加载中

    AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in . Xie Zhouli,Nolan Trevor M,Jiang Hao,Yin Yanhai Frontiers in plant science 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 . In addition, we leverage publically available 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. 10.3389/fpls.2019.00228
    Advances in AP2/ERF super-family transcription factors in plant. Feng Kai,Hou Xi-Lin,Xing Guo-Ming,Liu Jie-Xia,Duan Ao-Qi,Xu Zhi-Sheng,Li Meng-Yao,Zhuang Jing,Xiong Ai-Sheng Critical reviews in biotechnology In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding. 10.1080/07388551.2020.1768509
    Evolution of the APETALA2 Gene Lineage in Seed Plants. Zumajo-Cardona Cecilia,Pabón-Mora Natalia Molecular biology and evolution Gene duplication is a fundamental source of functional evolutionary change and has been associated with organismal diversification and the acquisition of novel features. The APETALA2/ETHYLENE RESPONSIVE ELEMENT-BINDING FACTOR (AP2/ERF) genes are exclusive to vascular plants and have been classified into the AP2-like and ERF-like clades. The AP2-like clade includes the AINTEGUMENTA (ANT) and the euAPETALA2 (euAP2) genes, both regulated by miR172 Arabidopsis has two paralogs in the euAP2 clade, namely APETALA2 (AP2) and TARGET OF EAT3 (TOE3) that control flowering time, meristem determinacy, sepal and petal identity and fruit development. euAP2 genes are likely functionally divergent outside Brassicaceae, as they control fruit development in tomato, and regulate inflorescence meristematic activity in maize. We studied the evolution and expression patterns of euAP2/TOE3 genes to assess large scale and local duplications and evaluate protein motifs likely related with functional changes across seed plants. We sampled euAP2/TOE3 genes from vascular plants and have found three major duplications and a few taxon-specific duplications. Here, we report conserved and new motifs across euAP2/TOE3 proteins and conclude that proteins predating the Brassicaceae duplication are more similar to AP2 than TOE3. Expression data show a shift from restricted expression in leaves, carpels, and fruits in non-core eudicots and asterids to a broader expression of euAP2 genes in leaves, all floral organs and fruits in rosids. Altogether, our data show a functional trend where the canonical A-function (sepal and petal identity) is exclusive to Brassicaceae and it is likely not maintained outside of rosids. 10.1093/molbev/msw059
    CYTOKININ RESPONSE FACTORs Gating Environmental Signals and Hormones. Kim Jungmook Trends in plant science CYTOKININ RESPONSE FACTORs (CRFs) encode transcription factors belonging to a small family within the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) superfamily. Recent studies have revealed the biological functions of some arabidopsis CRFs, providing insight into the role of these plant transcription factors in integrating environmental and hormonal signals for plant adaptation. 10.1016/j.tplants.2016.10.004
    The evolution of euAPETALA2 genes in vascular plants: from plesiomorphic roles in sporangia to acquired functions in ovules and fruits. Zumajo-Cardona Cecilia,Pabón-Mora Natalia,Ambrose Barbara A Molecular biology and evolution The field of evolutionary developmental biology (evo-devo) 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 APETALA2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR (AP2/ERF) 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 spatio-temporal 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 during development are most likely due to changes in regulatory regions. 10.1093/molbev/msab027
    ERF Gene Clusters: Working Together to Regulate Metabolism. Shoji Tsubasa,Yuan Ling Trends in plant science Plants produce structurally diverse specialized metabolites, including bioactive alkaloids and terpenoids, in response to biotic and abiotic environmental stresses. The APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family of transcription factors (TFs) play key roles in regulating biosynthesis of specialized metabolites. Increasing genomic and functional evidence shows that a subset of the ERF genes occurs in clusters on the chromosomes. These jasmonate-responsive ERF TF gene clusters control the biosynthesis of many important metabolites, from natural products, such as nicotine and steroidal glycoalkaloids (SGAs), to pharmaceuticals, such as artemisinin, vinblastine, and vincristine. Here, we review the function, regulation, and evolution of ERF clusters and highlight recent advances in understanding the distinct roles of clustered ERF genes and their possible application in metabolic engineering. 10.1016/j.tplants.2020.07.015
