Identification of OsMYC2-regulated senescence-associated genes in rice

OsJAZ10 negatively modulates the drought tolerance by integrating hormone signaling with systemic electrical activity in rice

Jasmonic acid (JA) plays crucial functions in plant stress response, and the synergistic interaction between JA and abscisic acid (ABA) signaling is implicated to help plants adapt to environmental challenges, whereas the underlying molecular mechanism still needs to be revealed. Here, we report that OsJAZ10, a repressor in the JA signaling, represses rice drought tolerance via inhibition of JA and ABA biosynthesis. Function loss of OsJAZ10 markedly enhances, while overexpression of OsJAZ10ΔJas reduces rice drought tolerance. The osjaz10 mutant is more sensitive to exogenous ABA and MeJA, and produces higher levels of ABA and JA after drought treatment, indicating OsJAZ10 represses the biosynthesis of these two hormones. Mechanistic study demonstrated that OsJAZ10 physically interacts with OsMYC2. Transient transcriptional regulation assays showed that OsMYC2 activates the expression of ABA-biosynthetic gene OsNCED2, JA-biosynthetic gene OsAOC, and drought-responsive genes OsRAB21 and OsLEA3, while OsJAZ10 prevents OsMYC2 transactivation of these genes. Further, the electrophoretic mobility shift assay (EMSA) confirmed that OsMYC2 directly binds to the promoters of OsNCED2 and OsRAB21. Electrical activity has been proposed to activate JA biosynthesis. Interestingly, OsJAZ10 inhibits the propagation of osmotic stress-elicited systemic electrical signals, indicated by the significantly increased PEG-elicited slow wave potentials (SWPs) in osjaz10 mutant, which is in accordance with the elevated JA levels. Collectively, our findings establish that OsJAZ10 functions as a negative regulator in rice drought tolerance by repressing JA and ABA biosynthesis, and reveal an important mechanism that plants integrate electrical events with hormone signaling to enhance the adaption to environmental stress.

Mutation of Leaf Senescence 1 Encoding a C2H2 Zinc Finger Protein Induces ROS Accumulation and Accelerates Leaf Senescence in Rice

Premature senescence of leaves causes a reduced yield and quality of rice by affecting plant growth and development. The regulatory mechanisms underlying early leaf senescence are still unclear. The Leaf senescence 1 (LS1) gene encodes a C2H2-type zinc finger protein that is localized to both the nucleus and cytoplasm. In this study, we constructed a rice mutant named leaf senescence 1 (ls1) with a premature leaf senescence phenotype using CRISPR/Cas9-mediated editing of the LS1 gene. The ls1 mutants exhibited premature leaf senescence and reduced chlorophyll content. The expression levels of LS1 were higher in mature or senescent leaves than that in young leaves. The contents of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD) were significantly increased and catalase (CAT) activity was remarkably reduced in the ls1 plants. Furthermore, a faster decrease in pigment content was detected in mutants than that in WT upon induction of complete darkness. TUNEL and staining experiments indicated severe DNA degradation and programmed cell death in the ls1 mutants, which suggested that excessive ROS may lead to leaf senescence and cell death in ls1 plants. Additionally, an RT-qPCR analysis revealed that most senescence-associated and ROS-scavenging genes were upregulated in the ls1 mutants compared with the WT. Collectively, our findings revealed that LS1 might regulate leaf development and function, and that disruption of LS1 function promotes ROS accumulation and accelerates leaf senescence and cell death in rice.

