Overexpression of cotton RAV1 gene in Arabidopsis confers transgenic plants high salinity and drought sensitivity

Comprehensive analysis of pepper (Capsicum annuum) RAV genes family and functional identification of CaRAV1 under chilling stress

BACKGROUND

Despite its known significance in plant abiotic stress responses, the role of the RAV gene family in the response of Capsicum annuum to chilling stress remains largely unexplored.

RESULTS

In this study, we identified and characterized six members of the CaRAV gene subfamily in pepper plants through genome-wide analysis. Subsequently, the CaRAV subfamily was classified into four branches based on homology with Arabidopsis thaliana, each exhibiting relatively conserved domains within the branch. We discovered that light response elements accounted for the majority of CaRAVs, whereas low-temperature response elements were specific to the NGA gene subfamily. After pepper plants were subjected to chilling stress, qRT‒PCR analysis revealed that CaRAV1, CaRAV2 and CaNGA1 were significantly induced in response to chilling stress, indicating that CaRAVs play a role in the response to chilling stress. Using virus-induced gene silencing (VIGS) vectors, we targeted key members of the CaRAV gene family. Under normal growth conditions, the MDA content and SOD enzyme activity of the silenced plants were slightly greater than those of the control plants, and the REC activity was significantly greater than that of the control plants. The levels of MDA and electrolyte leakage were greater in the silenced plants after they were exposed to chilling stress, and the POD and CAT enzyme activities were significantly lower than those in the control, which was particularly evident under repeated chilling stress. In addition, the relative expression of CaPOD and CaCAT was greater in V2 plants upon repeated chilling stress, especially CaCAT was significantly greater in V2 plants than in the other two silenced plants, with 3.29 and 1.10 increases within 12 and 24 h. These findings suggest that CaRAV1 and CaNGA1 positively regulate the response to chilling stress.

CONCLUSIONS

Silencing of key members of the CaRAV gene family results in increased susceptibility to chilling damage and reduced antioxidant enzyme activity in plants, particularly under repeated chilling stress. This study provides valuable information for understanding the classification and putative functions of RAV transcription factors in pepper plants.

PbGBF3 enhances salt response in pear by upregulating PbAPL2 and PbSDH1 and reducing ABA-mediated salt sensitivity

Pear is a widely cultivated fruit crop, but its distribution and sustainable production are significantly limited by salt stress. This study used RNA-Seq time-course analysis, WGCNA, and functional enrichment analysis to uncover the molecular mechanisms underlying salt stress tolerance in Pyrus ussuriensis. We identified an ABA-related regulatory module, PbGBF3-PbAPL2-PbSDH1, as crucial in this response. PbGBF3, a bZIP transcription factor, enhances salt tolerance by upregulating PbAPL2 and PbSDH1. Overexpression of PbGBF3 improved salt tolerance in Pyrus communis calli and Arabidopsis, while silencing it reduced tolerance in Pyrus betulifolia. Functional assays showed that PbGBF3 binds to the promoters of PbAPL2 and PbSDH1, increasing their expression. PbAPL2 and PbSDH1, key enzymes in starch synthesis and the sorbitol pathway, respectively, enhance salt tolerance by increasing AGPase activity, soluble sugar content, and SDH activity, improving ROS scavenging and ion balance. Our findings suggest that the PbGBF3-PbAPL2 and PbGBF3-PbSDH1 modules positively regulate salt tolerance by enhancing ABA signaling and reducing ABA-mediated growth inhibition. These insights provide a foundation for developing salt-tolerant pear cultivars.

Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans

BACKGROUND

Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported.

RESULTS

In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells.

CONCLUSIONS

These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.

SmRAV1, an AP2 and B3 Transcription Factor, Positively Regulates Eggplant's Response to Salt Stress

Salt stress is a lethal abiotic stress threatening global food security on a consistent basis. In this study, we identified an AP2 and B3 domain-containing transcription factor (TF) named SmRAV1, and its expression levels were significantly up-regulated by NaCl, abscisic acid (ABA), and hydrogen peroxide (H2O2) treatment. High expression of SmRAV1 was observed in the roots and sepal of mature plants. The transient expression assay in Nicotiana benthamiana leaves revealed that SmRAV1 was localized in the nucleus. Silencing of SmRAV1 via virus-induced gene silencing (VIGS) decreased the tolerance of eggplant to salt stress. Significant down-regulation of salt stress marker genes, including SmGSTU10 and SmNCED1, was observed. Additionally, increased H2O2 content and decreased catalase (CAT) enzyme activity were recorded in the SmRAV1-silenced plants compared to the TRV:00 plants. Our findings elucidate the functions of SmRAV1 and provide opportunities for generating salt-tolerant lines of eggplant.

