A Jasmonate-Activated MYC2-Dof2.1-MYC2 Transcriptional Loop Promotes Leaf Senescence in Arabidopsis

Regeneration and defense: unveiling the molecular interplay in plants

In both plants and animals, tissue or organ regeneration typically follows wounding, which also activates defense responses against pathogenic microbes and herbivores. Both intrinsic and environmental cues guide the molecular decisions between regeneration and defense. In animal studies, extensive research has highlighted the role of various microbes - including pathogenic, commensal, and beneficial species - in influencing the signaling interplay between immunity and regeneration. Conversely, most plant regeneration studies are conducted under sterile conditions, which leaves a gap in our understanding of how plant innate immunity influences regeneration pathways. Recent findings have begun to elucidate the roles of key defense pathways in modulating plant regeneration and the crosstalk between these two processes. These studies also explore how microbes might influence the molecular choice between defense and regeneration in plants. This review examines the molecular mechanisms governing the balance between plant regeneration and innate immunity, with a focus on the emerging role of aging and microbial interactions in shaping these processes.

MYB47 delays leaf senescence by modulating jasmonate pathway via direct regulation of CYP94B3/CYP94C1 expression in Arabidopsis

Leaf senescence is a complex genetic process intricately regulated by multiple layers of control. Transcription factors, as master regulators of gene expression, play crucial roles in initiating and progressing leaf senescence. Through screening an activation-tagged mutant library, we identified MYB47 as a negative regulator of leaf senescence. Constitutive or inducible overexpression of MYB47 significantly delays leaf senescence, while loss-of-function mutants exhibit accelerated senescence. Transcriptome analysis revealed a marked suppression of jasmonic acid (JA) signaling in MYB47 overexpression lines. Conversely, the myb47 mutants display elevated JA levels and reduced expression of JA catabolic genes, CYP94B3 and CYP94C1. Biochemical evidence demonstrated that MYB47 directly binds to the promoters of CYP94B3 and CYP94C1, upregulating their expression. Consequently, JA contents are significantly reduced in MYB47 overexpression lines. Overexpressing CYP94B3 or CYP94C1 in myb47 mutants alleviates their early senescence phenotype. Furthermore, JA induces MYB47 expression, forming a negative feedback loop (JA-MYB47-CYP94B3/C1-JA) that fine-tunes leaf senescence. Our findings reveal a novel regulatory module involving MYB47 and JA signaling that governs leaf senescence. By stimulating JA catabolism and attenuating JA signaling, MYB47 plays a crucial role in delaying leaf senescence.

Genome-Wide Identification and Functional Characterization of the Dof Family in Dendrobium officinale

The Dof gene family represents a class of plant-specific transcription factors that play crucial regulatory roles in various biological processes, including plant growth, development, and responses to abiotic stress. However, genome-wide identification and functional characterization of the Dof gene family remain unexplored in Dendrobium officinale. In this study, we performed a genome-wide identification and functional analysis of the DoDof gene family. A total of 28 Dof family members were identified and named DoDof1-28 based on genome annotation data. Phylogenetic analysis classified these genes into four major groups (A-D) and further subdivided them into nine subfamilies. Gene structure analysis revealed that most DoDofs lack introns, with no distinct specificity observed among different subfamilies and considerable diversity within the same subfamily. Sequence alignment analysis demonstrated that all DoDof proteins contain a conserved Dof domain consisting of 52 amino acids, which includes a C2-C2 zinc finger motif and a DNA-binding domain. MEME analysis revealed that the conserved motif composition exhibits a certain degree of conservation among DoDof proteins, but significant differences exist across subfamilies. Expression pattern analysis demonstrated that DoDofs have exhibited diverse expression profiles across different developmental stages, tissues, and under abiotic stresses (such as low temperature, salinity, and drought) in D. officinale, suggesting their potential roles in plant development and stress responses. Subcellular localization analysis indicated that DoDof15, DoDof22, and DoDof24 are localized exclusively in the nucleus. Yeast one-hybrid assays revealed that DoDof22 binds to the promoter of the ABA receptor DoPYL9, while DoDof15 and DoDof24 bind to the promoter of the bHLH transcription factor DobHLH68. These results suggest that DoDof proteins may regulate the growth, development, and stress response processes of D. officinale by binding to the promoters of target genes. This study provides critical insights into the functional roles of Dof transcription factors in Orchidaceae family and establishes a theoretical foundation for molecular breeding and stress resistance improvement in D. officinale.

Transcriptome analyses for revealing leaf abscission of Cyclocarya paliurus stem segments in vitro

Leaf abscission of Cyclocarya paliurus stem segments in vitro is very serious, and more than 90% of the leaves gradually fall off with prolonged culture time, which hinders breeding. This study investigated the molecular mechanism of leaf abscission. The emerged leaves of C. paliurus stem segments were cultured for 22 days (T0) in vitro; leaves at 27 days (T1) and leaves that had fallen after ≥ 32 days (T2) were used as materials for analysis of the physiological characteristics and transcriptome data. During the leaf abscission process of C. paliurus, the Indole-3-acetic acid (IAA) content gradually decreased, whereas the carotenoid, 1-aminocyclopropane-1-carboxylic acid (ACC) and lignin contents and pectinase and cellulase activities significantly increased; 1807 and 10,908 DEGs were obtained in T0 vs T1 and T1 vs T2, respectively. The plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway and flavonoid biosynthesis pathway were significantly enriched in the KEGG metabolic pathway analysis. The differential expression of related genes affected AUX and Ethylene (ETH) biosynthesis and signal transduction, lignin synthesis, ROS metabolism, leaf color changes. Weighted gene coexpression network analysis (WGCNA) identified 10 hub genes (U-box protein, ERF5, ERF109, ERF4, SAUR36, CML19, MYC2-like,SPHK1, TOE3, POD55) that interact to activate abscission signaling, which subsequently influences the genes expression involved in the biosynthesis and signal transduction of auxin and ethylene; this resulted in an imbalance of endogenous hormone levels in the leaves, leading to the upregulation of pectinase, cellulase, and lignin biosynthesis genes and acceleration of the rupture of the abscission zone (AZ) cell and vascular cell wall, which ultimately led to leaf abscission. The present study illustrates a regulatory mechanism of leaf abscission of C. paliurus stem segments in vitro, which provides potential application value for guiding the inhibition of leaf abscission in vitro.

GH3 Gene Family Identification in Chinese White Pear (Pyrus bretschneideri) and the Functional Analysis of PbrGH3.5 in Fe Deficiency Responses in Tomato

Iron (Fe) deficiency poses a major threat to pear (Pyrus spp.) fruit yield and quality. The Gretchen Hagen 3 (GH3) plays a vital part in plant stress responses. However, the GH3 gene family is yet to be characterized, and little focus has been given to the function of the GH3 gene in Fe deficiency responses. Here, we identified 15 GH3 proteins from the proteome of Chinese white pear (Pyrus bretschneideri) and analyzed their features using bioinformatics approaches. Structure domain and motif analyses showed that these PbrGH3s were relatively conserved, and phylogenetic investigation displayed that they were clustered into two groups (GH3 I and GH3 II). Meanwhile, cis-acting regulatory element searches of the corresponding promoters revealed that these PbrGH3s might be involved in ABA- and drought-mediated responses. Moreover, the analysis of gene expression patterns exhibited that most of the PbrGH3s were highly expressed in the calyxes, ovaries, and stems of pear plants, and some genes were significantly differentially expressed in normal and Fe-deficient pear leaves, especially for PbrGH3.5. Subsequently, the sequence of PbrGH3.5 was isolated from the pear, and the transgenic tomato plants with PbrGH3.5 overexpression (OE) were generated to investigate its role in Fe deficiency responses. It was found that the OE plants were more sensitive to Fe deficiency stress. Compared with wild-type (WT) plants, the rhizosphere acidification and ferric reductase activities were markedly weakened, and the capacity to scavenge reactive oxygen species was prominently impaired in OE plants under Fe starvation conditions. Moreover, the expressions of Fe-acquisition-associated genes, such as SlAHA4, SlFRO1, SlIRT1, and SlFER, were all greatly repressed in OE leaves under Fe depravation stress, and the free IAA level was dramatically reduced, while the conjugated IAA contents were notably escalated. Combined, our findings suggest that pear PbrGH3.5 negatively regulates Fe deficiency responses in tomato plants, and might help enrich the molecular basis of Fe deficiency responses in woody plants.

