Genome-wide analysis of the ERF gene family in Arabidopsis and rice

SmDREB A1-10 Is Required for SmTTF30-Mediated Hypoxia Stress Tolerance in Salix matsudana

Frequent flooding events induced by extreme weather significantly threaten plant growth and productivity. Salix matsudana, a willow species, demonstrates exceptional tolerance to hypoxia and submergence stress, providing an ideal model for exploring underlying molecular mechanisms. This study highlights the roles of two transcriptional factors and their interplay in enhancing hypoxia and submergence stress resilience in Salix matsudana. SmTTF30, a GT-1 trihelix transcription factor, is specifically induced under root hypoxia, with its promoter enriched in hypoxia-responsive elements. Functional analyses reveal that overexpression of SmTTF30 in Arabidopsis thaliana improves submergence tolerance, whereas its downregulation in Salix matsudana results in heightened submergence stress sensitivity. SmDREB A1-10, identified through yeast one-hybrid screening and dual-luciferase assays as an upstream regulator of SmTTF30, directly interacts with its promoter. Overexpression of SmDREB A1-10 in Arabidopsis thaliana also enhances submergence tolerance, similar to SmTTF30. Virus-induced gene silencing (VIGS) experiments confirm that silencing SmDREB A1-10 diminishes SmTTF30 expression and hypoxia-responsive gene activation, exacerbating submergence stress effects. These findings unveil a regulatory cascade involving SmDREB A1-10 and SmTTF30 in submergence stress responses, providing insights into transcriptional networks governing submergence tolerance in trees.

Involvement of sweet cherry PavPP2C59 in negatively regulating fruitlet abscission and fruit ripening

Abnormal fruitlet drop poses a significant challenge to the cherry industry, and ABA is known to be involved in organ abscission. The protein phosphatase 2Cs (PP2Cs) plays a crucial role in ABA signaling; however, their functions in the abscission of sweet cherry fruitlets remain unexplored. Currently, 17 F-clade PP2C members were identified in the sweet cherry, among which PavPP2C59 was significantly downregulated in fruit ripening and abscission. The PavPP2C59 promoter exhibited GUS expression activity in the abscission petals of Arabidopsis thaliana, which decreased during silique development and ripening and responded to IAA or ABA treatment. Overexpression of PavPP2C59 in A. thaliana promoted root elongation, delayed petal abscission, and shortened silique length. Yeast one-hybrid and dual-luciferase reporter assays demonstrated that PavDOF18 and PavERF110 interacted with the PavPP2C59 promoter and inhibited its transcription, respectively. PavDOF18 and PavERF110 are localized in the nucleus as transcriptional repressors and have regulatory functions in fruit development and abscission. Y2H and luciferase complementation imaging assays revealed that PavPP2C59 interacts with PavRDUF1, which may lead to its ubiquitination and subsequent degradation. These findings indicate that PavPP2C59 negatively regulates fruitlet abscission and ripening in sweet cherry, providing new insights for a better understanding of fruit abscission in plants.

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage laboratory and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, and molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Realizing the yield potential of Narrow Leaf 1 (NAL1) in rice: The way forward

Yield, a key parameter targeted by breeders to increase rice productivity is a complex trait, governed by source sink interactions and also subject to genotype x environmental effects. Over the last two decades, QTL mapping and map-based cloning have identified several loci and genes related to yield in rice. Among them, a variant of Narrow Leaf 1 (NAL1), a gene conferring pleiotropic effects in rice, has been inadvertently selected during domestication to enhance yield in japonica rice. In this review, we synthesize recent literature on NAL1 in rice, including molecular function, association with auxin transport, associated interactome, regulation at transcriptional and post-transcriptional levels that impact the narrow leaf phenotype. Causes of NAL1 pleiotropic effects are also examined, in addition to trade-offs between yield and photosynthesis conferred by distinct NAL1 variants. Finally, we suggest that the distinct allelic variants of NAL1, leading to partial or full functionality, found in indica and japonica rice backgrounds respectively integrate source-sink interactions to optimize rice yield in a given eco-physiological context. To realize the benefits of the fully functional NAL1 in conferring yield benefits under field conditions, genotype background is crucial and a systems approach is essential to elucidate the causes for such differences. The way forward to enhancing yield in japonica rice (with fully functional NAL1) further by introgression of additional sink and source traits from indica rice is outlined.

Transcriptomic profiling reveals bud dormancy stage dynamics in Japanese cedar (Cryptomeria japonica) throughout the nongrowing period

This study aimed to characterize the vegetative bud status of Japanese cedar (Cryptomeria japonica [L.f.] D. Don) throughout the nongrowing period (October-March). Based on the results of twig experiments and transcriptome analysis, we divided the nongrowing period into four stages. Buds were estimated to form between October and November (stage 1), with bud hardening continuing until December (stage 2). Endodormancy was released and transitioned into ecodormancy in mid-to-late December, with the timing varying by genotype. Buds endured harsh winter conditions during January and February (stage 3) and prepared for subsequent growth in March (stage 4). The number of days to bud burst (DBB) under forcing conditions gradually decreased after the transition to ecodormancy, culminating in bud burst in the field in late April. Transcriptome analysis identified key genes presumed to regulate these stages, such as CONSTANS-like and core clock genes. Furthermore, analysis of three genotypes with differing dormancy characteristics revealed DBB-associated genes, indicating the potential involvement of phytohormone cytokinins in regulating bud burst. Additionally, the PEBP- and SVP-like genes, known for their roles in dormancy regulation in other tree species, exhibited distinct expression patterns in Japanese cedar, highlighting variations in dormancy control mechanisms. This study is the first to categorize bud dormancy stages in conifers during the nongrowing period based on molecular data, and the results provide foundational insights for future investigations into conifer dormancy.

TOUSLED KINASE INTERACTING PROTEIN 1 (TKI1) interacts with SIN3-LIKES (SNLs) to promote flowering in Arabidopsis

TOUSLED KINASE INTERACTING PROTEIN 1 (TKI1) is a SANT/Myb domain-containing protein, which binds DNA and may function as a transcription factor, and is characterized as an interacting protein with TOUSLED (TSL) in Arabidopsis. However, it remains largely unknown what biological functions of TKI1 for few reports about TKI1 in the literature. Here we first identified that TKI1 interacts with SIN3-LIKEs (SNLs) and the responsible interaction domains are the C-terminal domain of TKI1 and the PAH (Paired Amphipathic Helix) domains of SNLs respectively in yeast. Then, we further confirmed the interactions between TKI1 and SNLs (SNL1-SNL6) in vitro or in vivo using multiple different protein-protein interaction methods. In addition, TKI1 and SNL3 are co-expressed in all the examined tissues here, and TKI1 and SNL3 are co-localized in the nucleus, indicating they may function together in plant. Furthermore, Genetic analysis with knockout mutants showed that both TKI1 and SNLs promote flowering with an additive effect in long days (LDs), however TKI1 induces flowering but SNLs inhibit flowering in short days (SDs). Finally, the flowering repressor FLOWERING LOCUS C (FLC) and its homolog MADS AFFECTING FLOWERING 4 (MAF4) were up-regulated, and the flowering activator FLOWERING LOCUS T (FT) and CONSTANS (CO) were down-regulated in tki1, snl1/2/3/4/5 and snl1/2/3/4/5 tki1 mutants, compared with Col-0. Therefore, our results increase our understanding of the biological functions of TKI1, and reveal that TKI1 physically interacts with SNLs and they both induce flowering in LDs, and indicate that TKI1 and SNLs may function together to regulate flowering gene expression to promote flowering in Arabidopsis.

