Binding of the wheat basic leucine zipper protein EmBP-1 to nucleosomal binding sites is modulated by nucleosome positioning

Identification of a 193 bp promoter region of TaNRX1-D gene from common wheat that contributes to osmotic or ABA stress inducibility in transgenic Arabidopsis

BACKGROUND

Cloning and characterizing the drought-inducible promoters is essential for their use in crop resistance's genetic improvement. Previous studies have shown that the TaNRX1-D gene participates in regulating the response of wheat to drought stress. However, its promoter has not yet been identified.

OBJECTIVE

In this study, we aimed to characterize the promoter of the TaNRX1-D gene.

METHODS

The promoter of TaNRX1-D (named P0, 2081 bp) was isolated from common wheat with several cis-acting elements that regulate in response to abiotic stresses and some core cis-acting elements. Functional verification of the promoter, eight 5'-deletion fragments of TaNRX1-D promoter, was fused to the β-glucuronidase (GUS) gene P0::GUS ~ P7::GUS and transformed into Arabidopsis, respectively. Agrobacterium-mediated GUS transient assay the P6a and P6b promoter regions in tobacco leaves under normal, osmotic or ABA stress.

RESULTS

Activity analysis of the full-length promoter (P0) showed that the intensity of stronger β-glucuronidase (GUS) staining in the roots and leaves was obtained during the growth of transgenic Arabidopsis. P0::GUS displayed the GUS activity was much higher in the roots and leaves than in other parts of the transgenic plant under normal conditions, which was similarly within wheat. Analysis of the 5'-deletion fragments revealed that P0::GUS ~ P6::GUS responded well upon exposure to osmotic (polyethylene glycol-6000, PEG6000) and abscisic acid (ABA) stress treatments and expressed significantly higher GUS activity than the CaMV35S promoter (35S::GUS), while P7::GUS did not. GUS transient assay in tobacco leaves showed that the GUS activities of P6a and P6b were lower than P6 in the PEG6000 and ABA stresses.

CONCLUSION

The 193 bp (P6) segment was considered the core region of TaNRX1-D responding to PEG6000 or ABA treatment. GUS activity assay in transgenic Arabidopsis showed that this segment was sufficient for the PEG6000 or ABA stress response. The identified 193 bp promoter of TaNRX1-D in this study will help breed osmotic or ABA tolerant crops. The 36 bp segment between P6 and P6b (-193 to -157 bp) was considered the critical sequence for the TaNRX1-D gene responding to PEG6000 or ABA treatment.

Functional characterization of a cotton late embryogenesis-abundant D113 gene promoter in transgenic tobacco

Previous studies have shown that mRNA and protein encoded by late embryogenesis-abundant (LEA) gene D113 from Gossypium hirsutum L. accumulate at high levels in mature seeds and also in response to abscisic acid (ABA) in young embryo. In this study, we studied the expression of four promoter 5' deletion constructs (-1383, -974, -578 and -158) of the LEA D113 gene fused to beta-glucuronidase (GUS). GUS activity analysis revealed that the -578 promoter fragment was necessary to direct seed-specific GUS expression in transgenic tobacco plants (Nicotiana tabacum L.). To further investigate the expression pattern of LEA D113 promoter under environmental stresses, 2-week-old transgenic tobacco seedlings were exposed to ABA, dehydration, high salinity and cold treatments. GUS activity in the seedlings was quantified fluorimetrically, and expression was also observed by histochemical staining. An apparent increase in GUS activity was found in plants harboring constructs -1383, -974 and -578 after 24 h of ABA or high-salinity treatments, as well as after 10 days of dehydration. By contrast, only a slight increase was observed in all the three lines after cold treatment. Virtually no change in expression was found in construct -158 in response to dehydration, salinity and cold, but there was a moderate response to ABA, suggesting that the region between -574 and -158 was necessary for dehydration- and salinity-dependent expression, whereas ABA-responsive cis-acting elements might be located in the -158 region of the promoter.

Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene

The chromatin structure of the pea plastocyanin gene (PetE) was examined at three different transcriptional states by investigating the acetylation states of histones H3 and H4 and the nuclease accessibility of the gene in pea roots, etiolated shoots, and green shoots. The acetylation states of histones associated with different regions of PetE were analyzed by chromatin immunoprecipitation with antibodies specific for acetylated or nonacetylated histone H3 or H4 tails, followed by polymerase chain reaction quantification. Comparison of pea tissues indicated that histone hyperacetylation was associated with increased PetE transcription in green shoots. Moreover, hyperacetylation of both histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified. Time-course digestions of nuclei with micrococcal nuclease and DNaseI indicated that the enhancer/promoter region was more resistant to digestion in the inactive gene in pea roots than was the same region in the active gene in shoots, whereas the transcribed region of PetE was digested similarly among the tissues. This finding indicates that transcription is accompanied by changes in the nuclease accessibility of the enhancer/promoter region only. Moreover, these results indicate that the changes in nuclease accessibility are organ specific, whereas histone hyperacetylation is light dependent, and they suggest that changes in nuclease accessibility precede histone hyperacetylation during PetE activation.

Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene

The chromatin structure of the pea plastocyanin gene (PetE) was examined at three different transcriptional states by investigating the acetylation states of histones H3 and H4 and the nuclease accessibility of the gene in pea roots, etiolated shoots, and green shoots. The acetylation states of histones associated with different regions of PetE were analyzed by chromatin immunoprecipitation with antibodies specific for acetylated or nonacetylated histone H3 or H4 tails, followed by polymerase chain reaction quantification. Comparison of pea tissues indicated that histone hyperacetylation was associated with increased PetE transcription in green shoots. Moreover, hyperacetylation of both histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified. Time-course digestions of nuclei with micrococcal nuclease and DNaseI indicated that the enhancer/promoter region was more resistant to digestion in the inactive gene in pea roots than was the same region in the active gene in shoots, whereas the transcribed region of PetE was digested similarly among the tissues. This finding indicates that transcription is accompanied by changes in the nuclease accessibility of the enhancer/promoter region only. Moreover, these results indicate that the changes in nuclease accessibility are organ specific, whereas histone hyperacetylation is light dependent, and they suggest that changes in nuclease accessibility precede histone hyperacetylation during PetE activation.

Permeabilized Arabidopsis protoplasts provide new insight into the chromatin structure of plant alcohol dehydrogenase genes

New data from permeabilized protoplasts have expanded our view of the 5'DNase I hypersensitive area of the Arabidopsis Adh gene derived from nuclei. DNase I hypersensitivity analyses conducted with permeabilized protoplasts from Arabidopsis cell cultures indicates that there are four distinct sites of hypersensitivity centered around positions -425, -325, -200, and -60. The hypersensitive site at -200 coincides with an in vitro hypersensitive site created by purified transcription factors bound to a G-box element. The G-box is a functional cis element that plays a role in the signal transduction of hypoxia and other stresses in Adh. The data presented in this paper support the notion that G-box-related elements may also play a role in defining chromatin structure. The new Arabidopsis data are discussed within the context of what is known about the chromatin structures and regulation of two other plant Adh genes; maize Adh1 and Adh2. The chromatin of the maize Adh1 promoter is divided into a region that is constitutively hypersensitive to DNase I (-700 to -160) and an inducibly hypersensitive region (-140 and -40). There are several sequence elements within the hypersensitive regions bound by proteins in vivo. The anaerobic response element is the most well characterized and functions in the detection of hypoxia. The maize Adh2 gene promoter is constitutively hypersensitive to DNase I, with the exception of a small region that extends to include the TATA box as the gene becomes active. Several cis elements in the Adh2 promoter are bound by factors in vivo. One, at -160, is a functional element that acts as an activator in vascular tissue. The overall goal of our research with the Adh genes from maize and Arabidopsis is to gain further insight into the relationships between the regulation of gene transcription and chromatin structure in plants as it is clear that all the necessary components that characterize regulated gene activity may not be found simply by elucidating the linear sequence of nucleotides that lie 5' to the protein coding regions and finding proteins capable of binding the promoter in vitro.

The seed-specific transactivator, ABI3, induces oleosin gene expression

A microspore-derived cell suspension culture of Brassica napus was used as a host for expression studies involving seed oleosin genes. The suspension culture was previously shown to display biochemistry and gene expression typical of zygotic embryos. Using a biolistic, transient expression approach we demonstrate that the seed-specific activator ABI3 promotes oleosin gene expression in these cultures. Co-bombardment of an oleosin promoter-GUS fusion and a full-length ABI3 gene from Arabidopsis resulted in four to six-fold enhancement of GUS expression. Deletion analysis was performed to identify which oleosin upstream sequences were required for ABI3 regulation. These studies found that a truncated oleosin promoter containing 160 bp of 5' regulatory sequence was sufficient to confer ABI3 responsiveness. Mutation of a canonical abscisic acid response element within this 160 bp region had a dramatic effect on basal expression, reducing levels to 25% of control. However, this mutation had no significant effect on ABI3 transactivation, indicating that the reduction in basal oleosin expression was distinct from the ABI3 response. These results also suggest that ABI3-mediated transactivation occurs through either a less-conserved ABRE element or other abscisic acid-independent sequences within the minimal promoter. Together, these data provide the first direct evidence that ABI3 mediates oleosin transactivation.