ArNAC148 induces Acer rubrum leaf senescence by activating the transcription of the ABA receptor gene ArPYR13

Acer rubrum, an ornamental tree known for its stunning autumn colors, has an elusive molecular mechanism that governs its leaf senescence. We performed the genome-wide analysis of NAC transcription factor genes and PYRABACTIN RESISTANCE1-LIKE (PYLs) and found that ArNAC148 and ArPYL13 were significantly upregulated in senescing leaves as compared to mature leaves. Subcellular localization studies confirmed the nuclear localization of ArNAC148 and the cytoplasmic localization of ArPYL13. Electrophoretic mobility shift assay and yeast one-hybrid assay demonstrated that ArNAC148 directly binds to the promoter of ArPYL13. Luciferase reporter assays further showed that ArNAC148 activates the transcription of ArPYL13. The transient expression of ArNAC148 and ArPYL13 in tobacco leaves promoted chlorophyll degradation, increased H2O2 level, MDA contents, and electrolyte leakage in response to abscisic acid (ABA). Moreover, the virus-induced gene silencing of ArNAC148 and ArPYL13 in A. rubrum produced results that were opposite to those observed in transient expression experiments. Our findings suggest that ArNAC148 induces leaf senescence by directly activating the transcription of ArPYL13, providing insights into the ABA-mediated regulatory mechanisms governing leaf senescence in A. rubrum. This study offers new perspectives for researchers to explore the roles of NAC and PYL genes in regulating leaf senescence in woody ornamental plants.

Hydrogen peroxide participates in leaf senescence by inhibiting CHLI1 activity

KEY MESSAGE

Hydrogen peroxide promoted leaf senescence by sulfenylating the magnesium chelating protease I subunit (CHLI1) in the chlorophyll synthesis pathway, and inhibited its activity to reduce chlorophyll synthesis. Leaf senescence is the final and crucial stage of plant growth and development, during which chlorophyll experiences varying degrees of destruction. It is well-known that the higher ROS accumulation is a key factor for leaf senescence, but whether and how ROS regulates chlorophyll synthesis in the process are unknown. Here, we report that H2O2 inhibits chlorophyll synthesis during leaf senescence via the I subunit of magnesium-chelatase (CHLI1). During leaf senescence, the decrease of chlorophyll content is accompanied by the increase of H2O2 accumulation, as well as the inhibition of catalase (CAT) genes expression. The mutant cat2-1, with increased H2O2 shows an accelerated senescence phenotype and decreased CHLI1 activity compared with the wild type. H2O2 inhibits CHLI1 activity by sulfenylating CHLI1 during leaf senescence. Consistent with this, the chli1 knockout mutant displays the same premature leaf senescence symptom as cat2-1, while overexpression of CHLI1 in cat2-1 can partially restore its early senescence phenotype. Taken together, these results illustrate that CAT2-mediated H2O2 accumulation during leaf senescence represses chlorophyll synthesis through sulfenylating CHLI1, and thus inhibits its activity, providing a new insight into the pivotal role of chlorophyll synthesis as a participant in orchestrating the leaf senescence.

The transcription factor MYC2 positively regulates terpene trilactone biosynthesis through activating GbGGPPS expression in Ginkgo biloba

Terpene trilactones (TTLs) have important medicinal value, but their low content in Ginkgo biloba leaves makes their exploitation extremely costly, thereby limiting the development of TTL-related industries. It was found that exogenous methyl jasmonate (MeJA) treatment increased the accumulation of TTLs, but the molecular mechanism is still unclear. Here, we identified two bHLH transcription factors in G. biloba, with the protein subcellular localizations in the nucleus. Expression of GbMYC2s was strongly induced by MeJA treatment, and the interactions between GbJAZs and GbMYC2s were demonstrated by yeast two-hybrid and bimolecular fluorescence complementation experiments. Overexpression of GbMYC2_4 and GbMYC2_5 enhanced Arabidopsis root sensitivity and significantly increased TTL content. In addition, GbGGPPS was found to be a common target of GbMYC2_4 and GbMYC2_5 by yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase reporter assays and DAP-seq, and they achieved regulation of GbGGPPS by binding to the G-box. Further findings revealed that GbMYC2_4 and GbMYC2_5 bind the G-box not universally but selectively. Our study revealed that jasmonic acid signaling mediates TTL biosynthesis through the GbJAZ-GbMYC2-GbGGPPS module, which enriches the terpenoid biosynthesis regulatory networks and provides a research basis and target genes for enhancing TTL content through genetic engineering.

RsOBP2a, a member of OBF BINDING PROTEIN transcription factors, inhibits two chlorophyll degradation genes in green radish

The green radish (Raphanus sativus L.) contains abundant chlorophyll (Chl). DOF-type transcription factor OBF BINDING PROTEIN (OBP) plays crucial functions in plant growth, development, maturation and responses to various abiotic stresses. However, the metabolism by which OBP transcription factors regulate light-induced Chl metabolism in green radish is not well understood. In this study, six OBP genes were identified from the radish genome, distributed unevenly across five chromosomes. Among these genes, RsOBP2a showed significantly higher expression in the green flesh compared to the white flesh of green radish. Analysis of promoter elements suggested that RsOBPs might be involved in stress responses, particularly in light-related processes. Overexpression of RsOBP2a led to increase Chl levels in cotyledons and adventitious roots of radish, while silencing RsOBP2a expression through TYMV-induced gene silencing accelerated leaf senescence. Further investigations revealed that RsOBP2a was localized in the nucleus and served as a transcriptional repressor. RsOBP2a was induced by light and directly suppressed the expression of STAYGREEN (SGR) and RED CHLOROPHYLL CATABOLITE REDUCTASE (RCCR), thereby delaying senescence in radish. Overall, a novel regulatory model involving RsOBP2a, RsSGR, and RsRCCR was proposed to govern Chl metabolism in response to light, offering insights for the enhancement of green radish germplasm.

HASTY-mediated miRNA dynamics modulate nitrogen starvation-induced leaf senescence in Arabidopsis

Nitrogen (N) deficiency responses are essential for plant survival and reproduction. Here, via an expression genome-wide association study (eGWAS), we reveal a mechanism that regulates microRNA (miRNA) dynamics necessary for N deficiency responses in Arabidopsis. Differential expression levels of three NAC transcription factor (TF) genes involved in leaf N deficiency responses among Arabidopsis accessions are most significantly associated with polymorphisms in HASTY (HST), which encodes an importin/exportin family protein responsible for the generation of mature miRNAs. HST acts as a negative regulator of N deficiency-induced leaf senescence, and the disruption and overexpression of HST differently modifies miRNA dynamics in response to N deficiency, altering levels of miRNAs targeting transcripts. Interestingly, N deficiency prevents the interaction of HST with HST-interacting proteins, DCL1 and RAN1, and some miRNAs. This suggests that HST-mediated regulation of miRNA dynamics collectively controls regulations mediated by multiple N deficiency response-associated NAC TFs, thereby being central to the N deficiency response network.

