Abiotic stresses such as extreme temperature, drought, high salinity, cold and waterlogging often result in significant losses to the yields of economically important crops such as soybean (Glycine max L.). Transcription factors (TFs) which bind to DNA through specific cis-regulatory sequences either activate or repress gene transcription have been reported to act as control switches in stress signaling. Recent completion of the soybean genomic sequence has open wide opportunities for large-scale identification and annotations of regulatory TFs in soybean for functional studies. Within the soybean genome, we identified 5,035 TF models which grouped into 61 families. Detailed annotations of soybean TF genes can be accessed at SoybeanTFDB (soybeantfdb.psc.riken. jp). Moreover, we have reported a new idea of high throughput prediction and selection of abiotic stress responsive TFs based on the existence of known stress responsive cis-element(s) located in the promoter regions of respective TFs and GO annotations. We, therefore, have provided a basic platform for the genomewide analysis of regulatory mechanisms underlying abiotic stress responses and a reliable tool for prediction and selection of stress responsive TFs for further functional studies and genetic engineering.
soybean; transcrition factor; cis-element; abiotic stress; gene ontology
The two-component signaling systems (TCSs), which mediate the histidine-aspartate signaling, control diverse biological processes of many organisms, including cell division, cell growth and proliferation and responses to environmental stimuli and growth regulators. We have provided in planta evidence that the cytokinin (CK) responsive TCS mediates abscisic acid (ABA) and osmotic stress responses. By using loss-of-function approach we have demonstrated that the three cytokinin (CK) receptor histidine kinases AHK2, AHK3 and AHK4/CRE1 act as negative regulators in ABA, drought and high salinity stress signalings. Genome-wide expression profiling of the stress-tolerant double mutant suggested that CK receptor kinases mediate osmotic stress response in both an ABA-dependent and ABA-independent manner. Additionally, we showed evidence for the role of CK in mediating stress responses, judging from the fact that AHK4 requires the CK to function as a negative regulator in osmotic stress response. Our results suggested that cross-talk exists among CK, ABA and osmotic stress signaling pathways, and that CK signaling and CK metabolism may play crucial roles not only in plant growth and development but also in osmotic stress signaling.
two-component systems; osmotic stress; abscisic acid; cytokinin; microarray
The plant-specific NAC transcription factors play important roles in plant response to drought stress. Here, we have compared the expression levels of a subset of GmNAC genes in drought-tolerant DT51 and drought-sensitive MTD720 under both normal and drought stress conditions aimed at identifying correlation between GmNAC expression levels and drought tolerance degree, as well as potential GmNAC candidates for genetic engineering. The expression of 23 selected dehydration-responsive GmNACs was assessed in both stressed and unstressed root tissues of DT51 and MTD720 using real-time quantitative PCR. The results indicated that expression of GmNACs was genotype-dependent. Seven and 13 of 23 tested GmNACs showed higher expression levels in roots of DT51 in comparison with MTD720 under normal and drought stress conditions, respectively, whereas none of them displayed lower transcript levels under any conditions. This finding suggests that the higher drought tolerance of DT51 might be positively correlated with the higher induction of the GmNAC genes during water deficit. The drought-inducible GmNAC011 needs to be mentioned as its transcript accumulation was more than 76-fold higher in drought-stressed DT51 roots relative to MTD720 roots. Additionally, among the GmNAC genes examined, GmNAC085, 092, 095, 101 and 109 were not only drought-inducible but also more highly up-regulated in DT51 roots than in that of MTD720 under both treatment conditions. These data together suggest that GmNAC011, 085, 092, 095, 101 and 109 might be promising candidates for improvement of drought tolerance in soybean by biotechnological approaches.