An ethylene response factor negatively regulates red light induced resistance of melon to powdery mildew by inhibiting ethylene biosynthesis

Powdery mildew is a common serious disease threatening global melon production. Red light can improve plant resistance to powdery mildew by inducing endogenous ethylene synthesis; however, the underlying molecular mechanism requires elucidation. In this study, an ERF transcription factor CmRAP2-13 was identified, silencing it significantly improved melon seedlings resistance to powdery mildew. Further research found that CmRAP2-13 inhibited the expression of key ethylene synthesis genes CmACS10 and CmERF27 by binding to GCC-box in the promoters, thus inhibiting ethylene biosynthesis. At the same time, protein-level interaction between CmRAP2-13 and CmERF27 also occurred. When CmRAP2-13 existed, the transcriptional activation of CmERF27 on CmACS10 was interfered and weakened. However, red light pretreatment notably decreased the expression of CmRAP2-13, and this process was influenced by phytochrome B, the red light receptor. Analysis of defence-related gene expression following ethephon application and CmRAP2-13 silencing revealed that CmRAP2-13 acted as a negative regulator of melon seedling resistance to powdery mildew, functioning as a convergence point for red light and ethylene signalling. Taken together, red light induced CmRAP2-13 and played a negative role in regulating Podosphaera xanthii infection in melons. Powdery mildew infection produced ethylene, which further inhibited CmRAP2-13 expression and formed a feedback regulation loop to participate in disease resistance. Our research on CmRAP2-13 deciphers the important regulatory network of red light-induced ethylene production in melon powdery mildew resistance, which can be used as a potential target of genetic engineering to enhance plant protection against powdery mildew.

Comparative transcriptome analysis of emerging young and mature leaves of Bienertia sinuspersici, a single-cell C4 plant

Background

Efficient carbon capture by plants is crucial to meet the increasing demands for food, fiber, feed, and fuel worldwide. One potential strategy to improve the photosynthetic performance of plants is the conversion of C3-type crops to C4-type crops, enabling them to perform photosynthesis at higher temperatures and with less water. C4-type crops, such as corn, possess a distinct Kranz anatomy, where photosynthesis occurs in two distinct cell types. Remarkably, Bienertia sinuspersici is one of the four known land plant species that perform C4 photosynthesis within a single cell. This unique single-cell C4 (SCC4) anatomy is characterized by dimorphic chloroplasts and corresponding intracellular biochemistry. Because young, emergent Bienertia leaves first exhibit C3anatomy and then differentiate into the C4 anatomy as the leaves mature, Bienertia represents an excellent system to explore the basis for a C3 to C4 transition.

Methods

To gain insight into the genes and pathways associated with the C3 to C4 transition between emerging young and mature Bienertia sinuspersici leaves, a comparative transcriptome analysis was conducted in which global gene expression and gene ontologies were compared between the two stages.

Results

In the emergent leaf, differentially expressed genes and enrichment of ontologies associated with the cell cycle and cytoskeletal dynamics were observed, while the mature leaf displayed enrichment of processes associated with photosynthesis and cellular energetics. Additionally, numerous transcription factors (TFs) associated with metabolic homeostasis, hormone and stress signaling, and developmental regulation were expressed throughout development, with unique TF expression profiles at each stage. These data expand our insights into the molecular basis of Binertia's unique cellular compartmentalization, chloroplast dimorphism, and single-cell C4 biochemistry and provide information that will be useful in the ongoing efforts to transform C3-type crops into C4 type.

An AP2-Family Gene Correlates with the Double-Flower Trait in Petunia × hybrida

The double-flower trait is highly valued in ornamental plants due to its unique aesthetic appeal, yet its genetic basis varies significantly across different species. While AGAMOUS (AG) and APETALA2 (AP2)-like genes have been demonstrated to play crucial roles in floral organ identity regulation in the model plant Arabidopsis thaliana, the underlying mechanisms governing double-flower formation in many ornamental species remain largely unexplored. In this study, we examined the inheritance pattern of this trait and identified a genetic variant associated with petal number variation. Crosses between the single-flowered cultivar 'Baccarat White' (BW) and the semi-double cultivar 'Duo Lavender' (DL) produced a 1:1 segregation of single and semi-double flowers in the F1 generation, while self-pollination of DL yielded a 1:2:1 segregation of single, semi-double, and double flowers. These results indicate that the double-flower trait follows a single-gene, semi-dominant inheritance model. Whole-genome sequencing of BW and DL followed by sequence analysis of floral organ identity genes revealed no significant differences in B-class (PhGLO1, PhGLO2, PhDEF, and PhTM6) or C-class (pMADS3 and FBP6) genes between the two cultivars. Notably, a 10 kb insertion upstream of the miR172 target site in the PhBOB gene was detected in DL. PCR genotyping of 192 F1 progenies demonstrated complete co-segregation between this insertion and the double-flower phenotype, suggesting a strong genetic association. Moreover, qRT-PCR analysis showed that PhBOB expression was significantly elevated in DL-exhibiting a 69-fold increase in petals compared to BW-implying that its overexpression disrupts the petal-to-stamen identity transition. Additionally, another AP2 family gene, PhROB3, was upregulated in semi-double flowers, with a 10-fold higher expression in the petals and stamens of DL relative to BW, suggesting its potential role in floral organ differentiation. This study elucidates the molecular regulatory mechanism underlying the double-flower trait in petunia, highlighting the role of PhBOB in floral organ identity specification and providing new insights into the potential function of PhROB3 in double-flower development.

Genome-wide identification and expression analysis of the DREB gene family in foxtail millet (Setaria Italica L.)

BACKGROUND

Dehydration response element binding factors (DREBs) are a family of plant-specific transcription factors that regulate plant responses.

RESULTS

In this study, members of the SiDREB gene family were identified and analyzed in terms of their physicochemical properties, phylogeny, and structure of the encoded proteins. The expression patterns of the DREB transcription factors in foxtail millet under stress were analysed by combining the qRT-PCR data for foxtail millet after exposure to low temperature, abscisic acid (ABA), and osmotic stress (20% PEG 6000). There were 56 SiDREB genes, which were divided into six subgroups, that were located on nine chromosomes of foxtail millet. Chromosomal localization showed that the SiDREB genes were unevenly distributed across nine foxtail millet chromosomes. Furthermore, qRT‒PCR experiments revealed that 19 SiDREB genes play a role in the response to abiotic stress and ABA.

CONCLUSIONS

The results of this study lay a foundation for further research on the functions of the DREB genes in foxtail millet and will be beneficial foe the genetic improvement of this species.

AP2 transcription factor CsAIL6 negatively regulates citric acid accumulation in citrus fruits by interacting with a WD40 protein CsAN11

Citric acid accumulation is an essential process in citrus fruits that determines fruit flavor and marketability. The MBW complex transcription factor genes, CsAN11, CsAN1, and CsPH4 play key roles in regulating citric acid accumulation. Although how to regulate CsAN1 or CsPH4 was widely investigated, studies on the regulation of CsAN11 are scarce. In this study, we characterized the AP2/ERF (APETALA2/ethylene response factor) transcription factor gene CsAIL6, which is lowly expressed in high-acid citrus varieties and highly expressed in low-acid citrus varieties. Overexpressing CsAIL6 obviously decreased the citric acid content in citrus fruits, calli, or tomatoes, whereas silencing CsAIL6 significantly increased the fruit citric acid content. Additionally, transcript levels of CsAN11, CsAN1, and CsPH4 were significantly increased by silencing CsAIL6; only the CsAN11 transcript level was significantly decreased by overexpressing CsAIL6. Similarly, only the tomato AN11 (SIAN11) transcript level in CsAIL6 stably overexpressing fruits was markedly lower than that in wild-type (WT) fruits. Further experiments revealed that overexpressing CsAN11 significantly increased the organic acid content but had no obvious influence on the CsAIL6 transcript level; in addition, CsAIL6 only interacts with CsAN11, rather than with CsAN1 and CsPH4 of the MBW complex. Taken together, our findings verified that CsAIL6 negatively regulates citric acid accumulation through directly interacting with the WD40 protein CsAN11, which provides a new mechanism for citric acid accumulation in fruits through the regulation of the MBW complex.

