Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize

Cloning, characterization, and transformation of the phosphoethanolamine N-methyltransferase gene (ZmPEAMT1) in maize (Zea mays L.)

N-methylation of phosphoethanolamine, the committing step in choline (Cho) biosynthesis in plants, is catalyzed by S-adenosyl-L-methionine: phosphoethanolamine N-methyltransferase (PEAMT, EC 2.1.1.103). Herein we report the cloning and characterization of the novel maize phosphoethanolamine N-methyltransferase gene (ZmPEAMT1) using a combination of bioinformatics and a PCR-based allele mining strategy. The cDNA sequence of ZmPEAMT1 gene is 1,806 bp in length and translates a 495 amino acids peptide. The upstream promoter sequence of ZmPEAMT1 were obtained by TAIL-PCR, and contained four kinds of putative cis-acting regulatory elements, including stress-responsive elements, phytohormone-responsive elements, pollen developmental special activation elements, and light-induced signal transduction elements, as well as several other structural features in common with the promoter of rice and Arabidopsis homologies. RT-PCR analysis showed that expression of ZmPEAMT1 was induced by salt stress and suppressed by high temperature. Over-expression of ZmPEAMT1 enhanced the salt tolerance, root length, and silique number in transgenic Arabidopsis. These data indicated that ZmPEAMT1 maybe involved in maize root development and stress resistance, and maybe having a potential application in maize genetic engineering.

Evolutionary Processes During the Formation of the Plant-Specific Dof Transcription Factor Family

We found 19 putative genes for plant-specific Dof transcription factors in the moss Physcomitrella patens and one Dof gene in the green alga Chlamydomonas reinhardtii, but no identifiable Dof gene in the red alga Cyanidioschyzon merolae and the diatom Thalassiosira pseudonana, suggesting that the origin of the Dof transcription factors pre-dates the divergence of the green algae and the ancestors of terrestrial plants. The phylogenetic analyses contended that the Dof family in angiosperms formed through a series of evolutionary processes, including intensive duplications of a specific ancestral gene after the divergence of the moss and the angiosperm lineages.

Molecular cloning and characterization of the rubber elongation factor gene and its promoter sequence from rubber tree (Hevea brasiliensis): A gene involved in rubber biosynthesis

Hevea rubber tree (Hevea brasiliensis) is the only plant species being cultivated for commercial production of rubber in the world. In order to meet ever increasing rubber demand, it is a prerequisite to identify and characterize a key gene involved in rubber biosynthesis and over-expression of rubber biosynthesis gene will eventually lead to enhance the latex (rubber) production in transgenic Hevea plants. Rubber elongation factor (REF) is a major protein located on the surface of large rubber particles in latex and is involved which is involved in rubber biosynthesis in H. brasiliensis. We report here cloning and characterization of REF gene as well as its 5' promoter region from Hevea. REF gene (1367bp) has three exons interrupted by two introns and encoded a 138 amino acid peptide containing an open reading frame of 414bp with a calculated MW of 14,700Da. Nucleotide sequence analysis showed that 1.3kb genomic DNA showed 100% homology to REF cDNA from Hevea. Southern blot hybridization of genomic DNA with REF gene probe revealed that REF gene is encoded by a small gene family consisting of two members. RNA blot analysis indicated that REF transcript is highly expressed in high yielding clone than in low yielder. The cloned 5' promoter region has a putative TATA element at -150 and CAAT box at -221 position. To identify the regulatory role of REF promoter, chimaeric fusion between REF promoter sequence and the β-glucuronidase (GUS) coding, uidA gene was constructed and used to transform tobacco and Arabidopsis. Expression of the uidA reporter gene was detected histochemically in the transformed tobacco plants where, GUS activity was detected in the leaf and petiole of transformed plants. The stable integration of REF:uidA fusion into the tobacco genome was further confirmed by PCR amplification and Southern blot analysis. A histochemical study of stable transformants demonstrated that the 5' upstream region of REF can drive strong GUS gene expression specifically in the vascular tissues (xylem and phloem) of leaf, stem and midribs of transgenic Arabidopsis. GUS staining revealed that REF:GUS expression was also induced by wounding. The results suggested that the cloned REF promoter is capable of directing gene expression. Our ultimate goal is to produce transgenic Hevea plants with enhanced latex yield by over expression of REF protein.

Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes

The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per haploid genome. Comparison of RPBF genomic and cDNA sequences revealed that the genomic copy is interrupted by one long intron of 1,892 bp in the 5' noncoding region. We demonstrated by transient expression in rice callus protoplasts that the isolated RPBF trans-activated several storage protein genes via an AAAG target sequence located within their promoters, and with methylation interference experiments the additional AAAG-like sequences in promoters of genes expressed in maturing seeds were recognized by the RPBF protein. Binding was sequence specific, since mutation of the AAAG motif or its derivatives decreased both binding and trans-activation by RPBF. Synergism between RPBF and RISBZ1 recognizing the GCN4 motif [TGA(G/C)TCA] was observed in the expression of many storage protein genes. Overexpression of both transcription factors gave rise to much higher levels of expression than the sum of individual activities elicited by either RPBF or RISBZ1 alone. Furthermore, mutation of recognition sites suppressed reciprocal trans-activation ability, indicating that there are mutual interactions between RISBZ1 and RPBF. The RPBF gene is predominantly expressed in maturing endosperm and coordinately expressed with seed storage protein genes, and is involved in the quantitative regulation of genes expressed in the endosperm in cooperation with RISBZ1.

Isolation and characterization of TaDof1 transcription factor in wheat (Triticum. aestivum. L)

The Dof (DNA binding with one finger) proteins are plant specific transcription factors. Dof proteins are apparently encoded by a multiple gene family in higher plants. However, only one Dof gene, WPBF, was reported in wheat. In this study, a member of Dof gene family, TaDof1, was cloned from wheat. TaDof1 encode 291 amino acids, with a predicted molecular mass of 30.348 kDa. At its N-terminal end, a 52 amino acid stretch typical of Dof domain and two serine-rich stretches were observed. Sequence alignment indicated that, in Dof domain, TaDof1 share more than 75% identity with other Dof proteins of different species. TaDof1 was expressed highly in leaves and sheaths, but lowly in roots, and constitutively expressed in developing seeds of 2-12 DAP. It was interesting to note that TaDof1 was differentially expressed between hybrids F1 and parents in root, sheath and leaf. The implication of the differential expression patterns of TaDof1 was discussed in related to the up-regulation of C4 pathway related gene in hybrid rice and heterosis.

Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor

Wheat prolamin-box binding factor (WPBF) was shown to be an activator of Triticum aestivum L. storage protein genes. Three homoeologous genes encoding this transcription factor were isolated from a bacterial artificial chromosome genomic library and sequenced. The genes all have two exons separated by an intron of approximately 1,000 bp where the second exon contains the entire coding sequence. Many differences were found between homoeologous sequences, but none of them is predicted to significantly alter the sequence of the putative encoded protein. The three homoeologous genes are specifically expressed in grain from 3 to 39 days after anthesis. The allelic variation of a genetically diverse collection of 27 bread wheat lines was assessed. One, five, and one single-nucleotide polymorphisms (SNPs) were detected in the wPbf genes for the A, B, and D genomes, respectively. Physical and genetic mapping utilizing some of the SNPs identified confirmed that wPbf genes are located close to the centromeres on the homoeologous group 5 chromosomes. The low level of allelic diversity found in wPbf genes may suggest that these genes play a key role and are thus constrained by selection.