comparative expression analysis; drought stress; NAC transcription factor; real-time quantitative PCR; soybean
In plants, transient changes in calcium concentrations of cytosol have been observed during stress conditions like high salt, drought, extreme temperature and mechanical disturbances. Calcium-dependent protein kinases (CDPKs) play important roles in relaying these calcium signatures into downstream effects. In this study, a stress-responsive CDPK gene, ZoCDPK1 was isolated from a stress cDNA generated from ginger using rapid amplification of cDNA ends (RLM-RACE) – PCR technique and characterized its role in stress tolerance. An important aspect seen during the analysis of the deduced protein is a rare coupling between the presence of a nuclear localization sequence in the junction domain and consensus sequence in the EF-hand loops of calmodulin-like domain. ZoCDPK1 is abundantly expressed in rhizome and is rapidly induced by high-salt stress, drought, and jasmonic acid treatment but not by low temperature stress or abscissic acid treatment. The sub-cellular localization of ZoCDPK1-GFP fusion protein was studied in transgenic tobacco epidermal cells using confocal laser scanning microscopy. Over-expression of ginger CDPK1 gene in tobacco conferred tolerance to salinity and drought stress as reflected by the high percentage of seed germination, higher relative water content, expression of stress responsive genes, higher leaf chlorophyll content, increased photosynthetic efficiency and other photosynthetic parameters. In addition, transgenic tobacco subjected to salinity/drought stress exhibited 50% more growth during stress conditions as compared to wild type plant during normal conditions. T3 transgenic plants are able to grow to maturity, flowers early and set viable seeds under continuous salinity or drought stress without yield penalty. The ZoCDPK1 up-regulated the expression levels of stress-related genes RD21A and ERD1 in tobacco plants. These results suggest that ZoCDPK1 functions in the positive regulation of the signaling pathways that are involved in the response to salinity and drought stress in ginger and it is likely operating in a DRE/CRT independent manner.
The worldwide production of maize (Zea mays L.) is frequently impacted by water scarcity and as a result, increased drought tolerance is a priority target in maize breeding programs. While DREB transcription factors have been demonstrated to play a central role in desiccation tolerance, whether or not natural sequence variations in these genes are associated with the phenotypic variability of this trait is largely unknown. In the present study, eighteen ZmDREB genes present in the maize B73 genome were cloned and systematically analyzed to determine their phylogenetic relationship, synteny with rice, maize and sorghum genomes; pattern of drought-responsive gene expression, and protein transactivation activity. Importantly, the association between the nucleic acid variation of each ZmDREB gene with drought tolerance was evaluated using a diverse population of maize consisting of 368 varieties from tropical and temperate regions. A significant association between the genetic variation of ZmDREB2.7 and drought tolerance at seedling stage was identified. Further analysis found that the DNA polymorphisms in the promoter region of ZmDREB2.7, but not the protein coding region itself, was associated with different levels of drought tolerance among maize varieties, likely due to distinct patterns of gene expression in response to drought stress. In vitro, protein-DNA binding assay demonstrated that ZmDREB2.7 protein could specifically interact with the target DNA sequences. The transgenic Arabidopsis overexpressing ZmDREB2.7 displayed enhanced tolerance to drought stress. Moreover, a favorable allele of ZmDREB2.7, identified in the drought-tolerant maize varieties, was effective in imparting plant tolerance to drought stress. Based upon these findings, we conclude that natural variation in the promoter of ZmDREB2.7 contributes to maize drought tolerance, and that the gene and its favorable allele may be an important genetic resource for the genetic improvement of drought tolerance in maize.
Water scarcity is one of the most severe threats to maize production worldwide. Although research has demonstrated that DREB-type transcription factors play important roles in plant water stress response, whether the specific genetic variants in DREB genes contribute to plant drought tolerance is largely unknown. Taking advantages of recent technical and methodological advance, we systematically analyzed all the functional DREB genes in maize and examined their associations with the natural variation in drought tolerance of 368 maize varieties collected from tropical and temperate regions. A significant association in the ZmDREB2.7 gene with drought tolerance was detected in that the DNA polymorphisms in the gene promoter region, but not those in the protein coding region, contributed to observed variations in maize drought tolerance, probably due to the distinct gene expression patterns in response to the stress. Overexpressing ZmDREB2.7 in Arabidopsis resulted in enhanced tolerance to drought stress. Moreover, a favorable ZmDREB2.7 allele, identified from drought-tolerant varieties, was effective in improving plant tolerance to drought stress when it was introduced into a drought-sensitive background. ZmDREB2.7 and its favorable allele represent a valuable genetic resource for enhancing maize drought tolerance by marker assisted breeding and transformation technology.