    Tobacco drought stress responses reveal new targets for Solanaceae crop improvement. Rabara Roel C,Tripathi Prateek,Reese R Neil,Rushton Deena L,Alexander Danny,Timko Michael P,Shen Qingxi J,Rushton Paul J BMC genomics BACKGROUND:The Solanaceae are an economically important family of plants that include tobacco (Nicotiana tabacum L.), tomato, and potato. Drought is a major cause of crop losses. RESULTS:We have identified major changes in physiology, metabolites, mRNA levels, and promoter activities during the tobacco response to drought. We have classified these as potential components of core responses that may be common to many plant species or responses that may be family/species-specific features of the drought stress response in tobacco or the Solanaceae. In tobacco the largest increase in any metabolite was a striking 70-fold increase in 4-hydroxy-2-oxoglutaric acid (KHG) in roots that appears to be tobacco/Solanaceae specific. KHG is poorly characterized in plants but is broken down to pyruvate and glyoxylate after the E. coli SOS response to facilitate the resumption of respiration. A similar process in tobacco would represent a mechanism to restart respiration upon water availability after drought. At the mRNA level, transcription factor gene induction by drought also showed both core and species/family specific responses. Many Group IX Subgroup 3 AP2/ERF transcription factors in tobacco appear to play roles in nicotine biosynthesis as a response to herbivory, whereas their counterparts in legume species appear to play roles in drought responses. We observed apparent Solanaceae-specific drought induction of several Group IId WRKY genes. One of these, NtWRKY69, showed ABA-independent drought stress-inducible promoter activity that moved into the leaf through the vascular tissue and then eventually into the surrounding leaf cells. CONCLUSIONS:We propose components of a core metabolic response to drought stress in plants and also show that some major responses to drought stress at the metabolome and transcriptome levels are family specific. We therefore propose that the observed family-specific changes in metabolism are regulated, at least in part, by family-specific changes in transcription factor activity. We also present a list of potential targets for the improvement of Solanaceae drought responses. 10.1186/s12864-015-1575-4
    The chrysanthemum leaf and root transcript profiling in response to salinity stress. Cheng Peilei,Gao Jiaojiao,Feng Yitong,Zhang Zixin,Liu Yanan,Fang Weimin,Chen Sumei,Chen Fadi,Jiang Jiafu Gene RNA-Seq was applied to capture the transcriptome of the leaf and root of non-treated and salinity-treated chrysanthemum cv. 'Jinba' plants. A total of 206,868 unigenes of mean length 849 nt and of N50 length 1363 nt was identified; of these about 64% (> 132,000) could be functionally assigned. Depending on the severity of the salinity stress, differential transcription was observed for genes encoding proteins involved in osmotic adjustment, in ion transport, in reactive oxygen species scavenging and in the regulation of abscisic acid (ABA) signaling. The root stress response was dominated by the up-regulation of genes involved in ion transport, while that of the leaf reflected the plant's effort to make osmotic adjustments and to regulate Ca transport. An array of known transcription factors (WRKY, AP2/ERF, MYB, bHLH and NAC) were differentially transcribed. 10.1016/j.gene.2018.06.075
    Genome-wide identification and analysis of AP2/ERF transcription factors related to camptothecin biosynthesis in Camptotheca acuminata. Hu Ya-Ting,Xu Zhi-Chao,Tian Ya,Gao Ran-Ran,Ji Ai-Jia,Pu Xiang-Dong,Wang Yu,Liu Xia,Song Jing-Yuan Chinese journal of natural medicines Camptotheca acuminata produces camptothecin (CPT), a monoterpene indole alkaloid (MIA) that is widely used in the treatment of lung, colorectal, cervical, and ovarian cancers. Its biosynthesis pathway has attracted significant attention, but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors (TFs) remains unclear. In this study, a systematic analysis of the AP2/ERF TFs family in C. acuminata was performed, including phylogeny, gene structure, conserved motifs, and gene expression profiles in different tissues and organs (immature bark, cotyledons, young flower, immature fruit, mature fruit, mature leaf, roots, upper stem, and lower stem) of C. acuminata. A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (26 genes), DREB (61 genes), ERF (92 genes), RAV (18 genes), and Soloist (one gene). The combination of gene expression patterns in different C. acuminata tissues and organs, the phylogenetic tree, the co-expression analysis with biosynthetic genes, and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C. acuminata might be involved in CPT synthesis regulation, which exhibit relatively high expression levels in the upper stem or immature bark. Among these, four genes (CacAP2/ERF123, CacAP2/ERF125, CacAP2/ERF126, and CacAP2/ERF127) belong to the ERF-B2 subgroup; two genes (CacAP2/ERF149 and CacAP2/ERF152) belong to the ERF-B3 subgroup; and two more genes (CacAP2/ERF095 and CacAP2/ERF096) belong to the DREB-A6 subgroup. These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C. acuminata. 10.1016/S1875-5364(20)30070-4