High temperature-responsive DEAR4 condensation confers thermotolerance through recruiting TOPLESS in Arabidopsis nucleus

Global warming is harmful to plants and threatens crop yields in the world. In contrast to other abiotic stresses, the molecular mechanisms for plant high temperature perception and signaling are still not fully understood. Here, we report that transcription factor DREB AND EAR MOTIF PROTEIN 4 (DEAR4) positively regulates heat tolerance in Arabidopsis thaliana. We further reveal that DEAR4 proteins undergo liquid-liquid phase separation (LLPS) and high temperature could induce DEAR4 condensate formation in the nucleus. Moreover, DEAR4 recruits the transcriptional co-repressor TOPLESS (TPL) into the nuclear speckles under high temperature. The high temperature triggered DEAR4-TPL co-condensates enhance their transcriptional repression activity through modulating histone deacetylation levels of GASA5, which is a reported negative regulator of HEAT SHOCK PROTEINs (HSPs). A genome-wide transcriptional landscape study confirms that DEAR4 induces the expression of multiple HSPs. Taken together, we illustrate a transcriptional repression mechanism mediated by DEAR4 through LLPS to confer plants thermotolerance and open a new avenue for translating this knowledge into crops for improving their heat resistance.

Molecular insights into DaERF108-mediated regulation on asperosaponin VI biosynthesis under cold tolerance in Dipsacus asper

Plants frequently modulate their hormonal signaling pathways in response to stress, thereby regulating the synthesis of secondary metabolites and adapting to fluctuations in their surroundings. The APETALA2/ethylene-responsive factor (AP2/ERF) domain transcription factors are important in regulating abiotic stress tolerance. The accumulation of asperosaponin VI in the root was significantly enhanced under low temperature stress, which exhibited a correlation with the AP2/ERF family. However, the involvement of AP2/ERF in regulating asperosaponin VI biosynthesis under cold stress remains ambiguous. Under cold stress conditions below 10 °C, we observed the accumulation of asperosaponin VI and an increase in jasmonic acid (JA) levels. This response was attributed to the activation of the JA synthesis pathway induced by low temperatures. Additionally, a comprehensive analysis of the full-length transcriptome of Dipsacus asper identified a total of 80 DaAP2/ERF transcription factors, which exhibited significant homology with Arabidopsis thaliana and Citrus ERFs based on phylogenetic analysis. Furthermore, qRT-PCR analysis demonstrated that both cold stress and methyl jasmonate (MeJA) induction upregulated DaERF108 expression. The expression of DaERF108 is notably upregulated in the leaves and during the early stages of growth and development of D. asper, while subcellular localization analysis confirmed its presence in the nucleus. The overexpression of DaERF108 significantly enhanced the accumulation of oleanolic acid, a precursor of asperosaponin VI, and activated the triterpenoid biosynthesis pathway in Arabidopsis roots. Additionally, the overexpression of DaERF108 induced the activation of the terpenoid synthesis pathway under cold stress conditions. Notably, there was a positive correlation between DaERF108 expression and genes involved in asperosaponin VI biosynthesis, particularly with 3-hydroxy-3-methylglutaryl coenzyme A synthase (DaHMGS). The interaction between DaERF108 and the GCC-box element in the DaHMGS promoter was demonstrated by LUC and Y1H assays, leading to enhanced activity. These findings suggest that DaERF108 specifically binds to the G-box element, thereby regulating DaHMGS gene expression, activating the JA signaling pathway, and promoting asperosaponin VI biosynthesis in response to cold stress.

Genome-Wide Identification and Expression of the ERF Gene Family in Populus trichocarpa and Their Responses to Nitrogen and Abiotic Stresses

The ethylene response factor (ERF) family is a prominent plant-specific transcription factor family, which plays a crucial role in modulating plant growth and stress tolerance. In this study, a total of 210 ERFs were identified in Populus trichocarpa, comprising 29 AP2 (APETALA2) subfamily members, 176 ERF subfamily members, and 5 RAV (related to ABI3/VP1) subfamily members. The duplication events of the PtERF family members exclusively occurred within the subfamilies. A total of 168 duplication pairs were found among 161 PtERF genes, and all of them were fragment duplications. Gene structure analysis revealed that most ERF subfamily members only had one exon without introns, the AP2 subfamily members had six or more introns and exons, and RAV subfamily members lacked introns except for PtERF102. Considerable cis-acting elements associated with plant growth and development, stress response, hormone response, and light response were detected in the promoters of PtERF genes. The expression levels of PtERFs were highest in roots across tissues and in winter among seasons. Furthermore, the nitrate and urea stimulated the expression of PtERF genes. The co-expression network analysis based on PtERFs indicated their potential roles in hormone signaling, acyltransferase activity, and response to chemicals. This study provides novel insights into investigating the role of PtERFs in environmental stress in poplar species.

Genome-Wide Identification and Expression Profiling of Dehydration-Responsive Element-Binding Family Genes in Flax (Linum usitatissimum L.)

Dehydration-responsive element-binding (DREB) transcription factors are ubiquitous in plants and regulate plant growth, development, signal transduction, and responses to stress, particularly drought stress. However, DREB genes in flax have not previously been studied. This study conducted a comprehensive and systematic analysis of the DREB gene family in flax (Linum usitatissimum L.). A total of 59 LuDREB genes were identified in Longya-10 (a breeding variety), with an uneven distribution across all 15 chromosomes. Further analysis revealed significant variations among LuDREB members, with predictions indicating that these proteins are hydrophilic and localized in the nucleus and cytoplasm. A phylogenetic analysis classified the LuDREB genes into six subgroups, a classification further supported by gene structure and motif composition. Members within the same subgroup exhibited structural conservation, suggesting functional redundancy. The duplication analysis identified 30 pairs of segmentally duplicated LuDREB genes and one pair of tandemly duplicated genes, indicating that segmental duplication was the primary driver of LuDREB gene expansion. A comparative collinearity analysis revealed that most LuDREB genes had orthologs in other plant species, suggesting that this gene family has remained relatively conserved throughout evolution. Cis-acting element analysis identified numerous hormone- and stress-responsive elements in LuDREB promoters, and the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) results confirmed the role of all LuDREB genes in drought stress response. In addition, transcriptome analysis revealed that LuDREB49 and LuDREB56 exhibited high expression levels in the capsules, whereas LuDREB3 and LuDREB36 showed significantly higher expression levels in the stems, suggesting that these LuDREB genes may have specialized functions in capsule or stem development. Collectively, this study provides a comprehensive overview of LuDREB genes, offering valuable insights into their roles in flax growth, development, and stress responses.

Functional analysis of the StERF79 gene in response to drought stress in potato (Solanum tuberosum L.)

BACKGROUND

The AP2/ERF (APETALA 2/ethylene-responsive element binding factors) is a class of superfamily of plant-specific transcription factor that play an important regulatory role in many physiological and biochemical processes in plants.

RESULTS

In this study, overexpression of the StERF79 gene increased drought tolerance in potato plants, whereas StERF79 RNA interference expression (RNAi) lines decreased drought tolerance in potato plants. In addition, the superoxide dismutase (SOD), peroxide dismutase (POD), and catalase (CAT) activities, as well as proline (Pro) content of StERF79 transgenic lines, showed significantly higher results than those of the wild type (WT) potato plants under natural drought stress conditions, while the malondialdehyde (MDA) content was lower. The StERF79 transcription factor can respond to drought stress by interacting with a DRE cis-acting element in the promoter region of the downstream target gene (StDHN-2), and activating its expression, the result was validated by using yeast one hybrid (Y1H), Dual-Luciferase and β-glucuronidase (GUS) staining assays both in vivo and in vitro. The StDHN-2 gene is a member of the dehydrin (DHN) subfamily of the potato plant late embryonic developmentally abundant (LEA) protein family. LEA, hydrophilic proteins found in plants, serve as cellular dewatering protectants to prevent desiccation during various stresses.

CONCLUSION

The results could provide novel knowledge into the functional analysis of the StERF79 gene in positive regulation of the StDHN-2 gene to drought response and its possible mechanisms in potato plants.

CLINICAL TRIAL NUMBER

Not applicable.