In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many of which were formed by genome duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain and an auxin/indole acetic acid (AUX/IAA) dimerization domain, whereas the remaining eight members lack the dimerization domain. Phylogenetic analysis of the ARFs from soybean and Arabidopsis revealed both similarity and divergence between the two ARF families, as well as enabled us to predict the functions of the GmARFs. Using quantitative real-time polymerase chain reaction (qRT-PCR) and available soybean Affymetrix array and Illumina transcriptome sequence data, a comprehensive expression atlas of GmARF genes was obtained in various organs and tissues, providing useful information about their involvement in defining the precise nature of individual tissues. Furthermore, expression profiling using qRT-PCR and microarray data revealed many water stress-responsive GmARFs in soybean, albeit with different patterns depending on types of tissues and/or developmental stages. Our systematic analysis has identified excellent tissue-specific and/or stress-responsive candidate GmARF genes for in-depth in planta functional analyses, which would lead to potential applications in the development of genetically modified soybean cultivars with enhanced drought tolerance.
ARF transcription factor family; soybean; structural analysis; expression analysis; water stress
Phosphorus (P)-deficiency is a major abiotic stress that limits legume growth in many types of soils. The relationship between Medicago and Sinorhizobium, is known to be affected by different environmental conditions. Recent reports have shown that, in combination with S. meliloti 2011, Medicago truncatula had a lower symbiotic efficiency than Medicago sativa. However, little is known about how Medicago–Sinorhizobium is affected by P-deficiency at the whole-plant level. The objective of the present study was to compare and characterize the symbiotic efficiency of N2 fixation of M. truncatula and M. sativa grown in sand under P-limitation. Under this condition, M. truncatula exhibited a significantly higher rate of N2 fixation. The specific activity of the nodules was much higher in M. truncatula in comparison to M. sativa, partially as a result of an increase in electron allocation to N2versus H+. Although the main organic acid, succinate, exhibited a strong tendency to decrease under P-deficiency, the more efficient symbiotic ability observed in M. truncatula coincided with an apparent increase in the content of malate in its nodules. Our results indicate that the higher efficiency of the M. truncatula symbiotic system is related to the ability to increase malate content under limited P-conditions.
Medicago sativa; Medicago truncatula; nitrogen fixation; nodule; symbiosis; phosphorus
Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.
tree crops; transcription factor; database; expression; cis-motif
Soybean (Glycine max) productivity is adversely affected by drought stress worldwide, including Vietnam. In the last few years, we have made a great effort in the development of drought-tolerant soybean cultivars by breeding and/or radiation-induced mutagenesis. One of the newly developed cultivars, the DT2008, showed enhanced drought tolerance and stable yield in the field conditions. The purpose of this study was to compare the drought-tolerant phenotype of DT2008 and Williams 82 (W82) by assessing their water loss and growth rate under dehydration and/or drought stress conditions as a means to provide genetic resources for further comparative and functional genomics. We found that DT2008 had reduced water loss under both dehydration and drought stresses in comparison with W82. The examination of root and shoot growths of DT2008 and W82 under both normal and drought conditions indicated that DT2008 maintains a better shoot and root growth rates than W82 under both two growth conditions. These results together suggest that DT2008 has better drought tolerance degree than W82. Our results open the way for further comparison of DT2008 and W82 at molecular levels by advanced omic approaches to identify mutation(s) involved in the enhancement of drought tolerance of DT2008, contributing to our understanding of drought tolerance mechanisms in soybean. Mutation(s) identified are potential candidates for genetic engineering of elite soybean varieties to improve drought tolerance and biomass.