Reciprocal inhibition of expression between RAV1 and BES1 modulates plant growth and development in Arabidopsis

RAV1 (Related to ABI3/VP1) is a plant-specific B3 and AP2 domain-containing transcription factor that acts as a negative regulator of growth in many plant species. The expression of RAV1 is downregulated by brassinosteroids (BRs); large-scale transcriptome analyses have shown that the expression of RAV1 was previously targeted by BRI1-EMS-SUPPRESOR1 (BES1) and BRASSINAZOLE-RESISTANT1 (BZR1), which are critical transcription factors for the BR-signaling process. Using RAV1-overexpressing transgenic plants, we showed that RAV1 overexpression reduced the BR signaling capacity, resulting in the downregulation of BR biosynthetic genes and BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, is directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa; RAV1 is also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to RAV1 and BES1 because RAV1 exhibited binding activity to the BZR1 promoter but did not repress BZR1 expression. We observed that constitutively activated BR signaling phenotypes in bes1-D were attenuated by the repression of endogenous BES1 expression in transgenic bes1-D plants overexpressing RAV1. RNA-sequencing analysis of RAV1-overexpressing transgenic plants and bes1-D mutant plants revealed differentially expressed genes by RAV1 and BES1 and genes that were oppositely co-regulated by RAV1 and BES1. RAV1 and BES1 regulated different transcriptomes but co-regulated a specific set of genes responsible for the balance between growth and defense. These results suggested that the mutual inhibitory transcriptional activities of RAV1 and BES1 provide fine regulatory mechanisms for plant growth and development.

Comprehensive analysis of cucumber RAV family genes and functional characterization of CsRAV1 in salt and ABA tolerance in cucumber

The RAV (related to ABI3 and VP1) transcription factors are specific and exist in plants, which contain a B3 DNA binding domain and/or an APETALA2 (AP2) DNA binding domain. RAVs have been extensively studied in plants, and more and more evidences show that RAVs are involved in various aspects of plant growth and development, stress resistance and hormone signal transduction. However, the systematic analysis of RAV family in cucumber is rarely reported. In this study, eight CsRAV genes were identified in cucumber genome and we further comprehensively analyzed their protein physicochemical properties, conserved domains, gene structure and phylogenetic relationships. The synteny analysis and gene duplications of CsRAV genes were also analysed. Cis-element analysis revealed that the CsRAVs promoter contained several elements related to plant hormones and abiotic stress. Expression analysis showed that NaCl and ABA could significantly induce CsRAV genes expression. Subcellular localization revealed that all CsRAVs were localized in the nucleus. In addition, 35S:CsRAV1 transgenic Arabidopsis and cucumber seedlings enhanced NaCl and ABA tolerance, revealing CsRAV1 may be an important regulator of abiotic stress response. In conclusion, comprehensive analysis of CsRAVs would provide certain reference for understanding the evolution and function of the CsRAV genes.

Identification of Brachypodium distachyon B3 genes reveals that BdB3-54 regulates primary root growth

B3 is a class of plant-specific transcription factors with important roles in plant development and growth. Here, we identified 69 B3 transcription factors in Brachypodium distachyon that were unevenly distributed across all five chromosomes. The ARF, REM, LAV, and RAV subfamilies were grouped based on sequence characteristics and phylogenetic relationships. The phylogenetically related members in the B3 family shared conserved domains and gene structures. Expression profiles showed that B3 genes were widely expressed in different tissues and varied in response to different abiotic stresses. BdB3-54 protein from the REM subfamily was located in the nucleus by subcellular localization and processed transcriptional activation activity. Overexpression of BdB3-54 in Arabidopsis increased primary root length. Our study provides a basis for further research on the functions of BdB3 genes.