Multiomics unraveled that gibberellin signaling underlies adaptation of rice to ciprofloxacin stress: Calling for concerns on the adverse effects of pharmaceutical residues in water during agricultural irrigations

Residual concentrations of antibiotics in water can reach ng mL-1 - µg mL-1 levels, which pose high risks to crops during irrigation; however, the interactions between rice and antibiotics, as well as the defense mechanisms of rice at their early growth phase remain unclear. In this study, we investigated the uptake dynamics of a ubiquitously found antibiotic, ciprofloxacin (CIP) at 0.1, 1, 6.5, and 20 µg mL-1 in rice seedlings. We found gradually bioaccumulated CIP induced significant physiological changes including inhibited growth of roots and leaves of rice seedlings, and decreased pigment contents, which can be caused by disrupted homeostasis of reactive oxygen species. Integrating roots transcriptomics, metabolomics, and validation experiments, we found that rice seedlings synthesized more gibberellins to trigger the expression of transcription factors such as group VII ethylene response factors, which induced metabolic reprogramming to yield more fatty acids derivates. These compounds including eicosanoids, isoprenoids, and fatty acids and conjugates can act as signaling molecules, as well as antioxidants and energy sources to achieve rice recovery. This conclusion is supported by the evidence showing that adding gibberellins in rice seedlings culture decreased the accumulated CIP and improved rice growth; whilst, disrupting gibberellin signaling pathway using paclobutrazol as an inhibitor increased uptaken CIP in both roots and leaves with augmenting the antibiotic stress on rice. This study has demonstrated a gibberellin-based defense mechanism in rice for defense of CIP stress, which might have significant environmental applications since we can add minor gibberellins to reduce bioaccumulated CIP with simultaneously promoting rice growth at their early phases.

Mechanism Analysis of OsbHLH34-OsERF34 Mediated Regulation of Rice Resistance to Sheath Blight

Transcription factors are pivotal molecules involved in transcriptional and post-transcriptional regulation in plants, playing a crucial role in combating biological stress. Here, we have characterized a regulatory factor, OsbHLH34, which governs the response of rice to infection by Rhizoctonia solani AG1-IA. The expression of OsbHLH34 significantly impacts the susceptibility of rice to Rhizoctonia solani infection. Through the generation of OsbHLH34 knockout and overexpressing rice plants, we observed that OsbHLH34 acts as a positive regulator of rice resistance against rice sheath blight. The average lesion area of overexpression plants was 14.3%, the average lesion area of wildtype plants was 36%, and the average lesion area of mutant plants was 67.6%. Transcriptome and qRT-PCR analysis showed that OsbHLH34 regulates OsERF34, which is a key transcription factor for ethylene biosynthesis and resistance to sheath blight. By employing yeast one-hybrid and dual luciferase assays, we demonstrated that OsbHLH34 directly interacts with the promoter of OsERF34, thereby activating its transcription. Both in vitro and in vivo experiments confirmed OsERF34 as a direct target of OsbHLH34. These findings not only enhance our understanding of the molecular mechanisms underpinning rice disease resistance but also offer novel targets for the improvement of rice disease resistance through breeding strategies.

Cloning of the DlERF10 gene from Diospyros lotus L. and cold tolerance analysis of the DlERF10 gene in transgenic tobacco plants

In the north of China, Diospyros plants are vulnerable to low-temperature damage in winter and is considered as a major factor restricting the development of the persimmon industry in Northern China. Diospyros lotus L. is featured by high survival potential of seedlings, cold tolerance, and grafting affinity with D. kaki Thunb. D. lotus has been frequently used as rootstocks for Diospyros spp. ERF transcriptional factors are a subfamily of the AP2/ERF gene family and play an important role in plant growth and stress tolerance. To explore the structure and function of the ERF transcription factors in D. lotus, we performed RT-PCR to clone DlERF10 from the leaves. The DlERF10 gene was 1104 bp long, encoding 367 amino acids. In order to deeply study the cold tolerance of DlERF10 gene, the pBI121-DlERF10 overexpression vector was constructed, and agrobacterium-mediated transformation was carried out to transfer the gene into tobacco plants. The wild-type and transgenic tobacco plants were subjected to low-temperature stress. The results showed that the transgenic plants were less severely damaged by low-temperature stress than the wild-type plants. Besides, the SOD, POD and CAT activities of leaves enhanced, and PRO contents of leaves increased, while the MDA content decreased. It was concluded that the DlERF10 gene increased the activity of protective enzymes in tobacco plants, thereby strengthening the tolerance to low-temperature stress. The present study proposes a candidate gene for engineering cold stress tolerance in Diospyros spp.

An AP2/ERF transcription factor GhERF109 negatively regulates plant growth and development in cotton

Cotton is an important source of natural fibers. The AP2/ethylene response factor (ERF) family is one of the largest plant-specific transcription factors (TFs) groups, playing key roles in plant growth and development. However, the role of ERF TFs in cotton's growth and development remains unclear. In this study, we identified GhERF109, a nuclear-localized ERF, which showed significant expression differences between ZM24 and pag1 cotton. Heterologous overexpression of GhERF109 in Arabidopsis resulted in reduced plant height, shortened root length, and reduced silique lengths compared to wild-type (WT) plants. In contrast, silencing GhERF109 in cotton led to a significant increase in plant height due to the elongation of stem cells. Overexpression of GhERF109 in cotton also produced a compact plant type with a notable reduction in height. RNA-seq analysis of GhERF109-silenced plants revealed 4123 differentially expressed genes (DEGs), with many upregulated genes involved in auxin response, polar transport, cell expansion, cell cycle regulation, brassinolide (BL) biosynthesis, and very long-chain fatty acid (VLCFA) pathways. These findings suggest that GhERF109 integrates auxin and other signaling pathways to suppress plant growth, providing valuable genetic material for breeding programs to improve mechanized cotton harvesting.

Genetic variations in ZmEREB179 are associated with waterlogging tolerance in maize

Maize (Zea mays) is highly susceptible to waterlogging stress, which reduces both the yield and quality of this important crop. However, the molecular mechanism governing waterlogging tolerance is poorly understood. In this study, we identify a waterlogging- and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor (ERF) localized in the nucleus. Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress. Conversely, the zmereb179 knockout mutants are more tolerant to waterlogging, suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance. A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes, including ZmEREB180. We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression. Notably, the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter (Hap2) are highly associated with waterlogging resistance. The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations, highlighting its potential applications in breeding programs. Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.

Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales

Co-option of gene regulatory networks leads to the acquisition of new cell types and tissues. Stomata, valves formed by guard cells (GCs), are present in most land plants and regulate CO2 exchange. The transcription factor (TF) FAMA globally regulates GC differentiation. In the Brassicales, FAMA also promotes the development of idioblast myrosin cells (MCs), another type of specialized cell along the vasculature essential for Brassicales-specific chemical defences. Here we show that in Arabidopsis thaliana, FAMA directly induces the TF gene WASABI MAKER (WSB), which triggers MC differentiation. WSB and STOMATAL CARPENTER 1 (SCAP1, a stomatal lineage-specific direct FAMA target), synergistically promote GC differentiation. wsb mutants lacked MCs and the wsb scap1 double mutant lacked normal GCs. Evolutionary analyses revealed that WSB is conserved across stomatous angiosperms. We propose that the conserved and reduced transcriptional FAMA-WSB module was co-opted before evolving to induce MC differentiation.

MsERF17 Promotes Ethylene-Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

Drought is an important factor that affects plant anthocyanin biosynthesis. However, the underlying molecular mechanisms remain elusive. Ethylene response factors (ERFs) are pivotal regulators in plant growth and environmental responses, particularly in anthocyanin biosynthesis. This study investigated the leaf colour transition from green to red in Malus spectabilis under drought conditions. This transition was primarily attributed to the accumulation of anthocyanins, specifically cyanidin-3,5-diglucoside and cyanidin-3-O-galactoside. Our findings elucidate the pivotal role of MsERF17 in drought-induced anthocyanin biosynthesis. Biochemical and molecular analyses showed that MsERF17 positively regulates anthocyanin synthesis by binding to promoters of MsbHLH3 and MsF3' H, thereby activating their expression. Moreover, transient overexpression and virus-induced gene silencing of MsERF17 in fruit peel and leaves, respectively, regulated anthocyanin synthesis. The stable transformation of calli further corroborated the positive regulatory function of MsERF17 in anthocyanin biosynthesis. Our results provide novel insights into the mechanism by which MsERF17, induced by ethylene, promotes anthocyanin accumulation through the positive regulation of MsbHLH3 and MsF3'H expression under drought conditions in M. spectabilis leaves.