Advances in functional studies of plant MYC transcription factors

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

A structure-redesigned intrinsically disordered peptide that selectively inhibits a plant transcription factor in jasmonate signaling

Plant hormone-related transcription factors (TFs) are key regulators of plant development, responses to environmental stress such as climate changes, pathogens, and pests. These TFs often function as families that exhibit genetic redundancy in higher plants, and are affected by complex crosstalk mechanisms between different plant hormones. These properties make it difficult to analyze and control them in many cases. In this study, we introduced a chemical inhibitor to manipulate plant hormone-related TFs, focusing on the jasmonate (JA) and ethylene (ET) signaling pathways, with the key TFs MYC2/3/4 and EIN3/EIL1. This study revealed that JAZ10CMID, the binding domain of the repressor involved in the desensitization of both TFs, is an intrinsically disordered region in the absence of binding partners. Chemical inhibitors have been designed based on this interaction to selectively inhibit MYC TFs while leaving EIN3/EIL1 unaffected. This peptide inhibitor effectively disrupts MYC-mediated responses while activating EIN3-mediated responses and successfully uncouples the crosstalk between JA and ET signaling in Arabidopsis thaliana. Furthermore, the designed peptide inhibitor was also shown to selectively inhibit the activity of MpMYC, an ortholog of AtMYC in Marchantia polymorpha, demonstrating its applicability across different plant species. This underscores the potential of using peptide inhibitors for specific TFs to elucidate hormone crosstalk mechanisms in non-model plants without genetic manipulation. Such a design concept for chemical fixation of the disordered structure is expected to limit the original multiple binding partners and provide useful chemical tools in chemical biology research.

Arabidopsis thaliana MYC2 and MYC3 Are Involved in Ethylene-Regulated Hypocotyl Growth as Negative Regulators

The ethylene-regulated hypocotyl elongation of Arabidopsis thaliana involves many transcription factors. The specific role of MYC transcription factors in ethylene signal transduction is not completely understood. The results here revealed that two MYCs, MYC2 and MYC3, act as negative regulators in ethylene-suppressed hypocotyl elongation. Etiolated seedlings of the loss-of-function mutant of MYC2 or MYC3 were significantly longer than wild-type seedlings. Single- or double-null mutants of MYC2 and MYC3 displayed remarkably enhanced response to ACC(1-aminocyclopropane-1-carboxylate), the ethylene precursor, compared to wild-type seedlings. MYC2 and MYC3 directly bind to the promoter zone of ERF1, strongly suppressing its expression. Additionally, EIN3, a key component in ethylene signaling, interacts with MYC2 or MYC3 and significantly suppresses their binding to ERF1's promoter. MYC2 and MYC3 play crucial roles in the ethylene-regulated expression of functional genes. The results revealed the novel role and functional mechanism of these transcription factors in ethylene signal transduction. The findings provide valuable information for deepening our understanding of their role in regulating plant growth and responding to stress.

Transcription factor NtNAC56 regulates jasmonic acid-induced leaf senescence in tobacco

Leaf senescence is a vital aspect of plant physiology and stress responses and is induced by endogenous factors and environmental cues. The plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factor family influences growth, development, and stress responses in Arabidopsis (Arabidopsis thaliana) and other species. However, the roles of NACs in tobacco (Nicotiana tabacum) leaf senescence are still unclear. Here, we report that NtNAC56 regulates leaf senescence in tobacco. Transgenic plants overexpressing NtNAC56 (NtNAC56-OE) showed induction of senescence-related genes and exhibited early senescence and lower chlorophyll content compared to wild-type (WT) plants and the Ntnac56-19 mutant. In addition, root development and seed germination were inhibited in the NtNAC56-OE lines. Transmission electron microscopy observations accompanied by physiological and biochemical assays revealed that NtNAC56 overexpression triggers chloroplast degradation and reactive oxygen species accumulation in tobacco leaves. Transcriptome analysis demonstrated that NtNAC56 activates leaf senescence-related genes and jasmonic acid (JA) biosynthesis pathway genes. In addition, the JA content of NtNAC56-OE plants was higher than in WT plants, and JA treatment induced NtNAC56 expression. We performed DNA affinity purification sequencing to identify direct targets of NtNAC56, among which we focused on LIPOXYGENASE 5 (NtLOX5), a key gene in JA biosynthesis. A dual-luciferase reporter assay and a yeast one-hybrid assay confirmed that NtNAC56 directly binds to the TTTCTT motif in the NtLOX5 promoter. Our results reveal a mechanism whereby NtNAC56 regulates JA-induced leaf senescence in tobacco and provide a strategy for genetically manipulating leaf senescence and plant growth.

Sequential activation of strigolactone and salicylate biosynthesis promotes leaf senescence

Leaf senescence is a complex process strictly regulated by various external and endogenous factors. However, the key signaling pathway mediating leaf senescence remains unknown. Here, we show that Arabidopsis SPX1/2 negatively regulate leaf senescence genetically downstream of the strigolactone (SL) pathway. We demonstrate that the SL receptor AtD14 and MAX2 mediate the age-dependent degradation of SPX1/2. Intriguingly, we uncover an age-dependent accumulation of SLs in leaves via transcriptional activation of SL biosynthetic genes by the transcription factors (TFs) SPL9/15. Furthermore, we reveal that SPX1/2 interact with the WRKY75 subclade TFs to inhibit their DNA-binding ability and thus repress transcriptional activation of salicylic acid (SA) biosynthetic gene SA Induction-Deficient 2, gating the age-dependent SA accumulation in leaves at the leaf senescence onset stage. Collectively, our new findings reveal a signaling pathway mediating sequential activation of SL and salicylate biosynthesis for the onset of leaf senescence in Arabidopsis.

SlMYC2 promotes SlLBD40-mediated cell expansion in tomato fruit development

As a plant-specific transcription factor, lateral organ boundaries domain (LBD) protein was reported to regulate plant growth and stress response, but the functional research of subfamily II genes is limited. SlMYC2, a master regulator of Jasmonic acid response, has been found to exhibit high expression levels in fruit and has been implicated in the regulation of fruit ripening and resistance to Botrytis. However, its role in fruit expansion remains unknown. In this study, we present evidence that a subfamily II member of LBD, namely SlLBD40, collaborates with SlMYC2 in the regulation of fruit expansion. Overexpression of SlLBD40 significantly promoted fruit growth by promoting mesocarp cell expansion, while knockout of SlLBD40 showed the opposite result. Similarly, SlMYC2 knockout resulted in a significant decrease in cell expansion within the fruit. Genetic analysis indicated that SlLBD40-mediated cell expansion depends on the expression of SlMYC2. SlLBD40 bound to the promoter of SlEXPA5, an expansin gene, but did not activate its expression directly. While, the co-expression of SlMYC2 and SlLBD40 significantly stimulated the activation of SlEXPA5, leading to an increase in fruit size. SlLBD40 interacted with SlMYC2 and enhanced the stability and abundance of SlMYC2. Furthermore, SlMYC2 directly targeted and activated the expression of SlLBD40, which is essential for SlLBD40-mediated fruit expansion. In summary, our research elucidates the role of the interaction between SlLBD40 and SlMYC2 in promoting cell expansion in tomato fruits, thus providing novel insights into the molecular genetics underlying fruit growth.

Dof1.7 and NIGT1 transcription factors mediate multilayered transcriptional regulation for different expression patterns of NITRATE TRANSPORTER2 genes under nitrogen deficiency stress

Elucidating the mechanisms regulating nitrogen (N) deficiency responses in plants is of great agricultural importance. Previous studies revealed that decreased expression of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) transcriptional repressor genes upon N deficiency is involved in N deficiency-inducible gene expression in Arabidopsis thaliana. However, our knowledge of the mechanisms controlling N deficiency-induced changes in gene expression is still limited. Through the identification of Dof1.7 as a direct target of NIGT1 repressors and a novel N deficiency response-related transcriptional activator gene, we here show that NIGT1 and Dof1.7 transcription factors (TFs) differentially regulate N deficiency-inducible expression of three high-affinity nitrate transporter genes, NRT2.1, NRT2.4, and NRT2.5, which are responsible for most of the soil nitrate uptake activity of Arabidopsis plants under N-deficient conditions. Unlike NIGT1 repressors, which directly suppress NRT2.1, NRT2.4, and NRT2.5 under N-sufficient conditions, Dof1.7 directly activated only NRT2.5 but indirectly and moderately activated NRT2.1 and NRT2.4 under N-deficient conditions, probably by indirectly decreasing NIGT1 expression. Thus, Dof1.7 converted passive transcriptional activation into active and potent transcriptional activation, further differentially enhancing the expression of NRT2 genes. These findings clarify the mechanism underlying different expression patterns of NRT2 genes upon N deficiency, suggesting that time-dependent multilayered transcriptional regulation generates complicated expression patterns of N deficiency-inducible genes.