Identification of AP2/ERF transcription factors in Tetrastigma hemsleyanum revealed the specific roles of ERF46 under cold stress

Tetrastigma hemsleyanum (T. hemsleyanum) is a traditional medicinal plant that is widely used in China. Cultivated T. hemsleyanum usually encounters cold stress, limiting its growth and quality at key developmental stages. APETALA2 (AP2)/ethylene-responsive factor (ERF) transcription factors (TFs) comprise one of the largest gene superfamilies in plants and are widely involved in biotic and abiotic stresses. To reveal the roles of AP2/ERF TFs during T. hemsleyanum development, 70 AP2/ERF TFs were identified in T. hemsleyanum. Among them, 18 and 2 TFs were classified into the AP2 and RAV families, respectively. The other 50 TFs belonged to the ERF family and were further divided into the ERF and (dehydration reaction element binding factor) DREB subfamilies. The ERF subfamily contained 46 TFs, while the DREB subfamily contained 4 TFs. Phylogenetic analysis indicated that AP2/ERF TFs could be classified into five groups, in which 10 conserved motifs were confirmed. Several motifs were group- or subgroup-specific, implying that they were significant for the functions of the AP2/ERF TFs of these clades. In addition, 70 AP2/ERF TFs from the five groups were used for an expression pattern analysis under three low-temperature levels, namely, -4, 0, and 4°C. The majority of these AP2/ERF TFs exhibited a positive response to cold stress conditions. Specifically, ThERF5, ThERF31, ThERF46, and ThERF55 demonstrated a more sensitive response to cold stress. Moreover, AP2/ERF TFs exhibited specific expression patterns under cold stress. Transient overexpression and RNA interference indicated that ThERF46 has a specific tolerance to cold stress. These new insights provide the basis for further studies on the roles of AP2/ERF TFs in cold stress tolerance in T. hemsleyanum.

Genome-Wide Analysis of the RAV Gene Family in Wheat and Functional Identification of TaRAV1 in Salt Stress

RAV transcription factors (TFs) are unique to higher plants and contain both B3 and APETALA2 (AP2) DNA binding domains. Although sets of RAV genes have been identified from several species, little is known about this family in wheat. In this study, 26 RAV genes were identified in the wheat genome. These wheat RAV TFs were phylogenetically clustered into three classes based on their amino acid sequences. A TaRAV gene located on chromosome 1D was cloned and named TaRAV1. TaRAV1 was expressed in roots, stems, leaves, and inflorescences, and its expression was up-regulated by heat while down-regulated by salt, ABA, and GA. Subcellular localization analysis revealed that the TaRAV1 protein was localized in the nucleus. The TaRAV1 protein showed DNA binding activity in the EMSA assay and transcriptional activation activity in yeast cells. Overexpressing TaRAV1 enhanced the salt tolerance of Arabidopsis and upregulated the expression of SOS genes and other stress response genes. Collectively, our data suggest that TaRAV1 functions as a transcription factor and is involved in the salt stress response by regulating gene expression in the SOS pathway.

NtRAV4 negatively regulates drought tolerance in Nicotiana tabacum by enhancing antioxidant capacity and defence system

KEY MESSAGE

NtRAV4 is a nucleus-localised protein and no self-activation effect. ntrav4 mutants maintain the steady state of the ROS system under drought stress by enhancing antioxidant capacity and defence system. The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) family plays an important role in plant responses to environmental stresses. In this study, we identified a novel NtRAV4 TF, a member of RAV subfamily among AP2/ERF gene family, which have AP2 and B3 domain in its N- and C-terminus, respectively. Subcellular localisation and self-activation activity analysis revealed that NtRAV4 localised in the nucleus and had no self-activation effect. The overexpression and gene editing vectors of NtRAV4 were constructed by homologous recombination and CRISPR/Cas9 gene editing methods, and transformed into tobacco by agrobacterium-mediated method. ntrav4 led to the appearance of termination codon in advance and lacked the unique B3 domain of RAV subfamily protein. Further analysis displayed that knockout of the NtRAV4 in tobacco increased drought tolerance with high relative water content, accompanied by reduced stomatal aperture, density, and stomatal opening ratio compared to overexpression lines and WT. Moreover, ntrav4 knockout plants also exhibited increased osmotic tolerance with low malondialdehyde (MDA) and ion leakage (EL), less accumulation of O2•- and H2O2, and high enzymatic antioxidant (SOD, POD, CAT) activities, non-enzymatic antioxidant (AsA-GSH cycle) contents and hormone (IAA, ABA, GA3, and ZR) levels under drought stress. Furthermore, ntrav4 mutants in tobacco improved the expression levels of ROS-related proline synthesis and stress-responsive genes under osmotic stress. Our results indicate that NtRAV4 negatively regulates plant tolerance to drought stress by reducing water loss and activating the antioxidant system and stress-related gene expression to maintain the steady state of the ROS system.