Genomic organization of the AODEF gene in Asparagus officinalis L

The perianths of Liliaceae plants, such as lily and tulip, have two whorls of almost identical petaloid organs, which are called tepals. According to the modified ABC model proposed in tulip, the class B genes are expressed in whorl 1 as well as whorls 2 and 3, so that the organs of whorls 1 and 2 have the same petaloid structure. The floral structure of asparagus (Asparagus officinalis L.) is similar to that of Liliaceae plants, however, the expression of B-class genes (AODEF, AOGLOA, AOGLOB) was not found in whorl 1, but was confined to whorls 2 and 3. This result does not support the modified ABC model in asparagus. In order to gain a better understanding of asparagus flower development, we have characterized a genomic clone of the AODEF gene. We compared the genomic organization and promoter sequence of AODEF with three well-studied DEF-like genes, DEFICIENS (Antirrhinum), APETALA3 (Arabidopsis), and OSMADS16 (rice). Exon-intron structures of these genes are well-conserved except for the large fifth intron in the AODEF gene and the OSMADS16 gene. Putative cis-elements including CArG-boxes were found in the promoter region and forty-two microsatellites were found in the AODEF genomic sequence.

Disruption of the glycolate dehydrogenase gene in the high-CO2-requiring mutant HCR89 ofChlamydomonas reinhardtii

One of the most notable contrasts between the photorespiratory pathway of higher plants and that of many of the green algae including Chlamydomonas reinhardtii lies in the enzymes that serve for oxidation of glycolate to glyoxylate. The gene disrupted by insertional mutagenesis in a high-CO2-requiring mutant, HCR89, of C. reinhardtii was determined to encode glycolate dehydrogenase (EC 1.1.99.14), which serves as the counterpart of glycolate oxidase (EC 1.1.3.15) in classical higher plant photorespiration. Neither glycolate nor D-lactate oxidation from the membrane fraction of HCR89 was detected. Excretion of over-accumulated glycolate into media due to the absence of glycolate dehydrogenase activity was observed for HCR89 under both high- and low-CO2conditions. Chlamydomonas glycolate dehydrogenase, CrGDH, with a molecular mass of 118 851 Da, comprises a relatively hydrophobic N-terminal region, a FAD-containing domain homologous to the D subunit of the glycolate oxidase complex from Escherischia coli, and an iron–sulfur cluster containing domain homologous to the C subunit of anaerobic glycerol-3-phosphate dehydrogenase complex from Escherichia coli. The second Cys residue in the second iron–sulfur cluster motif of CrGDH is replaced by Asp, as CxxDxxCxxxCP, indicating the second iron–sulfur cluster coordinates most likely 3Fe–4S instead of 4Fe–4S. The membrane association of the glycolate dehydrogenase activity agrees with three predicted transmembrane regions on the iron–sulfur domain.Key words: algae, Chlamydomonas, CO2, glycolate, lactate, mitochondria, photorespiration, photosynthesis.

Metabolic engineering with Dof1 transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions

Utilization of transcription factors might be a powerful approach to modification of metabolism for a generation of crops having superior characteristics because a single transcription factor frequently regulates coordinated expression of a set of key genes for respective pathways. Here, we apply the plant-specific Dof1 transcription factor to improve nitrogen assimilation, the essential metabolism including the primary assimilation of ammonia to carbon skeletons to biosynthesize amino acids and other organic compounds involving nitrogen in plants. Expressing Dof1 induced the up-regulation of genes encoding enzymes for carbon skeleton production, a marked increase of amino acid contents, and a reduction of the glucose level in transgenic Arabidopsis. The results suggest cooperative modification of carbon and nitrogen metabolisms on the basis of their intimate link. Furthermore, elementary analysis revealed that the nitrogen content increased in the Dof1 transgenic plants (approximately 30%), indicating promotion of net nitrogen assimilation. Most significantly, the Dof1 transgenic plants exhibit improved growth under low-nitrogen conditions, an agronomically important trait. These results highlight the great utility of transcription factors in engineering metabolism in plants.

One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat

Four hundred and seventy-eight microsatellite markers derived from expressed sequence tags (EST-SSRs) were screened among three mapping populations (W-7984xOpata 85, WOpop; LumaixHanxuan, LHpop; WenmaixShanhongmai, WSpop). The number of polymorphic EST-SSR primer pairs found in WOpop, LHpop and WSpop was 92, 58 and 29 respectively. A total of 101 EST-SSR loci amplified from 88 primer sets were distributed over the 20 chromosomes of the reference maps (no markers were located on chromosome 4B). These 101 mapped EST-SSR markers add to the existing 450 microsatellite loci previously mapped in bread wheat. Seventy-four of the 101 loci showed significant similarities to known genes, including 24 genes involved in metabolism, 4 in cellular structures, 9 in stress resistance, 12 in transcription, 2 in development, 2 transporters and 21 storage proteins. Besides gliadin and glutenin, most of the 53 genes with putative functions were mapped for the first time by EST-SSR markers in bread wheat. Sequence alignment of the mapped wheat EST-SSR loci allowed tentative assignment of functionality to the other members of grasses family. Colinearity combined with homology information offers an attractive approach to comparative genomics.

Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants

Dof (DNA-binding with one finger) domain proteins are plant-specific transcription factors with a highly conserved DNA-binding domain, which presumably includes a single C(2)-C(2) zinc finger. During the past decade, numerous Dof domain proteins have been identified in both monocots and dicots including maize, barley, wheat, rice, tobacco, Arabidopsis, pumpkin, potato, and pea. Biochemical, molecular biological and molecular genetic analyses revealed that Dof domain proteins function as a transcriptional activator or a repressor involved in diverse plant-specific biological processes. Although more physiological roles of Dof domain proteins would be elucidated in future because of numerous Dof domain proteins in plants, it is already evident that the Dof domain proteins play critical roles as transcriptional regulators in plant growth and development. Here I summarize our current knowledge about Dof domain proteins.

Photomorphogenic responses in maize seedling development

As an emerging maize (Zea mays) seedling senses light, there is a decrease in the rate of mesocotyl elongation, an induction of root growth, and an expansion of leaves. In leaf tissues, mesophyll and bundle sheath cell fate is determined, and the proplastids of each differentiate into the dimorphic chloroplasts typical of each cell type. Although it has been inferred from recent studies in several model plant species that multiple photoreceptor systems mediate this process, surprisingly little is known of light signal transduction in maize. Here, we examine two photomorphogenic responses in maize: inhibition of mesocotyl elongation and C4 photosynthetic differentiation. Through an extensive survey of white, red, far-red, and blue light responses among a diverse collection of germplasm, including a phytochrome-deficient mutant elm1, we show that light response is a highly variable trait in maize. Although all inbreds examined appear to have a functional phytochrome signal transduction pathway, several lines showed reduced sensitivity to blue light. A significant correlation was observed between light response and subpopulation, suggesting that light responsiveness may be a target of artificial selection. An examination of C4 gene expression patterns under various light regimes in the standard W22 inbred and elm1 indicate that cell-specific patterns of C4 gene expression are maintained in fully differentiated tissues independent of light quality. To our knowledge, these findings represent the first comprehensive survey of light response in maize and are discussed in relation to maize breeding strategies.

Functional dissections between GAMYB and Dof transcription factors suggest a role for protein-protein associations in the gibberellin-mediated expression of the RAmy1A gene in the rice aleurone

In the germinated cereal aleurone layer, gibberellic acids (GA) induce expression of a number of genes encoding hydrolytic enzymes that participate in the mobilization of stored molecules. Previous analyses suggest that the key events controlling the GA-regulated gene expression in the aleurone are formation of active transcription machinery referred to as the GA responsive complex, followed by recruiting GAMYB. In general, bipartite promoter contexts composed of the GA-responsive element and the pyrimidine box are observed within the regulatory regions of cereal GA-responsive genes. Protein factors that recognize each promoter sequence were identified and distinct effects on the GA-mediated activation of gene expression have been also investigated; however, the connection and intercalation between two promoter motifs remain obscure. In this study, I have evaluated cooperative function of GAMYB and a pyrimidine box-binding protein OsDOF3 that influenced the promoter activity of the most predominant GA-responsive gene (RAmy1A) of rice (Oryza sativa). Transient expression of OsDOF3 in the germinated aleurone prolonged GAMYB function on the reporter expression in the absence of GA. The synergistic effect required a set of DNA bindings of two proteins on the RAmy1A promoter region. The yeast two-hybrid assay showed the physical interaction of GAMYB and OsDOF3 in yeast cells, indicating that the association of GAMYB and OsDOF3 may be a functional unit in transcription regulation. The results showed the accessory function of OsDOF3 responsible for a dosage-dependent mediation of GA signaling that leads to high-level expression of physiological target genes.

Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid

Overexpression of a salicylic-acid (SA)-inducible Arabidopsis DNA binding with one finger (Dof) transcription factor, called OBF-binding protein 3 (OBP3; AtDof3.6), has previously been shown to result in growth defects. In this study, suppressive subtraction hybridization (SSH) was used to isolate genes induced in an OBP3-overexpression line and several putative clones, called OBP3-responsive genes (ORGs), were isolated. The link with the induced expression levels of these genes and OBP3 overexpression was confirmed by analysing additional OBP3-overexpression lines. ORG1 through ORG4 are novel genes, while ORG5 is an extensin gene, AtExt1. While ORG4 has no similarity with other proteins in the database, ORG1 has weak similarity in different regions of the predicted protein with CDC2 and fibrillin. ORG2 and ORG3 share 80% overall identity in their deduced amino acid sequences and contain a basic helix-loop-helix DNA-binding domain, suggesting that ORG2 and ORG3 may be transcription factors. The expression of the ORG1, ORG2 and ORG3 genes was co-regulated under all conditions examined including upregulation by SA and downregulation by jasmonic acid (JA). Fifteen OBP3-silenced lines were generated to further explore the function of OBP3. Although there were no visible phenotypic changes in any of these lines, the expression of ORG1, ORG2 and ORG3 was reduced. Among the ORG genes, ORG1, ORG2 and ORG3 contained the highest number of potential Dof-binding sites in the promoter region, and their expression was significantly increased within 3 h after induction of OBP3 expression using an inducible promoter system, and closely reflected the expression levels of the exogenous OBP3 protein. The results from the gain-of-function and loss-of-function experiments suggest that the ORG1, ORG2 and ORG3 genes are direct target genes of OBP3.

The interaction of DOF transcription factors with nucleosomes depends on the positioning of the binding site and is facilitated by maize HMGB5

The expression of genes involved in C(4) photosynthesis in maize is under tight tissue-specific and light-dependent control. There is strong evidence that this control is at least in part brought about by DOF transcription factors binding to the respective promoters. We analyzed the interaction of DOF1 and DOF2 proteins with a functional and a cryptic endogenous binding site derived from the maize phosphoenolpyruvate carboxylase promoter (-300 bp region) in the nucleosomal context. Various DNA fragments comprising this promoter region were reconstituted into mononucleosomes from purified components, resulting in different positions of the DOF binding sites on the nucleosome surface. Binding of recombinant transcription factors to the different types of nucleosomes was examined using electrophoretic mobility shift assays. Changing the translational position of the binding site on the nucleosome surface strongly affected the efficiency of the interaction with the DOF factors. Deletion of individual recognition motifs revealed a positive impact of DOF protein binding to the main binding site on interactions with the cryptic binding site. The addition of the chromosomal high-mobility group (HMG) protein HMGB5 to the binding reaction mixture facilitated nucleosome binding of the transcription factor independent from the position of the recognition sites. The relevance of the data for the activation of the promoter in vivo is discussed.

SAD: a new DOF protein from barley that activates transcription of a cathepsin B-like thiol protease gene in the aleurone of germinating seeds

Functional analysis of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, has identified a GA-responsive complex (GARC) as a tripartite element containing a pyrimidine-box motif 5'-CCTTTT-3'. We describe here the characterization of a new barley gene (Sad gene) encoding a transcription factor (SAD) of the DNA binding with One Finger (DOF) class that binds to the pyrimidine box in vitro and activates transcription of a GA-induced protease promoter in bombarded aleurone layers. RT-PCR and in situ hybridization analyses showed that the Sad transcripts accumulated in all tissues analysed, being especially abundant in the scutellum and aleurone cells upon seed germination. The SAD protein, expressed in bacteria, binds in a specific manner to two oligonucleotides containing the sequence 5'-G/CCTTTT/C-3', derived from the promoter region of the Al21 gene encoding a cathepsin B-like cysteine protease. Although the Sad transcript accumulation did not respond to external GA-incubation in aleurone cells, in transient expression experiments in co-bombarded aleurone layers, SAD trans-activated transcription from the Al21 promoter in a similar manner as did GAMYB, a MYB protein previously shown to respond to GA and to activate several hydrolase gene promoters in barley aleurone cells. In vivo interaction between the GAMYB and SAD proteins was shown in the yeast two-hybrid system, where GAMYB potentiates the SAD trans-activation capacity through interaction with its C-terminal domain.

