The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element

CsRAP2-7 negatively regulates cuticular wax biosynthesis and drought resistance in citrus by directly activating CsACO1

Cuticular wax plays an important role in enhancing plant stress tolerance. While positive regulators of cuticular wax biosynthesis are well-studied, negative regulators remain largely unexplored in citrus. In the present paper, we screened and cloned an AP2/ERF family gene, CsRAP2-7, from navel orange. This gene is localized to the nucleus and induced by drought and ABA treatments. Overexpression of CsRAP2-7 in lemon upregulates ethylene biosynthesis while concurrently inhibiting cuticular wax accumulation and reducing cuticular permeability, collectively leading to a marked decline in drought tolerance. CsRAP2-7 mediates its regulatory role by directly binding to the promoter of CsACO1, an ethylene biosynthetic gene, thereby activating its transcription. These results suggest that CsRAP2-7 play a negative role in regulating cuticular wax biosynthesis and drought resistance by directly mediating CsACO1 expression.

The ZmAHL25-ZmPUB19-ZmMPK5 Module Positively Regulates Resistance to Rhizoctonia solani in Maize

Ubiquitin-mediated proteolysis is a crucial mechanism in plant defenses against pathogens. However, the role of E3 ubiquitin ligases in the maize (Zea mays) defense response against Rhizoctonia solani, a major soil-borne fungal pathogen that causes banded leaf and sheath blight, remains unclear. We previously identified the maize ZmPUB19 gene, which encodes a U-box E3 ubiquitin ligase and is upregulated upon R. solani infection, suggesting its potential involvement in maize defense responses. In this study, we established that ZmPUB19 positively influences the maize defense response to R. solani. In vitro and in vivo experiments revealed that ZmPUB19 interacts with and ubiquitinates the mitogen-activated protein kinase ZmMPK5, resulting in ZmMPK5 degradation in response to R. solani infection. The Zmmpk5 mutant demonstrated superior resistance to R. solani compared to the wild type. Additionally, we identified an AT-Hook Motif Nuclear Localized (AHL) transcription factor, ZmAHL25, which binds to the AT-rich cis-element in the ZmPUB19 promoter and activates its expression under R. solani attack. Notably, decreased expression of ZmAHL25 increased maize susceptibility to R. solani. Collectively, our findings show that the ZmAHL25-ZmPUB19-ZmMPK5 module plays a positive role in regulating maize defense responses to R. solani infection.

Genome-wide analysis of Q binding reveals a regulatory network that coordinates wheat grain yield and grain protein content

Wheat is an important cereal crop used to produce diverse and popular food worldwide because of its high grain yield (GY) and grain protein content (GPC). However, GY and GPC are usually negatively correlated. We previously reported that favorable alleles of the wheat domestication gene Q can synchronously increase GY and GPC, but the underlying mechanisms remain largely unknown. In this study, we investigated the regulatory network involving Q associated with GY and GPC in young grains through DNA affinity purification sequencing and transcriptome sequencing analyses, electrophoretic mobility shift and dual-luciferase assays, and transgenic approaches. Three Q-binding motifs, namely TTAAGG, AAACA[A/T]A, and GTAC[T/G]A, were identified. Notably, genes related to photosynthesis or carbon and nitrogen metabolism were enriched and regulated by Q. Moreover, Q was revealed to bind directly to its own gene and the glutamine synthetase gene TaGSr-4D to increase expression, thereby influencing nitrogen assimilation during the grain filling stage and increasing GPC. Considered together, our study findings provide molecular evidence of the positive regulatory effects of Q on wheat GY and GPC.

CRF12 specifically regulates the flowering time of Arabidopsis thaliana under non-inductive conditions

The flowering time of Arabidopsis thaliana, a model plant, is significantly accelerated when exposed to long-day (LD) conditions, as it is a typical LD plant. Consequently, the investigation of the flowering regulatory network in A. thaliana under LD conditions has garnered considerable attention in the study of flowering signals, resulting in a significant breakthrough. While many LD plants, including A. thaliana, exhibit delayed flowering under non-inductive short-day (SD) conditions, they are still capable of flowering. Nevertheless, research on the regulation of flowering induction in LD plants under non-inductive SD conditions has been limited. This study demonstrated the involvement of CYTOKININ RESPONSE FACTORS 12 (CRF12) in the regulation of flowering in A. thaliana under non-inductive conditions. Analysis of the expression patterns revealed that the activation of CRF12 expression and protein stability occurred exclusively in non-inductive environments. Molecular and genetic analyses revealed that under a non-inductive photoperiod of 12 h of light and 12 h of darkness, CRF12, CONSTANS (CO), and TARGET OF EAT 1/2 (TOE1/2) engage in competitive interactions to regulate flowering time, while in a SD photoperiod of 8 h of light and 16 h of darkness, CRF12 modulates flowering time by inhibiting the activity of TOE1/2.

Molecular regulation and domestication of parthenocarpy in cucumber

Parthenocarpy is a pivotal trait that enhances the yield and quality of fruit crops by enabling the development of seedless fruits. Here we unveil a molecular framework for the regulation and domestication of parthenocarpy in cucumber (Cucumis sativus L.). We previously discovered a natural non-parthenocarpic mutant and demonstrated that the AP2-like transcription factor NON-PARTHENOCARPIC FRUIT 1 (NPF1) is a central regulator of parthenocarpy through activating YUC4 expression and promoting auxin biosynthesis in ovules. A Phe-to-Ser substitution at amino acid residue 7 results in a stable form of NPF1 that is localized in the nucleus. An A-to-G polymorphism (SNP-383) within an NPF1-binding site in the YUC4 promoter significantly enhances the activation of NPF1 towards YUC4, leading to an increased rate of parthenocarpy. Additionally, NPF1 influences bitterness by reducing cucurbitacin C biosynthesis through the suppression of Bt expression. Our results suggest a two-step evolutionary model for parthenocarpy and fruit bitterness during cucumber domestication.