Molecular intricacies of intrinsically disordered proteins and drought stress in plants

Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) are renowned for their dynamic structural characteristics and conformational adaptability, allowing them to assume diverse conformations in response to prevailing environmental conditions. This inherent flexibility facilitates their interactions with molecular targets, enabling them to engage in numerous cellular processes without any excessive energy consumption. This adaptability is instrumental in shaping cellular complexity and enhancing adaptability. Notably, most investigations into IDPs/IDRs have concentrated on non-plant organisms, while this comprehensive review explores their multifaceted functions with a perspective of plant resilience to drought stress. Furthermore, the impact of IDPs on plant stress is discussed, highlighting their involvement in diverse biological processes extending beyond mere stress adaptation. This review incorporates a broad spectrum of methodological approaches, ranging from computational tools to experimental techniques, employed for the systematic study of IDPs. We also discussed limitations, challenges, and future directions in this dynamic and evolving field, aiming to provide insights into the unexplored facets of IDPs/IDRs in the intricate landscape of plant responses to drought stress.

Repressor MrERF4 and Activator MrERF34 Synergistically Regulate High Flavonol Accumulation Under UV-B Irradiation in Morella rubra Leaves

Flavonols are important plant photoprotectants to defence UV-B irradiation, however, the underlying transcriptional regulatory mechanism of rapid flavonol accumulation in response to UV-B remains unknown. In this study, content of flavonols was significantly induced from 0.11 to 3.80 mg/g fresh weight by UV-B irradiation in leaves of Morella rubra seedlings. MrERF34 was identified as an activator that can regulate the expression of MrFLS2, and promoted flavonol biosynthesis with activator MrMYB12 under UV-B treatment. Transient overexpression of MrERF34 resulted in higher flavonol accumulation, while virus-induced gene silencing of MrERF34 reduced the content of flavonols in bayberry leaves. We further demonstrated that a repressor MrERF4 inhibited the expression of MrERF34 and MrMYB12 as well as MrFLS2 via ERF-associated-amphiphilic repression motif. Exposure to UV-B reduced the promoter activity and transcription of MrERF4, which weakened the inhibitory effect of MrERF4 on MrERF34, MrMYB12, and MrFLS2, leading to a tremendous accumulation of flavonols. Such inhibitory roles of MrERF4 in regulation of flavonol biosynthesis were further validated by transient overexpression in leaves of Nicotiana benthamiana and M. rubra. These findings enrich the synergistical regulatory mechanisms between repressor and activators in flavonol biosynthesis, and provide new insights into photoprotectants biosynthesis to mitigate UV-B stress in plants.

TaERFL1a enhances drought resilience through DHAR-mediated ASA-GSH biosynthesis in wheat

Wheat is one of the important cereal crops around the world, but it often suffers from abiotic stresses, which threaten food security. Thus, it is critical to identify the genes that determine drought tolerance in wheat. AP2/ERFs are known to regulate drought stress in various crops. In this study, TaERFL1a-overexpressing wheat transgenic lines (TaERFL1a-OEs) were used to determine drought resilience mechanism. After 12 d without watering, the growth phenotype of TaERFL1a-OEs was better than that of the wild type (WT), whose activities of superoxide dismutase and catalase, and contents of ascorbate acid (ASA) and glutathione (GSH) were significantly increased, while malondialdehyde content was significantly decreased. Transcriptome analysis revealed that 28,520 genes were differentially expressed between TaERFL1a-OEs and WT under drought condition. Further analysis found that these DEGs were involved in multiple stress-response processes, especially in the ASA-GSH pathway. qPCR revealed that the expression levels of GPX, DHAR, and MDHAR, which are suggested to be participated in ASA-GSH biosynthesis, were significantly up-regulated in TaERFL1a-OEs under drought stress, especially the DHAR gene. Moreover, dual-luciferase and luciferase complementation imaging revealed that TaERFL1a was more promoted DHAR transcription to a greater extent than other genes. Furthermore, yeast one-hybrid, electrophoretic mobility shift assay, and chromatin immunoprecipitation combined with qPCR revealed that TaERFL1a regulates DHAR expression by binding to the cis-element ERF in DHAR promoter and promotes the transcription of later in vivo and in vitro. Overall, our results provided molecular regulatory evidence for TaERFL1a in wheat drought stress and suggested candidate genes for improving drought-tolerant wheat breeding.

Ethylene modulates wheat response to phosphate deficiency

Ethylene is involved in the response to P deficiency in some model plants such as Arabidopsis and rice, but its role in wheat remains unclear. Following our recent study demonstrating the role of differentially expressed genes encoding ethylene response factors (ERFs) in response to P starvation in wheat, this study aims to investigate remodeling of the ethylene pathway and the physiological roles of ethylene in wheat under P deficiency using transcriptome analysis and the addition of the exogenous ethylene analogue, ethephon, or ethylene inhibitors. ERFs with at least a 2-fold expression change upon P deficiency had a distribution biased towards chromosome 4B. A group of genes encoding aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase were up-regulated under P starvation, suggesting an increase in ACC and ethylene content, which was verified by biochemical measurements and gas chromatography-mass spectrometry analysis. Under P deficiency, both root and shoot biomass decreased with application of exogenous ethephon or ethylene inhibitors, while root fork numbers and root surface area decreased upon ethephon treatment. Phosphate (Pi) concentrations in roots and old leaves increased with ethephon treatment, and Pi redistribution in roots and younger leaves was altered under Pi starvation. Our findings can guide breeding of germplasm with high Pi efficiency.

Genome-Wide Identification and Functional Analysis of AP2/ERF Gene Family in Passiflora edulis Sims

The Apetala2/Ethylene Responsive Factor (AP2/ERF) family represents a critical group of transcription factors in plants, recognized for their roles in growth, development, fruit ripening, and postharvest processes. This study aimed to identify and characterize the AP2/ERF gene family in passion fruit (Passiflora edulis Sims) and investigate their potential roles in flavor enhancement. A total of 91 PeAP2/ERF genes were identified and classified into five subfamilies. Chromosome localization and collinearity analysis demonstrated their distribution across all nine chromosomes of passion fruit, with tandem duplication events identified as a key driver of family expansion. Exon-intron configurations and motif compositions were highly conserved among PeAP2/ERF genes. Promoter cis-acting element analysis indicated potential regulation by environmental signals, including abiotic and biotic stresses, as well as hormonal cues. Postharvest storage induced the expression of 59 PeAP2/ERF genes over time. Notably, PeAP2-10 was found to enhance the expression of PeSTP6, a gene associated with sugar transport, suggesting its potential influence on the flavor profile of passion fruit. These findings provide valuable insights into the functional roles of PeAP2/ERF genes in passion fruit, highlighting their significance in postharvest management and flavor quality enhancement strategies.

Ethylene response factor SlERF.D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12

Ripening is crucial for the development of fleshy fruits that release their seeds following consumption by frugivores and are important contributors to human health and nutritional security. Many genetic ripening regulators have been identified, especially in the model system tomato, yet more remain to be discovered and integrated into comprehensive regulatory models. Most tomato ripening genes have been studied in pericarp tissue, though recent evidence indicates that locule tissue is a site of early ripening-gene activities. Here, we identified and functionally characterized an Ethylene Response Factor (ERF) gene, SlERF.D6, by investigating tomato transcriptome data throughout plant development, emphasizing genes elevated in the locule during fruit development and ripening. SlERF.D6 loss-of-function mutants resulting from CRISPR/Cas9 gene editing delayed ripening initiation and carotenoid accumulation in both pericarp and locule tissues. Transcriptome analysis of lines altered in SlERF.D6 expression revealed multiple classes of altered genes including ripening regulators, in addition to carotenoid, cell wall, and ethylene pathway genes, suggesting comprehensive ripening control. Distinct regulatory patterns in pericarp versus locule tissues were observed, indicating tissue-specific activity of this transcription factor (TF). Analysis of SlERF.D6 interaction with target promoters revealed an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) TF (SlDEAR2) as a target of SlERF.D6. Furthermore, we show that a third TF gene, SlTCP12, is a target of SlDEAR2, presenting a tricomponent module of ripening control residing in the larger SlERF.D6 regulatory network.