Genome-wide analysis of basic helix-loop-helix genes in Dendrobium catenatum and functional characterization of DcMYC2 in jasmonate-mediated immunity to Sclerotium delphinii

Dendrobium catenatum, belonging to the Orchidaceae, is a precious Chinese herbal medicine. Sclerotium delphinii (P1) is a broad-spectrum fungal disease, which causes widespread loss in the near-wild cultivation of D. catenatum. Thus, resistance breeding of D. catenatum has become the key to solve this problem. The basic helix-loop-helix (bHLH) gene family is closely related to plant resistance to external stresses, but the related research in D. catenatum is not deep enough yet. Phylogenetic analysis showed that 108 DcbHLH genes could be divided into 23 subgroups. Promoter cis-acting elements revealed that DcbHLHs contain a large number of stress-related cis-acting elements. Transcriptome analysis of MeJA and P1 treatment manifested that exogenous MeJA can change the expression pattern of most bHLH genes, especially the IIIe subgroup, including inhibiting the expression of DcbHLH026 (MYC2a) and promoting the expression of DcbHLH027 (MYC2b). Subcellular localization indicated that they were located in the nucleus. Furthermore, exogenous MeJA treatment significantly delayed disease time and reduced lesion size after infection with P1. DcMYC2b-overexpression Arabidopsis lines showed significantly smaller lesions after being infected with P1 than the wild type, indicating that DcMYC2b functions as an important positive regulator in D. catenatum defense against P1. Our findings shed more insights into the critical role of the DcbHLH family in plants and the resistance breeding of D. catenatum.

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

The Mutation of Rice MEDIATOR25, OsMED25, Induces Rice Bacterial Blight Resistance through Altering Jasmonate- and Auxin-Signaling

Rice bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most severe diseases of rice. However, the regulatory mechanisms of rice defense against Xoo remain poorly understood. The rice MEDIATOR25, OsMED25—a subunit of the mediator multiprotein complex that acts as a universal adaptor between transcription factors (TFs) and RNA polymerase II—plays an important role in jasmonic acid (JA)-mediated lateral root development in rice. In this study, we found that OsMED25 also plays an important role in JA- and auxin-mediated resistance responses against rice bacterial blight. The osmed25 loss-of-function mutant exhibited high resistance to Xoo. The expression of JA-responsive defense-related genes regulated by OsMYC2, which is a positive TF in JA signaling, was downregulated in osmed25 mutants. Conversely, expression of some OsMYC2-independent JA-responsive defense-related genes was upregulated in osmed25 mutants. Furthermore, OsMED25 interacted with some AUXIN RESPONSE FACTORS (OsARFs) that regulate auxin signaling, whereas the mutated osmed25 protein did not interact with the OsARFs. The expression of auxin-responsive genes was downregulated in osmed25 mutants, and auxin-induced susceptibility to Xoo was not observed in osmed25 mutants. These results indicate that OsMED25 plays an important role in the stable regulation of JA- and auxin-mediated signaling in rice defense response.

Transcriptional Programs and Regulators Underlying Age-Dependent and Dark-Induced Senescence in Medicago truncatula

In forage crops, age-dependent and stress-induced senescence reduces forage yield and quality. Therefore, delaying leaf senescence may be a way to improve forage yield and quality as well as plant resilience to stresses. Here, we used RNA-sequencing to determine the molecular bases of age-dependent and dark-induced leaf senescence in Medicago truncatula. We identified 6845 differentially expressed genes (DEGs) in M3 leaves associated with age-dependent leaf senescence. An even larger number (14219) of DEGs were associated with dark-induced senescence. Upregulated genes identified during age-dependent and dark-induced senescence were over-represented in oxidation–reduction processes and amino acid, carboxylic acid and chlorophyll catabolic processes. Dark-specific upregulated genes also over-represented autophagy, senescence and cell death. Mitochondrial functions were strongly inhibited by dark-treatment while these remained active during age-dependent senescence. Additionally, 391 DE transcription factors (TFs) belonging to various TF families were identified, including a core set of 74 TFs during age-dependent senescence while 759 DE TFs including a core set of 338 TFs were identified during dark-induced senescence. The heterologous expression of several senescence-induced TFs belonging to NAC, WKRY, bZIP, MYB and HD-zip TF families promoted senescence in tobacco leaves. This study revealed the dynamics of transcriptomic responses to age- and dark-induced senescence in M. truncatula and identified senescence-associated TFs that are attractive targets for future work to control senescence in forage legumes.