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

BACKGROUND

Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified.

RESULTS

To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the binding sites and target genes of ZmMYC2. A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classic cis-elements like the G-box and E-box that are bound by MYC2, some new motifs are also revealed to be recognized by ZmMYC2, such as nGCATGCAnn, AAAAAAAA, CACGTGCGTGCG. The binding sites of many ZmMYC2 regulating genes are identified by IGV-sRNA.

CONCLUSIONS

All together, abundant target genes of ZmMYC2 are characterized with their binding sites, providing the basis to construct the regulatory network of ZmMYC2 and better understanding for JA signaling in maize.

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

Introduction: DNA-binding with one finger (Dof) transcription factors (TFs) are a unique family of TFs found in higher plants that regulate plant responses to light, hormones, and abiotic stresses. The specific involvement of Dof genes in the response to environmental stresses remains unknown in D. huoshanense. Methods: A total of 22 Dof family genes were identified from the D. huoshanense genome. Results: Chromosome location analysis showed that DhDof genes were distributed on 12 chromosomes, with the largest number of Dof genes located on chromosome 8. The phylogenetic tree revealed that DhDofs could be categorized into 11 distinct subgroups. In addition to the common groups, DhDof4, DhDof5, DhDof17, and the AtDof1.4 ortholog were clustered into the B3 subgroup. Group E was a newly identified branch, among which DhDof6, DhDof7, DhDof8, and DhDof9 were in an independent branch. The conserved motifs and gene structure revealed the differences in motif number and composition of DhDofs. The dof domain near the N-terminus was highly conserved and contained a C2-C2-type zinc finger structure linked with four cysteines. Microsynteny and interspecies collinearity revealed gene duplication events and phylogenetic tree among DhDofs. Large-scale gene duplication had not occurred among the DhDofs genes and only in one pair of genes on chromosome 13. Synteny blocks were found more often between D. huoshanense and its relatives and less often between Oryza sativa and Arabidopsis thaliana. Selection pressure analysis indicated that DhDof genes were subject to purifying selection. Expression profiles and correlation analyses revealed that the Dof gene under hormone treatments showed several different expression patterns. DhDof20 and DhDof21 had the highest expression levels and were co-expressed under MeJA induction. The cis-acting element analysis revealed that each DhDof had several regulatory elements involved in plant growth as well as abiotic stresses. qRT-PCR analysis demonstrated that DhDof2 was the main ABA-responsive gene and DhDof7 was the main cold stress-related gene. IAA suppressed the expression of some Dof candidates, and SA inhibited most of the candidate genes. Discussion: Our results may provide new insights for the further investigation of the Dof genes and the screening of the core stress-resistance genes.

Jasmonate signaling pathway confers salt tolerance through a NUCLEAR FACTOR-Y trimeric transcription factor complex in Arabidopsis

Jasmonate (JA) is a well-known phytohormone essential for plant response to biotic stress. Recently, a crucial role of JA signaling in salt resistance has been highlighted; however, the specific regulatory mechanism remains largely unknown. In this study, we found that the NUCLEAR FACTOR-Y (NF-Y) subunits NF-YA1, NF-YB2, and NF-YC9 form a trimeric complex that positively regulates the expression of salinity-responsive genes, whereas JASMONATE-ZIM DOMAIN protein 8 (JAZ8) directly interacts with three subunits and acts as the key repressor to suppress both the assembly of the NF-YA1-YB2-YC9 trimeric complex and the transcriptional activation activity of the complex. When plants encounter high salinity, JA levels are elevated and perceived by the CORONATINE INSENSITIVE (COI) 1 receptor, leading to the degradation of JAZ8 via the 26S proteasome pathway, thereby releasing the activity of the NF-YA1-YB2-YC9 complex, initiating the activation of salinity-responsive genes, such as MYB75, and thus enhancing the salinity tolerance of plants.

Epoxyalcohol Synthase Branch of Lipoxygenase Cascade

Oxylipins are one of the most important classes of bioregulators, biosynthesized through the oxidative metabolism of unsaturated fatty acids in various aerobic organisms. Oxylipins are bioregulators that maintain homeostasis at the cellular and organismal levels. The most important oxylipins are mammalian eicosanoids and plant octadecanoids. In plants, the main source of oxylipins is the lipoxygenase cascade, the key enzymes of which are nonclassical cytochromes P450 of the CYP74 family, namely allene oxide synthases (AOSs), hydroperoxide lyases (HPLs), and divinyl ether synthases (DESs). The most well-studied plant oxylipins are jasmonates (AOS products) and traumatin and green leaf volatiles (HPL products), whereas other oxylipins remain outside of the focus of researchers' attention. Among them, there is a large group of epoxy hydroxy fatty acids (epoxyalcohols), whose biosynthesis has remained unclear for a long time. In 2008, the first epoxyalcohol synthase of lancelet Branchiostoma floridae, BfEAS (CYP440A1), was discovered. The present review collects data on EASs discovered after BfEAS and enzymes exhibiting EAS activity along with other catalytic activities. This review also presents the results of a study on the evolutionary processes possibly occurring within the P450 superfamily as a whole.

The N-terminal α2 helix element is critical for the activity of the rice transcription factor MYC2

Jasmonates (JAs) are a class of phytohormones that play a crucial role in plant growth, development, and environmental stress responses. Central to JA signaling are the MYC2-type transcription factors, as they activate the expression of JA-responsive genes. We previously used CRISPR-Cas9-based genome editing to engineer rice OsMYC2 and yielded a mutant (myc2-5) with a single amino acid (aa) deletion (75I) outside the known functional domains of the protein. This myc2-5 mutant also showed some JA-deficient phenotypes, promoting us to investigate how 75I deletion affects JA responses. The mutation is found in the α2 helix element at the N-terminal of OsMYC2. The deletion of 75I in OsMYC2 rendered plants deficient in most of the JA responses, including root growth, leaf senescence, spikelet development, and resistance to pathogens and herbivores. Biochemical assays revealed that the 75I deletion markedly reduced OsMYC2 protein accumulation, subsequently diminishing its transcriptional activity. However, the deletion did not influence the protein's subcellular localization, DNA-binding capability, or its interactions with JAZ transcriptional repressors and the Mediator complex subunit MED25. Additionally, the screening of seven other deletions in the α2 helix further reinforces the importance of this protein element. Our results highlight the significance of the α2 helix in the N-terminus for OsMYC2's functionality, primarily through modulating its protein levels. This insight expands our knowledge of JA signaling and opens new avenues for research into the yet-to-be-explored domains of the MYC2 protein, with the potential to tailor JA responses in rice and other plant species.

Spliceosomal protein U2B″ delays leaf senescence by enhancing splicing variant JAZ9β expression to attenuate jasmonate signaling in Arabidopsis

The regulatory framework of leaf senescence is gradually becoming clearer; however, the fine regulation of this process remains largely unknown. Here, genetic analysis revealed that U2 small nuclear ribonucleoprotein B (U2B″), a component of the spliceosome, is a negative regulator of leaf senescence. Mutation of U2B″ led to precocious leaf senescence, whereas overexpression of U2B″ extended leaf longevity. Transcriptome analysis revealed that the jasmonic acid (JA) signaling pathway was activated in the u2b″ mutant. U2B″ enhances the generation of splicing variant JASMONATE ZIM-DOMAIN 9β (JAZ9β) with an intron retention in the Jas motif, which compromises its interaction with CORONATINE INSENSITIVE1 and thus enhances the stability of JAZ9β protein. Moreover, JAZ9β could interact with MYC2 and obstruct its activity, thereby attenuating JA signaling. Correspondingly, overexpression of JAZ9β rescued the early senescence phenotype of the u2b″ mutant. Furthermore, JA treatment promoted expression of U2B″ that was found to be a direct target of MYC2. Overexpression of MYC2 in the u2b″ mutant resulted in a more pronounced premature senescence than that in wild-type plants. Collectively, our findings reveal that the spliceosomal protein U2B″ fine-tunes leaf senescence by enhancing the expression of JAZ9β and thereby attenuating JA signaling.