Isolation and promoter analysis of two genes encoding different endo-beta-1,4-glucanases in the non-climacteric strawberry

Two endo-beta-1,4-glucanase (EGase; EC 3.2.1.4.) genes, highly expressed during ripening of the non-climacteric strawberries (Fragariaxananassa Duch. cv. Chandler), were isolated. Serial promoter deletions of both genes (i.e. FaEG1 and FaEG3) fused to GUS were transiently assayed in strawberry fruits by using a technique recently developed in this laboratory. Although differences were observed with the short fragments, GUS activity became comparable with the largest fragments of both promoters. The apparently similar strength of the two largest promoter fragments was in contrast with previous results of Northern analyses which demonstrated different transcripts amounts for the two genes. The inclusion of the 3' flanking region of both genes in the transient assays showed that, in the case of FaEG3, the 3' region had a down-regulating effect on the expression of GUS, and this might account for the lower amount of FaEG3 mRNA usually observed in ripe fruits compared to that of FaEG1. Downstream instability elements might be involved in such down-regulation.

The Dof family of plant transcription factors

Dof proteins are members of a major family of plant transcription factors. The proteins have similar DNA-binding properties because of the highly conserved DNA-binding domain. However, recent studies are disclosing their diverse roles in gene expression when associated with plant-specific phenomena including light, phytohormone and defense responses, seed development and germination. Based on the structural diversity indicated by the complete catalog of Arabidopsis Dof proteins, Dof genes appear to have evolved multiple times, preceding and paralleling the diversification of angiosperms. Such gene multiplication might have led to the functional diversification of Dof proteins proceeding differently in distinct plant species.

Specificity of the stimulatory interaction between chromosomal HMGB proteins and the transcription factor Dof2 and its negative regulation by protein kinase CK2-mediated phosphorylation

The high mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that can contribute to transcriptional control by interaction with certain transcription factors. Using the transcription factor Dof2 and five different maize HMGB proteins, we have examined the specificity of the HMGB-transcription factor interaction. The HMG-box DNA binding domain of HMGB1 is sufficient for the interaction with Dof2. Although all tested HMGB proteins can interact with Dof2, the various HMGB proteins stimulate the binding of Dof2 to its DNA target site with different efficiencies. The HMGB5 protein is clearly the most potent facilitator of Dof2 DNA binding. Maximal stimulation of the DNA binding by the HMGB proteins requires association of HMGB and Dof2 prior to DNA binding. HMGB5 and Dof2 form a ternary complex with the DNA, but within the protein-DNA complex the interaction of HMGB5 and Dof2 is different from that in solution, as in contrast to the proteins in solution, they cannot be cross-linked with glutaraldehyde when bound to DNA. Phosphorylation of HMGB1 by protein kinase CK2 abolishes the interaction with Dof2 and the stimulation of Dof2 DNA binding. These findings indicate that transcription factors may recruit certain members of the HMGB family as assistant factors.

A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone

Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5'-CCTTTT-3'. We describe here that BPBF, a barley (Hordeum vulgare) transcription factor of the DOF (DNA-Binding with One Finger) class, previously shown to be an activator of reserve protein encoding genes during development, also has a role in the control of hydrolase genes following seed germination. Northern-blot, reverse transcriptase-polymerase chain reaction, and in situ hybridization analyses evidenced that the transcripts of the BPBF-encoding gene (Pbf), besides being present during endosperm development, are also expressed in aleurone cells of germinated seeds where they are induced by GA, an effect counteracted by abscisic acid. Electrophoretic mobility shift assays have shown that the BPBF protein binds specifically to the pyrimidine box motif in vitro within the different sequence contexts that naturally occur in the promoters of genes encoding a cathepsin B-like protease (Al21) and a low-isoelectric point alpha-amylase (Amy2/32b), both induced in the aleurone layers in response to GA. In transient expression experiments, BPBF repressed transcription of the Al21 promoter in GA-treated barley aleurone layers and reverted the GAMYB-mediated activation of this protease promoter.