Applications of CRISPR/Cas9 as New Strategies for Short Breeding to Drought Gene in Rice

Recent unpredictable climate change is the main reason for the decline in rice yield. In particular, drought stress is a major constraint in reducing yield and quality for rice at rainfed agriculture areas, such as Asia and South America. CRISPR/Cas9 provides an effective solution for gene function study and molecular breeding due to specific editing of targeted genome sequences. In addition, CRISPR/Cas9 application can significantly reduce the time required to develop new cultivars with improved traits compared to conventional complex and time-consuming breeding. Here, drought-induced gene Oryza sativa Senescence-associated protein (OsSAP) was edited by CRISPR/Cas9. To investigate the possible role of OsSAP in drought stress, genome-editing plants were subjected to drought stress until the soil moisture content reached 20%, and the reactive oxygen species (ROS) scavenging efficiency of genome-editing plants were decreased. When the genome-editing plants were subjected to drought stress, survival rate, shoot length, root length, content of chlorophyll number of tiller, and 1,000-grain weight decreased, and more H₂O₂ and O₂ ^- were detected in leaves. In addition, expression levels of several critical stress-related transcription factors were decreased in the OsSAP genome-editing plant. These results suggest that OsSAP function as a positive regulator during drought stress response in rice. We analyzed the expression of OsSAP and Cas9 in T₀ and T₁ plants as well as T₂ seeds. As the course of generation advancement progressed, Cas9 expression remained stable or weakened but the OsSAP expression was continuously removed from the T₀ plant. The coefficient of variation (CV) in both T₁ plants and T₂ seeds was lower than 5%. Overall, our results suggest that CRISPR/Cas9 could be a novel and important tool for efficiently generating specific and inheritable targeted genome editing in rice, with short breeding cycles.

Insights into Gene Regulation of Jasmonate-Induced Whole-Plant Senescence of Tobacco under Non-Starvation Conditions

Jasmonate (JA)-induced plant senescence has been mainly studied with a dark/starvation-promoted system using detached leaves; yet, the induction of whole-plant senescence by JA remains largely unclear. This work reports the finding of a JA-induced whole-plant senescence of tobacco under light/non-starvation conditions and the investigation of underlying regulations. Methyl jasmonate (MeJA) treatment induces the whole-plant senescence of tobacco in a light-intensity-dependent manner, which is suppressed by silencing of NtCOI1 that encodes the receptor protein of JA-Ile (the bioactive derivative of JA). MeJA treatment could induce the senescence-specific cysteine protease gene SAG12 and another cysteine protease gene SAG-L1 to high expression levels in the detached leaf patches under dark conditions but failed to induce their expression in tobacco whole plants under light conditions. Furthermore, MeJA attenuates the RuBisCo activase (RCA) level in the detached leaves but has no effect on this protein in the whole plant under light conditions. A genome-wide transcriptional assay also supports the presence of a differential regulatory pattern of senescence-related genes during MeJA-induced whole-plant senescence under non-starvation conditions and results in the finding of a chlorophylase activity increase in this process. We also observed that the MeJA-induced senescence of tobacco whole plants is reversible, which is accompanied by a structural change of chloroplasts. This work provides novel insights into JA-induced plant senescence under non-starvation conditions and is helpful to dissect the JA-synchronized process of whole-plant senescence.

TaWRKY13-A Serves as a Mediator of Jasmonic Acid-Related Leaf Senescence by Modulating Jasmonic Acid Biosynthesis