Recent advances in cellular degradation and nuclear control of leaf senescence

Senescence is the final stage of plant growth and development, and is a highly regulated process at the molecular, cellular, and organismal levels. When triggered by age, hormonal, or environmental cues, plants actively adjust their metabolism and gene expression to execute the progression of senescence. Regulation of senescence is vital for the reallocation of nutrients to sink organs, to ensure reproductive success and adaptations to stresses. Identification and characterization of hallmarks of leaf senescence are of great importance for understanding the molecular regulatory mechanisms of plant senescence, and breeding future crops with more desirable senescence traits. Tremendous progress has been made in elucidating the genetic network underpinning the metabolic and cellular changes in leaf senescence. In this review, we focus on three hallmarks of leaf senescence - chlorophyll and chloroplast degradation, loss of proteostasis, and activation of senescence-associated genes (SAGs), and discuss recent findings of the molecular players and the crosstalk of senescence pathways.

A truncated ETHYLENE INSENSITIVE3-like protein, GhLYI, regulates senescence in cotton

Numerous endogenous and environmental signals regulate the intricate and highly orchestrated process of plant senescence. Ethylene (ET), which accumulates as senescence progresses, is a major promoter of leaf senescence. The master transcription activator ETHYLENE INSENSITIVE3 (EIN3) activates the expression of a wide range of downstream genes during leaf senescence. Here, we found that a unique EIN3-LIKE 1 (EIL1) gene, cotton LINT YIELD INCREASING (GhLYI), encodes a truncated EIN3 protein in upland cotton (Gossypium hirsutum L.) that functions as an ET signal response factor and a positive regulator of senescence. Ectopic expression or overexpression of GhLYI accelerated leaf senescence in both Arabidopsis (Arabidopsis thaliana) and cotton. Cleavage under targets and tagmentation (CUT&Tag) analyses revealed that SENESCENCE-ASSOCIATED GENE 20 (SAG20) was a target of GhLYI. Electrophoretic mobility shift assay (EMSA), yeast 1-hybrid (Y1H), and dual-luciferase transient expression assay confirmed that GhLYI directly bound the promoter of SAG20 to activate its expression. Transcriptome analysis revealed that transcript levels of a series of senescence-related genes, SAG12, NAC-LIKE, ACTIVATED by APETALA 3/PISTILLATA (NAP/ANAC029), and WRKY53, are substantially induced in GhLYI overexpression plants compared with wild-type (WT) plants. Virus-induced gene silencing (VIGS) preliminarily confirmed that knockdown of GhSAG20 delayed leaf senescence. Collectively, our findings provide a regulatory module involving GhLYI-GhSAG20 in controlling senescence in cotton.

Jasmonic acid regulates lignin deposition in poplar through JAZ5-MYB/NAC interaction

Jasmonic acid (JA) is a phytohormone involved in plant defense, growth, and development, etc. However, the regulatory mechanisms underlying JA-mediated lignin deposition and secondary cell wall (SCW) formation remain poorly understood. In this study, we found that JA can inhibit lignin deposition and SCW thickening in poplar trees through exogenous MeJA treatment and observation of the phenotypes of a JA synthesis mutant, opdat1. Hence, we identified a JA signal inhibitor PtoJAZ5, belonging to the TIFY gene family, which is involved in the regulation of secondary vascular development of Populus tomentosa. RT-qPCR and GUS staining revealed that PtoJAZ5 was highly expressed in poplar stems, particularly in developing xylem. Overexpression of PtoJAZ5 inhibited SCW thickening and down-regulated the expression of SCW biosynthesis-related genes. Further biochemical analysis showed that PtoJAZ5 interacted with multiple SCW switches NAC/MYB transcription factors, including MYB3 and WND6A, through yeast two-hybrid and bimolecular fluorescent complementation experiments. Transcriptional activation assays demonstrated that MYB3-PtoJAZ5 and WND6A-PtoJAZ5 complexes regulated the expression of lignin synthetic genes. Our results suggest that PtoJAZ5 plays a negative role in JA-induced lignin deposition and SCW thickening in poplar and provide new insights into the molecular mechanisms underlying JA-mediated regulation of SCW formation.

Genome-wide association study of ear tip barrenness in waxy maize

Ear tip-barrenness (ETB), which results from aborted kernels or infertile florets at the ear tip, is an undesirable factor affecting the yield and quality of waxy maize. To uncover the genetic basis of ETB, a genome-wide association study (GWAS) was conducted using the genotype with 27,354 SNPs and phenotype with three environments. Five SNPs that distributed on chromosomes 1, 3 and 6, were identified to be significantly associated with ETB based on the threshold of false discovery rate (FDR) at 0.05. Among these significant loci, three SNPs were clustered together and colocalized with genomic regions previously reported. The average length of ETB decreased almost linearly from the inbred lines containing no favorable alleles across the three loci (1.75 cm) to those with one (1.18 cm), two (0.94 cm) and three (0.65 cm) favorable alleles. Moreover, three important genes, Zm00001d030028, Zm00001d041510 and Zm00001d038676 were predicted for three significant QTLs, respectively. These results promote the understanding genetic basis for ETB and will be useful for breeding waxy maize varieties with high-quality and high-yield.

ABI5 promotes heat stress-induced chlorophyll degradation by modulating the stability of MYB44 in cucumber

The yellowing of leaves caused by the decomposition of chlorophyll (Chl) is a characteristic event during senescence, which can be induced by various environmental stresses. However, the molecular mechanisms of high temperature-induced Chl degradation in horticultural plants remain poorly understood. Here, we found that heat stress induced Chl degradation and the expression of ABI5 and MYB44 in cucumber. Silencing of ABI5 compromised heat stress-induced Chl degradation, and the transcription of pheophytinase (PPH) and pheophorbide a oxygenase (PAO), two key genes in Chl catabolic pathway, but silencing of MYB44 exhibited the opposite results. Furthermore, ABI5 interacted with MYB44 in vitro and in vivo. ABI5 positively regulated heat stress-induced Chl degradation through two pathways. ABI5 directly bound to PPH and PAO promoters to promote their expression, leading to accelerating Chl degradation. On the other hand, the interaction between ABI5 and MYB44 reduced the binding of MYB44 to PPH and PAO promoters and led to the ubiquitination-depended protein degradation of MYB44, thereby alleviating the transcription inhibitory effect of MYB44 on PPH and PAO. Taken together, our findings propose a new regulatory network for ABI5 in regulating heat stress-induced Chl degradation.

Transcription Factors-Regulated Leaf Senescence: Current Knowledge, Challenges and Approaches

Leaf senescence is a complex biological process regulated at multiple levels, including chromatin remodeling, transcription, post-transcription, translation, and post-translational modifications. Transcription factors (TFs) are crucial regulators of leaf senescence, with NAC and WRKY families being the most studied. This review summarizes the progress made in understanding the regulatory roles of these families in leaf senescence in Arabidopsis and various crops such as wheat, maize, sorghum, and rice. Additionally, we review the regulatory functions of other families, such as ERF, bHLH, bZIP, and MYB. Unraveling the mechanisms of leaf senescence regulated by TFs has the potential to improve crop yield and quality through molecular breeding. While significant progress has been made in leaf senescence research in recent years, our understanding of the molecular regulatory mechanisms underlying this process is still incomplete. This review also discusses the challenges and opportunities in leaf senescence research, with suggestions for possible strategies to address them.

Exploring the metabolic basis of growth/defense trade-offs in complex environments with Nicotiana attenuata plants cosilenced in NaMYC2a/b expression

In response to challenges from herbivores and competitors, plants use fitness-limiting resources to produce (auto)toxic defenses. Jasmonate signaling, mediated by MYC2 transcription factors (TF), is thought to reconfigure metabolism to minimize these formal costs of defense and optimize fitness in complex environments. To study the context-dependence of this metabolic reconfiguration, we cosilenced NaMYC2a/b by RNAi in Nicotiana attenuata and phenotyped plants in the field and increasingly realistic glasshouse setups with competitors and mobile herbivores. NaMYC2a/b had normal phytohormonal responses, and higher growth and fitness in herbivore-reduced environments, but were devastated in high herbivore-load environments in the field due to diminished accumulations of specialized metabolites. In setups with competitors and mobile herbivores, irMYC2a/b plants had lower fitness than empty vector (EV) in single-genotype setups but increased fitness in mixed-genotype setups. Correlational analyses of metabolic, resistance, and growth traits revealed the expected defense/growth associations for most sectors of primary and specialized metabolism. Notable exceptions were some HGL-DTGs and phenolamides that differed between single-genotype and mixed-genotype setups, consistent with expectations of a blurred functional trichotomy of metabolites. MYC2 TFs mediate the reconfiguration of primary and specialized metabolic sectors to allow plants to optimize their fitness in complex environments.