Constitutive protein-DNA interactions on the abscisic acid-responsive element before and after developmental activation of the rab28 gene

Transcription of the rab28 gene from maize is induced in late embryo development and in response to abscisic acid. We have studied the regulation of the activity of the rab28 promoter in embryos. Two abscisic acid-responsive elements (ABREs) were necessary for expression in embryos of transgenic Arabidopsis and in transient transformation in maize embryos. In vivo footprinting showed that there was protein binding to the ABREs and to other cis elements in the promoter in young embryos before expression of rab28. This shows that the rab28 promoter is in an open chromatin structure before developmental activation. The ABREs are important for the induction and have protein binding in young embryos. Nuclear proteins extracted from embryos before activation of rab28 bound to the ABREs in band shift assays. A complex with different mobility was formed between nuclear proteins and the ABREs after induction of rab28 suggesting a modification of the ABRE-binding factor or an exchange of proteins. The footprints on the ABREs were unaltered by induction with abscisic acid or during developmental activation of rab28. These results indicate that constitutive binding of transcription factor(s) on the ABRE is central in embryonic regulation of the rab28 gene.

Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins

The basic leucine zipper (bZIP) proteins are one of the largest and most conserved groups of eukaryotic transcription factors/repressors. Two major subgroups among the plant bZIP proteins have been identified as G-box (CCACGTGG) or C-box (TGACGTCA) binding proteins based on their DNA binding specificity and the amino acid sequences of their basic regions. We have investigated how plant bZIP proteins determine their DNA binding specificity by mutation of the basic domain of the G-box-binding protein EmBP-1. Four subregions of the EmBP-1 basic domain that differ from the C-box-binding protein TGA1a were substituted singly or in combination with the corresponding regions of TGA1a. DNA binding experiments with the mutant proteins demonstrated that binding specificity of plant bZIP proteins is determined independently by two regions, the core basic region and the hinge region. These two regions have an additive effect on DNA binding specificity. PCR-assisted binding-site selections using key mutants demonstrated that only G-box and C-box binding specificity can be generated by combinations of amino acids in the basic domains of EmBP-1 and TGA1a. These results suggest that factorial contributions of the amino acid residues in the basic domain combine to determine DNA-binding specificity of bZIP proteins.

PLANT TRANSCRIPTION FACTOR STUDIES

▪ Abstract  Major advances have been made in understanding the role of transcription factors in gene expression in yeast, Drosophila, and man. Transcription factor modification, synergistic events, protein-protein interactions, and chromatin structure have been successfully integrated into transcription factor studies in these organisms. While many putative transcription factors have been isolated from plants, most of them are only poorly characterized. This review summarizes examples where molecular biological techniques have been successfully employed to study plant transcription factors. The functional analysis of transcription factors is described as well as techniques for studying the interactions of transcription factors with other proteins and with DNA.

Protein binding to the abscisic acid-responsive element is independent of VIVIPAROUS1 in vivo

The plant hormone abscisic acid and the transcriptional activator VIVIPAROUS1 have a synergistic effect on transcription during embryo development. An abscisic acid-responsive element (ABRE) mediates induction by abscisic acid and VIVIPAROUS1, but the mechanism involved has not been determined. In this study, we explore the interaction between abscisic acid and VIVIPAROUS1 and its effect on the ABRE from the maize rab28 gene. In transient transformation experiments, abscisic acid stimulated transcription via several elements, whereas activation by VIVIPAROUS1 was mediated exclusively through the ABRE. In vivo footprinting showed only minor differences in binding to the ABRE between wild-type and VIVIPAROUS1-deficient embryos, suggesting that VIVIPAROUS1 stimulates transcription through the ABRE without major changes in protein-DNA interactions. A factor that bound to the ABRE in electrophoretic mobility shift assays was present at the same developmental stages as rab28 mRNA and had binding characteristics similar to those observed by in vivo footprinting. This suggests that the factor binds to the ABRE in the rab28 promoter in vivo. We discuss the constraints that our results put on the possible mechanism for action of VIVIPAROUS1 in vivo.