Leaf senescence is crucial for crop yield and quality. Transcriptional regulation is a key step for integrating various senescence-related signals into the nucleus. However, few regulators of senescence implicating transcriptional events have been functionally characterized in wheat. Based on our RNA-seq data, we identified a WRKY transcription factor, TaWRKY13-A, that predominately expresses at senescent stages. By using the virus-induced gene silencing (VIGS) method, we manifested impaired transcription of TaWRKY13-A leading to a delayed leaf senescence phenotype in wheat. Moreover, the overexpression (OE) of TaWRKY13-A accelerated the onset of leaf senescence under both natural growth condition and darkness in Brachypodium distachyon and Arabidopsis thaliana. Furthermore, by physiological and molecular investigations, we verified that TaWRKY13-A participates in the regulation of leaf senescence via jasmonic acid (JA) pathway. The expression of JA biosynthetic genes, including AtLOX6, was altered in TaWRKY13-A-overexpressing Arabidopsis. We also demonstrated that TaWRKY13-A can interact with the promoter of AtLOX6 and TaLOX6 by using the electrophoretic mobility shift assay (EMSA) and luciferase reporter system. Consistently, we detected a higher JA level in TaWRKY13-A-overexpressing lines than that in Col-0. Moreover, our data suggested that TaWRKY13-A is partially functional conserved with AtWRKY53 in age-dependent leaf senescence. Collectively, this study manifests TaWRKY13-A as a positive regulator of JA-related leaf senescence, which could be a new clue for molecular breeding in wheat.

Rice MEDIATOR25, OsMED25, is an essential subunit for jasmonate-mediated root development and OsMYC2-mediated leaf senescence

The Mediator multiprotein complex acts as a universal adaptor between transcription factors (TFs) and RNA polymerase II. MEDIATOR25 (MED25) has an important role in jasmonic acid (JA) signaling in Arabidopsis. However, no research has been conducted on the role of MED25 in JA signaling in rice, which is one of the most important food crops globally and is a model plant for molecular studies in other monocotyledonous species. In the present study, we isolated the loss-of function mutant of MED25, osmed25, through the map-based cloning and phenotypic complementation analysis by the introduction of OsMED25 and investigated the role of OsMED25 in JA signaling in rice. The osmed25 mutants had longer primary (seminal) roots than those of the wild-type (WT) and exhibited JA-insensitive phenotypes. S-type lateral root densities in osmed25 mutants were lower than those in the WT, whereas L-type lateral root densities in osmed25 mutants were higher than those in the WT. Furthermore, the osmed25 mutants retarded JA-regulated leaf senescence under dark-induced senescence. Mutated osmed25 protein could not interact with OsMYC2, which is a positive TF in JA signaling in rice. The expression of JA-responsive senescence-associated genes was not upregulated in response to JA in the osmed25 mutants. The results suggest that OsMED25 participates in JA-mediated root development and OsMYC2-mediated leaf senescence in rice.

Current Understanding of Leaf Senescence in Rice

Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.

Low Light/Darkness as Stressors of Multifactor-Induced Senescence in Rice Plants

Leaf senescence, as an integral part of the final development stage for plants, primarily remobilizes nutrients from the sources to the sinks in response to different stressors. The premature senescence of leaves is a critical challenge that causes significant economic losses in terms of crop yields. Although low light causes losses of up to 50% and affects rice yield and quality, its regulatory mechanisms remain poorly elucidated. Darkness-mediated premature leaf senescence is a well-studied stressor. It initiates the expression of senescence-associated genes (SAGs), which have been implicated in chlorophyll breakdown and degradation. The molecular and biochemical regulatory mechanisms of premature leaf senescence show significant levels of redundant biomass in complex pathways. Thus, clarifying the regulatory mechanisms of low-light/dark-induced senescence may be conducive to developing strategies for rice crop improvement. This review describes the recent molecular regulatory mechanisms associated with low-light response and dark-induced senescence (DIS), and their effects on plastid signaling and photosynthesis-mediated processes, chloroplast and protein degradation, as well as hormonal and transcriptional regulation in rice.

Apple BT2 protein negatively regulates jasmonic acid-triggered leaf senescence by modulating the stability of MYC2 and JAZ2

Jasmonic acid (JA) is shown to induce leaf senescence. However, the underlying molecular mechanism is not well understood, especially in woody plants such as fruit trees. In this study, we are interested in exploring the biological role of MdBT2 in JA-mediated leaf senescence. We found that MdBT2 played an antagonistic role in MdMYC2-promoted leaf senescence. Our results revealed that MdBT2 interacted with MdMYC2 and accelerated its ubiquitination degradation, thus negatively regulated MdMYC2-promoted leaf senescence. In addition, MdBT2 acted as a stabilizing factor to improve the stability of MdJAZ2 through direct interaction, thereby inhibited JA-mediated leaf senescence. Furthermore, our results also showed that MdBT2 interacted with a subset of JAZ proteins in apple, including MdJAZ1, MdJAZ3, MdJAZ4 and MdJAZ8. Our investigations provide new insight into molecular mechanisms of JA-modulated leaf senescence. The dynamic JA-MdBT2-MdJAZ2-MdMYC2 regulatory module plays an important role in JA-modulated leaf senescence.