Interaction of methionine sulfoxide reductase B5 with SlMYC2 stimulates the transcription of MeJA-mediated autophagy-related genes in tomato fruit

Methyl jasmonate (MeJA) has been shown to induce autophagy in various plant stress responses and metabolic pathways. MYC2 is involved in MeJA-mediated postharvest fruit biological metabolism, but it is unclear how it affects MeJA-induced fruit autophagy. In this study, we noticed that silencing SlMYC2 significantly reduced the increase in autophagy-related genes (SlATGs) expression induced by MeJA. SlMYC2 could also bind to the promoters of several SlATGs, including SlATG13a, SlATG13b, SlATG18a, and SlATG18h, and activate their transcript levels. Moreover, SlMsrB5, a methionine sulfoxide reductase, could interact with SlMYC2. Methionine oxidation in SlMYC2 and mimicking sulfoxidation in SlMYC2 by mutation of methionine-542 to glutamine reduced the DNA-binding ability and transcriptional activity of SlMYC2, respectively. SlMsrB5 partially repaired oxidized SlMYC2 and restored its DNA-binding ability. On the other hand, silencing SlMsrB5 inhibited the transcript levels of SlMYC2-targeted genes (SlATG13a, SlATG13b, SlATG18a, and SlATG18h). Similarly, dual-luciferase reporter (DLR) analysis revealed that SlMsrB5-SlMYC2 interaction significantly increased the ability of SlMYC2-mediated transcriptional activation of SlATG13a, SlATG13b, SlATG18a, and SlATG18h. These findings demonstrate that SlMsrB5-mediated cyclic oxidation/reduction of methionine in SlMYC2 influences SlATGs expression. Collectively, these findings reveal the mechanism of SlMYC2 in SlATGs transcriptional regulation, providing insight into the mechanism of MeJA-mediated postharvest fruit quality regulation.

Cold stress triggers freezing tolerance in wheat (Triticum aestivum L.) via hormone regulation and transcription of related genes

Low temperatures limit the geographic distribution and yield of plants. Hormones play an important role in coordinating the growth and development of plants and their tolerance to low temperatures. However, the mechanisms by which hormones affect plant resistance to extreme cold stress in the natural environment are still unclear. In this study, two winter wheat varieties with different cold resistances, Dn1 and J22, were used to conduct targeted plant hormone metabolome analysis on the tillering nodes of winter wheat at 5 °C, -10 °C and -25 °C using an LC-ESI-MS/MS system. We screened 39 hormones from 88 plant hormone metabolites and constructed a partial regulatory network of auxin, jasmonic acid and cytokinin. GO analysis and enrichment of KEGG pathways in different metabolites showed that the 'plant hormone signal transduction' pathway was the most common. Our study showed that extreme low temperature increased the most levels of auxin, cytokinin and salicylic acid, and decreased levels of jasmonic acid and abscisic acid, and that levels of auxin, jasmonic acid and cytokinin in Dn1 were higher than those in J22. These changes in hormone levels were associated with changes in gene expression in synthesis, catabolism, transport and signal transduction pathways. These results differ from the previous hormone regulation mechanisms, which were mostly obtained at 4 °C. Our results provide a basis for further understanding the molecular mechanisms by which plant endogenous hormones regulate plant freezing stress tolerance.

MYC2: A Master Switch for Plant Physiological Processes and Specialized Metabolite Synthesis

The jasmonic acid (JA) signaling pathway plays important roles in plant defenses, development, and the synthesis of specialized metabolites synthesis. Transcription factor MYC2 is a major regulator of the JA signaling pathway and is involved in the regulation of plant physiological processes and specialized metabolite synthesis. Based on our understanding of the mechanism underlying the regulation of specialized metabolite synthesis in plants by the transcription factor MYC2, the use of synthetic biology approaches to design MYC2-driven chassis cells for the synthesis of specialized metabolites with high medicinal value, such as paclitaxel, vincristine, and artemisinin, seems to be a promising strategy. In this review, the regulatory role of MYC2 in JA signal transduction of plants to biotic and abiotic stresses, plant growth, development and specialized metabolite synthesis is described in detail, which will provide valuable reference for the use of MYC2 molecular switches to regulate plant specialized metabolite biosynthesis.

DOF transcription factors: Specific regulators of plant biological processes

Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.

Overexpression of SmMYC2 enhances salt resistance in Arabidopsis thaliana and Salvia miltiorrhiza hairy roots

Soil salinity significantly affects both Salvia miltiorrhiza growth and development as well as seed germination throughout field cultivation and production. The basic helix-loop-helix (bHLH) transcription factor (TF) MYC2 contributes significantly to plant stress resistance as a key regulator of the jasmonic acid signaling pathway. In transgenic S. miltiorrhiza hairy roots, SmMYC2 has been shown to promote the accumulation of tanshinone and salvianolic acid, but its role in S. miltiorrhiza of resistance to abiotic stress is unclear. Herein, we found methyl jasmonate (MeJA), NaCl, and PEG treatment all significantly increased SmMYC2 expression. In response to salt stress, SmMYC2 overexpression in yeast increased its rate of growth. Additionally, overexpression of SmMYC2 transgenic Arabidopsis thaliana and S. miltiorrhiza hairy root showed that it might improve salt resistance in transgenic plant. In particular, compared to WT, overexpression of SmMYC2 transgenic Arabidopsis had higher levels of three antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), proline (Pro) content, and ABA-dependent and ABA-independent genes expression. They also had lower levels of malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. What's more, overexpression of SmMYC2 increases the expression of flavonoid synthesis genes and the accumulation of related components in Arabidopsis. These findings imply that SmMYC2 functions as a positive regulator that regulates plant tolerance to salt through ABA-dependent and independent signaling pathways.

A jasmonate-responsive bHLH transcription factor TaMYC2 positively regulates triterpenes biosynthesis in Taraxacum antungense Kitag

Dandelion is a well-known traditional medical herb, also used as functional food. Dandelion possesses many medical properties, such as anti-bacterial and antioxidant activity and contains a variety of triterpenes, such as α-amyrin, β-amyrin, taraxerol and taraxasterol. In this study, we found that triterpenes biosynthesis was promoted by methyl jasmonate (MeJA), while the transcriptional mechanism underlying triterpenes biosynthesis was rarely investigated. Here, a MeJA-induced bHLH transcription factor TaMYC2 was identified. The content of taraxasterol and taraxerol in dandelion was obviously enhanced in overexpression TaMYC2 transgenic lines and expression level of the squalene synthase gene (TaSS) was elevated to about 3-5 folds compared with the control lines. Dual-LUC, Y1H and EMSA experiments revealed that TaMYC2 bound to the E-box motif in the promoter of TaSS and activated its transcription. Taken together, this study suggested that TaMYC2 acted as a positive regulator for bioengineering approaches to produce high content triterpenes-producing dandelions.

Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest

Perennial rice is a new type of rice that allows the harvest of rice for multiple years without growing new seedlings annually. This technology represents a green and sustainable agricultural production mode with many advantages for balancing agricultural ecology and food security. However, the differences in regeneration patterns between perennial and annual rice and the gene regulatory pathways of the apical dominance in axillary bud growth after harvest in perennial rice are still unclear. In this study, perennial rice (PR23) and annual rice (Chugeng28) were used to investigate axillary bud growth patterns before and after apical spike removal. After elimination of apical dominance at different development stages, perennial rice rhizome axillary buds at the compression nodes germinated more rapidly than others and developed into new seedlings. The axillary buds at the high-position nodes in annual rice grew faster than those at other nodes. Furthermore, the global gene expression patterns of PR23 rhizome buds at compression nodes grown for 1, 3, 4, and 5 days after apical spike removal were analyzed by transcriptome sequencing. Compared with the control buds without apical removal, 264, 3,484, 2,095, and 3,398 genes were up-regulated, and 674, 3,484, 1,594, and 1,824 genes were down-regulated in the buds grown for 1, 3, 4, and 5 days after apical spike removal, respectively. Trend analysis of the expressed genes at different time points was performed and co-expression network was constructed to identify key genes in rhizome axillary bud regrowth. The results showed that 85 hub genes involved in 12 co-regulatory networks were mainly enriched in the light system, photosynthesis-antenna protein, plant hormone signal transduction, ABC transporter and metabolic pathways, which suggested that hormone and photosynthetic signals might play important roles in the regulation of rhizome axillary bud regeneration in perennial rice. Overall, this study clarified the differences in the regeneration patterns of axillary buds between perennial and annual rice and provided insight into the complex regulatory networks during the regeneration of rhizome axillary buds in perennial rice.

Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate

DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding.

Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton ( Gossypium hirsutum and Gossypium barbadense , AADD) and its extant AA ( Gossypium arboreum ) and DD ( Gossypium raimondii ) progenitors. We observed distinct DHS distributions between G. arboreum and G. raimondii . In contrast, the DHSs of the two subgenomes of G. hirsutum and G. barbadense showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids Gossypium darwinii and G. hirsutum var. yucatanense , but absent from a resynthesized hybrid of G. arboreum and G. raimondii , suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative cis -regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.

Genome-Wide Identification of DOF Gene Family and the Mechanism Dissection of SbDof21 Regulating Starch Biosynthesis in Sorghum

Starch is one of the main utilization products of sorghum (Sorghum bicolor L.), the fifth largest cereal crop in the world. Up to now, the regulation mechanism of starch biosynthesis is rarely documented in sorghum. In the present study, we identified 30 genes encoding the C2-C2 zinc finger domain (DOF), with one to three exons in the sorghum genome. The DOF proteins of sorghum were divided into two types according to the results of sequence alignment and evolutionary analysis. Based on gene expressions and co-expression analysis, we identified a regulatory factor, SbDof21, that was located on chromosome 5. SbDof21 contained two exons, encoding a 36.122 kD protein composed of 340 amino acids. SbDof21 co-expressed with 15 genes involved in the sorghum starch biosynthesis pathway, and the Pearson correlation coefficients (PCCs) with 11 genes were greater than 0.9. The results of qRT-PCR assays indicated that SbDof21 is highly expressed in sorghum grains, exhibiting low relative expression levels in the tissues of roots, stems and leaves. SbDOF21 presented as a typical DOF transcription factor (TF) that was localized to the nucleus and possessed transcriptional activation activity. Amino acids at positions 182–231 of SbDOF21 formed an important structure in its activation domain. The results of EMSA showed that SbDOF21 could bind to four tandem repeats of P-Box (TGTAAAG) motifs in vitro, such as its homologous proteins of ZmDOF36, OsPBF and TaPBF. Meanwhile, we also discovered that SbDOF21 could bind and transactivate SbGBSSI, a key gene in sorghum amylose biosynthesis. Collectively, the results of the present study suggest that SbDOF21 acts as an important regulator in sorghum starch biosynthesis, exhibiting potential values for the improvement of starch contents in sorghum.

ARF2-PIF5 interaction controls transcriptional reprogramming in the ABS3-mediated plant senescence pathway

One of the hallmarks of plant senescence is the global transcriptional reprogramming coordinated by a plethora of transcription factors (TFs). However, mechanisms underlying the interactions between different TFs in modulating senescence remain obscure. Previously, we discovered that plant ABS3 subfamily MATE transporter genes regulate senescence and senescence-associated transcriptional changes. In a genetic screen for mutants suppressing the accelerated senescence phenotype of the gain-of-function mutant abs3-1D, AUXIN RESPONSE FACTOR 2 (ARF2) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) were identified as key TFs responsible for transcriptional regulation in the ABS3-mediated senescence pathway. ARF2 and PIF5 (as well as PIF4) interact directly and function interdependently to promote senescence, and they share common target genes such as key senescence promoting genes ORESARA 1 (ORE1) and STAY-GREEN 1 (SGR1) in the ABS3-mediated senescence pathway. In addition, we discovered reciprocal regulation between ABS3-subfamily MATEs and the ARF2 and PIF5/4 TFs. Taken together, our findings reveal a regulatory paradigm in which the ARF2-PIF5/4 functional module facilitates the transcriptional reprogramming in the ABS3-mediated senescence pathway.

The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

Morphological, Transcriptome, and Hormone Analysis of Dwarfism in Tetraploids of Populus alba × P. glandulosa

Breeding for dwarfism is an important approach to improve lodging resistance. Here, we performed comparative analysis of the phenotype, transcriptome, and hormone contents between diploids and tetraploids of poplar 84K (Populus alba × P. glandulosa). Compared with diploids, the indole-3-acetic acid (IAA) and gibberellin (GA₃) contents were increased, whereas the jasmonic acid (JA) and abscisic acid (ABA) contents were decreased in tetraploids. RNA-sequencing revealed that differentially expressed genes (DEGs) in leaves of tetraploids were mainly involved in plant hormone pathways. Most DEGs associated with IAA and GA promotion of plant growth and development were downregulated, whereas most DEGs associated with ABA and JA promotion of plant senescence were upregulated. Weighted gene co-expression network analysis indicated that certain transcription factors may be involved in the regulation of genes involved in plant hormone pathways. Thus, the altered expression of some genes in the plant hormone pathways may lead to a reduction in IAA and GA contents, as well as an elevation in ABA and JA contents, resulting in the dwarfing of tetraploids. The results show that polyploidization is a complex biological process affected by multiple plant hormone signals, and it provides a foundation for further exploration of the mechanism of tetraploids dwarfing in forest trees.

SlJAZ10 and SlJAZ11 mediate dark-induced leaf senescence and regeneration

During evolutionary adaptation, the mechanisms for self-regulation are established between the normal growth and development of plants and environmental stress. The phytohormone jasmonate (JA) is a key tie of plant defence and development, and JASMONATE-ZIM DOMAIN (JAZ) repressor proteins are key components in JA signalling pathways. Here, we show that JAZ expression was affected by leaf senescence from the transcriptomic data. Further investigation revealed that SlJAZ10 and SlJAZ11 positively regulate leaf senescence and that SlJAZ11 can also promote plant regeneration. Moreover, we reveal that the SlJAV1-SlWRKY51 (JW) complex could suppress JA biosynthesis under normal growth conditions. Immediately after injury, SlJAZ10 and SlJAZ11 can regulate the activity of the JW complex through the effects of electrical signals and Ca²⁺ waves, which in turn affect JA biosynthesis, causing a difference in the regeneration phenotype between SlJAZ10-OE and SlJAZ11-OE transgenic plants. In addition, SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. Together, SlJAZ10 and SlJAZ11 not only act as repressors of JA signalling to leaf senescence, but also regulate plant regeneration through coordinated electrical signals, Ca²⁺ waves, hormones and transcriptional regulation. Our study provides critical insights into the mechanisms by which SlJAZ11 can induce regeneration.

In plants, senescence is the final stage of development, but regeneration can help them beyond the stage. Plants regeneration is essential for propagation, and in cultivated crops to maintain excellent traits as close as possible. JA signaling can sense environmental signals and integrate various regulatory mechanisms to ensure plants regeneration occurs under optimal conditions. In this work, the JAZ-JAV1-WRKY51 complexes with reported was further optimized, the function of SlJAZ10 and SlJAZ11 was identified to promote inhibitory activity of SlJAV1-SlWRKY51 complex which negatively regulated JA biosynthesis by direct binding of the W-box of the SlAOC promoter. The results of further investigation suggest that the differences in regulation of electrical signals, Ca²⁺ waves, hormones and transcriptional regulation are responsible for the regeneration between SlJAZ10 and SlJAZ11. In addition, we have found that SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. In summary, despite both SlJAZ10 and SlJAZ11 can function as senescence, only SlJAZ11 has an important promoting function for regeneration.

