response to dehydration and rehydration were investigated in four Caragana species with isohydric (Caragana spinosa and C. pruinosa) and anisohydric (C. intermedia and C. microphylla) traits. Two isohydric species with ABA-induced stomatal closure exhibited more sensitive g_s and K_leaf to decreasing ψ_leaf than two anisohydric species which exhibited a switch from ABA to water potential-driven stomatal closure during dehydration. Following rehydration, the recovery of gas exchange was not associated with a decrease in ABA level but was strongly limited by the degradation of the ethylene emission rate in all species. Furthermore, two anisohydric species with low drought-induced ethylene production exhibited more rapid recovery in gas exchange upon rehydration. Our results indicated that ethylene is a key factor regulating the drought-recovery ability in terms of gas exchange, which may shape species adaptation to drought and potential species distribution.

Arabidopsis FHY3 and FAR1 Function in Age Gating of Leaf Senescence

Leaf senescence is the terminal stage of leaf development. Both light and the plant hormone ethylene play important roles in regulating leaf senescence. However, how they coordinately regulate leaf senescence during leaf development remains largely unclear. In this study, we show that FHY3 and FAR1, two homologous proteins essential for phytochrome A-mediated light signaling, physically interact with and repress the DNA binding activity of EIN3 (a key transcription factor essential for ethylene signaling) and PIF5 (a bHLH transcription factor negatively regulating light signaling), and interfere with their DNA binding to the promoter of ORE1, which encodes a key NAC transcription factor promoting leaf senescence. In addition, we show that FHY3, PIF5, and EIN3 form a tri-protein complex(es) and that they coordinately regulate the progression of leaf senescence. We show that during aging or under dark conditions, accumulation of FHY3 protein decreases, thus lifting its repression on DNA binding of EIN3 and PIF5, leading to the increase of ORE1 expression and onset of leaf senescence. Our combined results suggest that FHY3 and FAR1 act in an age gating mechanism to prevent precocious leaf senescence by integrating light and ethylene signaling with developmental aging.

HbWRKY82, a novel IIc WRKY transcription factor from Hevea brasiliensis associated with abiotic stress tolerance and leaf senescence in Arabidopsis

WRKY group transcription factors of model plants and major crops are confirmed to play essential roles in stress responses, senescence, secondary metabolism processes and hormone signal transduction. Previous studies have identified 81 HbWRKY genes from Hevea brasiliensis (the Pará rubber tree), but the functions of HbWRKYs in response to abiotic stresses and leaf senescence are unclear. In this study, one novel group IIc WRKY transcription factor named HbWRKY82 was identified and characterized as a stress-associated WRKY in rubber tree. Transient expression and transcriptional activation analyses indicated that HbWRKY82 encoded a nuclear protein and functioned as a transcription activator. The transcription levels of HbWRKY82 were induced by exogenous Ethrel (ET) (ethylene releaser) and abscisic acid (ABA) stimulations, down-regulated in tapping panel dryness rubber trees, and also exhibits significant decrease during the progression of leaf senescence. Overexpression of HbWRKY82 in Arabidopsis improved the tolerance to dehydration and salinity, and decreased the sensitivity to exogenous ABA. Moreover, real-time quantitative PCR analysis demonstrated that HbWRKY82 regulated the transcriptional expression of several stress-responsive genes (DREB1A, ERD10, HKT1, P5CS, RD22, RD29B, SKOR), leaf senescence marker genes (EIN3, WRKY53, NAP), ROS-related genes (RbohD, CSD1, CSD2, FSD3) and hormone signaling genes (EIN3, ABF3, ABF4). Collectively, our findings suggested that HbWRKY82 might function as an important transcriptional regulator in ET- and ABA-mediated leaf senescence and abiotic stress responses, and also be involved in tapping panel dryness, latex flow and regeneration processes of rubber trees via participating in the ET and reactive oxygen species signaling pathways.

Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives

Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.

Vitamin E Is Superior to Vitamin C in Delaying Seedling Senescence and Improving Resistance in Arabidopsis Deficient in Macro-Elements

Nitrogen (N), phosphorus (P), and potassium (K) are three essential macro-elements for plant growth and development. Used to improve yield in agricultural production, the excessive use of chemical fertilizers often leads to increased production costs and ecological environmental pollution. Vitamins C and E are antioxidants that play an important role in alleviating abiotic stress. However, there are few studies on alleviating oxidative stress caused by macro-element deficiency. Here, we used Arabidopsis vitamin E synthesis-deficient mutant vte4 and vitamin C synthesis-deficient mutant vtc1 on which exogenous vitamin E and vitamin C, respectively, were applied at the bolting stage. In the deficiency of macro-elements, the Arabidopsis chlorophyll content decreased, malondialdehyde (MDA) content and relative electric conductivity increased, and reactive oxygen species (ROS) accumulated. The mutants vtc1 and vte4 are more severely stressed than the wild-type plants. Adding exogenous vitamin E was found to better alleviate stress than adding vitamin C. Vitamin C barely affected and vitamin E significantly inhibited the synthesis of ethylene (ETH) and jasmonic acid (JA) genes, thereby reducing the accumulation of ETH and JA that alleviated the senescence caused by macro-element deficiency at the later stage of bolting in Arabidopsis. A deficiency of macro-elements also reduced the yield and germination rate of the seeds, which were more apparent in vtc1 and vte4, and adding exogenous vitamin C and vitamin E, respectively, could restore them. This study reported, for the first time, that vitamin E is better than vitamin C in delaying seedling senescence caused by macro-element deficiency in Arabidopsis.

An Arabidopsis NAC domain transcription factor, ATAF2, promotes age-dependent and dark-induced leaf senescence

Leaf senescence is controlled developmentally and environmentally and is affected by numerous genes, including transcription factors. An Arabidopsis NAC domain transcription factor, ATAF2, is known to regulate biotic stress responses. Recently, we have demonstrated that ATAF2 upregulates ORE1, a key regulator of leaf senescence. Here, to investigate the function of ATAF2 in leaf senescence further, we generated and analyzed overexpressing transgenic and T-DNA inserted mutant lines. Transient expression analysis indicated that ATAF2 upregulates several NAC domain transcription factors that regulate senescence. Indeed, ATAF2 overexpression induced the expression of senescence-related genes, thereby accelerating leaf senescence, whereas the expression of such genes in ataf2 mutants was lower than that of wild-type plants. Furthermore, the ataf2 mutants exhibited significant delays in dark-induced leaf senescence. It was also found that ATAF2 induces the expression of transcription factors, which both promotes and represses leaf senescence. The present study demonstrates that ATAF2 promotes leaf senescence in response to developmental and environmental signals.

Cytosolic Invertase-Mediated Root Growth Is Feedback Regulated by a Glucose-Dependent Signaling Loop

The disaccharide Suc cannot be utilized directly; rather, it is irreversibly hydrolyzed by invertase to the hexoses Glc and Fru to shape plant growth. In this context, Glc controls the stability of the transcription factor Ethylene-Insensitive3 (EIN3) via the function of Hexokinase1 (HXK1), a Glc sensor. Thus, invertase, especially the major neutral cytosolic invertase (CINV), constitutes a key point of control for plant growth. However, the cognate regulatory mechanisms that modulate CINV activity remain unclear. Here, we demonstrate that in Arabidopsis (Arabidopsis thaliana), EIN3 binds directly to both the promoters of Production of Anthocyanin Pigment1 (PAP1) and Phosphatidylinositol Monophosphate 5-Kinase 9 (PIP5K9), repressing and enhancing, respectively, their expression. Subsequently, PAP1 binds directly to and promotes transcription of the Cytosolic Invertase1 (CINV1) promoter, while PIP5K9 interacts with and negatively regulates CINV1. The accumulated CINV1 subsequently hydrolyzes Suc, releasing the sequestered signaling cue, Glc, which has been shown to negatively regulate the stability of EIN3 via HXK1. We conclude that a CINV1-Glc-HXK1-EIN3-PAP1/PIP5K9-CINV1 loop contributes to the modulation of CINV1 activity regulating root growth by Glc signaling.