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.

A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics

Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.

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.

Overexpression of jasmonate-responsive OsbHLH034 in rice results in the induction of bacterial blight resistance via an increase in lignin biosynthesis

OsbHLH034 acts as a positive regulator in jasmonate signaling in rice. Jasmonic acid (JA) is a plant hormone under strict regulation by various transcription factors (TFs) that acts as a signaling compound in the regulation of plant defense responses and development. Here, we report that a basic helix-loop-helix (bHLH)-type TF, OsbHLH034, plays an important role in the JA-mediated resistance response against rice bacterial blight caused by Xanthomonas oryzae pv. oryzae. The expression of OsbHLH034 was upregulated at a late phase after JA treatment. OsbHLH034 interacted with a Jasmonate ZIM-domain (JAZ) protein, OsJAZ9, in both plant and yeast cells. Transgenic rice plants overexpressing OsbHLH034 exhibited a JA-hypersensitive phenotype and increased resistance against rice bacterial blight. Conversely, OsbHLH034-overexpressing plants exhibited high sensitivity to salt stress. The expression of some JA-responsive secretory-type peroxidase genes was upregulated in the OsbHLH034-overexpressing rice plants. Concomitantly, the lignin content significantly increased in these transgenic plants compared to that in the wild-type. These results indicate that OsbHLH034 acts as a positive regulator of the JA-mediated defense response in rice.

Rice ETHYLENE RESPONSE FACTOR 101 Promotes Leaf Senescence Through Jasmonic Acid-Mediated Regulation of OsNAP and OsMYC2

Leaf senescence is the final stage of leaf development and an important step that relocates nutrients for grain filling in cereal crops. Senescence occurs in an age-dependent manner and under unfavorable environmental conditions such as deep shade, water deficit, and high salinity stresses. Although many transcription factors that modulate leaf senescence have been identified, the mechanisms that regulate leaf senescence in response to environmental conditions remain elusive. Here, we show that rice (Oryza sativa) ETHYLENE RESPONSE FACTOR 101 (OsERF101) promotes the onset and progression of leaf senescence. OsERF101 encodes a predicted transcription factor and OsERF101 transcript levels rapidly increased in rice leaves during dark-induced senescence (DIS), indicating that OsERF101 is a senescence-associated transcription factor. Compared with wild type, the oserf101 T-DNA knockout mutant showed delayed leaf yellowing and higher chlorophyll contents during DIS and natural senescence. Consistent with its delayed-yellowing phenotype, the oserf101 mutant exhibited downregulation of genes involved in chlorophyll degradation, including rice NAM, ATAF1/2, and CUC2 (OsNAP), STAY-GREEN (SGR), NON-YELLOW COLORING 1 (NYC1), and NYC3 during DIS. After methyl jasmonate treatment to induce rapid leaf de-greening, the oserf101 leaves retained more chlorophyll compared with wild type, indicating that OsERF101 is involved in promoting jasmonic acid (JA)-induced leaf senescence. Consistent with the involvement of JA, the expression of the JA signaling genes OsMYC2/JA INSENSITIVE 1 (OsJAI1) and CORONATINE INSENSITIVE 1a (OsCOI1a), was downregulated in the oserf101 leaves during DIS. Transient transactivation and chromatin immunoprecipitation assays revealed that OsERF101 directly binds to the promoter regions of OsNAP and OsMYC2, which activate genes involved in chlorophyll degradation and JA signaling-mediated leaf senescence. These results demonstrate that OsERF101 promotes the onset and progression of leaf senescence through a JA-mediated signaling pathway.