Potassium (K) is an important plant macronutrient that has various functions throughout the whole plant over its entire life span. Cytokinins (CKs) are known to regulate macronutrient homeostasis by controlling the expression of nitrate, phosphate and sulfate transporters. Although several studies have described how CKs signal deficiencies for some macronutrients, the roles of CKs in K signaling are poorly understood. CK content has been shown to decrease under K-starved conditions. Specifically, a CK-deficient mutant was more tolerant to low K than wild-type; however, a plant with an overaccumulation of CKs was more sensitive to low K. These results suggest that K deprivation alters CK metabolism, leading to a decrease in CK content. To investigate this phenomenon further, several Arabidopsis lines, including a CK-deficient mutant and CK receptor mutants, were analyzed in low K conditions using molecular, genetic and biochemical approaches. ROS accumulation and root hair growth in low K were also influenced by CKs. CK receptor mutants lost the responsiveness to K-deficient signaling, including ROS accumulation and root hair growth, but the CK-deficient mutant accumulated more ROS and exhibited up-regulated expression of HAK5, which is a high-affinity K uptake transporter gene that is rapidly induced by low K stress in ROS- and ethylene-dependent manner in response to low K. From these results, we conclude that a reduction in CK levels subsequently allows fast and effective stimulation of low K-induced ROS accumulation, root hair growth and HAK5 expression, leading to plant adaptation to low K conditions.
Brassinosteroids (BRs) and polyamines (PAs) regulate various responses to abiotic stress, but their involvement in the regulation of copper (Cu) homeostasis in plants exposed to toxic levels of Cu is poorly understood. This study provides an analysis of the effects of exogenously applied BRs and PAs on radish (Raphanus sativus) plants exposed to toxic concentrations of Cu. The interaction of 24-epibrassinolide (EBR, an active BR) and spermidine (Spd, an active PA) on gene expression and the physiology of radish plants resulted in enhanced tolerance to Cu stress. Results indicated that the combined application of EBR and Spd modulated the expression of genes encoding PA enzymes and genes that impact the metabolism of indole-3-acetic acid (IAA) and abscisic acid (ABA) resulting in enhanced Cu stress tolerance. Altered expression of genes implicated in Cu homeostasis appeared to be the main effect of EBR and Spd leading to Cu stress alleviation in radish. Ion leakage, in vivo imaging of H2O2, comet assay, and improved tolerance of Cu-sensitive yeast strains provided further evidence for the ability of EBR and Spd to improve Cu tolerance significantly. The study indicates that co-application of EBR and Spd is an effective approach for Cu detoxification and the maintenance of Cu homeostasis in plants. Therefore, the use of these compounds in agricultural production systems should be explored.