    [Research progress on effect of AP2/ERF transcription factors in regulating secondary metabolite biosynthesis]. Liang Xiao,Rui-Bing Chen,Yu W U,Lei Zhang Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica AP2/ERF transcription factor is a kind of transcription factors widely existing in plants, and contains at least a conserved AP2/ERF domain composed of about 60-70 amino acids. AP2/ERF transcription factors are widely involved in a variety of physiological processes in plants, including plant development, fruit ripening, flower development and other plant development processes, as well as such stress response processes as damage, pathogen defense, high-salt condition and drought. In recent years, secondary metabolic engineering that takes transcription factors as genetic manipulation targets has developed rapidly in improving the content of active ingredients and the quality of medicinal plants. This paper reviews the recent progress in the regulation of secondary metabolites biosynthesis with AP2/ERF transcription factors, and provides theoretical basis for the exploration of efficient regulatory targets, the regulation of secondary metabolites in medicinal plants, the targeted improvement of the content of active ingredients in traditional Chinese medicine, and the sustainable supply of high-quality traditional Chinese medicines. 10.19540/j.cnki.cjcmm.20200804.602
    Dehydration responsive element binding transcription factors and their applications for the engineering of stress tolerance. Agarwal Pradeep K,Gupta Kapil,Lopato Sergiy,Agarwal Parinita Journal of experimental botany Dehydration responsive element binding (DREB) factors or CRT element binding factors (CBFs) are members of the AP2/ERF family, which comprises a large number of stress-responsive regulatory genes. This review traverses almost two decades of research, from the discovery of DREB/CBF factors to their optimization for application in plant biotechnology. In this review, we describe (i) the discovery, classification, structure, and evolution of DREB genes and proteins; (ii) induction of DREB genes by abiotic stresses and involvement of their products in stress responses; (iii) protein structure and DNA binding selectivity of different groups of DREB proteins; (iv) post-transcriptional and post-translational mechanisms of DREB transcription factor (TF) regulation; and (v) physical and/or functional interaction of DREB TFs with other proteins during plant stress responses. We also discuss existing issues in applications of DREB TFs for engineering of enhanced stress tolerance and improved performance under stress of transgenic crop plants. 10.1093/jxb/erx118
    Transcriptional factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants. Wang Meizhen,Qiu Xiaoxiao,Pan Xian,Li Caili Current pharmaceutical biotechnology BACKGROUND:Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceutically-valuable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. OBJECTIVE:Here we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. RESULTS AND CONCLUSION:Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically-valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds. 10.2174/1389201021666200622121809
    Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes. Zhuang Jing,Xiong Ai-Sheng,Peng Ri-He,Gao Feng,Zhu Bo,Zhang Jian,Fu Xiao-Yan,Jin Xiao-Feng,Chen Jian-Min,Zhang Zhen,Qiao Yu-Shan,Yao Quan-Hong Molecular biology reports Chinese cabbage (Brassica rapa subsp. pekinensis) is among the most important vegetables and is widely cultivated in world. Genes in the AP2/ERF family encode transcriptional regulators that serve a variety of functions in the plants. Expressed sequence tags (ESTs) are created by partially sequencing randomly isolated gene transcripts and have proved valuable in molecular biology. Starting from the database with 142 947 ESTs of B. rapa, 62 putative AP2/ERF family genes were identified by in silico cloning using the conserved AP2/ERF domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies (DREB, ERF, AP2 and RAV). Using large-scale available EST information as a source of expression data for digital expression profiling, differentially detected genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were detected in all tissues: most were detected only in some tissues but not in others. The maximum detected was that of BraERF-B2-5, and it was recorded from seed tissue. 10.1007/s11033-009-9763-4
    Discovery and expression profile analysis of AP2/ERF family genes from Triticum aestivum. Zhuang Jing,Chen Jian-Min,Yao Quan-Hong,Xiong Fei,Sun Chao-Cai,Zhou Xi-Rong,Zhang Jian,Xiong Ai-Sheng Molecular biology reports Throughout its development, common wheat, Triticum aestivum responds to different kinds of adverse abiotic and biotic stress by expressing specific genes that allow it to adapt to these stresses. In this process, genes in the AP2/ERF family encode transcriptional regulators involved in diverse developmental and physiological processes play critical roles. Here, we established an extensive picture of the AP2/ERF family genes in wheat. From 960, 174 ESTs of T. aestivum, 117 putative AP2/ERF family genes were identified by in silico analysis based on the presence of the conserved AP2/ERF domain amino acid sequence of Arabidopsis thaliana. Based on the model species A. thaliana, the AP2/ERF TFs from T. aestivum were classified into five subfamilies with the following number of members: DREB (57), ERF (47), AP2 (9), RAV (3) and Soloist (1). Using the available EST information as a source of expression data, the putative AP2/ERF family genes from T. aestivum were detected in nine kinds of tissues. Transcripts of the genes were shown to be most abundant in leaves, followed by roots and seeds, and the least abundant in stem. Most of the T. aestivum AP2/ERF family genes showed some tissue specificity. 10.1007/s11033-010-0162-7