The overexpression of OsSRO1a, which encodes an OsNINJA1- and OsMYC2-interacting protein, negatively affects OsMYC2-mediated jasmonate signaling in rice

OsNINJA1-interacting protein, OsSRO1a, acts as a mediator that suppresses OsMYC2 activity in response to JA. Jasmonic acid (JA) is an important plant hormone for the stable growth and development of higher plants. The rice gene NOVEL INTERACTOR OF JAZ1 (OsNINJA1) interacts with Jasmonate ZIM-domain (JAZ) proteins and is a repressor of JA signaling. In this study, we identified several OsNINJA1-interacting proteins in rice from a yeast two-hybrid screen. Among the newly identified genes, we focused on SIMILAR TO RCD ONE1a (OsSRO1a) and investigated its role in JA signaling. Full-length OsSRO1a interacted with OsNINJA1 in plant cells but not in yeast cells. OsSRO1a also interacted with OsMYC2, a positive transcription factor in JA signaling, in both plant and yeast cells. The expression of OsSRO1a was upregulated at a late phase after JA treatment. Transgenic rice plants overexpressing OsSRO1a exhibited JA-insensitive phenotypes. In wild-type plants, JA induces resistance against rice bacterial blight, but this phenotype was suppressed in the OsSRO1a-overexpressing plants. Furthermore, the degradation of chlorophyll under dark-induced senescence conditions and the JA-induced upregulation of OsMYC2-responsive genes were suppressed in the OsSRO1a-overexpressing plants. These results suggest that OsSRO1a is a negative regulator of the OsMYC2-mediated JA signaling pathway in rice.

Natural variation in the expression and catalytic activity of a naringenin 7-O-methyltransferase influences antifungal defenses in diverse rice cultivars

Phytoalexins play a pivotal role in plant-pathogen interactions. Whereas leaves of rice (Oryza sativa) cultivar Nipponbare predominantly accumulated the phytoalexin sakuranetin after jasmonic acid induction, only very low amounts accumulated in the Kasalath cultivar. Sakuranetin is synthesized from naringenin by naringenin 7-O-methyltransferase (NOMT). Analysis of chromosome segment substitution lines and backcrossed inbred lines suggested that NOMT is the underlying cause of differential phytoalexin accumulation between Nipponbare and Kasalath. Indeed, both NOMT expression and NOMT enzymatic activity are lower in Kasalath than in Nipponbare. We identified a proline to threonine substitution in Kasalath relative to Nipponbare NOMT as the main cause of the lower enzymatic activity. Expanding this analysis to rice cultivars with varying amounts of sakuranetin collected from around the world showed that NOMT induction is correlated with sakuranetin accumulation. In bioassays with Pyricularia oryzae, Gibberella fujikuroi, Bipolaris oryzae, Burkholderia glumae, Xanthomonas oryzae, Erwinia chrysanthemi, Pseudomonas syringae, and Acidovorax avenae, naringenin was more effective against bacterial pathogens and sakuranetin was more effective against fungal pathogens. Therefore, the relative amounts of naringenin and sakuranetin may provide protection against specific pathogen profiles in different rice-growing environments. In a dendrogram of NOMT genes, those from low-sakuranetin-accumulating cultivars formed at least two clusters, only one of which involves the proline to threonine mutation, suggesting that the low sakuranetin chemotype was acquired more than once in cultivated rice. Strains of the wild rice species Oryza rufipogon also exhibited differential sakuranetin accumulation, indicating that this metabolic diversity predates rice domestication.

Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

BACKGROUND

Due to their sessile life style, plant survival is dependent on the ability to build up fast and highly adapted responses to environmental stresses by modulating defense response and organ growth. The phytohormone jasmonate plays an essential role in regulating these plant responses to stress.