A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis

BACKGROUND

Leaf senescence comprises numerous cooperative events, integrates environmental signals with age-dependent developmental cues, and coordinates the multifaceted deterioration and source-to-sink allocation of nutrients. In crops, leaf senescence has long been regarded as an essential developmental stage for productivity and quality, whereas functional characterization of candidate genes involved in the regulation of leaf senescence has, thus far, been limited in wheat.

RESULTS

In this study, we analyzed the expression profiles of 97 WRKY transcription factors (TFs) throughout the progression of leaf senescence in wheat and subsequently isolated a potential regulator of leaf senescence, TaWRKY42-B, for further functional investigation. By phenotypic and physiological analyses in TaWRKY42-B-overexpressing Arabidopsis plants and TaWRKY42-B-silenced wheat plants, we confirmed the positive role of TaWRKY42-B in the initiation of developmental and dark-induced leaf senescence. Furthermore, our results revealed that TaWRKY42-B promotes leaf senescence mainly by interacting with a JA biosynthesis gene, AtLOX3, and its ortholog, TaLOX3, which consequently contributes to the accumulation of JA content. In the present study, we also demonstrated that TaWRKY42-B was functionally conserved with AtWRKY53 in the initiation of age-dependent leaf senescence.

CONCLUSION

Our results revealed a novel positive regulator of leaf senescence, TaWRKY42-B, which mediates JA-related leaf senescence via activation of JA biosynthesis and has the potential to be a target gene for molecular breeding in wheat.

Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence

BACKGROUND

To fully elucidate the roles and mechanisms of plant hormones in leaf senescence, we adopted an integrated analysis of both non-senescing and senescing leaves from red maple with transcriptome and metabolome data.

RESULTS

Transcription and metabolite profiles were generated through a combination of deep sequencing, third-generation sequencing data analysis, and ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS), respectively. We investigated the accumulation of compounds and the expression of biosynthesis and signaling genes for eight hormones. The results revealed that ethylene and abscisic acid concentrations increased during the leaf senescence process, while the contents of cytokinin, auxin, jasmonic acid, and salicylic acid continued to decrease. Correlation tests between the hormone content and transcriptional changes were analyzed, and in six pathways, genes closely linked with leaf senescence were identified.

CONCLUSIONS

These results will enrich our understanding of the mechanisms of plant hormones that regulate leaf senescence in red maple, while establishing a foundation for the genetic modification of Acer in the future.

Emerging Connections between Small RNAs and Phytohormones

Small RNAs (sRNAs), mainly including miRNAs and siRNAs, are ubiquitous in eukaryotes. sRNAs mostly negatively regulate gene expression via (post-)transcriptional gene silencing through DNA methylation, mRNA cleavage, or translation inhibition. The mechanisms of sRNA biogenesis and function in diverse biological processes, as well as the interactions between sRNAs and environmental factors, like (a)biotic stress, have been deeply explored. Phytohormones are central in the plant's response to stress, and multiple recent studies highlight an emerging role for sRNAs in the direct response to, or the regulation of, plant hormonal pathways. In this review, we discuss recent progress on the unraveling of crossregulation between sRNAs and nine plant hormones.