Functional roles of the birch BpRAV1 transcription factor in salt and osmotic stress response

RAV (Related to ABI3/VP1) transcription factors play vital roles in regulating plant response to abiotic stresses; however, the regulatory mechanisms underlying stress response are still poorly understood for most of the RAVgenes. In this study, a novel gene BpRAV1 was cloned from white birch (Betula platyphylla). BpRAV1 protein is localized in the nucleus and serves as a transcriptional activator. The expression of BpRAV1 was induced by salt and osmotic stress treatments. BpRAV1-overexpression birch seedlings exhibited dramatically less ROS accumulation and reduced cell death in response to salt and osmotic stresses. BpRAV1 can specifically bind to the known RAV1A element. In addition, a novel cis-acting element (termed RBS1) bound by BpRAV1 was identified by transcription factor (TF)- centered Y1H assay. BpRAV1 activated the RAV1A and RBS1 elements to induce the expression of SOD and POD genes, resulting in increased SOD and POD activities to enhance ROS scavenging ability, thus improving salt and osmotic stress tolerance. These results indicate that BpRAV1 is a positive regulator governing abiotic stress response.

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron-exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

MeRAV5 promotes drought stress resistance in cassava by modulating hydrogen peroxide and lignin accumulation

Cassava, an important food and energy crop, is relatively more resistant to drought stress than other crops. However, the molecular mechanism underlying this resistance remains elusive. Herein, we report that silencing a drought stress-responsive transcription factor MeRAV5 significantly reduced drought stress resistance, with higher levels of hydrogen peroxide (H₂ O₂ ) and less lignin during drought stress. Yeast two-hybrid, pull down and bimolecular fluorescence complementation (BiFC) showed that MeRAV5 physically interacted with peroxidase (MePOD) and lignin-related cinnamyl alcohol dehydrogenase 15 (MeCAD15) in vitro and in vivo. MeRAV5 promoted the activities of both MePOD and MeCAD15 to affect H₂ O₂ and endogenous lignin accumulation respectively, which are important in drought stress resistance in cassava. When either MeCAD15 or MeRAV5 was silenced, or both were co-silenced, cassava showed lower lignin content and drought-sensitive phenotype, whereas exogenous lignin alkali treatment increased drought stress resistance and alleviated the drought-sensitive phenotype of these silenced cassava plants. This study documents that the modulation of H₂ O₂ and lignin by MeRAV5 is essential for drought stress resistance in cassava.

Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress

Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress.

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BACKGROUND

The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus).

RESULTS

57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401.

CONCLUSION

This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

Genome-Wide Analysis of RAV Transcription Factors and Functional Characterization of Anthocyanin-Biosynthesis-Related RAV Genes in Pear

Related to ABSCISIC ACID INSENSITIVE3/VIVIPAROUS1 (ABI3/VP1, RAV), transcription factors (TFs) belonging to the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) TF family play critical roles in plant growth, development, and responses to abiotic and biotic stress. In this study, 11 novel RAV TFs were identified in pear (Pyrus bretschneideri Rehd). A phylogenetic analysis revealed that the TFs clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the RAVs in these clades. RAVs in Pyrus and Malus were closely related, and the former showed a collinear relationship. Analysis of their expression patterns in different tissues and at various growth stages and their responses to abiotic and biotic stress suggested that PbRAV6 and PbRAV7 play important roles in drought stress and salt stress, respectively. We investigated the function of RAVs in pear peel coloration using two red pear varieties with different color patterns and applying data from transcriptome analyses. We found that PbRAV6 participates in the regulation of pericarp color. These findings provide insight into a new TF family in pear and a basis for further studies on the response to drought stress and fruit coloration in this commercially important crop.