Abscisic acid; brassinosteroids; comet assay; copper transporters; Cu homeostasis; Cu-sensitive yeast; indole-3-acetic acid; oxidative stress; polyamines
Brassinosteroids (BRs) and polyamines (PAs) are well-established growth regulators playing key roles in stress management among plants. In the present study, we evaluated the effects of epibrassinolide (EBL, an active BR) and spermidine (Spd, an active PA) on the tolerance of radish to oxidative stress induced by Cr (VI) metal. Our investigation aimed to study the impacts of EBL (10−9 M) and/or Spd (1 mM) on the biochemical and physiological responses of radish (Raphanus sativus L.) under Cr-stress. Applications of EBL and/or Spd were found to improve growth of Cr-stressed seedlings in terms of root length, shoot length and fresh weight. Our data also indicated that applications of EBL and Spd have significant impacts, particularly when applied together, on the endogenous titers of PAs, free and bound forms of IAA and ABA in seedlings treated with Cr-stress. Additionally, co-applications of EBL and Spd modulated more remarkably the titers of antioxidants (glutathione, ascorbic acid, proline, glycine betaine and total phenol) and activities of antioxidant enzymes (guaicol peroxidase, catalase, superoxide dismutase and glutathione reductase) in Cr-stressed plants than their individual applications. Attenuation of Cr-stress by EBL and/or Spd (more efficient with EBL and Spd combination) was also supported by enhanced values of stress indices, such as phytochelatins, photosynthetic pigments and total soluble sugars, and reduction in malondialdehyde and H2O2 levels in Cr-treated seedlings. Diminution of ROS production and enhanced ROS scavenging capacities were also noted for EBL and/or Spd under Cr-stress. However, no significant reduction in Cr uptake was observed for co-application of EBL and Spd when compared to their individual treatments in Cr-stressed seedlings. Taken together, our results demonstrate that co-applications of EBL and Spd are more effective than their independent treatments in lowering the Cr-induced oxidative stress in radish, leading to improved growth of radish seedlings under Cr-stress.
Synthesis of polyunsaturated fatty acids (PUFAs) in the endoplasmic reticulum of plants typically involves the fatty acid desaturases FAD2 and FAD3, which use cytochrome b5 (Cb5) as an electron donor. Higher plants are reported to have multiple isoforms of Cb5, in contrast to a single Cb5 in mammals and yeast. Despite the wealth of information available on the roles of FAD2 and FAD3 in PUFA synthesis, information regarding the contributions of various Cb5 isoforms in desaturase-mediated reactions is limited.
The present functional characterization of Cb5 polypeptides revealed that all Arabidopsis Cb5 isoforms are not similarly efficient in ω-6 desaturation, as evidenced by significant variation in their product outcomes in yeast-based functional assays. On the other hand, characterization of Cb5 polypeptides of soybean (Glycine max) suggested that similar ω-6 desaturation efficiencies were shared by various isoforms. With regard to ω-3 desaturation, certain Cb5 genes of both Arabidopsis and soybean were shown to facilitate the accumulation of more desaturation products than others when co-expressed with their native FAD3. Additionally, similar trends of differential desaturation product accumulation were also observed with most Cb5 genes of both soybean and Arabidopsis even if co-expressed with non-native FAD3.
The present study reports the first description of the differential nature of the Cb5 genes of higher plants in fatty acid desaturation and further suggests that ω-3/ω-6 desaturation product outcome is determined by the nature of both the Cb5 isoform and the fatty acid desaturases.
Soil destruction by abiotic environmental conditions, such as high salinity, has resulted in dramatic losses of arable land, giving rise to the need of studying mechanisms of plant adaptation to salt stress aimed at creating salt-tolerant plants. Recently, it has been reported that cytokinins (CKs) regulate plant environmental stress responses through two-component systems. A decrease in endogenous CK levels could enhance salt and drought stress tolerance. Here, we have investigated the global transcriptional change caused by a reduction in endogenous CK content under both normal and salt stress conditions. Ten-day-old Arabidopsis thaliana wild-type (WT) and CK-deficient ipt1,3,5,7 plants were transferred to agar plates containing either 0 mM (control) or 200 mM NaCl and maintained at normal growth conditions for 24 h. Our experimental design allowed us to compare transcriptome changes under four conditions: WT-200 mM vs. WT-0 mM, ipt1,3,5,7-0 mM vs. WT-0 mM, ipt1,3,5,7-200 mM vs. ipt1,3,5,7-0 mM and ipt1,3,5,7-200 mM vs. WT-200 mM NaCl. Our results indicated that the expression of more than 10% of all of the annotated Arabidopsis genes was altered by CK deficiency under either normal or salt stress conditions when compared to WT. We found that upregulated expression of many genes encoding either regulatory proteins, such as NAC, DREB and ZFHD transcription factors and the calcium sensor SOS3, or functional proteins, such as late embryogenesis-abundant proteins, xyloglucan endo-transglycosylases, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins, may contribute to improved salt tolerance of CK-deficient plants. We also demonstrated that the downregulation of photosynthesis-related genes and the upregulation of several NAC genes may cause the altered morphological phenotype of CK-deficient plants. This study highlights the impact of CK regulation on the well-known stress-responsive signaling pathways, which regulate plant adaptation to high salinity as well as other environmental stresses.