Functional Studies on the LiAG1 Gene of Lilium 'Ice Pink Queen' in Flower Development

Lily (Lilium Asiatica Hybrida) is a globally known perennial herbaceous bulbous flower, popular for its large, colourful flowers and high economic and ornamental value. However, pollen generation is a severe issue that reduces the cosmetic value of lilies. In this study, the MADS transcription factor LiAG1 was isolated and identified from the Lilium Asiatica Hybrida 'Ice Pink Queen', a male-sterile variety obtained through several years of hybridisation in our laboratory. qRT-PCR revealed that LiAG1 expression was greater in lily anthers, especially during the half-opening stage. The transient expression in tobacco demonstrated that LiAG1 was located in the nucleus. In the 'Ice Pink Queen' lily, suppression of LiAG1 using TRV-VIGS (tobacco-rattle-virus-mediated virus-induced gene silencing) resulted in the disappearance of most of the tapetum layer and the absence of the microsporangia. Overexpression of LiAG1 in transgenic Arabidopsis and tobacco resulted in narrower and more involute leaves, plant dwarfing, earlier blooming, and better pollen viability. Overall, our results suggested that LiAG1 might play an important role in flower development, especially anther development, of Lilium Asiatica Hybrida 'Ice Pink Queen'.

Identification and characterization of two APETALA2 homolog genes in lotus (Nelumbo nucifera) involved in sepal and petal development

BACKGROUND

Lotus (Nelumbo nucifera) is a significant aquatic ornamental genus widely utilized in horticulture for its decorative, culinary, medicinal, and other practical uses. It presents a variety of flower shapes, including few-petalled, semi-double-petalled, double-petalled and thousand-petalled flowers, making it an ideal candidate for studying the flower development of aquatic plants. However, the molecular mechanism of floral development in lotus remains elusive.

RESULTS

In this study, two APETALA2 (AP2) homologues, NnAP2a and NnAP2b, were identified in lotus. Interestingly, both NnAP2a and NnAP2b proteins contained two conserved AP2 domains and were verified to be located primarily in the nucleus. Both NnAP2a and NnAP2b showed high expression levels in the floral buds and petals. Ectopic expression of NnAP2a and NnAP2b in Arabidopsis led to an increase in the number of petals and sepals compared to the wild type (WT). Meanwhile, each of the two NnAP2 genes was able to rescue the sepal and petal defective phenotype of the ap2-6 mutant in Arabidopsis. Furthermore, protein-protein interaction assays indicated that NnAP2s could form a protein complex with other proteins involved in floral organ development, such as AP3, PISTILLATA (PI), and SEPALLATA3 (SEP3).

CONCLUSIONS

These results suggest that NnAP2s could influence sepal and petal development in N. nucifera. Our findings not only provide some insights into molecular mechanism underlying sepal and petal development and formation of lotus, but also might help its breeding in improving flower morphology.

RICE LONG GRAIN 3 delays dark-induced senescence by downregulating abscisic acid signaling and upregulating reactive oxygen species scavenging activity

Leaf senescence is a complex developmental process influenced by abscisic acid (ABA) and reactive oxygen species (ROS), both of which increase during senescence. Understanding the regulatory mechanisms of leaf senescence can provide insights into enhancing crop yield and stress tolerance. In this study, we aimed to elucidate the role and mechanisms of rice (Oryza sativa) LONG GRAIN 3 (OsLG3), an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factor, in orchestrating dark-induced leaf senescence. The transcript levels of OsLG3 gradually increased during dark-induced and natural senescence. Transgenic plants overexpressing OsLG3 exhibited delayed senescence, whereas CRISPR/Cas9-mediated oslg3 mutants exhibited accelerated leaf senescence. OsLG3 overexpression suppressed senescence-induced ABA signaling by downregulating OsABF4 (an ABA-signaling-related gene) and reduced ROS accumulation by enhancing catalase activity through upregulation of OsCATC. In vivo and in vitro binding assays demonstrated that OsLG3 downregulated OsABF4 and upregulated OsCATC by binding directly to their promoter regions. These results demonstrate the critical role of OsLG3 in fine-tuning leaf senescence progression by suppressing ABA-mediated signaling while simultaneously activating ROS-scavenging mechanisms. These findings suggest that OsLG3 could be targeted to enhance crop resilience and longevity.

The miR172/TOE3 module regulates resistance to tobacco mosaic virus in tobacco

The outcome of certain plant-virus interaction is symptom recovery, which is accompanied with the emergence of asymptomatic tissues in which the virus accumulation decreased dramatically. This phenomenon shows the potential to reveal critical molecular factors for controlling viral disease. MicroRNAs act as master regulators in plant growth, development, and immunity. However, the mechanism by which miRNA participates in regulating symptom recovery remains largely unknown. Here, we reported that miR172 was scavenged in the recovered tissue of tobacco mosaic virus (TMV)-infected Nicotiana tabacum plants. Overexpression of miR172 promoted TMV infection, whereas silencing of miR172 inhibited TMV infection. Then, TARGET OF EAT3 (TOE3), an APETALA2 transcription factor, was identified as a downstream target of miR172. Overexpression of NtTOE3 significantly improved plant resistance to TMV infection, while knockout of NtTOE3 facilitated virus infection. Furthermore, transcriptome analysis indicated that TOE3 promoted the expression of defense-related genes, such as KL1 and MLP43. Overexpression of these genes conferred resistance of plant against TMV infection. Importantly, results of dual-luciferase assay, chromatin immunoprecipitation-quantitative PCR, and electrophoretic mobility shift assay proved that TOE3 activated the transcription of KL1 and MLP43 by binding their promoters. Moreover, overexpression of rTOE3 (the miR172-resistant form of TOE3) significantly reduced TMV accumulation compared to the overexpression of TOE3 (the normal form of TOE3) in miR172 overexpressing Nicotiana benthamiana plants. Taken together, our study reveals the pivotal role of miR172/TOE3 module in regulating plant immunity and in the establishment of recovery in virus-infected tobacco plants, elucidating a regulatory mechanism integrating plant growth, development, and immune response.

APETALA2-like Floral Homeotic Protein Up-Regulating FaesAP1_2 Gene Involved in Floral Development in Long-Homostyle Common Buckwheat

In the rosid species Arabidopsis thaliana, the AP2-type AP2 transcription factor (TF) is required for specifying the sepals and petals identities and confers a major A-function to antagonize the C-function in the outer floral whorls. In the asterid species Petunia, the AP2-type ROB TFs are required for perianth and pistil development, as well as repressing the B-function together with TOE-type TF BEN. In Long-homostyle (LH) Fagopyrum esculentum, VIGS-silencing showed that FaesAP2 is mainly involved in controlling filament and style length, but FaesTOE is mainly involved in regulating filament length and pollen grain development. Both FaesAP2 (AP2-type) and FaesTOE (TOE-type) are redundantly involved in style and/or filament length determination instead of perianth development. However, neither FaesAP2 nor FaesTOE could directly repress the B and/or C class genes in common buckwheat. Moreover, the FaesAP1_2 silenced flower showed tepal numbers, and filament length decreased obviously. Interestingly, yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) further suggested that FaesTOE directly up-regulates FaesAP1_2 to be involved in filament length determination in LH common buckwheat. Moreover, the knockdown of FaesTOE expression could result in expression down-regulation of the directly target FaesAP1_2 in the FaesTOE-silenced LH plants. Our findings uncover a stamen development pathway in common buckwheat and offer deeper insight into the functional evolution of AP2 orthologs in the early-diverging core eudicots.