    Global Transcriptome Analyses Reveal Differentially Expressed Genes of Six Organs and Putative Genes Involved in (Iso)flavonoid Biosynthesis in . Tian Mei,Zhang Xiang,Zhu Yan,Xie Guoyong,Qin Minjian Frontiers in plant science (L.) DC., a perennial herb of the family Iridaceae, is rich in a variety of (iso)flavonoids with significant organ-specific distribution and has a swollen rhizome that is widely used in East Asia as a traditional medicine. In the present study, comprehensive transcriptomes of six organs (root, rhizome, aerial stem, leaf, flower, and young fruit) of were obtained by high-throughput RNA-sequencing and assembly. A total of 423,661 unigenes (mean length = 618 bp, median length = 391 bp) were assembled and annotated in seven databases: Non-redundant protein sequences, Nucleotide sequences, Swiss-Prot, Protein family database, euKaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). A total of 4995 transcription factors were identified, including 408 MYB, 182 bHLH, 277 AP2/ERF, and 228 WRKY genes. A total of 129 cytochrome P450 unigenes belonging to 10 divergent clans were identified and grouped into clades in a phylogenetic tree that showed their inferred evolutionary relationship. Differentially expressed unigenes among the six organs were subjected to GO and KEGG enrichment analysis to profile the functions of each organ. Unigenes associated with (iso)flavonoid biosynthesis were then profiled by expression level analysis. Additionally, the complete coding sequences of six predicted enzymes essential to the (iso)flavonoid pathway were obtained, based on the annotated unigenes. This work reveals clear differences in expression patterns of genes among the six organs and will provide a sound platform to understand the (iso)flavonoid pathways in 10.3389/fpls.2018.01160
    Overexpression of a Phosphate Starvation Response AP2/ERF Gene From Physic Nut in Arabidopsis Alters Root Morphological Traits and Phosphate Starvation-Induced Anthocyanin Accumulation. Chen Yanbo,Wu Pingzhi,Zhao Qianqian,Tang Yuehui,Chen Yaping,Li Meiru,Jiang Huawu,Wu Guojiang Frontiers in plant science Physic nut ( L.) is highly tolerant of barren environments and a significant biofuel plant. To probe mechanisms of its tolerance mechanisms, we have analyzed genome-wide transcriptional profiles of 8-week-old physic nut seedlings subjected to Pi deficiency (P-) for 2 and 16 days, and Pi-sufficient conditions (P+) controls. We identified several phosphate transporters, purple acid phosphatases, and enzymes of membrane lipid metabolism among the 272 most differentially expressed genes. Genes of the miR399/PHO2 pathway (, miR399, and members of the SPX family) showed alterations in expression. We also found that expression of several transcription factor genes was modulated by phosphate starvation stress in physic nut seedlings, including an AP2/ERF gene (), which was down-regulated in both root and leaf tissues under Pi-deprivation. In -overexpressing Arabidopsis lines both numbers and lengths of first-order lateral roots were dramatically reduced, but numbers of root hairs on the primary root tip were significantly elevated, under both P+ and P- conditions. Furthermore, the transgenic plants accumulated less anthocyanin but had similar Pi contents to wild-type plants under P-deficiency conditions. Expression levels of the tested genes related to anthocyanin biosynthesis and regulation, and genes induced by low phosphate, were significantly lower in shoots of transgenic lines than in wild-type plants under P-deficiency. Our data show that down-regulation of the gene might contribute to the regulation of root system architecture and both biosynthesis and accumulation of anthocyanins in aerial tissues of plants under low Pi conditions. 10.3389/fpls.2018.01186
    Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress. Sharma Rinku,Singh Garima,Bhattacharya Sudeepto,Singh Ashutosh PloS one Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as-'photosynthesis', 'respiratory burst', 'response to hormone', 'signal transduction', 'metabolic process', 'response to water deprivation', which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules. 10.1371/journal.pone.0203266