The interactions between transcription factors (TFs) and cis-regulatory DNA sequences control gene expression, constituting the essential functional linkages of gene regulatory networks. The aim of this study is to identify and integrate all putative TFs from six grass species: Brachypodium distachyon, maize, rice, sorghum, barley, and wheat with significant information into an integrative database (GramineaeTFDB) for comparative genomics and functional genomics. For each TF, sequence features, promoter regions, domain alignments, GO assignment, FL-cDNA information, if available, and cross-references to various public databases and genetic resources are provided. Additionally, GramineaeTFDB possesses a tool which aids the users to search for putative cis-elements located in the promoter regions of TFs and predict the functions of the TFs using cis-element-based functional prediction approach. We also supplied hyperlinks to expression profiles of those TF genes of maize, rice, and barley, for which data are available. Furthermore, information about the availability of FOX and Ds mutant lines for rice and maize TFs, respectively, are also accessible through hyperlinks. Our study provides an important user-friendly public resource for functional analyses and comparative genomics of grass TFs, and understanding of the architecture of transcriptional regulatory networks and evolution of the TFs in agriculturally important cereal crops.
abiotic stress; cis-motif; database; grasses; transcription factor
Plant-specific NAC transcription factors (TFs) play important roles in regulating diverse biological processes, including development, senescence, growth, cell division and responses to environmental stress stimuli. Within the soybean genome, we identified 152 full-length GmNAC TFs, including 11 membrane-bound members. In silico analysis of the GmNACs, together with their Arabidopsis and rice counterparts, revealed similar NAC architecture. Next, we explored the soybean Affymetrix array and Illumina transcriptome sequence data to analyse tissue-specific expression profiles of GmNAC genes. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis and rice as seeding sequences identified 58 of the 152 GmNACs as putative stress-responsive genes, including eight previously reported dehydration-responsive GmNACs. We could design gene-specific primers for quantitative real-time PCR verification of 38 out of 50 newly predicted stress-related genes. Twenty-five and six GmNACs were found to be induced and repressed 2-fold or more, respectively, in soybean roots and/or shoots in response to dehydration. GmNAC085, whose amino acid sequence was 39%; identical to that of well-known SNAC1/ONAC2, was the most induced gene upon dehydration, showing 390-fold and 20-fold induction in shoots and roots, respectively. Our systematic analysis has identified excellent tissue-specific and/or dehydration-responsive candidate GmNAC genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
soybean; NAC transcription factors; dehydration; sequence analysis; expression analysis
Two-component systems (TCSs) play vital functions in the adaptation of plants to environmental stresses. To identify soybean TCS genes involved in the regulation of drought stress response, we performed tissue-specific expression profiling of all 83 putative TCS genes in plants subjected to dehydration. Under well-watered conditions, the majority of soybean TCS genes were expressed higher in the root tissues. Additionally, a high variability in transcript abundance was observed for the TCS genes in both roots and shoots. Under dehydration, TCS genes were more responsive in shoots than in roots. Further analysis indicated that 50% more TCS genes were repressed by dehydration than induced. Specifically, 18 genes were induced by 2-fold or more, whereas 33 genes were down-regulated at least 2-fold by dehydration. TCS genes putatively involved in cytokinin and ethylene signallings strongly responded to dehydration, suggesting that crosstalk exists between different hormonal and stress pathways. Our study provides the first glance into the complex regulatory roles of soybean TCSs underlying their functions in response to dehydration. Additionally, these systematic expression analyses identified excellent dehydration-responsive candidate genes to further clarify soybean TCS functions in drought response and to enable the development of improved drought tolerance in transgenic soybeans.