Apple SINA E3 ligase MdSINA3 negatively mediates JA-triggered leaf senescence by ubiquitinating and degrading the MdBBX37 protein

Jasmonic acid (JA) induces chlorophyll degradation and leaf senescence. B-box (BBX) proteins play important roles in the modulation of leaf senescence, but the molecular mechanism of BBX protein-mediated leaf senescence remains to be further studied. Here, we identified the BBX protein MdBBX37 as a positive regulator of JA-induced leaf senescence in Malus domestica (apple). Further studies showed that MdBBX37 interacted with the senescence regulatory protein MdbHLH93 to enhance its transcriptional activation on the senescence-associated gene MdSAG18, thereby promoting leaf senescence. Moreover, the JA signaling repressor MdJAZ2 interacted with MdBBX37 and interfered with the interaction between MdBBX37 and MdbHLH93, thereby negatively mediating MdBBX37-promoted leaf senescence. In addition, the E3 ubiquitin ligase MdSINA3 delayed MdBBX37-promoted leaf senescence through targeting MdBBX37 for degradation. The MdJAZ2-MdBBX37-MdbHLH93-MdSAG18 and MdSINA3-MdBBX37 modules realized the precise modulation of JA on leaf senescence. In parallel, our data demonstrate that MdBBX37 was involved in abscisic acid (ABA)- and ethylene-mediated leaf senescence through interacting with the ABA signaling regulatory protein MdABI5 and ethylene signaling regulatory protein MdEIL1, respectively. Taken together, our results not only reveal the role of MdBBX37 as an integration node in JA-, ABA- and ethylene-mediated leaf senescence, but also provide new insights into the post-translational modification of BBX proteins.

New Advances in the Regulation of Leaf Senescence by Classical and Peptide Hormones

Leaf senescence is the last stage of leaf development, manifested by leaf yellowing due to the loss of chlorophyll, along with the degradation of macromolecules and facilitates nutrient translocation from the sink to the source tissues, which is essential for the plants' fitness. Leaf senescence is controlled by a sophisticated genetic network that has been revealed through the study of the molecular mechanisms of hundreds of senescence-associated genes (SAGs), which are involved in multiple layers of regulation. Leaf senescence is primarily regulated by plant age, but also influenced by a variety of factors, including phytohormones and environmental stimuli. Phytohormones, as important signaling molecules in plant, contribute to the onset and progression of leaf senescence. Recently, peptide hormones have been reported to be involved in the regulation of leaf senescence, enriching the significance of signaling molecules in controlling leaf senescence. This review summarizes recent advances in the regulation of leaf senescence by classical and peptide hormones, aiming to better understand the coordinated network of different pathways during leaf senescence.

Identification of Long-Distance Transport Signal Molecules Associated with Plant Maturity in Tetraploid Cultivated Potatoes (Solanum tuberosum L.)

Maturity is a key trait for breeders to identify potato cultivars suitable to grow in different latitudes. However, the molecular mechanism regulating maturity remains unclear. In this study, we performed a grafting experiment using the early-maturing cultivar Zhongshu 5 (Z5) and the late-maturing cultivar Zhongshu 18 (Z18) and found that abscisic acid (ABA) and salicylic acid (SA) positively regulate the early maturity of potato, while indole-3-acetic acid (IAA) negatively regulated early maturity. A total of 43 long-distance transport mRNAs are observed to be involved in early maturity, and 292 long-distance transport mRNAs involved in late maturity were identified using RNA sequencing. Specifically, StMADS18, StSWEET10C, and StSWEET11 are detected to be candidate genes for their association with potato early maturity. Metabolomic data analysis shows a significant increase in phenolic acid and flavonoid contents increased in the scion of the early-maturing cultivar Z5, but a significant decrease in amino acid, phenolic acid, and alkaloid contents increased in the scion of the late-maturing cultivar Z18. This work reveals a significant association between the maturity of tetraploid cultivated potato and long-distance transport signal molecules and provides useful data for assessing the molecular mechanisms underlying the maturity of potato plants and for breeding early-maturing potato cultivars.

Emerging Roles of Plant DNA-Binding With One Finger Transcription Factors in Various Hormone and Stress Signaling Pathways

Coordinated transcriptional regulation of stress-responsive genes orchestrated by a complex network of transcription factors (TFs) and the reprogramming of metabolism ensure a plant's continued growth and survival under adverse environmental conditions (e.g., abiotic stress). DNA-binding with one finger (Dof) proteins, a group of plant-specific TF, were identified as one of several key components of the transcriptional regulatory network involved in abiotic stress responses. In many plant species, Dofs are often activated in response to a wide range of adverse environmental conditions. Dofs play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Moreover, Dofs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid, jasmonate, SA and redox signaling in response to many abiotic stresses. Taken together, we highlight a unique role of Dofs in hormone and stress signaling that integrates plant response to adverse environmental conditions with different aspects of plant growth and development.

Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner

Cis-regulatory elements are regions of noncoding DNA that regulate the transcription of neighboring genes. The study of cis-element architecture that functions in transcription regulation are essential. AAAG and ACGT are a class of cis-regulatory elements, known to interact with Dof and bZIP transcription factors respectively, and are known to regulate the expression of auxin response, gibberellin response, floral development, light response, seed storage proteins genes, biotic and abiotic stress genes in plants. Analysis of the frequency of occurrence of AAAG and ACGT motifs from varying spacer lengths (0–30 base pair) between these 2 motifs in both possible orientations—AAAG _(N) ACGT and ACGT _(N) AAAG, in the promoters and genome of Arabidopsis thaliana which indicated preferred orientation of AAAG _(N) ACGT over ACGT _(N) AAAG across the genome and in promoters. Further, microarray analysis revealed the involvement of these motifs in the genes downregulated under jasmonic acid response in an orientation-independent manner. These results were further confirmed by the transient expression studies with promoter-reporter cassettes carrying AAAG and ACGT motifs in both orientations. Furthermore, cluster analysis on genes with AAAG _(N) ACGT and ACGT _(N) AAAG motifs orientations revealed clusters of genes to be involved in ABA signaling, transcriptional regulation, DNA binding, and metal ion binding. These findings can be utilized in designing synthetic promoters for the development of stress-tolerant transgenic plants and also provides an insight into the roles of these motifs in transcriptional regulation.

The AP2/ERF transcription factor SlERF.F5 functions in leaf senescence in tomato

Our results confirmed that SlERF.F5 can directly regulate the promoter activity of ACS6 and interact with SlMYC2 to regulate tomato leaf senescence. The process of plant senescence is complex and highly coordinated, and is regulated by many endogenous and environmental signals. Ethylene and jasmonic acid are well-known senescence inducers, but their molecular mechanisms for inducing leaf senescence have not been fully elucidated. Here, we isolated an ETHYLENE RESPONSE FACTOR F5 (SlERF.F5) from tomato. Silencing of SlERF.F5 causes accelerated senescence induced by age, darkness, ethylene, and jasmonic acid. However, overexpression of SlERF.F5 would not promote senescence. Moreover, SlERF.F5 can regulate the promoter activity of ACS6 in vitro and in vivo. Suppression of SlERF.F5 resulted in increased sensitivity to ethylene and jasmonic acid, decreased accumulation of chlorophyll content, and inhibited the expression of chlorophyll- and light response-related genes. Compared with the wild type, the qRT-PCR analysis showed the expression levels of genes related to the ethylene biosynthesis pathway and the jasmonic acid signaling pathway in SlERF.F5-RNAi lines increased. Yeast two-hybrid experiments showed that SlERF.F5 and SlMYC2 (a transcription factor downstream of the JA receptor) can interact physically, thereby mediating the role of SlERF.F5 in jasmonic acid-induced leaf senescence. Collectively, our research provides new insights into how ethylene and jasmonic acid promote leaf senescence in tomato.