Dynamic Changes of DNA Methylation Induced by Heat Treatment Were Involved in Ethylene Signal Transmission and Delayed the Postharvest Ripening of Tomato Fruit

Deoxyribonucleic acid (DNA) methylation plays an important role in fruit ripening and senescence. Here, the role of DNA methylation of the CpG island of SlACS10, LeCTR1, LeEIN3, LeERT10, and SlERF-A1 genes induced by heat treatment (37 °C) in postharvest ripening of tomato fruit was studied. After heat treatment, the firmness and vitamin C content showed higher levels, the loss of aldehydes in volatile components was delayed, and the activities of methylase and demethylase decreased in tomato fruit. Moreover, in heat-treated fruit, significant changes in DNA methylation of SlACS10, LeCTR1, LeEIN3, LeERT10, and SlERF-A1 were induced, the expression of LeERT10 and LeEIN3 was inhibited, the expression of SlERF-A1 was increased, by which ethylene signal transmission might be suppressed and the postharvest ripening of tomato fruit was delayed. The present study provided valuable information for understanding the essential role of DNA methylation in the postharvest ripening of tomato fruit.

High Ambient Temperature Accelerates Leaf Senescence via PHYTOCHROME-INTERACTING FACTOR 4 and 5 in Arabidopsis

Leaf senescence is a developmental process by which a plant actively remobilizes nutrients from aged and photosynthetically inefficient leaves to young growing ones by disassembling organelles and degrading macromolecules. Senescence is accelerated by age and environmental stresses such as prolonged darkness. Phytochrome B (phyB) inhibits leaf senescence by inhibiting phytochrome-interacting factor 4 (PIF4) and PIF5 in prolonged darkness. However, it remains unknown whether phyB mediates the temperature signal that regulates leaf senescence. We found the light-activated form of phyB (Pfr) remains active at least four days after a transfer to darkness at 20°C but is inactivated more rapidly at 28°C. This faster inactivation of Pfr further increases PIF4 protein levels at the higher ambient temperature. In addition, PIF4 mRNA levels rise faster after the transfer to darkness at high ambient temperature via a mechanism that depends on ELF3 but not phyB. Increased PIF4 protein then binds to the ORE1 promoter and activates its expression together with ABA and ethylene signaling, accelerating leaf senescence at high ambient temperature. Our results support a role for the phy-PIF signaling module in integrating not only light signaling but also temperature signaling in the regulation of leaf senescence.

Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.

Transcription factor CDF4 promotes leaf senescence and floral organ abscission by regulating abscisic acid and reactive oxygen species pathways in Arabidopsis

Leaf senescence is a highly complex developmental process that is tightly controlled by multiple layers of regulation. Abscisic acid (ABA) and reactive oxygen species (ROS) are two well-known factors that promote leaf senescence. We show here that the transcription factor CDF4 positively regulates leaf senescence. Constitutive and inducible overexpression of CDF4 accelerates leaf senescence, while knockdown of CDF4 delays it. CDF4 increases endogenous ABA levels by upregulating the transcription of the ABA biosynthesis genes 9-cis-epoxycarotenoid dioxygenase 2, 3 (NCED2, 3) and suppresses H₂ O₂ scavenging by repressing expression of the catalase2 (CAT2) gene. NCED2, 3 knockout and CAT2 overexpression partially rescue premature leaf senescence caused by CDF4 overexpression. We also show that CDF4 promotes floral organ abscission by activating the polygalacturonase PGAZAT gene. Based on these results, we propose that the levels of CDF4, ABA, and ROS undergo a gradual increase driven by their interlinking positive feedback loops during the leaf senescence and floral organ abscission processes.

LSD 3.0: a comprehensive resource for the leaf senescence research community

The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.