soybean; two-component system; dehydration; expression profiling; RT-qPCR
In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms.
soybean; two-component systems; abiotic stress
Sequence-specific DNA-binding transcription factors (TFs) are often termed as ‘master regulators’ which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.
soybean; transcription factors; abiotic stress; database
BiP overexpression improves leaf water relations during droughts and delays drought-induced leaf senescence. However, whether BiP controls cellular homeostasis under drought conditions or simply delays dehydration-induced leaf senescence as the primary cause for water stress tolerance remains to be determined. To address this issue, we examined the drought-induced transcriptomes of BiP-overexpressing lines and wild-type (WT) lines under similar leaf water potential (ψw) values. In the WT leaves, a ψw reduction of −1.0 resulted in 1339 up-regulated and 2710 down-regulated genes; in the BiP-overexpressing line 35S::BiP-4, only 334 and 420 genes were induced and repressed, respectively, at a similar leaf ψw = −1.0 MPa. This level of leaf dehydration was low enough to induce a repertory of typical drought-responsive genes in WT leaves but not in 35S::BiP-4 dehydrated leaves. The responders included hormone-related genes, functional and regulatory genes involved in drought protection and senescence-associated genes. The number of differentially expressed genes in the 35S::BiP-4 line approached the wild type number at a leaf ψw = −1.6 MPa. However, N-rich protein (NRP)- mediated cell death signaling genes and unfolded protein response (UPR) genes were induced to a much lower extent in the 35S::BiP-4 line than in the WT even at ψw = −1.6 MPa. The heatmaps for UPR, ERAD (ER-associated degradation protein system), drought-responsive and cell death-associated genes revealed that the leaf transcriptome of 35S::BiP-4 at ψw = −1.0 MPa clustered together with the transcriptome of well-watered leaves and they diverged considerably from the drought-induced transcriptome of the WT (ψw = −1.0, −1.7 and −2.0 MPa) and 35S::BiP-4 leaves at ψw = −1.6 MPa. Taken together, our data revealed that BiP-overexpressing lines requires a much higher level of stress (ψw = −1.6 MPa) to respond to drought than that of WT (ψw = −1.0). Therefore, BiP overexpression maintains cellular homeostasis under water stress conditions and thus ameliorates endogenous osmotic stress.
In Arabidopsis, NAC (NAM, ATAF and CUC) transcription factors have been found to promote lateral root number through the auxin signaling pathway. In the present study, the role of water stress–inducible soybean GmNAC003 and GmNAC004 genes in the enhancement of lateral root development under water deficit conditions was investigated. Both genes were highly expressed in roots, leaves and flowers of soybean and were strongly induced by water stress and moderately induced by a treatment with abscisic acid (ABA). They showed a slight response to treatment with 2,4-dichlorophenoxyacetic acid (2,4-D). The transgenic Arabidopsis plants overexpressing GmNAC004 showed an increase in lateral root number and length under non-stress conditions and maintained higher lateral root number and length under mild water stress conditions compared to the wild-type (WT), while the transgenic plants overexpressing GmNAC003 did not show any response. However, LR development of GmNAC004 transgenic Arabidopsis plants was not enhanced in the water-stressed compared to the well-watered treatment. In the treatment with ABA, LR density of the GmNAC004 transgenic Arabidopsis was less suppressed than that of the WT, suggesting that GmNAC004 counteracts ABA-induced inhibition of lateral root development. In the treatment with 2,4-D, lateral root density was enhanced in both GmNAC004 transgenic Arabidopsis and WT plants but the promotion was higher in the transgenic plants. Conversely, in the treatment with naphthylphthalamic acid (NPA), lateral root density was inhibited and there was no difference in the phenotype of the GmNAC004 transgenic Arabidopsis and WT plants, indicating that auxin is required for the action of GmNAC004. Transcript analysis for a number of known auxin and ABA related genes showed that GmNAC004's role may suppress ABA signaling but promote auxin signaling to increase lateral root development in the Arabidopsis heterologous system.