RESULTS

To assess variation of plant growth responses and identify genetic determinants associated to JA treatment, we conducted a genome-wide association study (GWAS) using an original panel of Vietnamese rice accessions. The phenotyping results showed a high natural genetic variability of the 155 tested rice accessions in response to JA for shoot and root growth. The level of growth inhibition by JA is different according to the rice varieties tested. We conducted genome-wide association study and identified 28 significant associations for root length (RTL), shoot length (SHL), root weight (RTW), shoot weight (SHW) and total weight (TTW) in response to JA treatment. Three common QTLs were found for RTL, RTW and SHL. Among a list of 560 candidate genes found to co-locate with the QTLs, a transcriptome analysis from public database for the JA response allows us to identify 232 regulated genes including several JA-responsive transcription factors known to play a role in stress response.

CONCLUSION

Our genome-wide association study shows that common and specific genetic elements are associated with inhibition of shoot and root growth under JA treatment suggesting the involvement of a complex JA-dependent genetic control of rice growth inhibition at the whole plant level. Besides, numerous candidate genes associated to stress and JA response are co-located with the association loci, providing useful information for future studies on genetics and breeding to optimize the growth-defense trade-off in rice.

Rice DNA-Binding One Zinc Finger 24 (OsDOF24) Delays Leaf Senescence in a Jasmonate-Mediated Pathway

Leaf senescence is the final stage of leaf development and in cereal crops, the timing of senescence relative to grain filling has major effects on agronomic traits such as yield. Although many genetic factors are involved in the regulation of leaf senescence in cereals, the key regulators remain to be determined. Plant transcription factors with a conserved DOF (DNA-binding one zinc finger) domain play roles in multiple physiological processes. Here, we show a novel function for OsDOF24 as a repressor of leaf senescence in rice (Oryza sativa). In wild-type leaves, OsDOF24 expression rapidly decreased during natural senescence (NS) and dark-induced senescence (DIS). The gain-of-function mutant osdof24-D, which contains an enhancer-trap T-DNA in the OsDOF24 promoter, exhibited delayed leaf yellowing during NS and DIS. Transgenic plants overexpressing OsDOF24 showed the same phenotype during DIS. Reverse-transcription quantitative real-time PCR analysis revealed that senescence-associated genes (Osl85, Osl57 and OsNAP) and chlorophyll degradation genes (NYC1, NYC3 and SGR) were downregulated in the osdof24-D mutant during dark incubation. Among the phytohormones, only methyl jasmonate induced OsDOF24 expression. Furthermore, the reduced expression of jasmonate biosynthesis-related genes (OsLOX2, OsLOX8, OsHI-LOX, OsAOS1 and OsAOS2) in osdof24-D decreased endogenous jasmonate levels, resulting in delayed leaf senescence under DIS conditions. Yeast one-hybrid assays showed that OsDOF24 binds to the promoter region of OsAOS1. Taken together, our results demonstrate that OsDOF24 suppresses the induction of leaf senescence during vegetative growth by deactivating jasmonate biosynthetic pathways.

Jasmonic Acid-Induced VQ-Motif-Containing Protein OsVQ13 Influences the OsWRKY45 Signaling Pathway and Grain Size by Associating with OsMPK6 in Rice

Jasmonic acid (JA) is a plant hormone that plays an important role in the defense response and stable growth of rice. In this study, we investigated the role of the JA-responsive valine-glutamine (VQ)-motif-containing protein OsVQ13 in JA signaling in rice. OsVQ13 was primarily located in the nucleus and cytoplasm. The transgenic rice plants overexpressing OsVQ13 exhibited a JA-hypersensitive phenotype and increased JA-induced resistance to Xanthomonas oryzae pv. oryzae (Xoo), which is the bacteria that causes rice bacterial blight, one of the most serious diseases in rice. Furthermore, we identified a mitogen-activated protein kinase, OsMPK6, as an OsVQ13-associating protein. The expression of genes regulated by OsWRKY45, an important WRKY-type transcription factor for Xoo resistance that is known to be regulated by OsMPK6, was upregulated in OsVQ13-overexpressing rice plants. The grain size of OsVQ13-overexpressing rice plants was also larger than that of the wild type. These results indicated that OsVQ13 positively regulated JA signaling by activating the OsMPK6-OsWRKY45 signaling pathway in rice.