The floral repressors TEMPRANILLO1 and 2 modulate salt tolerance by regulating hormonal components and photo-protection in Arabidopsis

Members of the plant specific RAV family of transcription factors regulate several developmental and physiological processes. In the model plant Arabidopsis thaliana, the RAV TEMPRANILLO 1 (TEM1) and TEM2 control important phase changes such as the juvenile to adult and the vegetative to reproductive transitions. Besides their known regulatory function in plant development, a transcriptomics analysis of transgenic plants overexpressing TEM1 also revealed overrepresentation of Gene Ontology (GO) categories related to abiotic stress responses. Therefore, to investigate the biological relevance of these TEM-dependent transcriptomic changes and elucidate whether TEMs contribute to the modulation of plant growth in response to salinity, we analyzed the behavior of TEM gain and loss of function mutants subjected to mild and high salt stresses at different development stages. With respect to increasing salinity, TEM overexpressing plants were hypersensitive whereas the tem1 tem2 double mutants were more tolerant. Precisely, tem1 tem2 mutants germinated and flowered faster than the wild-type plants under salt stress conditions. Also, tem1 tem2 plants showed a delay in salt-induced leaf senescence, possibly as a consequence of downregulation of jasmonic acid biosynthesis genes. Besides a shorter life cycle and delayed senescence, tem1 tem2 mutants appeared to be better suited to withstand oxidative stress as they accumulated higher levels of α-tocopherol (an important antioxidant metabolite) and displayed a slower degradation of photosynthetic pigments. Taken together, our studies suggest novel and crucial roles for TEM in adaptive growth as they modulate plant development in response to environmental changes such as increasing soil salinity.

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

Expression of Three Related to ABI3/VP1 Genes in Medicago truncatula Caused Increased Stress Resistance and Branch Increase in Arabidopsis thaliana

Related to ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1(VP1)(RAV) transcription factors, which encode a B3 domain and an APETALA2(AP2) domain, belong to the APETALA2/ethylene-responsive element binding factor(AP2/ERF) or B3 superfamily and play an important role in regulating plant growth and development and responding to abiotic stress. Although there have been many functional studies on RAV, the functional differences between RAVs are not clear. Therefore, in this study, the functional differences of RAVs of Medicago truncatula were analyzed. Based on sequence data from the plant transcription factor database and the M. truncatula genome database, we cloned three RAV genes from M. truncatula, named MtRAV1, MtRAV2, and MtRAV3. The cis-acting elements of these genes promoters were predicted, and the expression patterns of MtRAVs under exogenous conditions (4°C, NaCl, Polyethylene Glycol, Abscisic acid) were analyzed. MtRAVs transgenic Arabidopsis thaliana were obtained and subjected to adversity treatment. Subcellular localization results indicated that MtRAVs were located in the nucleus. A much lower expression level was observed for MtRAV3 than the levels of MtRAV1 and MtRAV2 in M. truncatula for growth in normal conditions, but under 4°C or PEG and NaCl treatment, the expression level of MtRAV3 was significantly increased. Only the MtRAV3 overexpression transgenic plants showed strong cold resistance, but the overexpressed MtRAV1 and MtRAV2 transgenic plants showed no difference from wild type plants. MtRAV transgenic plants exhibited similar response to exogenous mannitol, NaCl, and ABA, and the expression of some adverse-related marker genes were up-regulated, such as COLD REGULATED 414 THYLAKOID MEMBRANE 1 (COR414-TM1), Arabidopsis thaliana drought-induced 21 (AtDI21), and Arabidopsis thaliana phosphatidylinositol-specific phospholipase C (ATPLC). MtRAVs transgenic Arabidopsis thaliana exhibited increasing of branch number. These results indicated that there was some function redundancy during MtRAVs proteins of M. truncatula, and MtRAV3 has increased function compared to the other two genes. The results of this study should provide the foundation for future application of MtRAVs in legumes.