    Arabidopsis ETHYLENE RESPONSE FACTOR 8 (ERF8) has dual functions in ABA signaling and immunity. Cao Feng Yi,DeFalco Thomas A,Moeder Wolfgang,Li Bo,Gong Yunchen,Liu Xiao-Min,Taniguchi Masatoshi,Lumba Shelley,Toh Shigeo,Shan Libo,Ellis Brian,Desveaux Darrell,Yoshioka Keiko BMC plant biology BACKGROUND:ETHYLENE RESPONSE FACTOR (ERF) 8 is a member of one of the largest transcription factor families in plants, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) superfamily. Members of this superfamily have been implicated in a wide variety of processes such as development and environmental stress responses. RESULTS:In this study we demonstrated that ERF8 is involved in both ABA and immune signaling. ERF8 overexpression induced programmed cell death (PCD) in Arabidopsis and Nicotiana benthamiana. This PCD was salicylic acid (SA)-independent, suggesting that ERF8 acts downstream or independent of SA. ERF8-induced PCD was abolished by mutations within the ERF-associated amphiphilic repression (EAR) motif, indicating ERF8 induces cell death through its transcriptional repression activity. Two immunity-related mitogen-activated protein kinases, MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) and MPK11, were identified as ERF8-interacting proteins and directly phosphorylated ERF8 in vitro. Four putative MPK phosphorylation sites were identified in ERF8, one of which (Ser103) was determined to be the predominantly phosphorylated residue in vitro, while mutation of all four putative phosphorylation sites partially suppressed ERF8-induced cell death in N. benthamiana. Genome-wide transcriptomic analysis and pathogen growth assays confirmed a positive role of ERF8 in mediating immunity, as ERF8 knockdown or overexpression lines conferred compromised or enhanced resistance against the hemibiotrophic bacterial pathogen Pseudomonas syringae, respectively. CONCLUSIONS:Together these data reveal that the ABA-inducible transcriptional repressor ERF8 has dual roles in ABA signaling and pathogen defense, and further highlight the complex influence of ABA on plant-microbe interactions. 10.1186/s12870-018-1402-6
    Arabidopsis Group IIId ERF proteins positively regulate primary cell wall-type CESA genes. Saelim Laddawan,Akiyoshi Nobuhiro,Tan Tian Tian,Ihara Ayumi,Yamaguchi Masatoshi,Hirano Ko,Matsuoka Makoto,Demura Taku,Ohtani Misato Journal of plant research The cell wall determines morphology and the environmental responses of plant cells. The primary cell wall (PCW) is produced during cell division and expansion, determining the cell shape and volume. After cell expansion, specific types of plant cells produce a lignified wall, known as a secondary cell wall (SCW). We functionally analyzed Group IIId Arabidopsis AP2/EREBP genes, namely ERF34, ERF35, ERF38, and ERF39, which are homologs of a rice ERF gene previously proposed to be related to SCW biosynthesis. Expression analysis revealed that these four genes are expressed in regions related to cell division and/or cell differentiation in seedlings (i.e., shoot apical meristems, the primordia of leaves and lateral roots, trichomes, and central cylinder of primary roots) and flowers (i.e., vascular tissues of floral organs and replums and/or valve margins of pistils). Overexpression of ERF genes significantly upregulated PCW-type, but not SCW-type, CESA genes encoding cellulose synthase catalytic subunits in Arabidopsis seedlings. Transient co-expression reporter analysis indicated that ERF35, ERF38, and ERF39 possess transcriptional activator activity, and that ERF34, ERF35, ERF38, and ERF39 upregulated the promoter activity of CESA1, a PCW-type CESA gene, through the DRECRTCOREAT elements, the core cis-acting elements known to be recognized by AP2/ERF proteins. Together, our findings show that Group IIId ERF genes are positive transcriptional regulators of PCW-type CESA genes in Arabidopsis and are possibly involved in modulating cellulose biosynthesis in response to developmental requirements and environmental stimuli. 10.1007/s10265-018-1074-1
    Corrigendum: AP2/ERF Family Transcription Factors ORA59 and RAP2.3 Interact in the Nucleus and Function Together in Ethylene Response. Kim Na Young,Jang Young Jin,Park Ohkmae K Frontiers in plant science [This corrects the article DOI: 10.3389/fpls.2018.01675.]. 10.3389/fpls.2019.00042
    An AP2/ERF gene, IbRAP2-12, from sweetpotato is involved in salt and drought tolerance in transgenic Arabidopsis. Li Yan,Zhang Huan,Zhang Qian,Liu Qingchang,Zhai Hong,Zhao Ning,He Shaozhen Plant science : an international journal of experimental plant biology The manipulation of APETALA2/ethylene responsive factor (AP2/ERF) genes in plants makes great contributions on resistance to abiotic stresses. Here, we cloned an AP2/ERF gene from the salt-tolerant sweetpotato line ND98 and named IbRAP2-12. IbRAP2-12 protein expressed in nuclear revealed by transient expression in tobacco epidermal cells, and IbRAP2-12 exhibited transcriptional activation using heterologous expression assays in yeast. IbRAP2-12 was induced by NaCl (200 mM), 20% polyethylene glycol (PEG) 6000, 100 μM abscisic acid (ABA), 100 μM ethephon and 100 μM methyl jasmonate (MeJA). IbRAP2-12-overexpressing Arabidopsis lines were more tolerant to salt and drought stresses than wild type plants. Transcriptome analysis showed that genes involved in the ABA signalling, JA signalling, proline biosynthesis and reactive oxygen species (ROS) scavenging processes were up-regulated in IbRAP2-12 overexpression lines under salt and drought stresses. In comparing with WT, the contents of ABA, JA and proline were significantly increased, while hydrogen peroxide (HO) and the rate of water loss were significantly reduced in transgenic lines under salt and drought stresses. All these results demonstrated the roles of IbRAP2-12 in enhancing salt and drought tolerance in transgenic Arabidopsis lines. Thus, this IbRAP2-12 gene can be used to increase the tolerance ability during abiotic stresses in plants. 10.1016/j.plantsci.2019.01.009