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

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

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)

Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.

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.

Overexpression of OsNINJA1 negatively affects a part of OsMYC2-mediated abiotic and biotic responses in rice

The plant hormone jasmonic acid (JA) plays an important role in defense response and plant development. Jasmonate ZIM-domain (JAZ) proteins act as transcriptional repressors of plant responses to JA. In this study, we found that OsNINJA1, which is a JAZ-interacting adaptor protein, plays an important role in JA signaling that is positively regulated by the transcription factor OsMYC2 in rice. The expression of OsNINJA1 was upregulated at an early phase after JA treatment, and OsNINJA1 interacted with several OsJAZ proteins in a C domain-dependent manner. Transgenic rice plants overexpressing OsNINJA1 exhibited a JA-insensitive phenotype and were more susceptible to rice bacterial blight caused by Xanthomonas oryzae pv. oryzae, which is one of the most serious diseases affecting rice. Furthermore, OsNINJA1 negatively affected JA-regulated leaf senescence under dark-induced senescence conditions. Finally, the expression of OsMYC2-responsive pathogenesis-related (PR) genes and senescence-associated genes (SAGs) tended to be downregulated in the OsNINJA1-overexpressing rice plants. These results indicate that OsNINJA1 acts as a negative regulator of OsMYC2-mediated JA signaling in rice.

Association of BrERF72 with methyl jasmonate-induced leaf senescence of Chinese flowering cabbage through activating JA biosynthesis-related genes

The ethylene response factor (ERF) and phytohormone jasmonate (JA) are reported to function in leaf senescence. The involvement of ERF in JA-mediated leaf senescence, however, needs to be elucidated. In the present work, we demonstrate a Chinese flowering cabbage ERF transcription factor (TF), BrERF72, that is associated with JA-promoted leaf senescence. Exogenous application of methyl jasmonate (MeJA)-accelerated leaf senescence of Chinese flowering cabbage, evidenced by the data that MeJA treatment led to the stronger reduction in the maximum quantum yield (Fv/Fm), photosynthetic electron transport rate (ETR), and total chlorophyll content, while significant induction in the expression of several senescence-associated genes (SAGs) including BrSAG12, BrSAG19, and chlorophyll catabolic genes (CCGs) BrPAO1, BrNYC1, BrPPH1, and BrSGR1. Increases in levels of endogenous JA and transcripts of JA biosynthetic genes BrLOX4, BrAOC3, and BrOPR3 were also found after MeJA treatment. BrERF72 was a MeJA-inducible, nucleus-localized protein, and possessed trans-activation ability. Transient overexpression of BrERF72 in tobacco leaves also promoted leaf senescence. More importantly, further experiments revealed that BrERF72 directly activated expression of BrLOX4, BrAOC3, and BrOPR3 through binding to their promoters via the GCC or DRE/CRT cis-element. Together, the novel JA-ERF association reported in our study uncovers a new insight into the transcriptional regulation of JA production mediated by ERF during JA-promoted leaf senescence in Chinese flowering cabbage.

Genetic Dissection of Leaf Senescence in Rice

Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon

BACKGROUND

As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae.

RESULTS

A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.

CONCLUSION

One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.

Phytohormone and Light Regulation of Chlorophyll Degradation

Degreening, due to the net loss of chlorophyll (Chl), is the most prominent symptom during the processes of leaf senescence, fruit ripening, and seed maturation. Over the last decade or so, extensive identifications of Chl catabolic genes (CCGs) have led to the revelation of the biochemical pathway of Chl degradation. As such, exploration of the regulatory mechanism of the degreening process is greatly facilitated. During the past few years, substantial progress has been made in elucidating the regulation of Chl degradation, particularly via the mediation of major phytohormones' signaling. Intriguingly, ethylene and abscisic acid's signaling have been demonstrated to interweave with light signaling in mediating the regulation of Chl degradation. In this review, we briefly summarize this progress, with an effort on providing a framework for further investigation of multifaceted and hierarchical regulations of Chl degradation.