CmRAV1 shows differential expression in two melon (Cucumis melo L.) cultivars and enhances salt tolerance in transgenic Arabidopsis plants

The growth and development of melon (Cucumis melo L.) are severely affected by soil salinization in many areas of the world, but the understanding of the molecular mechanisms underlying salt tolerance in melon remains limited. In this study, a new RAV (related to ABI3/VP1) gene, CmRAV1, was identified in melon. Protein structure homology analysis revealed that CmRAV1 contains an AP2 domain and a B3 domain, and subcellular localization assay revealed that CmRAV1 is localized in the nucleus. The transcript level of CmRAV1 was closely correlated with NaCl treatment, and the expression pattern of CmRAV1 differed between two cultivars (salt-tolerant and salt-sensitive cultivars) under NaCl treatment. In addition, yeasts transformed with CmRAV1 showed notably improved growth on medium containing 200 mM NaCl compared with wild-type ones. The overexpression of CmRAV1 in transgenic Arabidopsis thaliana resulted in enhanced salt tolerance at the seed germination and seedling growth stages. This study demonstrated that the expression of CmRAV1 was associated with saline stress and can potentially be utilized to improve plant salt tolerance.

GhWRKY6 Acts as a Negative Regulator in Both Transgenic Arabidopsis and Cotton During Drought and Salt Stress

Drought and high salinity are key limiting factors for cotton production. Therefore, research is increasingly focused on the underlying stress response mechanisms of cotton. We first identified and cloned a novel gene encoding the 525 amino acids in cotton, namely GhWRKY6. qRT-PCR analysis indicated that GhWRKY6 was induced by NaCl, PEG 6000 and ABA. Analyses of germination rate and root length indicated that overexpression of GhWRKY6 in Arabidopsis resulted in hypersensitivity to ABA, NaCl, and PEG 6000. In contrast, the loss-of-function mutant wrky6 was insensitive and had slightly longer roots than the wild-type did under these treatment conditions. Furthermore, GhWRKY6 overexpression in Arabidopsis modulated salt- and drought-sensitive phenotypes and stomatal aperture by regulating ABA signaling pathways, and reduced plant tolerance to abiotic stress through reactive oxygen species (ROS) enrichment, reduced proline content, and increased electrolytes and malondialdehyde (MDA). The expression levels of a series of ABA-, salt- and drought-related marker genes were altered in overexpression seedlings. Virus-induced gene silencing (VIGS) technology revealed that down-regulation of GhWRKY6 increased salt tolerance in cotton. These results demonstrate that GhWRKY6 is a negative regulator of plant responses to abiotic stress via the ABA signaling pathway.

GmRAV1 regulates regeneration of roots and adventitious buds by the cytokinin signaling pathway in Arabidopsis and soybean

The division and differentiation of cells are the basis of growth and development. Cytokinin plays an active role in cell growth division and differentiation. The Related to ABI3/VP1 (RAV) family comprises transcription factors in plants and all contain both AP2- and B3-like domains. In this study, GmRAV1 (Glycine max), which belongs to the AP2/ERF transcription factor family, was isolated and functionally characterized. Subcellular localization showed that GmRAV1 was localized to the nucleus and quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that GmRAV1 was induced by cytokinin. Furthermore, compared with wild-type plants, plants overexpressing GmRAV1 showed dwarfism and late maturity. In contrast, the mutant of TEMPRANILLO (tem1) and GmRAV-i plants had an opposite phenotype. More interestingly, a root and shoot regeneration experiment indicated that GmRAV1 is one of the most important positive regulators of the cytokinin signaling pathway, which is involved in promoting root and shoot regeneration. In addition, RNA-seq and qRT-PCR results indicated that GmRAV1 is related to the key factors involved in the cytokinin signaling pathway, namely, cytokinin oxidase (GmCKX6 and GmCKX7), purine permease (GmPUP1), cell cyclin-related genes (GmCycA2;4, GmCycD3 and GmCYC1), cyclin-dependent kinase (GmCDKB2), cell division cycle (GmCDC20), E2F transcription factors (GmE2FE) and authentic response regulator (GmARR9). In conclusion, GmRAV1, one of the most important positive regulators involved in promoting root and shoot regeneration, was induced by cytokinin and is related to the key factors of the cytokinin signaling pathways.

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice

Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.