    The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza. Zhang Yu,Ji Aijia,Xu Zhichao,Luo Hongmei,Song Jingyuan Plant molecular biology KEY MESSAGE:The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering. 10.1007/s11103-019-00845-7
    An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition. Wessels Bernard,Seyfferth Carolin,Escamez Sacha,Vain Thomas,Antos Kamil,Vahala Jorma,Delhomme Nicolas,Kangasjärvi Jaakko,Eder Michaela,Felten Judith,Tuominen Hannele The New phytologist Differentiation of xylem elements involves cell expansion, secondary cell wall (SCW) deposition and programmed cell death. Transitions between these phases require strict spatiotemporal control. The function of Populus ERF139 (Potri.013G101100) in xylem differentiation was characterized in transgenic overexpression and dominant repressor lines of ERF139 in hybrid aspen (Populus tremula × tremuloides). Xylem properties, SCW chemistry and downstream targets were analyzed in both types of transgenic trees using microscopy techniques, Fourier transform-infrared spectroscopy, pyrolysis-GC/MS, wet chemistry methods and RNA sequencing. Opposite phenotypes were observed in the secondary xylem vessel sizes and SCW chemistry in the two different types of transgenic trees, supporting the function of ERF139 in suppressing the radial expansion of vessel elements and stimulating accumulation of guaiacyl-type lignin and possibly also xylan. Comparative transcriptomics identified genes related to SCW biosynthesis (LAC5, LBD15, MYB86) and salt and drought stress-responsive genes (ANAC002, ABA1) as potential direct targets of ERF139. The phenotypes of the transgenic trees and the stem expression profiles of ERF139 potential target genes support the role of ERF139 as a transcriptional regulator of xylem cell expansion and SCW formation, possibly in response to osmotic changes of the cells. 10.1111/nph.15960
    The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Responses in Arabidopsis. Xie Zhouli,Nolan Trevor,Jiang Hao,Tang Buyun,Zhang Mingcai,Li Zhaohu,Yin Yanhai The Plant cell APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors have well-documented functions in stress responses, but their roles in brassinosteroid (BR)-regulated growth and stress responses have not been established. Here, we show that the Arabidopsis () stress-inducible AP2/ERF transcription factor TINY inhibits BR-regulated growth while promoting drought responses. -overexpressing plants have stunted growth, increased sensitivity to BR biosynthesis inhibitors, and compromised BR-responsive gene expression. By contrast, triple mutants have increased BR-regulated growth and BR-responsive gene expression. TINY positively regulates drought responses by activating drought-responsive genes and promoting abscisic acid-mediated stomatal closure. Global gene expression studies revealed that TINY and BRs have opposite effects on plant growth and stress response genes. TINY interacts with and antagonizes BRASSINOSTERIOID INSENSITIVE1-ETHYL METHANESULFONATE SUPRESSOR1 (BES1) in the regulation of these genes. Glycogen synthase kinase 3-like protein kinase BR-INSENSITIVE2 (BIN2), a negative regulator in the BR pathway, phosphorylates and stabilizes TINY, providing a mechanism for BR-mediated downregulation of TINY to prevent activation of stress responses under optimal growth conditions. Taken together, our results demonstrate that BR signaling negatively regulates TINY through BIN2 phosphorylation and TINY positively regulates drought responses, as well as inhibiting BR-mediated growth through TINY-BES1 antagonistic interactions. Our results thus provide insight into the coordination of BR-regulated growth and drought responses. 10.1105/tpc.18.00918
    The Recruitment Model of Metabolic Evolution: Jasmonate-Responsive Transcription Factors and a Conceptual Model for the Evolution of Metabolic Pathways. Shoji Tsubasa Frontiers in plant science Plants produce a vast array of structurally diverse specialized metabolites with various biological activities, including medicinal alkaloids and terpenoids, from relatively simple precursors through a series of enzymatic steps. Massive metabolic flow through these pathways usually depends on the transcriptional coordination of a large set of metabolic, transport, and regulatory genes known as a regulon. The coexpression of genes involved in certain metabolic pathways in a wide range of developmental and environmental contexts has been investigated through transcriptomic analysis, which has been successfully exploited to mine the genes involved in various metabolic processes. Transcription factors are DNA-binding proteins that recognize relatively short sequences known as -regulatory elements residing in the promoter regions of target genes. Transcription factors have positive or negative effects on