Raffinose synthase enhances drought tolerance through raffinose synthesis or galactinol hydrolysis in maize and Arabidopsis plants

Raffinose and its precursor galactinol accumulate in plant leaves during abiotic stress. RAFFINOSE SYNTHASE (RAFS) catalyzes raffinose formation by transferring a galactosyl group of galactinol to sucrose. However, whether RAFS contributes to plant drought tolerance and, if so, by what mechanism remains unclear. In this study, we report that expression of RAFS from maize (or corn, Zea mays) (ZmRAFS) is induced by drought, heat, cold, and salinity stresses. We found that zmrafs mutant maize plants completely lack raffinose and hyper-accumulate galactinol and are more sensitive to drought stress than the corresponding null-segregant (NS) plants. This indicated that ZmRAFS and its product raffinose contribute to plant drought tolerance. ZmRAFS overexpression in Arabidopsis enhanced drought stress tolerance by increasing myo-inositol levels via ZmRAFS-mediated galactinol hydrolysis in the leaves due to sucrose insufficiency in leaf cells and also enhanced raffinose synthesis in the seeds. Supplementation of sucrose to detached leaves converted ZmRAFS from hydrolyzing galactinol to synthesizing raffinose. Taken together, we demonstrate that ZmRAFS enhances plant drought tolerance through either raffinose synthesis or galactinol hydrolysis, depending on sucrose availability in plant cells. These results provide new avenues to improve plant drought stress tolerance through manipulation of the raffinose anabolic pathway.

Calcium-Dependent Protein Kinase CPK1 Controls Cell Death by In Vivo Phosphorylation of Senescence Master Regulator ORE1

Calcium-regulated protein kinases are key components of intracellular signaling in plants that mediate rapid stress-induced responses to changes in the environment. To identify in vivo phosphorylation substrates of CALCIUM-DEPENDENT PROTEIN KINASE1 (CPK1), we analyzed the conditional expression of constitutively active CPK1 in conjunction with in vivo phosphoproteomics. We identified Arabidopsis (Arabidopsis thaliana) ORESARA1 (ORE1), the developmental master regulator of senescence, as a direct CPK1 phosphorylation substrate. CPK1 phosphorylates ORE1 at a hotspot within an intrinsically disordered region. This augments transcriptional activation by ORE1 of its downstream target gene BIFUNCTIONAL NUCLEASE1 (BFN1). Plants that overexpress ORE1, but not an ORE1 variant lacking the CPK1 phosphorylation hotspot, promote early senescence. Furthermore, ORE1 is required for enhanced cell death induced by CPK1 signaling. Our data validate the use of conditional expression of an active enzyme combined with phosphoproteomics to decipher specific kinase target proteins of low abundance, of transient phosphorylation, or in yet-undescribed biological contexts. Here, we have identified that senescence is not just under molecular surveillance manifested by stringent gene regulatory control over ORE1 In addition, the decision to die is superimposed by an additional layer of control toward ORE1 via its posttranslational modification linked to the calcium-regulatory network through CPK1.

Expression profiling of the genes encoding ABA route components and the ACC oxidase isozymes in the senescing leaves of Populus tremula