Isolation and characterization of a Chlamydomonas gene that encodes a putative blue-light photoreceptor of the phototropin family

In the search for a Chlamydomonas reinhardtii photoreceptor that may mediate blue-light-induced responses we identified a gene that encodes a protein with a structure typical for that of members of the phototropin family, i.e. two LOV domains that may function in flavin mononucleotide binding and a ser/thr kinase domain. The amino acid sequences of these domains are closely related to those of higher plant phototropins. This single-copy gene (Phot) encodes a protein with a calculated molecular mass of 81.4 kDa which is distinctly smaller than the homologous proteins of higher plants that exhibit molecular masses around 120 kDa. Expression analyses revealed rather constant levels of Phot mRNA and Phot protein in vegetative cells incubated in the dark and in cells undergoing gametogenesis. Only vegetative cells in the light showed a reduced expression of the Phot gene. Cell fractionation studies revealed that the protein is membrane-associated. In higher plants, phototropins were shown to be bound to the plasma membrane. However, the expression of a Phot-GFP gene fusion in tobacco protoplasts revealed an association of the fusion protein with the endogenous membrane network of the cell.

A novel family of calmodulin-binding transcription activators in multicellular organisms

Screening of cDNA expression libraries derived from plants exposed to stress, with 35S-labeled recombinant calmodulin as a probe, revealed a new family of proteins containing a transcription activation domain and two types of DNA-binding domains designated the CG-1 domain and the transcription factor immunoglobulin domain, ankyrin repeats, and a varying number of IQ calmodulin-binding motifs. Based on domain organization and amino acid sequence comparisons, similar proteins, with the same domain organization, were identified in the genomes of other multicellular organisms including human, Drosophila, and Caenorhabditis, whereas none were found in the complete genomes of single cell eukaryotes and prokaryotes. This family of proteins was designated calmodulin-binding transcription activators (CAMTAs). Arabidopsis thaliana contains six CAMTA genes (AtCAMTA1-AtCAMTA6). The transcription activation domain of AtCAMTA1 was mapped by testing a series of protein fusions with the DNA-binding domain of the bacterial LexA transcription factor and two reporter genes fused to LexA recognition sequences in yeast cells. Two human proteins designated HsCAMTA1 and HsCAMTA2 were also shown to activate transcription in yeast using the same reporter system. Subcellular fractionation of Arabidopsis tissues revealed the presence of CAMTAs predominantly in the nucleus. Calmodulin binding assays identified a region of 25 amino acids capable of binding calmodulin with high affinity (K(d) = 1.2 nm) in the presence of calcium. We suggest that CAMTAs comprise a conserved family of transcription factors in a wide range of multicellular eukaryotes, which possibly respond to calcium signaling by direct binding of calmodulin.

Inactivation of the phloem-specific Dof zinc finger gene DAG1 affects response to light and integrity of the testa of Arabidopsis seeds

We show here that seeds from the knockout mutant of the Arabidopsis DAG1 gene encoding a Dof zinc finger transcription factor have an altered response to red and far-red light. Mutant dag1 seeds are induced to germinate by much lower red light fluence rates, and germination reaches more quickly a point where it is independent of phytochrome signaling. Moreover, although microscopic analysis reveals no obvious structural alterations in the seed coat (testa) of dag1 seeds, staining assays with different dyes point to an abnormal fragility of the testa. By extensive in situ mRNA hybridization analysis we show here that the gene, which is not expressed in the embryo, is specifically expressed in the phloem of all organs of the mother plant.