Allelic diversity of phytoene synthase gene influences the transcription level in citrus fruit among a citrus F1 hybrid population

Phytoene synthase (PSY) is one of the key regulatory enzyme on the biosynthesis and accumulation of carotenoid in citrus fruits. The transcriptional diversity of PSY is mainly attributed to the structural variation in promoter region among PSY alleles. In aim to clarify how this transcriptional diversity is regulated among them, PSY alleles responsible for carotenoid biosynthesis in the fruits are characterized and their promoter sequences were compared. Based on gene structure and expression pattern of PSY homologues on the clementine mandarin genome sequence, PSY alleles responsible for carotenoid biosynthesis are derived from a single locus in the scaffold 6. AG mapping population possessed four PSY alleles derived from parent lines of A255 and G434, and their F₁ individuals with PSY-g2 allele tended to have low transcription level. From sequence comparison of their promoter regions, the cis-motif alternation from MYBPZM to RAV1AAT might be a candidate to influence the transcription level. Among the ancestral pedigree varieties of AG mapping population, the transcription level of PSY correlated with genotypes of MYBPZM and RAV1AAT motifs in the promoter region of PSY alleles, so that homozygous genotype of MYBPZM showed higher transcription level while heterozygous genotype of MYBPZM and RAV1AAT showed lower transcription level.

GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana

Drought transcriptome analysis of finger millet (Eleusine coracana) by cDNA subtraction identified drought responsive genes that have a potential role in drought tolerance. Through virus-induced gene silencing (VIGS) in a related crop species, maize (Zea mays), several genes, including a G-BOX BINDING FACTOR 3 (GBF3) were identified as candidate drought stress response genes and the role of GBF3 in drought tolerance was studied in Arabidopsis thaliana. Overexpression of both EcGBF3 and AtGBF3 in A. thaliana resulted in improved tolerance to osmotic stress, salinity and drought stress in addition to conferring insensitivity to ABA. Conversely, loss of function of this gene increased the sensitivity of A. thaliana plants to drought stress. EcGBF3 transgenic A. thaliana results also suggest that drought tolerance of sensitive plants can be improved by transferring genes from far related crops like finger millet. Our results demonstrate the role of GBF3 in imparting drought tolerance in A. thaliana and indicate the conserved role of this gene in drought and other abiotic stress tolerance in several plant species.

Genome-Wide Analysis of the RAV Family in Soybean and Functional Identification of GmRAV-03 Involvement in Salt and Drought Stresses and Exogenous ABA Treatment

Transcription factors play vital roles in plant growth and in plant responses to abiotic stresses. The RAV transcription factors contain a B3 DNA binding domain and/or an APETALA2 (AP2) DNA binding domain. Although genome-wide analyses of RAV family genes have been performed in several species, little is known about the family in soybean (Glycine max L.). In this study, a total of 13 RAV genes, named as GmRAVs, were identified in the soybean genome. We predicted and analyzed the amino acid compositions, phylogenetic relationships, and folding states of conserved domain sequences of soybean RAV transcription factors. These soybean RAV transcription factors were phylogenetically clustered into three classes based on their amino acid sequences. Subcellular localization analysis revealed that the soybean RAV proteins were located in the nucleus. The expression patterns of 13 RAV genes were analyzed by quantitative real-time PCR. Under drought stresses, the RAV genes expressed diversely, up- or down-regulated. Following NaCl treatments, all RAV genes were down-regulated excepting GmRAV-03 which was up-regulated. Under abscisic acid (ABA) treatment, the expression of all of the soybean RAV genes increased dramatically. These results suggested that the soybean RAV genes may be involved in diverse signaling pathways and may be responsive to abiotic stresses and exogenous ABA. Further analysis indicated that GmRAV-03 could increase the transgenic lines resistance to high salt and drought and result in the transgenic plants insensitive to exogenous ABA. This present study provides valuable information for understanding the classification and putative functions of the RAV transcription factors in soybean.

Two Groups of Thellungiella salsuginea RAVs Exhibit Distinct Responses and Sensitivity to Salt and ABA in Transgenic Arabidopsis