Inhabitants of arid ecosystems face severe nitrogen and water limitations. Inventive adaptations by organisms occupying such habitats are essential for survival. This study describes a tri-party symbiotic interaction between a plant (Salsola inermis), a beetle (Conorhynchus pistor), and a bacterium (Klebsiella pneumonia). The weevil survives by living within a mud structure affixed to the plant roots, thus benefiting from increased carbon and water, and refuge from predators and parasites. Active nitrogen-fixing bacteria harbored within the weevil's gut mediate this interaction, by supplying nitrogen to the system, which eventually promotes seed development. We studied the correlation between the weevil's existence and (i) root carbon and nitrogen content, (ii) soil water content and (iii) seed weight. Roots hosting weevils contained more nitrogen, heavier seeds and less carbon. In addition, water content was higher around the roots than in open spaces a short distance from the plant stem. Bacterial studies and nitrogen-fixation analyses, including molecular and chemical assays, indicated atmospheric nitrogen fixation in the larval stage and identified the bacterium. The coexistence of weevil and bacterial behavior coinciding with the plant's life cycle was revealed here by a long period of field observations. Out of over 60,000 known weevils, this is the only report of a weevil living most of its life underground without harming plants. The unique tri-party interaction described herein shows the important ecological role of desert plant roots and provides an example of a sustainable consortium of living organisms coping with the challenging desert environment.
Inositol polyphosphatases are important regulators since they control the catabolism of phosphoinositol derivatives, which are often signaling molecules for cellular processes. Here we report on the characterization of one of their members in soybean, GmSAL1. In contrast to the substrate specificity of its Arabidopsis homologues (AtSAL1 and AtSAL2), GmSAL1 only hydrolyzes inositol-1,4,5-trisphosphate (IP3) but not inositol-1,3,4-trisphosphate or inositol-1,4-bisphosphate.The ectopic expression of GmSAL1 in transgenic Arabidopsis thaliana led to a reduction in IP3 signals, which was inferred from the reduction in the cytoplasmic signals of the in vivo biomarker pleckstrin homology domain–green florescent protein fusion protein and the suppression of abscisic acid-induced stomatal closure. At the cellular level, the ectopic expression of GmSAL1 in transgenic BY-2 cells enhanced vacuolar Na+ compartmentalization and therefore could partially alleviate salinity stress.
Calcineurin B-like protein-interacting protein kinases (CIPKs) have been found to be responsive to abiotic stress. However, their precise functions and the related molecular mechanisms in abiotic stress tolerance are not completely understood, especially in wheat. In the present study, TaCIPK29 was identified as a new member of CIPK gene family in wheat. TaCIPK29 transcript increased after NaCl, cold, methyl viologen (MV), abscisic acid (ABA) and ethylene treatments. Over-expression of TaCIPK29 in tobacco resulted in increased salt tolerance, which was demonstrated by higher germination rates, longer root lengths and better growth status of transgenic tobacco plants compared to controls when both were treated with salt stress. Physiological measurements indicated that transgenic tobacco seedlings retained high K+/Na+ ratios and Ca2+ content by up-regulating some transporter genes expression and also possessed lower H2O2 levels and reduced membrane injury by increasing the expression and activities of catalase (CAT) and peroxidase (POD) under salt stress. Moreover, transgenic lines conferred tolerance to oxidative stress by increasing the activity and expression of CAT. Finally, TaCIPK29 was located throughout cells and it preferentially interacted with TaCBL2, TaCBL3, NtCBL2, NtCBL3 and NtCAT1. Taken together, our results showed that TaCIPK29 functions as a positive factor under salt stress and is involved in regulating cations and reactive oxygen species (ROS) homeostasis.