gene transcription mediated by RNA polymerase II. Evolutionarily conserved transcription factors of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) and basic helix-loop-helix (bHLH) families have been identified as jasmonate (JA)-responsive transcriptional regulators of unrelated specialized pathways in distinct plant lineages. Here, I review the current knowledge and propose a conceptual model for the evolution of metabolic pathways, termed "recruitment model of metabolic evolution." According to this model, structural genes are repeatedly recruited into regulons under the control of conserved transcription factors through the generation of cognate -regulatory elements in the promoters of these genes. This leads to the adjustment of catalytic activities that improve metabolic flow through newly established passages. 10.3389/fpls.2019.00560
    Identification and functional characterization of the (Asteraceae) Clade III Cytokinin Response Factor (CRF). Melton Anthony E,Zwack Paul J,Rashotte Aaron M,Goertzen Leslie R Plant signaling & behavior Cytokinin Response Factor (CRF) genes are a subgroup of AP2/ERF domain-containing transcription factors that are defined by the CRF domain, from which five clades of CRF genes have been identified. Clade III CRFs are strongly induced by cytokinin, as well as other abiotic stress factors, such as oxidative stress. While this appears well studied for the Clade III CRFs in Arabidopsis and tomato, there have been almost no studies done outside of these model systems. This study expands upon that and represents the first CRF research in the Sunflower family, Asteraceae. Fifty Asterid Clade III CRF protein sequences were examined, and novel Clade III CRF C-terminus motifs were identified. Clade III CRF genes of and were assembled from genome-skimming and transcriptomic data. Expression experiments were conducted on to test responsiveness to both cytokinin and oxidative stress. Low levels of basal expression for the were found to be strongly induced in both treatment groups. These are the first experiments to show regulation of a nuclear gene in a species, and these results suggest there is broad conservation in the sequence, form, and regulation of Clade III CRF genes and proteins. 10.1080/15592324.2019.1633886
    Genome-Wide Identification and Expression Profiling of the Gene Family in L. Under Various Abiotic Stresses. Jin Xiaoyu,Yin Xiaofan,Ndayambaza Boniface,Zhang Zhengshe,Min Xueyang,Lin Xiaoshan,Wang Yanrong,Liu Wenxian DNA and cell biology The (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factor represents one of the largest plant-specific transcriptional regulators in plants. plays important roles in the regulation of various developmental processes and acts as a mediator in plant external stress responses. However, the research of the gene family is still limited in alfalfa ( L.), one of the most important forage legume species in the world. In the present study, a total of 159 genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, signal peptide prediction, and expression patterns under salt, drought, and low-temperature stresses of these genes were comprehensively analyzed. The genes family in alfalfa could be classified into 10 groups and predicted to be strongly homologous. Based on the structure and functions relationships, the III and IV subfamilies were more likely to play functions in abiotic stresses and 18 genes were selected for further quantitative real-time PCR validation in different stresses treatment. The results showed that all these genes were upregulated under three stresses except . This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole-genome level, which would provide primary understanding for exploring -mediated tolerance in alfalfa. 10.1089/dna.2019.4881
    Review - Cytokinin Response Factors: Responding to more than cytokinin. Hallmark H Tucker,Rashotte Aaron M Plant science : an international journal of experimental plant biology Cytokinin Response Factors (CRFs) are a family of transcription factors which make up a side branch of the classical cytokinin two-component signaling pathway. CRFs were originally identified and have been primarily studied in Arabidopsis thaliana, although orthologs have be found throughout all land plants. Research into the evolution of CRFs as sub-group members of the larger APETALA2/Ethylene Response Factor (AP2/ERF) family has yielded interesting and useful insights related to the functional roles of CRFs in plants. Recent studies of CRFs suggest that these transcription factors are a lot more than just a group of cytokinin related genes and play important roles in both plant development and environmental stress response. This review focuses on recent advances in understanding the roles of CRFs beyond cytokinin, in reproductive development and abiotic stress response, as well as to other environmental cues. 10.1016/j.plantsci.2019.110251