A transcriptional cascade mediated by two APETALA2 family members orchestrates carotenoid biosynthesis in tomato

Carotenoids are important nutrients for human health that must be obtained from plants since they cannot be biosynthesized by the human body. Dissecting the regulatory mechanism of carotenoid metabolism in plants represents the first step toward manipulating carotenoid contents in plants by molecular design breeding. In this study, we determined that SlAP2c, an APETALA2 (AP2) family member, acts as a transcriptional repressor to regulate carotenoid biosynthesis in tomato (Solanum lycopersicum). Knockout of SlAP2c in both the "MicroTom" and "Ailsa Craig" backgrounds resulted in greater lycopene accumulation, whereas overexpression of this gene led to orange-ripe fruit with significantly lower lycopene contents than the wild type. We established that SlAP2c represses the expression of genes involved in lycopene biosynthesis by directly binding to the cis-elements in their promoters. Moreover, SlAP2c relies on its EAR motif to recruit the co-repressors TOPLESS (TPL)2/4 and forms a complex with histone deacetylase (had)1/3, thereby reducing the histone acetylation levels of lycopene biosynthesis genes. Furthermore, SlAP2a, a homolog of SlAP2c, acts upstream of SlAP2c and alleviates the SlAP2c-induced repression of lycopene biosynthesis genes by inhibiting SlAP2c transcription during fruit ripening. Therefore, we identified a transcriptional cascade mediated by AP2 family members that regulates lycopene biosynthesis during fruit ripening in tomato, laying the foundation for the manipulation of carotenoid metabolism in plants.

The APETALA2-MYBL2 module represses proanthocyanidin biosynthesis by affecting formation of the MBW complex in seeds of Arabidopsis thaliana

Proanthocyanidins (PAs) are the second most abundant plant phenolic natural products. PA biosynthesis is regulated by the well-documented MYB/bHLH/WD40 (MBW) complex, but how this complex itself is regulated remains ill defined. Here, in situ hybridization and β-glucuronidase staining show that APETALA2 (AP2), a well-defined regulator of flower and seed development, is strongly expressed in the seed coat endothelium, where PAs accumulate. AP2 negatively regulates PA content and expression levels of key PA pathway genes. AP2 activates MYBL2 transcription and interacts with MYBL2, a key suppressor of the PA pathway. AP2 exerts its function by directly binding to the AT-rich motifs near the promoter region of MYBL2. Molecular and biochemical analyses revealed that AP2 forms AP2-MYBL2-TT8/EGL3 complexes, disrupting the MBW complex and thereby repressing expression of ANR, TT12, TT19, and AHA10. Genetic analyses revealed that AP2 functions upstream of MYBL2, TT2, and TT8 in PA regulation. Our work reveals a new role of AP2 as a key regulator of PA biosynthesis in Arabidopsis. Overall, this study sheds new light on the comprehensive regulation network of PA biosynthesis as well as the dual regulatory roles of AP2 in seed development and accumulation of major secondary metabolites in Arabidopsis.

Time-Course Transcriptomic Analysis Reveals Molecular Insights into the Inflorescence and Flower Development of Cardiocrinum giganteum

Cardiocrinum giganteum is an endemic species of east Asia which is famous for its showy inflorescence and medicinal bulbs. Its inflorescence is a determinate raceme and the flowers bloom synchronously. Morphological observation and time-course transcriptomic analysis were combined to study the process of inflorescence and flower development of C. giganteum. The results show that the autonomic pathway, GA pathway, and the vernalization pathway are involved in the flower formation pathway of C. giganteum. A varied ABCDE flowering model was deduced from the main development process. Moreover, it was found that the flowers in different parts of the raceme in C. giganteum gradually synchronized during development, which is highly important for both evolution and ecology. The results obtained in this work improve our understanding of the process and mechanism of inflorescence and flower development and could be useful for the flowering period regulation and breeding of C. giganteum.

Characterization of Two AGAMOUS-like Genes and Their Promoters from the Cymbidium faberi (Orchidaceae)

Arabidopsis AGAMOUS (AG) play roles in determining stamens' and carpels' identities, floral meristem determinacy, and repression of the A-function. Gynostemium fused by stamens and carpels is a characteristic reproductive structure in orchid flowers, which shows a considerable difference from the reproductive organs of eudicots and other monocot species. The molecular basis of orchid gynostemium development remains largely unknown. Here, we report the identification and functional characterization of two AG-like genes, CyfaAG1 and CyfaAG2, and their promoters from C. faberi. Both CyfaAG1 and CyfaAG2 are highly expressed in the anther cap, gynostemium, and ovary. Ectopic expression of CyfaAG1 and CyfaAG2 promotes early flowering of wild-type Arabidopsis. Moreover, ectopic expression of CyfaAG1 completely rescues floral defects in the Arabidopsis ag-1 mutant, while ectopic expression of CyfaAG2 only completes filament and carpel development. Our findings suggest that CyfaAG1 acts as an evolutionarily conserved C-function gene in determining reproductive organ identity and mediating floral meristem determinacy. CyfaAG2 redundantly mediates the C-function in floral meristem determinacy and gynostemium development. Our results provided more details to understand how the C-class function has been partitioned in orchids, and the roles of two AG orthologs in regulating gynostemium development in C. faberi.