The Mulberry WRKY Transcription Factor MaWRKYIIc7 Participates in Regulating Plant Drought Stress Tolerance

The sericulture industry is an important component of the agricultural industry. Drought stress can cause yellowing, premature ageing, and the shrinkage of mulberry (Morus alba L.) leaves, greatly damaging their quality and restricting the high-quality development of the sericulture industry. WRKY transcription factors play important roles in the plant drought stress response. In this study, we found that MaWRKYIIc7 of the mulberry WRKY TFs, had significantly higher expression levels in leaves than in other tissues and was induced to be expressed under drought stress. The MaWRKYIIc7 protein is located in the nucleus and plasma membrane, and its transcriptional activity depends mainly on the N-terminal sequence. The overexpression of MaWRKYIIc7 in Arabidopsis resulted in better drought tolerance. An analysis of the transient overexpression of MaWRKYIIc7 in mulberry seedlings under drought stress revealed that the transgenic seedlings presented decreased stomatal opening, decreased MDA content, increased ROS clearance ability, and increased the expression of ABA biosynthesis-related genes. The Y1H and Dual-luc results indicate that MaWRKYIIc7 can bind W-boxes to positively regulate MaNCED1 and MaRD29A, synergistically regulating the drought tolerance of mulberry. Overall, our research suggests that MaWRKYIIc7 can increase plant drought tolerance by promoting ROS clearance, adjusting stomatal opening, and activating the ABA signalling pathway.

Surviving floods: Escape and quiescence strategies of rice coping with submergence

Historical and recent insights into the molecular mechanisms of escape and quiescence strategies employed by rice to survive flooding.

Characterization of pecan PEBP family genes and the potential regulation role of CiPEBP-like1 in fatty acid synthesis

Phosphatidyl ethanolamine-binding protein (PEBP) plays important roles in plant growth and development. However, few studies have investigated the PEBP gene family in pecan (Carya illinoinensis), particularly the function of the PEBP-like subfamily. In this study, we identified 12 PEBP genes from the pecan genome and classified them into four subfamilies: MFT-like, FT-like, TFL1-like and PEBP-like. Multiple sequence alignment, gene structure, and conserved motif analyses indicated that pecan PEBP subfamily genes were highly conserved. Cis-element analysis revealed that many light responsive elements and plant hormone-responsive elements are found in CiPEBPs promoters. Additionally, RNA-seq and RT-qPCR showed that CiPEBP-like1 was highly expressed during kernel filling stage. GO and KEGG enrichment analysis further indicated that CiPEBP-like1 was involved in fatty acid biosynthesis and metabolism progress. Overexpression of CiPEBP-like1 led to earlier flowering and altered fatty acid composition in Arabidopsis seeds. RT-qPCR confirmed that CiPEBP-like1 promoted fatty acid synthesis by regulating the expression of key genes. Overall, this study contributes to a comprehensive understanding of the potential functions of the PEBP family genes and lay a foundation to modifying fatty acid composition in pecan kernel.

Transcriptomics highlights dose-dependent response of poplar to a phenanthrene contamination

Polycyclic aromatic hydrocarbon (PAH) contamination in industrial soils poses significant environmental challenges, necessitating cost-effective bioremediation approaches like tree-based phytoremediation. However, the defence mechanisms and adaptability of trees to PAH exposure remain poorly understood, while the identification of molecular markers could help in the detection of toxicity symptoms. This study explores the molecular response of Populus canadensis to a phenanthrene (PHE) contamination gradient (from 100 to 2000 mg kg-1) using RNA-seq analysis of roots and leaves after 4 weeks of exposure. Both differentially expressed genes (DEGs) and DRomics, a dose-response tool, identified transcriptomic changes, with about 50% of deregulated genes responding significantly at a benchmark dose (i.e. minimal dose that produces a significant effect) below 400 mg PHE kg-1. The highest number of DEGs was found both at a low concentration (200 and 700 mg kg-1) and at the highest concentrations (1500-2000 mg kg-1) for both roots and leaves. Ethylene signalling genes were activated via ABA-independent pathways at low concentrations and ABA-dependent pathways at high concentrations. Across the gradient, responses to oxidative stress were triggered, including reactive oxygen species scavenging and phenylpropanoid biosynthesis, specifically at 1500-2000 mg kg-1. Additionally, PHE disrupted pathways related to plant responses to biotic stress. These findings revealed unexpected dose-dependent transcriptomic shifts, demonstrating poplar's adaptive defence mechanisms against PHE toxicity.

Genome-wide identification and comparative analysis of the AP2/ERF gene family in Prunus dulcis and Prunus tenella: expression of PdAP2/ERF genes under freezing stress during dormancy

The AP2/ERF (APETALA2/ethylene responsive factor) transcription factor family, one of the largest in plants, plays a crucial role in regulating various biological processes, including plant growth and development, hormone signaling, and stress response. This study identified 114 and 116 AP2/ERF genes in the genomes of 'Wanfeng' almond (Prunus dulcis) and 'Yumin' wild dwarf almond (Prunus tenella), respectively. These genes were categorized into five subfamilies: AP2, DREB, ERF, RAV, and Soloist. The PdAP2/ERF and PtAP2/ERF members both demonstrated high conservation in protein motifs and gene structures. Members of both families were unevenly distributed across eight chromosomes, with 30 and 27 pairs of segmental duplications and 15 and 18 pairs of tandem repeated genes, respectively. The promoter regions of PdAP2/ERF and PtAP2/ERF family members contained numerous important cis-elements related to growth and development, hormone regulation, and stress response. Expression pattern analysis revealed that PdAP2/ERF family members exhibited responsive characteristics under freezing stress at different temperatures in perennial dormant branches. Quantitative fluorescence analysis indicated that PdAP2/ERF genes might be more intensely expressed in the phloem of perennial dormant branches of almond, with the opposite trend observed in the xylem. This study compared the characteristics of PdAP2/ERF and PtAP2/ERF gene family members and initially explored the expression patterns of PdAP2/ERF genes in the phloem and xylem of perennial dormant branches. The findings provide a theoretical foundation for future research on almond improvement and breeding, as well as the molecular mechanisms underlying resistance to freezing stress.

ERF114/115/109 are essential for jasmonate-repressed non-canonical JAZ8 activity in JA signaling

Jasmonate (JA), a key plant hormone, regulates various aspects of plant development and stress responses, primarily through the degradation of canonical jasmonate-ZIM domain (JAZ) proteins by the SCFCOI1 complex. While JAZ8, a non-canonical JAZ protein lacking the degron signal, has been shown to repress JA responses, the mechanism by which JA inhibits JAZ8 activity remains unclear. Here, we demonstrate that Arabidopsis ethylene response factor 114 (ERF114), ERF115, and ERF109 regulate JA signaling through interacting with JAZ8. This interaction disrupts the formation of the MYC2/3/4-JAZ8 and root hair defective 6 (RHD6)-JAZ8 complexes. We show that ERF114 positively regulates JA-induced transcriptional responses and that JA-promoted root hair growth is highly alleviated in erf114 mutants. Furthermore, the transcription of ERF114/115/109 is induced by JA in an MYC2-dependent manner, thus forming a positive feedback loop in JA signaling. Collectively, this study reveals a regulatory pathway in which ERF114/115/109 regulate JA signaling by targeting non-canonical JAZ proteins.