Molecular cloning and functional expression of the gene for a cotton Delta-12 fatty acid desaturase (FAD2)

Two overlapping genomic clones spanning 16.5 kb of cotton DNA were found to encompass a Delta-12 fatty acid desaturase (FAD2-3) gene. A partial FAD2-3 cDNA clone was also analyzed. The FAD2-3 gene has one large intron of 2967 bp entirely within its 5'-untranslated region, only 12 bp upstream from the ATG initiation codon. Several potential promoter elements, including several light-responsive motifs, occur in the 5'-flanking region. The continuous FAD2-3 coding region is 1155 bp and would encode a protein of 384 amino acids. The polypeptide has four putative membrane-spanning helices, indicative of an integral membrane protein, and is most likely localized in the endoplasmic reticulum. Yeast cells transformed with a plasmid construct containing the cotton FAD2-3 coding region accumulate an appreciable amount of linoleic acid (18:2), not normally present in wild-type yeast cells, indicating that the gene encodes a functional FAD2 enzyme.

Involvement of TAAAG elements suggests a role for Dof transcription factors in guard cell-specific gene expression

Due to their unique structure and function, guard cells have attracted much attention at the physiological level. Very little, however, is known about the molecular events involved in the determination and maintenance of guard cell specificity. The KST1 gene encodes a K+ influx channel of guard cells in potato, and was therefore chosen as a model to study regulation of guard cell-specific gene expression. Transgenic potato plants carrying a fusion between the KST1 promoter and the E. coli uidA (beta-glucuronidase) reporter gene revealed promoter activity in guard cells and in flowers. A detailed dissection of the KST1 promoter led to the discovery of two independent small TATA box-proximal regulatory units, each of which was sufficient to direct guard cell-specific gene transcription. Both fragments contain the sequence motif, 5'-TAAAG-3', which is related to known target sites for a novel class of zinc finger transcription factors, called Dof proteins. Block mutagenesis of these Dof target sites in the context of different promoter constructs dramatically reduced guard cell promoter activity. A Dof gene, StDof1, was cloned and shown to be expressed in epidermal fragments highly enriched for guard cells. In gel retardation experiments, the StDof1 protein interacted in a sequence-specific manner with a KST1 promoter fragment containing the TAAAG motif. These results provide evidence that TAAAG elements are target sites for trans-acting Dof proteins controlling guard cell-specific gene expression. Our data will add to the design of tailor-made guard cell promoters as a further tool in molecular engineering of guard cell function and, hence, control of stomatal carbon dioxide (CO2) uptake and water loss in crop plants.

The transcriptional activation domain of the plant-specific Dof1 factor functions in plant, animal, and yeast cells

Maize Dof1, one of the plant-specific Dof transcription factors, is involved in light-regulated gene expression. To elucidate the molecular mechanism underlying the activity of Dof1, in vivo functional analyses were carried out using transient expression assays with maize mesophyll protoplasts. The results suggest that the Dof domain alone, the region conserved among Dof factors, can mediate interaction with DNA in vivo and distinct Dof1 activities in greening and etiolated protoplasts. A region rich in basic amino acids was identified as a nuclear localization signal. Deletion analysis defined the transcriptional activation domain of 48 amino acids located in the C-terminus of Dof1. This activation domain was also found to be functional in both human cells and yeast, implying that Dof1 may stimulate transcription through a mechanism evolutionarily conserved among eukaryotes. A computer homology search with known transcription factors revealed that the activation domain of Dof1 displayed only a limited similarity to Activation domain II of animal transcription factor GATA-4. Mutational analysis revealed the critical role of a tryptophan residue within the activation domain of Dof1, as had been shown in Activation domain II of GATA-4.

Database-assisted promoter analysis

The analysis of regulatory sequences is greatly facilitated by database-assisted bioinformatic approaches. The TRANSFAC database contains information on transcription factors and their origins, functional properties and sequence-specific binding activities. Software tools enable us to screen the database with a given DNA sequence for interacting transcription factors. If a regulatory function is already attributed to this sequence then the database-assisted identification of binding sites for proteins or protein classes and subsequent experimental verification might establish functionally relevant sites within this sequence. The binding transcription factors and interacting factors might already be present in the database.