Transcription factor induction of vascular blood stem cell niches in vivo

The hematopoietic niche is a supportive microenvironment composed of distinct cell types, including specialized vascular endothelial cells that directly interact with hematopoietic stem and progenitor cells (HSPCs). The molecular factors that specify niche endothelial cells and orchestrate HSPC homeostasis remain largely unknown. Using multi-dimensional gene expression and chromatin accessibility analyses in zebrafish, we define a conserved gene expression signature and cis-regulatory landscape that are unique to sinusoidal endothelial cells in the HSPC niche. Using enhancer mutagenesis and transcription factor overexpression, we elucidate a transcriptional code that involves members of the Ets, Sox, and nuclear hormone receptor families and is sufficient to induce ectopic niche endothelial cells that associate with mesenchymal stromal cells and support the recruitment, maintenance, and division of HSPCs in vivo. These studies set forth an approach for generating synthetic HSPC niches, in vitro or in vivo, and for effective therapies to modulate the endogenous niche.

Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses

AP2/ERF (APETALA2/Ethylene Response Factor) is a family of transcription factors that play essential roles in regulating gene expression in response to various environmental stimuli, including biotic and abiotic stresses, hormone signaling, and developmental processes. Pisum sativum (L.), commonly known as garden pea, is a winter crop sensitive to high temperatures and can also be affected by extreme cold and drought conditions. This study performed a genome-wide analysis of AP2/ERF genes and identified 153 AP2/ERF genes in P. sativum. Based on the conserved AP2/ERF domain and sequence homology, they were classified into AP2 (APETALA2), ERF (Ethylene Response Factor), DREB (Dehydration responsive element-binding), RAV (Related to Abscisic Acid Insensitive 3/ Viviparous 1) and Soloist subfamily. The DREB and ERF subfamily were further divided into groups A1-6 and B1-B6. Tandem and segmental duplication events were more frequent in the ERF subfamily, which can have important implications for their evolution and functional diversification. Under cold stress, the expression of DREB1A was highly induced in leaves, whereas DREB1B was suppressed. Similarly, the DREB2A, DREB2C, DREB2E, and DREB2F were induced in leaves under drought stress. The putative target genes of AP2/ERF transcription factors are highly diversified, suggesting that they play essential roles in various physiological responses in plants, including responses to biotic and abiotic stresses as well as developmental processes. Thus, this study of AP2/ERF genes and their functions provides valuable insight into how P. sativum responds to different environmental conditions, including cold and drought stresses.

Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching

Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.

Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize

Apetala2/ethylene response factor (AP2/ERF) is one of the largest families of transcription factors, regulating growth, development, and stress response in plants. Several studies have been conducted to clarify their roles in Arabidopsis and rice. However, less research has been carried out on maize. In this review, we systematically identified the AP2/ERFs in the maize genome and summarized the research progress related to AP2/ERF genes. The potential roles were predicted from rice homologs based on phylogenetic and collinear analysis. The putative regulatory interactions mediated by maize AP2/ERFs were discovered according to integrated data sources, implying that they involved complex networks in biological activities. This will facilitate the functional assignment of AP2/ERFs and their applications in breeding strategy.

An NKX-COUP-TFII morphogenetic code directs mucosal endothelial addressin expression

Immunoglobulin family and carbohydrate vascular addressins encoded by Madcam1 and St6gal1 control lymphocyte homing into intestinal tissues, regulating immunity and inflammation. The addressins are developmentally programmed to decorate endothelial cells lining gut post-capillary and high endothelial venules (HEV), providing a prototypical example of organ- and segment-specific endothelial specialization. We identify conserved NKX-COUP-TFII composite elements (NCCE) in regulatory regions of Madcam1 and St6gal1 that bind intestinal homeodomain protein NKX2-3 cooperatively with venous nuclear receptor COUP-TFII to activate transcription. The Madcam1 element also integrates repressive signals from arterial/capillary Notch effectors. Pan-endothelial COUP-TFII overexpression induces ectopic addressin expression in NKX2-3+ capillaries, while NKX2-3 deficiency abrogates expression by HEV. Phylogenetically conserved NCCE are enriched in genes involved in neuron migration and morphogenesis of the heart, kidney, pancreas and other organs. Our results define an NKX-COUP-TFII morphogenetic code that targets expression of mucosal vascular addressins.

The APETALA2a/DWARF/BRASSINAZOLE-RESISTANT 1 module contributes to carotenoid synthesis in tomato fruits

Ethylene (ET) signaling plays a critical role in the ripening of climacteric fruits such as tomato. Brassinosteroids (BRs) were found to promote the ripening of both climacteric and non-climacteric fruits. However, the mechanism of interaction between ET and BRs during fruit ripening is unclear. Here, we found that BR synthesis and signaling increased after the onset of fruit ripening. Overexpression of the BR synthesis gene DWARF (DWF) promotedfruit softening, lycopene synthesis and ET production, whereas defect of DWF inhibited them. BRASSINAZOLE RESISTANT 1 (BZR1) as a key component of BR signaling, enhanced fruit lycopene content by directly activating the transcription of PSY1 gene. Interestingly, the increases in BR synthesis and BZR1 protein levels were dependent on ET signaling. Knocking out the ET-induced APETALA2a (AP2a) suppressed the expression of DWF and BR accumulation. Molecular assays demonstrated that AP2a was a positive regulator of DWF expression. Furthermore, 28-homobrassinolide, a bioactive BR, partially compensated the defects of lycopene accumulation and expression of PSY1 in ap2a mutant fruits. The results demonstrated that AP2a mediated ET signaling to regulate BR synthesis and signaling. BRs played critical roles in lycopene synthesis after onset of fruit ripening.

FaesAP3_1 Regulates the FaesELF3 Gene Involved in Filament-Length Determination of Long-Homostyle Fagopyrum esculentum

The identification downstream genes of floral organ identity regulators are critical to revealing the molecular mechanisms underlying floral morphogenesis. However, a general regulatory pathway between floral organ identity genes and their downstream targets is still unclear because of the lack of studies in nonmodel species. Here, we screened a direct downstream target gene, FaesELF3, of a stamen identity transcription factor, FaesAP3_1, in long-homostyle (LH) Fagopyrum esculentum moench by using yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) assays. Furthermore, FaesAP3_1-silenced LH plants that produced flowers with part stamens or anthers homeotically converted into a tepaloid structure, and FaesELF3-silenced plants that had flowers with part stamens consisting of a short filament and empty anther (male sterile anther). All these suggested that transcription factor (TF) FaesAP3_1 directly activates FaesELF3 in order to regulate filament elongation and pollen grain development in LH buckwheat. Our data also suggested that other stamen development pathways independent of FaesAP3_1 remain in F. esculentum.