The AP2/ERF Transcription Factor ERF56 Negatively Regulating Nitrate-Dependent Plant Growth in Arabidopsis

ERF56, a member of the APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor (TF) family, was reported to be an early nitrate-responsive TF in Arabidopsis. But the function of ERF56 in nitrate signaling remains not entirely clear. This study aimed to investigate the role of ERF56 in nitrate-dependent plant growth and nitrate signaling. We confirmed with reverse transcription quantitative PCR (RT-qPCR) that the transcription of ERF56 is quickly induced by nitrate. ERF56 overexpressors displayed decreased nitrate-dependent plant growth, while erf56 mutants exhibited increased plant growth. Confocal imaging demonstrated that ERF56 is localized into nuclei. Assays with the glucuronidase (GUS) reporter showed that ERF56 is mainly expressed at the region of maturation of roots and in anthers. The dual-luciferase assay manifested that the transcription of ERF56 is not directly regulated by NIN-LIKE PROTEIN 7 (NLP7). The transcriptome analysis identified 1038 candidate genes regulated by ERF56 directly. A gene ontology (GO) over-representation analysis showed that ERF56 is involved in the processes of water transport, inorganic molecule transmembrane transport, secondary metabolite biosynthesis, and cell wall organization. We revealed that ERF56 represses nitrate-dependent growth through regulating the processes of inorganic molecule transmembrane transport, the secondary metabolite biosynthesis, and cell wall organization.

Unraveling the occurrence of hyperhydricity in oil palm somatic embryos during somatic embryogenesis process

The propagation of oil palm through somatic embryogenesis is the most effective method of cloning this palm tree; however, in vitro cultivation can lead to abnormalities in plant tissue, such as hyperhydricity. The present study aimed to evaluate the difference in anatomical, morphological, and histochemical characteristics, and gene expression in normal (Nm) and hyperhydric (Hh) somatic embryos of oil palm. For this purpose, Nm and Hh somatic embryos were collected from the differentiation medium and were submitted to anatomical and histochemical analyses to assess the nucleus/cytoplasm ratio (toluidine blue), starch (Lugol), and proteins (XP), as well as ultrastructural analyses via transmission electron microscopy. Additionally, gene expression analyses were performed to gain a better understanding on the molecular aspect of hyperhydric abnormality. A higher quantity of differentiated Nm somatic embryos per explant was observed, with a germination rate close to zero in Hh somatic embryos. Additionally, a higher accumulation of proteins and starch was found in Nm somatic embryos when compared to Hh embryos. It was also noted that in Nm somatic embryos, protein reserves were primarily located in the proximal region (embryonic axis), whereas starch reserves were mainly accumulated in the distal region of the somatic embryos. Hh somatic embryos exhibit insignificant starch reserves, and a greater number of intercellular spaces were observed compared to Nm somatic embryos. However, some Hh somatic embryos displayed histochemical characteristics similar to Nm, which could explain the occurrence of reversions from the Hh state to the Nm state observed in this study. Regarding molecular analyses, the gene expression results obtained showed that out of the 19 genes analyzed, 17 were upregulated in hyperhydric embryos when compared to the control condition (normal somatic embryos). Genes involved in stress response, energy metabolism, defense, membrane transport, hormonal regulation, and development were positively regulated, especially those involved in ethylene synthesis and energetic metabolism. To the best of our knowledge, this is the first in-depth study addressing hyperhydricity in oil palm during somatic embryogenesis.

ETHYLENE RESPONSE FACTOR6, A Central Regulator of Plant Growth in Response to Stress

ETHYLENE RESPONSE FACTOR6 (ERF6) has emerged as a central player in stress-induced plant growth inhibition. It orchestrates complex pathways that enable plants to acclimate and thrive in challenging environments. In response to various abiotic and biotic stresses, ERF6 is promptly activated through both ethylene-dependent and -independent pathways, and contributes to enhanced stress tolerance mechanisms by activating a broad spectrum of genes at various developmental stages. Despite the crucial role of ERF6, there is currently a lack of published comprehensive insights into its function in plant growth and stress response. In this respect, based on the tight connection between ethylene and ERF6, we review the latest research findings on how ethylene regulates stress responses and the mechanisms involved. In addition, we summarize the trends and advances in ERF6-mediated plant performance under optimal and stressful conditions. Finally, we also highlight key questions and suggest potential paths to unravel the ERF6 regulon in future research.

The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation

Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. In Arabidopsis, two enzymes share overlapping functions to produce TAGs, namely acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in a dgat1-1/pdat1-2 double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue-specific expression of either gene has not yet been identified. We transformed a dgat1-1/dgat1-1//PDAT1/pdat1-2 parent with transgenic constructs containing the Arabidopsis DGAT1 promoter fused to the AtDGAT1 open reading frame either with or without the first intron. Triple homozygous plants were obtained, however, in the absence of the DGAT1 first intron anthers fail to fill with pollen, seed yield is c. 10% of wild-type, seed oil content remains reduced (similar to dgat1-1/dgat1-1), and non-Mendelian segregation of the PDAT1/pdat1-2 locus occurs. Whereas plants expressing the AtDGAT1pro:AtDGAT1 transgene containing the first intron mostly recover phenotypes to wild-type. This study establishes that a combination of the promoter and first intron of AtDGAT1 provides the proper context for temporal and tissue-specific expression of AtDGAT1 in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes in Arabidopsis.

Kiwifruit spatiotemporal multiomics networks uncover key tissue-specific regulatory processes throughout the life cycle

Kiwifruit (Actinidia chinensis), a recently commercialized horticultural crop, is rich in various nutrient compounds. However, the regulatory networks controlling the dynamic changes in key metabolites among different tissues remain largely unknown. Here, high-resolution spatiotemporal datasets obtained by ultraperformance liquid chromatography-tandem mass spectrometry methodology and RNA-seq were employed to investigate the dynamic changes in the metabolic and transcriptional landscape of major kiwifruit tissues across different developmental stages, including from fruit skin, outer pericarp, inner pericarp, and fruit core. Kiwifruit spatiotemporal regulatory networks (KSRN) were constructed by integrating the 1,243 identified metabolites and co-expressed genes into 10 different clusters and 11 modules based on their biological functions. These networks allowed the generation of a global map for the major metabolic and transcriptional changes occurring throughout the life cycle of different kiwifruit tissues and discovery of the underlying regulatory networks. KSRN predictions confirmed previously established regulatory networks, including the spatiotemporal accumulation of anthocyanin and ascorbic acid (AsA). More importantly, the networks led to the functional characterization of three transcription factors: an A. chinensis ethylene response factor 1, which negatively controls sugar accumulation and ethylene production by perceiving the ripening signal, a basic-leucine zipper 60 (AcbZIP60) transcription factor, which is involved in the biosynthesis of AsA as part of the L-galactose pathway, and a transcription factor related to apetala 2.4 (RAP2.4), which directly activates the expression of the kiwi fruit aroma terpene synthase gene AcTPS1b. Our findings provide insights into spatiotemporal changes in kiwifruit metabolism and generate a valuable resource for the study of metabolic regulatory processes in kiwifruit as well as other fruits.

Arabidopsis DREB26/ERF12 and its close relatives regulate cuticular wax biosynthesis under drought stress condition

Land plants have evolved a hydrophobic cuticle on the surface of aerial organs as an adaptation to ensure survival in terrestrial environments. Cuticle is mainly composed of lipids, namely cutin and intracuticular wax, with epicuticular wax deposited on plant surface. The composition and permeability of cuticle have a large influence on its ability to protect plants against drought stress. However, the regulatory mechanisms underlying cuticular wax biosynthesis in response to drought stress have not been fully elucidated. Here, we identified three AP2/ERF transcription factors (DREB26/ERF12, ERF13 and ERF14) involved in the regulation of water permeability of the plant surface. Transmission electron microscopy revealed thicker cuticle on the leaves of DREB26-overexpressing (DREB26OX) plants, and thinner cuticle on the leaves of transgenic plants expressing SRDX repression domain-fused DREB26 (DREB26SR). Genes involved in cuticular wax formation were upregulated in DREB26OX and downregulated in DREB26SR. The levels of very-long chain (VLC) alkanes, which are a major wax component, increased in DREB26OX leaves and decreased in DREB26SR leaves. Under dehydration stress, water loss was reduced in DREB26OX and increased in DREB26SR. The erf12/13/14 triple mutant showed delayed growth, decreased leaf water content, and reduced drought-inducible VLC alkane accumulation. Taken together, our results indicate that the DREB26/ERF12 and its closed family members, ERF13 and ERF14, play an important role in cuticular wax biosynthesis in response to drought stress. The complex transcriptional cascade involved in the regulation of cuticular wax biosynthesis under drought stress conditions is discussed.