    Mutually Regulated AP2/ERF Gene Clusters Modulate Biosynthesis of Specialized Metabolites in Plants. Paul Priyanka,Singh Sanjay Kumar,Patra Barunava,Liu Xiaoyu,Pattanaik Sitakanta,Yuan Ling Plant physiology APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) gene clusters regulate the biosynthesis of diverse specialized metabolites, including steroidal glycoalkaloids in tomato () and potato (), nicotine in tobacco (), and pharmaceutically valuable terpenoid indole alkaloids in Madagascar periwinkle (). However, the regulatory relationships between individual AP2/ERF genes within the cluster remain unexplored. We uncovered intracluster regulation of the AP2/ERF regulatory circuit, which consists of , , and ORCA3 and ORCA5 activate by directly binding to a GC-rich motif in the promoter. ORCA5 regulates its own expression through a positive autoregulatory loop and indirectly activates In determining the functional conservation of AP2/ERF clusters in other plant species, we found that GC-rich motifs are present in the promoters of analogous AP2/ERF clusters in tobacco, tomato, and potato. Intracluster regulation is evident within the tobacco () cluster. Moreover, overexpression of in tobacco and of in hairy roots activates nicotine and terpenoid indole alkaloid pathway genes, respectively, suggesting that the AP2/ERFs are functionally equivalent and are likely to be interchangeable. Elucidation of the intracluster and mutual regulation of transcription factor gene clusters advances our understanding of the underlying molecular mechanism governing regulatory gene clusters in plants. 10.1104/pp.19.00772
    Increased Leaf Nicotine Content by Targeting Transcription Factor Gene Expression in Commercial Flue-Cured Tobacco ( L.). Liu Hai,Kotova Tatyana I,Timko Michael P Genes Nicotine, the most abundant pyridine alkaloid in cultivated tobacco ( L.), is a potent inhibitor of insect and animal herbivory and a neurostimulator of human brain function. Nicotine biosynthesis is controlled developmentally and can be induced by abiotic and biotic stressors via a jasmonic acid (JA)-mediated signal transduction mechanism involving members of the APETALA 2/ethylene-responsive factor (AP2/ERF) and basic helix-loop-helix (bHLH) transcription factor (TF) families. AP2/ERF and bHLH TFs work combinatorically to control nicotine biosynthesis and its subsequent accumulation in tobacco leaves. Here, we demonstrate that overexpression of the tobacco NtERF32, NtERF221/ORC1, and NtMYC2a TFs leads to significant increases in nicotine accumulation in T2 transgenic K326 tobacco plants before topping. Up to 9-fold higher nicotine production was achieved in transgenics overexpressing NtERF221/ORC1 under the control of a constitutive GmUBI3 gene promoter compared to wild-type plants. The constitutive 2XCaMV35S promoter and a novel JA-inducible 4XGAG promoter were less effective in driving high-level nicotine formation. Methyljasmonic acid (MeJA) treatment further elevated nicotine production in all transgenic lines. Our results show that targeted manipulation of NtERF221/ORC1 is an effective strategy for elevating leaf nicotine levels in commercial tobacco for use in the preparation of reduced risk tobacco products for smoking replacement therapeutics. 10.3390/genes10110930
    Overexpression of an AP2/ERF family gene, BpERF13, in birch enhances cold tolerance through upregulating CBF genes and mitigating reactive oxygen species. Lv Kaiwen,Li Jiang,Zhao Kai,Chen Su,Nie Jeff,Zhang Wenli,Liu Guifeng,Wei Hairong Plant science : an international journal of experimental plant biology The AP2/ERF (APETALA2/ethylene-responsive factor) family of transcription factors (TF) is involved in regulating biotic and abiotic stress responses in plants. To explore the role of AP2/ERFs in cold tolerance in woody plants, BpERF13 was cloned and characterized in Betula platyphylla (white birch), a species primarily found in Asia in temperate and boreal climates. Based on phylogenetic analysis, BpERF13 is a member of the IXb subfamily of ERFs. Using qRT-PCR, we found that BpERF13 was differentially expressed in different tissues, and its expression could be induced by cold treatment (4 °C). BpERF13 protein, fused with GFP, was exclusively localized to nuclei. To further assess the role of BpERF13 in cold tolerance, BpERF13 overexpression (OE) transgenic lines were generated in B. platyphylla and used for cold stress treatment and biochemical/physiological studies. BpERF13 overexpression lines had significantly increased tolerance to subfreezing treatment and reduced reactive oxygen species. Using a TF-centered yeast one-hybrid (Y1H) experimental system, we showed that BpERF13 could bind to LTRECOREATCOR15 and MYBCORE cis-elements to activate a reporter gene. ChIP-seq and ChIP-PCR experiments further demonstrated that BpERF13 bound to these cis-elements when present in the 5' proximal regions of superoxide dismutase (SOD), peroxidase (POD), and C-repeat-binding factor (CBF) genes. qRT-PCR was employed to examine the expression levels of these genes in response to cold stress; SOD, POD, and CBF genes were significantly upregulated in BpERF13 transgenic lines compared to wild-type plants in response to cold stress. These results indicate that the transcription factor BpERF13 regulates physiological processes underlying cold tolerance in woody plants. 10.1016/j.plantsci.2019.110375