A banana transcriptional repressor MaAP2a participates in fruit starch degradation during postharvest ripening

Fruit postharvest ripening is a crucial course for many fruits with significant conversion of biosubstance, which forms an intricate regulatory network. Ethylene facilitates the ripening process in banana with a remarkable change of fruit starch, but the mechanism adjusting the expression of starch degradation-related enzyme genes is incompletely discovered. Here, we describe a banana APETALA2 transcription factor (MaAP2a) identified as a transcriptional repressor with its powerful transcriptional inhibitory activity. The transcriptional level of MaAP2a gradually decreased with the transition of banana fruit ripening, suggesting a passive role of MaAP2a in banana fruit ripening. Moreover, MaAP2a is a classic nucleoprotein and encompasses transcriptional repressor domain (EAR, LxLxLx). More specifically, protein-DNA interaction assays found that MaAP2a repressed the expression of 15 starch degradation-related genes comprising MaGWD1, MaPWD1, MaSEX4, MaLSF1, MaBAM1-MaBAM3, MaAMY2B/2C/3A/3C, MaMEX1/2, and MapGlcT2-1/2-2 via binding to the GCC-box or AT-rich motif of their promoters. Overall, these results reveal an original MaAP2a-mediated negative regulatory network involved in banana postharvest starch breakdown, which advances our cognition on banana fruit ripening and offers additional reference values for banana varietal improvement.

The AP2/ERF transcription factor LATE FLOWERING SEMI-DWARF suppresses long-day-dependent repression of flowering

The vegetative-to-reproductive transition requires the complex, coordinated activities of many transcriptional regulators. Rice (Oryza sativa), a facultative short-day (SD) plant, flowers early under SD (≤10 h light/day) and late under long-day (LD; ≥14 h light/day) conditions. Here, we demonstrate that rice LATE FLOWERING SEMI-DWARF (LFS) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factor that promotes flowering under non-inductive LD conditions. LFS showed diurnal expression peaking at dawn, and transcript levels increased gradually until heading. Mutation of LFS delayed flowering under LD but not SD conditions. Expression of the LD-specific floral repressor gene LEAFY COTYLEDON2 AND FUSCA3-LIKE 1 (OsLFL1) was upregulated in lfs knockout mutants, and LFS bound directly to the GCC-rich motif in the OsLFL1 promoter, repressing OsLFL1 expression. This suggests that increased LFS activity during vegetative growth gradually attenuates OsLFL1 activity. Subsequent increases in Early heading date 1, Heading date 3a, and RICE FLOWERING LOCUS T 1 expression result in flowering under non-inductive LD conditions. LFS did not affect the expression of other OsLFL1 regulators, including OsMADS50, OsMADS56, VERNALIZATION INSENSITIVE3-LIKE 2, and GERMINATION DEFECTIVE 1, or interact with them. Our results demonstrate the novel roles of LFS in inducing flowering under natural LD conditions.

Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae)

Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.

Characterization of PISTILLATA-like Genes and Their Promoters from the Distyly Fagopyrum esculentum

Arabidopsis PISTILLATA (PI) encodes B-class MADS-box transcription factor (TF), and works together with APETALA3 (AP3) to specify petal and stamen identity. However, a small-scale gene duplication event of PI ortholog was observed in common buckwheat and resulted in FaesPI_1 and FaesPI_2. FaesPI_1 and FaesPI_2 were expressed only in the stamen of dimorphic flower (thrum and pin) of Fagopyrum esculentum. Moreover, intense beta-glucuronidase (GUS) staining was found in the entire stamen (filament and anther) in pFaesPI_1::GUS transgenic Arabidopsis, while GUS was expressed only in the filament of pFaesPI_2::GUS transgenic Arabidopsis. In addition, phenotype complementation analysis suggested that pFaesPI_1::FaesPI_1/pFaesPI_2::FaesPI_2 transgenic pi-1 Arabidopsis showed similar a flower structure with stamen-like organs or filament-like organs in the third whorl. This suggested that FaesPI_2 only specified filament development, but FaesPI_1 specified stamen development. Meanwhile, FaesPI_1 and FaesPI_2 were shown to function redundantly in regulating filament development, and both genes work together to require a proper stamen identity. The data also provide a clue to understanding the roles of PI-like genes involved in floral organ development during the early evolution of core eudicots and also suggested that FaesPI_1 and FaesPI_2 hold the potential application in bioengineering to develop a common buckwheat male sterile line.

The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato

Soil salinity and drought limit sweet potato yield. Scavenging of reactive oxygen species (ROS) by peroxidases (PRXs) is essential during plant stress responses, but how PRX expression is regulated under abiotic stress is not well understood. Here, we report that the B-box (BBX) family transcription factor IbBBX24 activates the expression of the class III peroxidase gene IbPRX17 by binding to its promoter. Overexpression of IbBBX24 and IbPRX17 significantly improved the tolerance of sweet potato to salt and drought stresses, whereas reducing IbBBX24 expression increased their susceptibility. Under abiotic stress, IbBBX24- and IbPRX17-overexpression lines showed higher peroxidase activity and lower H₂ O₂ accumulation compared with the wild-type. RNA sequencing analysis revealed that IbBBX24 modulates the expression of genes encoding ROS scavenging enzymes, including PRXs. Moreover, interaction between IbBBX24 and the APETALA2 (AP2) protein IbTOE3 enhances the ability of IbBBX24 to activate IbPRX17 transcription. Overexpression of IbTOE3 improved the tolerance of tobacco plants to salt and drought stresses by scavenging ROS. Together, our findings elucidate the mechanism underlying the IbBBX24-IbTOE3-IbPRX17 module in response to abiotic stress in sweet potato and identify candidate genes for developing elite crop varieties with enhanced abiotic stress tolerance.

Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

The Evolution of euAPETALA2 Genes in Vascular Plants: From Plesiomorphic Roles in Sporangia to Acquired Functions in Ovules and Fruits

The field of evolutionary developmental biology can help address how morphological novelties evolve, a key question in evolutionary biology. In Arabidopsis thaliana, APETALA2 (AP2) plays a role in the development of key plant innovations including seeds, flowers, and fruits. AP2 belongs to the AP2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR family which has members in all viridiplantae, making it one of the oldest and most diverse gene lineages. One key subclade, present across vascular plants is the euAPETALA2 (euAP2) clade, whose founding member is AP2. We reconstructed the evolution of the euAP2 gene lineage in vascular plants to better understand its impact on the morphological evolution of plants, identifying seven major duplication events. We also performed spatiotemporal expression analyses of euAP2/TOE3 genes focusing on less explored vascular plant lineages, including ferns, gymnosperms, early diverging angiosperms and early diverging eudicots. Altogether, our data suggest that euAP2 genes originally contributed to spore and sporangium development, and were subsequently recruited to ovule, fruit and floral organ development. Finally, euAP2 protein sequences are highly conserved; therefore, changes in the role of euAP2 homologs during development are most likely due to changes in regulatory regions.