The ERF transcription factor ZbERF3 promotes ethylene-induced anthocyanin biosynthesis in Zanthoxylum bungeanum

Ethylene regulates fruit ripening, and in Zanthoxylum bungeanum, fruit color deepened with increasing of ethylene during fruit ripening. However, the molecular mechanism of this physiological process was still unclear. In this study, through the combined analysis of transcriptome and metabolome, it was found that ethylene release was consistent with anthocyanin synthesis, and ethylene response factors (ERFs) were significantly related to anthocyanin biosynthesis during the fruit ripening of Z. bungeanum. Ethylene treatment significantly induced fruit coloration and promoted anthocyanin synthesis and the expression of ZbERF3. Furthermore, Yeast one-hybrid assays and Luciferase reporter assays demonstrated that ZbERF3 directly bound to the promoter of ZbMYB17 and transcriptionally activated its expression. What's more, it was demonstrated that ZbMYB17 directly bound to the promoter of ZbANS, promoting anthocyanin biosynthesis. Overall, this study revealed the mechanism of ERF and MYB synergistically regulating the coloration of Z. bungeanum fruit.

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

An AP2/ERF member LlERF012 confers thermotolerance via activation of HSF pathway in lily

Heat stress transcription factors (HSFs) are core factors of plants in response to heat stress (HS), but their regulatory network is complicated and remains elusive in a large part, especially HSFBs. In this study, we reported that the LlERF012-LlHSFA1 module participates in heat stress response (HSR) by directly regulating HSF pathway in lily (Lilium longiflorum). LlHSFB1 was confirmed as a positive regulator in lily thermotolerance and a heat-inducible AP2/ERF member LlERF012 (Ethylene Response Factor 012) was further identified to be a direct trans-activator of LlHSFB1. Overexpression of LlERF012 elevated the thermotolerance of transgenic Arabidopsis and lily, but silencing LlERF012 reduced thermotolerance in lily. Further analysis showed LlERF012 interacted with LlHSFA1, which led to enhanced transactivation activity and DNA-binding capability of LlERF012. In addition, LlERF012 also directly activated the expression of LlHSFA1 by binding its promoter. As expected, we found that LlERF012 bound the promoters of LlHSFA2, LlHSFA3A, and LlHSFA3B to stimulate their expression, and LlERF012-LlHSFA1 interaction enhanced these activation effects. Overall, our data suggested that LlERF012 was a key factor for lily thermotolerance and the LlERF012-LlHSFA1 interaction synergistically regulated the activity of the HSF pathway including the class A and B members, which might be of great significance for coordinating the functions of different HSFs.

Genome-Wide Identification and Expression Analysis of the AP2/ERF Transcription Factor Gene Family in Hybrid Tea Rose Under Drought Stress

Drought stress is an important factor that reduces plant biomass production and quality. The APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) gene family is widely involved in biological processes such as plant growth, development, and stress response. However, the characteristics of the AP2/ERF gene family in hybrid tea rose (Rosa × hybrida) and their potential functions in responding to drought stress are still unclear. In the current study, 127 AP2/ERF genes were identified in hybrid tea rose. Phylogenetic analysis showed that the corresponding 127 AP2/ERF transcription factors belonged to five subfamilies. There was a large number of cis-acting elements in the AP2/ERF gene promoters related to regulation of stress response, growth and development. By examining the RNA sequencing data in the PlantExp database, the RhAP2/ERF genes exhibiting tissue-specific and stress-responsive expression in rose were identified. Furthermore, three candidate RhAP2/ERF genes (RhDREB36, RhERF59, and RhDREB44) that might participate in drought response were determined via qRT-PCR analysis in rose cultivars under drought treatment. Subcellular localization analysis revealed that RhDREB44 was located in the nucleus. These results provide a foundation for exploring the regulatory functions of RhAP2/ERF genes in the growth and development of roses, as well as for selecting key genes for future molecular breeding.

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.

Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the AP2/ERF gene family in quinoa (Chenopodium quinoa Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150 CqAP2/ERF genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative CqAP2/ERF genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many cis-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of CqAP2/ERF genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the CqAP2/ERF gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive CqAP2/ERF genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the AP2/ERF gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.

Biomass enhancement and activation of transcriptional regulation in sorghum seedling by plasma-activated water

Introduction

Recent advancements in agricultural technology have highlighted the potential of eco-friendly innovations, such as plasma-activated water (PAW), for enhancing seed germination, growth, and biomass production.

Methods

In this study, we investigated the effects of PAW irrigation on young sorghum seedlings through phenotypic and transcriptional analyses. We measured growth parameters, including seedling height, stem thickness, and biomass, across five sorghum varieties: BTx623, Sodamchal, Noeulchal, Baremae, and Hichal. Additionally, we performed detailed analyses of stem cross-sections to evaluate the structural changes induced by PAW. Whole transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and to perform Gene Ontology (GO) analysis.

Results

Phenotypic analysis revealed significant growth enhancements in PAW-treated seedlings compared to the control group, with notable increases in seedling height, stem thickness, and biomass. Stem cross-section analysis confirmed that PAW treatment led to the enlargement of primordia tissue, leaf sheath (LS1 and LS2), and overall stem tissue area. Transcriptomic analysis revealed that 78% of the DEGs were upregulated in response to PAW, indicating that PAW acts as a positive regulator of gene expression. Gene Ontology (GO) analysis further showed that PAW treatment predominantly upregulated genes associated with transmembrane transport, response to light stimulus, oxidoreductase activity, and transcriptional regulation. Additionally, an enriched AP2/EREBP transcription binding motif was identified.

Conclusion

These findings suggest that PAW not only enhances sorghum seedling growth through transcriptional regulation but also has the potential to optimize agricultural practices by increasing crop yield. The upregulation of genes involved in critical biological processes underscores the need for further exploration of PAW's potential in improving the productivity of sorghum and possibly other crops.

Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue 'The evolution of plant metabolism'.

Genome-wide identification and analysis of ERF transcription factors related to abiotic stress responses in Nelumbo nucifera

BACKGROUND

Ethylene-responsive factor (ERF) transcription factors belong to the APETALA2/ERF (AP2/ERF) superfamily, and play crucial roles in plant development process and stress responses. However, the function of ERF proteins (especially for their role in response to abiotic stresses) remains scarce in Nelumbo nucifera, which is an important aquatic plant with high ornamental, economic, and ecological values.

RESULTS

A total of 107 ERF genes were identified from the N. nucifera genome, and phylogenetic analysis classified these genes into 11 groups. The NnERF genes in the same group exhibited similar gene structure and conserved motifs, and they were unevenly distributed across the 8 chromosomes, with three pairs of tandem duplications and 21 pairs of segmental duplications. Synteny analysis revealed 44 and 39 of NnERF genes were orthologous to those in Arabidopsis thaliana and Oryza sativa, respectively. Tissue-specific expression patterns analysis of NnERF showed that 26 NnERF genes were expressed in all tested tissues, in which five genes exhibited high expression levels. Furthermore, 16 NnERF genes were selected for exploring their responses to different abiotic stresses, including cold, salt, drought, and Cd stresses. qRT-PCR analysis revealed that all these 16 investigated genes were regulated by at least one stress treatment, and 12 genes responded to all the stress treatments with different expression patterns or levels, suggesting their potential roles in diverse abiotic stress tolerance of N. nucifera. Additionally, two representative stress-related NnERFs (Nn3g19628 and Nn1g06033) were confirmed to be nuclear-localized proteins and displayed transcriptional activation.

CONCLUSIONS

In this study, we conducted a genome-wide identification and analysis of NnERF gene family related to abiotic stress responses in N. nucifera, which provides valuable information for further functional validation of these genes in stress responses, and forms a foundation for stress tolerance breeding in N. nucifera and other aquatic ornamental plants.