Containing both AP2 domain and B3 domain, RAV (Related to ABI3/VP1) transcription factors are involved in diverse functions in higher plants. A total of eight TsRAV genes were isolated from the genome of Thellungiella salsuginea and could be divided into two groups (A- and B-group) based on their sequence similarity. The mRNA abundance of all Thellungiella salsuginea TsRAVs followed a gradual decline during seed germination. In Thellungiella salsuginea seedling, transcripts of TsRAVs in the group A (A-TsRAVs) were gradually and moderately reduced by salt treatment but rapidly and severely repressed by ABA treatment. In comparison, with a barely detectable constitutive expression, the transcriptional level of TsRAVs in the group B (B-TsRAVs) exhibited a moderate induction in cotyledons when confronted with ABA. We then produced the “gain-of-function” transgenic Arabidopsis plants for each TsRAV gene and found that only 35S:A-TsRAVs showed weak growth retardation including reduced root elongation, suggesting their roles in negatively controlling plant growth. Under normal conditions, the germination process of all TsRAVs overexpressing transgenic seeds was inhibited with a stronger effect observed in 35S:A-TsRAVs seeds than in 35S:B-TsRAVs seeds. With the presence of NaCl, seed germination and seedling root elongation of all plants including wild type and 35S:TsRAVs plants were retarded and a more severe inhibition occurred to the 35S:A-TsRAV transgenic plants. ABA treatment only negatively affected the germination rates of 35S:A-TsRAV transgenic seeds but not those of 35S:B-TsRAV transgenic seeds. All 35S:TsRAVs transgenic plants showed a similar degree of reduction in root growth compared with untreated seedlings in the presence of ABA. Furthermore, the cotyledon greening/expansion was more severely inhibited 35S:A-TsRAVs than in 35S:B-TsRAVs seedlings. Upon water deficiency, with a wider opening of stomata, 35S:A-TsRAVs plants experienced a faster transpirational water loss than wild type and 35S:B-TsRAVs lines. Taken together, our results suggest that two groups of TsRAVs perform distinct regulating roles during plant growth and abiotic defense including drought and salt, and A-TsRAVs are more likely than B-TsRAVs to act as negative regulators in the above-mentioned biological processes.

Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon

APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plant, and play essential roles in growth, development and stress response. Except a few members, the AP2/EREBP family has not been characterized in Brachypodium distachyon, a model plant of Poaceae. We performed a genome-wide study of this family in B. distachyon by phylogenetic analyses, transactivation assays and transcript profiling. A total of 149 AP2/EREBP genes were identified and divided into four subfamilies, i.e., ERF (ethylene responsive factor), DREB (dehydration responsive element binding gene), RAV (related to ABI3/VP) and AP2. Tandem duplication was a major force in expanding B. distachyon AP2/EREBP (BdAP2/EREBP) family. Despite a significant expansion, genomic organizations of BdAP2/EREBPs were monotonous as the majority of them, except those of AP2 subfamily, had no intron. An analysis of transcription activities of several closely related and duplicated BdDREB genes showed their functional divergence and redundancy in evolution. The expression of BdAP2/EREBPs in different tissues and the expression of DREB/ERF subfamilies in B. distachyon, wheat and rice under abiotic stresses were investigated by next-generation sequencing and microarray profiling. Our results are valuable for further function analysis of stress tolerant AP2/EREBP genes in B. distachyon.

Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis

Salt is a major environmental stress factor that can affect rice growth and yields. Recent studies suggested that members of the AP2/ERF domain-containing RAV (related to ABI3/VP1) TF family are involved in abiotic stress adaptation. However, the transcriptional response of rice RAV genes (OsRAVs) to salt has not yet been fully characterized. In this study, the expression patterns of all five OsRAVs were examined under salt stress. Only one gene, OsRAV2, was stably induced by high-salinity treatment. Further expression profile analyses indicated that OsRAV2 is transcriptionally regulated by salt, but not KCl, osmotic stress, cold or ABA (abscisic acid) treatment. To elucidate the regulatory mechanism of the stress response at the transcriptional level, we isolated and characterized the promoter region of OsRAV2 (P OsRAV2 ). Transgenic analysis indicated that P OsRAV2 is induced by salt stress but not osmotic stress or ABA treatment. Serial 5' deletions and site-specific mutations in P OsRAV2 revealed that a GT-1 element located at position -664 relative to the putative translation start site is essential for the salt induction of P OsRAV2 . The regulatory function of the GT-1 element in the salt induction of OsRAV2 was verified in situ in plants with targeted mutations generated using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system. Taken together, our results indicate that the GT-1 element directly controls the salt response of OsRAV2. This study provides a better understanding of the putative functions of OsRAVs and the molecular regulatory mechanisms of plant genes under salt stress.