Plant Transcription Factors Involved in Drought and Associated Stresses

Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.

APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley

Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.

Root system architecture, physiological analysis and dynamic transcriptomics unravel the drought-responsive traits in rice genotypes

Drought is the major abiotic factors that limit crop productivity worldwide. To withstand stress conditions, plants alter numerous mechanisms for adaption and tolerance. Therefore, in the present study, 106 rice varieties were screened for drought tolerance phenotype via exposing different concentrations of polyethylene glycol 6000 (PEG) in the hydroponic nutrient medium at the time interval of 1, 3, and 7 days to evaluate the changes in their root system architecture. Further, based on root phenotype obtained after PEG-induced drought, two contrasting varieties drought-tolerant Heena and -sensitive Kiran were selected to study transcriptional and physiological alterations at the same stress durations. Physiological parameters (photosynthesis rate, stomatal conductance, transpiration), and non-enzymatic antioxidants (carotenoids, anthocyanins, total phenol content) production indicated better performance of Heena than Kiran. Comparatively higher accumulation of carotenoid and anthocyanin content and the increased photosynthetic rate was also observed in Heena. Root morphology (length, numbers of root hairs, seminal roots and adventitious roots) and anatomical data (lignin deposition, xylem area) enable tolerant variety Heena to better maintain membrane integrity and relative water content, which also contribute to comparatively higher biomass accumulation in Heena under drought. In transcriptome profiling, significant drought stress-associated differentially expressed genes (DEGs) were identified in both the varieties. A total of 1033 and 936 uniquely upregulated DEGs were found in Heena and Kiran respectively. The significant modulation of DEGs that were mainly associated with phytohormone signaling, stress-responsive genes (LEA, DREB), transcription factors (TFs) (AP2/ERF, MYB, WRKY, bHLH), and genes involved in photosynthesis and antioxidative mechanisms indicate better adaptive nature of Heena in stress tolerance. Additionally, the QTL-mapping analysis showed a very high number of DEGs associated with drought stress at AQHP069 QTL in Heena in comparison to Kiran which further distinguishes the drought-responsive traits at the chromosomal level in both the contrasting varieties. Overall, results support the higher capability of Heena over Kiran variety to induce numerous genes along with the development of better root architecture to endure drought stress.

Parallel evolution of apetalous lineages within the buttercup family (Ranunculaceae): outward expansion of AGAMOUS1, rather than disruption of APETALA3-3

Complete loss of petals, or becoming apetalous, has occurred independently in many flowering plant lineages. However, the mechanisms underlying the parallel evolution of naturally occurring apetalous lineages remain largely unclear. Here, by sampling representatives of all nine apetalous genera/tribes of the family Ranunculaceae and conducting detailed morphological, expression, molecular evolutionary and functional studies, we investigate the mechanisms underlying parallel petal losses. We found that while non-expression/downregulation of the petal identity gene APETALA3-3 (AP3-3) is tightly associated with complete petal losses, disruptions of the AP3-3 orthologs were unlikely to be the real causes for the parallel evolution of apetalous lineages. We also found that, compared with their close petalous relatives, naturally occurring apetalous taxa usually bear slightly larger numbers of stamens, whereas the number of sepals remains largely unchanged, suggestive of petal-to-stamen rather than petal-to-sepal transformations. In addition, in the recently originated apetalous genus Enemion, the petal-to-stamen transformations have likely been caused by the mutations that led to the elevation and outward expansion of the expression of the C-function gene, AGAMOUS1 (AG1). Our results not only provide a general picture of parallel petal losses within the Ranunculaceae but also help understand the mechanisms underlying the independent originations of other apetalous lineages.

Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica)

Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing. In this context, twenty-six genes distributed among eleven chromosomes in Indica rice encoding AP2 transcription-factor subfamily were identified and their diverse haplotypes were studied. Phylogenetic analysis of OsAP2 TF family-members grouped them into three clades indicating conservation of clades among cereals. Segmental duplications were observed to be principal route of evolution, supporting the higher positive selection-pressure, which were estimated to be originated about 10.57 to 56.72 million years ago (MYA). Conserved domain analysis and intron-exon distribution pattern of identified OsAP2s revealed their exclusive distribution among the specific clades of the phylogenetic tree. Moreover, the members of osa-miR172 family were also identified potentially targeting four OsAP2 genes. The real-time quantitative expression profiling of OsAP2s under heat stress conditions in contrasting indica rice genotypes revealed the differential expression pattern of OsAP2s (6 genes up-regulated and 4 genes down-regulated) in stress- and genotype-dependent manner. These findings unveiled the evolutionary pathways of AP2-TF in rice, and can help the functional characterization under developmental and stress responses.

Genome-wide AP2/ERF gene family analysis reveals the classification, structure, expression profiles and potential function in orchardgrass (Dactylis glomerata)

The AP2/ERF transcription factor (TF) family is of great importance in developmental regulation and responses to stress and pathogenic stimuli. Orchardgrass (Dactylis glomerata), a perennial cold-season forage of high quality in the world's temperate zones, contributes to grazing land through mixed sowing with alfalfa (Medicago sativa) and white clover (Trifolium repens). However, little is known about AP2/ERF TFs in orchardgrass. In this study, 193 AP2/ERF genes were classified into five subfamilies and 13 subgroups through phylogenetic analysis. Chromosome structure analysis showed that AP2/ERF family genes in orchardgrass were distributed on seven chromosomes and specific conservative sequences were found in each subgroup. Exon-intron structure and motifs in the same subgroup were almost identical, and the unique motifs contributed to the classification and functional annotation of DgERFs. Expression analysis showed tissue-specific expression of DgERFs in roots and flowers, with most DgERFs widely expressed in roots. The expression levels of each subgroup (subgroups Vc, VIIa, VIIIb, IXa, and XIa) were high at the before-heading and heading stages (BH_DON and H_DON). In addition, 12 DgERFs in various tissues and five DgERFs associated with abiotic stresses were selected for qRT-PCR analysis showed that four dehydration-responsive element binding (DREB) genes and one ERF subfamily gene in orchardgrass were regulated with PEG, heat and salt stresses. DgERF056 belonged to ERF subfamily was involved in the processes of flowering and development stage. This study systematic explored the DgERFs at the genome level for the first time, which lays a foundation for a better understanding of AP2/ERF gene function in Dactylis glomerata and other types of forage.