Abscisic acid (ABA) triggers and regulates, while ethylene modulates autumn leaf senescence. The expression profiles of genes encoding ABA route components and the ACC oxidase isozymes were investigated in Populus tremula during the early and moderate stages of autumn leaf senescence. The targets of interest were Ptre-HAB1-like genes (Ptre-HAB1, Ptre-HAB3a and Ptre-HAB3b), the subclass 3 of Ptre-SnRK2s genes (Ptre-SnRK2.6a, Ptre-SnRK2.6b and Ptre-SnRK2.6b) and Ptre-RbohD1, Ptre-RbohF1, and Ptre-RbohF2 genes encoding the poplar components, which are counterparts of the ABA route key regulators or the counterparts of its secondary messengers, such as Homology to ABA-insensitive 1 (HAB1), Sucrose non-fermenting 1-related protein kinases 2 (SnRK2s) or Respiratory burst oxidase D and Respiratory burst oxidase F (RbohD and RbohF, respectively) in Arabidopsis, and Ptre-ACO3, Ptre-ACO5, and Ptre-ACO6 genes encoding ACC oxidase isozymes involved in ethylene biosynthesis. The fold change in their expression levels enabled to distinguish the distinct expression patterns for the following pairs of genes: Ptre-HAB3a and Ptre-SnRK2.6a, Ptre-HAB3b and Ptre-SnRK2.2, and Ptre-HAB1 and Ptre-SnRK2.6b, where each pair involves the genes encoding the negative and positive regulators of ABA route, respectively. Among the investigated genes, the fold change of expression was the highest for Ptre-ACO3, Ptre-ACO6, and Ptre-SnRK2.6b genes during both the studied stages, and additionally for Ptre-HAB1 and Ptre-RbohD1 genes during the moderate stage. In contrast, the Ptre-RbohF1 and Ptre-RbohF2 genes exhibited only the transient upregulation at the early stage of senescence. In an in vitro study, the ability of protein kinases Ptre-SnRK2.6a and Ptre-SnRK2.6b to phosphorylate the N-terminal regions of Ptre-RbohD1 and Ptre-RbohF2 was studied; the activity of Ptre-SnRK2.6b against the studied Ptre-Rbohs was noticeably lower than that exhibited by Ptre-SnRK2.6a. It seems that despite the high similarity of their polypeptides, Ptre-SnRK2.6a and Ptre-SnRK2.6b may play different biological roles; nonetheless, it requires in vivo confirmation. Surprisingly, the highest protein kinase activity against the Ptre-Rbohs was detected in the heterologous reaction with AT-SnRK2.6/OST1 which suggests that the discussed interactions are evolutionary conserved.

ETHYLENE INSENSITIVE 3 suppresses plant de novo root regeneration from leaf explants and mediates age-regulated regeneration decline

Powerful regeneration ability enables plant survival when plants are wounded. For example, adventitious roots can regenerate from the cutting site in detached Arabidopsis thaliana leaf explants, even in the absence of any exogenous plant hormone treatment. This process is known as de novo root regeneration (DNRR). Although the developmental program underlying DNRR is known, the precise regulatory mechanisms underlying DNRR are not completely understood. Here, we show that ethylene treatment or genetic activation of transcription factor ETHYLENE INSENSITIVE 3 (EIN3) strongly suppresses DNRR rates, while a mutant lacking EIN3 and its homolog EIL1 (ein3 eil1) displays a higher DNRR capacity. Previous reports have shown that the sequential induction of WUSCHEL RELATED HOMEOBOX 11 (WOX11)/WOX12 and WOX5/WOX7 expression is required for the establishment of DNRR. We found that EIN3 directly targets WOX11 and WOX5 promoter regions to suppress their transcription. Furthermore, older plants show enhanced EIN3 activity, and repressed expression of WOX11 and WOX5 Taken together, these results illustrate that plant aging at least partially takes advantage of EIN3 as a negative regulator to suppress DNRR through inhibiting the activation of WOX genes.

Small RNA sequencing revealed various microRNAs involved in ethylene-triggered flowering process in Aechmea fasciata

Ethylene-triggered flowering is a common phenomenon in plants of the family Bromeliaceae, but its molecular mechanism remains unclear. As a classical group of small RNAs, microRNAs play an essential role in the regulation of flowering. In this study, we found that various miRNAs participate in the ethylene-triggered flowering process in Aechmea fasciata via small RNA sequencing using juvenile and adult plants treated with ethylene for 24 hours. Finally, 63 known miRNAs, 52 novel miRNAs and 1721 target genes were identified or predicted. Expression changes of specific miRNAs were validated by qRT-PCR and northern blotting. Some predicted targets, including SPL, GAMYB and ARF, were verified in RLM-RACE experiments. Gene Ontology (GO) and KEGG analysis showed that numerous developmental and RNA-related processes were enriched. Integrated analysis of the transcriptomic data with small RNA sequencing revealed that numerous miRNAs and targets involved in ethylene-triggered flowering in A. fasciata. Our study is helpful for illuminating the molecular basis of the ethylene-triggered flowering phenomenon in Bromeliaceae.

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.