Genome-Wide Identification and Characterization of APETALA2/Ethylene-Responsive Element Binding Factor Superfamily Genes in Soybean Seed Development

Glycine max is one of the most important grain and oil crops, and improvement of seed yield is one of the major objectives in soybean breeding. The AP2/ERF superfamily members are involved in regulating flower and seed development in many species, and therefore play key roles in seed yield. However, it is still unknown that how many AP2/ERF members were presented in the G. max genome and whether these AP2/ERF family members function in flower and seed development in G. max. Here, we identified 380 AP2/ERF superfamily genes in the G. max genome. Phylogenetic analysis showed that 323 members were grouped into the ERF family, and 49 into the AP2 family. Among the AP2 family, 14 members of the euAP2 lineage showed high identity with their orthologs, and eight member of the ANT lineage were expressed highly in the seeds. Furthermore, seven of them (GmAP2-1 to GmAP2-7) were successfully cloned and over-expressed in Arabidopsis thaliana. The transgenic Arabidopsis plants over-expressing these GmAP2 genes flowered earlier relative to the wild type control. The seed length and width, and seed area of these over-expression lines were increased compared with the wild type, and seed weight of over-expression lines of GmAP2-1, GmAP2-4, GmAP2-5, and GmAP2-6 were greater than those of the wild type. Furthermore, the seed number per silique of the over-expression lines for GmAP2 genes were not affected except GmAP2-5. Collectively, GmAP2-1, GmAP2-4, and GmAP2-6 played important roles in regulating seed weight by affecting seed length, width and area, and further controlling seed yield.

Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development

EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.

Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice

BACKGROUND

Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is particularly severely affected. The present study was performed to identify the molecular nature and function of the SUI4 gene during internode elongation.

RESULTS

Our previous study showed that the SUI4 gene was mapped to a 1.1-Mb interval on chromosome 7 (Ji et al. 2014). In order to isolate the gene responsible for the sui4 phenotype, genomic DNA resequencing of sui4 mutants and wild-type plants and reciprocal transformation of wild-type and mutant alleles of the putative SUI4 gene was performed. The data revealed that the causative mutation of sui4 was a T to A nucleotide substitution at the microRNA172 binding site of Os07g0235800, and that SUI4 is a new allele of the previously reported gene SUPERNUMERARY BRACT (SNB), which affects flower structure. In order to understand the effect of this mutation on expression of the SUI4/SNB gene, SUI4/SNB native promoter-fuzed GUS transgenics were examined, along with qRT-PCR analysis at various developmental stages. In sui4 mutants, the SUI4/SNB gene was upregulated in the leaves, culms, and panicles, especially when internodes were elongated. In culms, SUI4/SNB was expressed in the nodes and the lower parts of elongating internodes. In order to further explore the molecular nature of SUI4/SNB during internode elongation, RNA-seq and qRT-PCR analysis were performed with RNAs from the culms of sui4 mutants and wild-type plants in the booting stage. The data showed that in sui4 mutants, genes deactivating bioactive gibberellins and cytokinin were upregulated while genes related to cell expansion and cell wall synthesis were downregulated.

CONCLUSION

In summary, this paper shows that interaction between SUI4/SNB and microRNA172 could determine internode elongation during the reproductive stage in rice plants. Due to a mutation at the microRNA172 binding site in sui4 mutants, the expression of SUI4/SNB was enhanced, which lowered the activities of cell expansion and cell wall synthesis and consequently resulted in shortened internodes.

APETALA2 control of barley internode elongation

Many plants dramatically elongate their stems during flowering, yet how this response is coordinated with the reproductive phase is unclear. We demonstrate that microRNA (miRNA) control of APETALA2 (AP2) is required for rapid, complete elongation of stem internodes in barley, especially of the final ‘peduncle’ internode directly underneath the inflorescence. Disrupted miR172 targeting of AP2 in the Zeo1.b barley mutant caused lower mitotic activity, delayed growth dynamics and premature lignification in the peduncle leading to fewer and shorter cells. Stage- and tissue-specific comparative transcriptomics between Zeo1.b and its parent cultivar showed reduced expression of proliferation-associated genes, ectopic expression of maturation-related genes and persistent, elevated expression of genes associated with jasmonate and stress responses. We further show that applying methyl jasmonate (MeJA) phenocopied the stem elongation of Zeo1.b, and that Zeo1.b itself was hypersensitive to inhibition by MeJA but less responsive to promotion by gibberellin. Taken together, we propose that miR172-mediated restriction of AP2 may modulate the jasmonate pathway to facilitate gibberellin-promoted stem growth during flowering.

Summary: Regulation of reproductive stem elongation in barley by APETALA2 suggests a pivotal role for phase change repression of JA-associated responses to promote internode growth.

Ectopic expression of the Aechmea fasciata APETALA2 gene AfAP2-2 reduces seed size and delays flowering in Arabidopsis

The Bromeliaceae family, which is distributed pantropically, is one of the most morphologically diverse families. Except for the edible pineapple (Ananas comosus), the vast majority of bromeliads cultivated worldwide are appreciated mainly for their ornamental value. As subtropical and tropical flowering plants, these bromeliads, among with Aechmea fasciata, have significant economic importance. However, the molecular mechanism of flowering in bromeliads remains unrevealed. In this study, an APETALA2 (AP2) homologue, AfAP2-2, which belongs to the AP2/ethylene response element binding protein (AP2/EREBP) transcription factor superfamily, was identified in A. fasciata. AfAP2-2 contains two conserved AP2 domains and is a nuclear-localized transactivator. The expression level of AfAP2-2 was predominantly higher in vegetative organs of the reproductive phase than in those of the vegetative phase. Ectopic expression of AfAP2-2 in Arabidopsis specifically delayed flowering in short-day (SD) conditions. Furthermore, the size and weight of seeds of AfAP2-2-overexpressing Arabidopsis plants were significantly reduced compared to those of the wild type (WT). Our findings suggest that AfAP2-2 might be a negative regulator of flowering and seed size and weight. These results may help facilitate the molecular breeding of bromeliads.

Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs

MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors. Among these, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors (AP2/ERFs) have emerged as key regulators of various stress responses, in which they also respond to hormones with improved plant survival during stress conditions. Apart from participation in specific stresses, AP2/ERFs are involved in a wide range of stress tolerance, enabling them to form an interconnected stress regulatory network. Additionally, many AP2/ERFs respond to the plant hormones abscisic acid (ABA) and ethylene (ET) to help activate ABA and ET dependent and independent stress-responsive genes. While some AP2/ERFs are implicated in growth and developmental processes mediated by gibberellins (GAs), cytokinins (CTK), and brassinosteroids (BRs). The involvement of AP2/ERFs in hormone signaling adds the complexity of stress regulatory network. In this review, we summarize recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis. In addition, we leverage publically available Arabidopsis gene networks and transcriptome data to investigate AP2/ERF regulatory networks, providing context and important clues about the roles of diverse AP2/ERFs in controlling hormone and stress responses.

Genome-wide identification of the AP2/ERF transcription factor family in pepper (Capsicum annuum L.)

The AP2/ERF family is one of the largest transcription factor families in the plant kingdom. AP2/ERF genes contributing to various processes including plant growth, development, and response to various stresses have been identified. In this study, 175 putative AP2/ERF genes were identified in the latest pepper genome database and classified into AP2, RAV, ERF, and Soloist subfamilies. Their chromosomal localization, gene structure, conserved motif, cis-acting elements within the promoter region, and subcellular locations were analyzed. Transient expression of CaAP2/ERF proteins in tobacco revealed that CaAP2/ERF064, CaAP2/ERF109, and CaAP2/ERF127 were located in the nucleus, while CaAP2/ERF171 was located in the nucleus and cytoplasm. Most of the CaAP2/ERF genes contained cis-elements within their promoter regions that responded to various stresses (HSE, LTR, MBS, Box-W1/W-box, and TC-rich repeats) and phytohormones (ABRE, CGTCA-motif, and TCA-element). Furthermore, RNA-seq analysis revealed that CaAP2/ERF genes showed differential expression profiles in various tissues as well as under biotic stresses. Moreover, qRT-PCR analysis of eight selected CaAP2/ERF genes also showed differential expression patterns in response to infection with Phytophthora capsici (HX-9) and in response to phytohormones (SA, MeJA, and ETH). This study will provide basic insights for further studies of the CaAP2/ERF genes involved in the interaction between pepper and P. capsici.

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

A transcription factor network responsive to high CO2/hypoxia is involved in deastringency in persimmon fruit

Plant responses to anaerobic environments are regulated by ethylene-response factors (ERFs) in both vegetative and productive organs, but the roles of other transcription factors (TFs) in hypoxia responses are poorly understood. In this study, eight TFs (DkbHLH1, DkMYB9/10/11, DkRH2-1, DkGT3-1, DkAN1-1, DkHSF1) were shown to be strongly up-regulated by an artificial high-CO2 atmosphere (1% O2 and 95% CO2). Dual-luciferase assays indicated that some TFs were activators of previously characterized DkERFs, including DkMYB10 for the DkERF9 promoter, DkERF18/19 and DkMYB6 for the DkERF19 promoter, and DkERF21/22 for the DkERF10 promoter. Yeast one-hybrid and cis-element mutagenesis confirmed these physical interactions with one exception. The potential roles of these TFs in persimmon fruit deastringency were analysed by investigating their transient over-expression (TOX) in persimmon fruit discs, which indicated that DkMYB6TOX, DkMYB10TOX, DkERF18TOX, and DkERF19TOX were all effective in causing insolubilization of tannins, concomitantly with the up-regulation of the corresponding genes. These results indicated that multiple TFs of different classes are responsive to high-CO2/hypoxia in fruit tissues, and that a TF-TF regulatory cascade is involved in the hypoxia responses involving the Group VII DkERF10, and DkERFs and DkMYBs.

An APETALA2 Homolog, RcAP2, Regulates the Number of Rose Petals Derived From Stamens and Response to Temperature Fluctuations

Rosa chinensis, which is a famous traditional flower in China, is a major ornamental plant worldwide. Long-term cultivation and breeding have resulted in considerable changes in the number of rose petals, while most wild Rosaceae plants have only one whorl consisting of five petals. The petals of double flowers reportedly originate from stamens, but the underlying molecular mechanism has not been fully characterized. In this study, we observed that the number of petals of R. chinensis 'Old Blush' flowers increased and decreased in response to low- and high-temperature treatments, respectively, similar to previous reports. We characterized these variations in further detail and found that the number of stamens exhibited the opposite trend. We cloned an APETALA2 homolog, RcAP2. A detailed analysis of gene structure and promoter cis-acting elements as well as RcAP2 temporospatial expression patterns and responses to temperature changes suggested that RcAP2 expression may be related to the number of petals from stamen origin. The overexpression of RcAP2 in Arabidopsis thaliana transgenic plants may induce the transformation of stamens to petals, thereby increasing the number of petals. Moreover, silencing RcAP2 in 'Old Blush' plants decreased the number of petals. Our results may be useful for clarifying the temperature-responsive mechanism involved in petaloid stamen production, which may be relevant for the breeding of new rose varieties with enhanced flower traits.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum

Variegated surface antigen expression is key to chronic infection and pathogenesis of the human malaria parasite Plasmodium falciparum. This protozoan parasite expresses distinct surface molecules that are encoded by clonally variant gene families such as var, rif and stevor. The molecular mechanisms governing activation of individual members remain ill-defined. To investigate the molecular events of the initial transcriptional activation process we focused on a member of the apicomplexan ApiAP2 transcription factor family predicted to bind to the 5′ upstream regions of the var gene family, AP2-exp (PF3D7_1466400). Viable AP2-exp mutant parasites rely on expressing no less than a short truncated protein including the N-terminal AP2 DNA-binding domain. RNA-seq analysis in mutant parasites revealed transcriptional changes in a subset of exported proteins encoded by clonally variant gene families. Upregulation of RIFINs and STEVORs was validated at the protein levels. In addition, morphological alterations were observed on the surface of the host cells infected by the mutants. This work points to a complex regulatory network of clonally variant gene families in which transcription of a subset of members is regulated by the same transcription factor. In addition, we highlight the importance of the non-DNA binding AP2 domain in functional gene regulation.