GT-1 binding site confers light responsive expression in transgenic tobacco

The promoter from the rice nuclear gene encoding chloroplast aldolase confers mesophyll-specific and light-regulated expression in transgenic tobacco

The rice genome contains at least four separate loci that encode aldolase isozymes. Among these, the aldolase P (AldP) gene, a nuclear gene coding for chloroplast aldolase, is expressed predominantly in the leaf blade mesophyll cells in rice. To dissect promoter elements that regulate such tissue- or cell type-specific expression, we constructed various AldP promoter-beta-glucuronidase (GUS) fusion genes and transferred them into Nicotiana tabacum (tobacco) plants. Analysis of GUS activities in the transgenic tobacco revealed the presence of at least two elements within 2.0 kb AldP promoter region. One is located within the segment from position -2.0 kb to -1.2 kb and acts as a negative element. The other is a positive element located between -1.2 kb and -0.31 kb that confers developmentally regulated, mesophyll cell-specific expression. In addition, the 1.2 kb rice promoter segment flanking the transcription start site contains an element(s) that serves as target for light induction in tobacco. The results suggest that the AldP gene promoter of rice, a monocot promoter, can function in an essentially physiological manner in the dicot tobacco plant.

Light intensity regulation of cab gene transcription is signaled by the redox state of the plastoquinone pool

The eukaryotic green alga Dunaliella tertiolecta acclimates to decreased growth irradiance by increasing cellular levels of light-harvesting chlorophyll protein complex apoproteins associated with photosystem II (LHCIIs), whereas increased growth irradiance elicits the opposite response. Nuclear run-on transcription assays and measurements of cab mRNA stability established that light intensity-dependent changes in LHCII are controlled at the level of transcription. cab gene transcription in high-intensity light was partially enhanced by reducing plastoquinone with 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU), whereas it was repressed in low-intensity light by partially inhibiting the oxidation of plastoquinol with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). Uncouplers of photosynthetic electron transport and inhibition of water splitting had no effect on LHCII levels. These results strongly implicate the redox state of the plastoquinone pool in the chloroplast as a photon-sensing system that is coupled to the light-intensity regulation of nuclear-encoded cab gene transcription. The accumulation of cellular chlorophyll at low-intensity light can be blocked with cytoplasmically directed phosphatase inhibitors, such as okadaic acid, microcystin L-R, and tautomycin. Gel mobility-shift assays revealed that cells grown in high-intensity light contained proteins that bind to the promoter region of a cab gene carrying sequences homologous to higher plant light-responsive elements. On the basis of these experimental results, we propose a model for a light intensity signaling system where cab gene expression is reversibly repressed by a phosphorylated factor coupled to the redox status of plastoquinone through a chloroplast protein kinase.

Binding site requirements and differential representation of TGF factors in nuclear ASF-1 activity

Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the octopine synthase promoter. This class of cis-acting elements can respond to auxin and salicylic acid treatments. Consistent with these observations, we have shown that ASF-1 can interact with promoter elements of an auxin-inducible tobacco gene GNT35, encoding a glutathione S-transferase. Characterization of the nuclear factors that make up ASF-1 activity in vivo will be an important step toward understanding this induction phenomenon. The TGA family of basic-leucine-zipper (bZIP) proteins are good candidates for the ASF-1 nuclear factor. However, there may be as many as seven distinct TGA genes in Arabidopsis, five of which have now been reported. In this study, we expressed the cDNAs that encode four of these five Arabidopsis TGA factors in vitro and compared their DNA-binding behavior using two types of TGACG-containing elements. With specific antisera prepared against three of the five known Arabidopsis TGA factors, we also investigated the relative abundance of these three proteins within the ASF-1 activities of root and leaf nuclear extracts. Our results indicate that these TGA factors bind to DNA with different degrees of cooperativity and their relative affinity toward as-1 also can differ significantly. The results of a supershift assay suggested that only one of the three TGA factors represented a significant component of nuclear ASF-1 activity. Arabidopsis TGA2 comprises approximately 33 and 50% of the ASF-1 activity detected in root and leaf nuclear extracts respectively. These results suggest that each member of the TGA factor family may be differentially regulated and that they may play different roles by virtue of their distinct DNA-binding characteristics. Furthermore, since transcripts for each of these factors can be detected in various plant tissues, post-transcriptional regulation may play an important part in determining their contribution to nuclear ASF-1 in a given cell type.

Molecular cloning of a small DNA binding protein with specificity for a tissue-specific negative element within the rps1 promoter

A cDNA encoding a specific binding activity for the tissue-specific negative cis-element S1F binding site of spinach rps1 was isolated from a spinach cDNA expression library. This cDNA of 0.7 kb encodes an unusual small peptide of only 70 amino acids, with a basic domain which contains a nuclear localization signal and a putative DNA binding helix. This protein, named S1Fa, is highly conserved between dicotyledonous and monocotyledonous plants and may represent a novel class of DNA binding proteins. The corresponding mRNA is accumulated more in roots and in etiolated seedlings than in green leaves. This expression pattern is correlated with the tissue-specific function of the S1F binding site which represses the rps1 promoter preferentially in roots and in etiolated plants.

Functional dissection of circadian clock- and phytochrome-regulated transcription of the Arabidopsis CAB2 gene

Both the circadian clock and phytochrome regulate expression of the Arabidopsis genes encoding the light-harvesting chlorophyll a/b-binding proteins (CAB genes). Phytochrome activates CAB transcription, and it has been proposed that the circadian clock negatively regulates CAB transcription. The tobacco nuclear proteins CUF-1 (CAB upstream factor 1) and CGF-1 (CAB GATA factor 1) bind the Arabidopsis CAB2 promoter, and the CGF-1 binding site is contained within a minimal clock- and phytochrome-regulated region of the promoter. We have used in vivo cab2::luciferase gene bioluminescence markers containing site-directed mutations in the CUF-1 and CGF-1 binding sites to define the role of these proteins in CAB2 regulation and to further delineate the terminal genomic targets of the phytochrome and circadian clock signal transduction pathways. Results from these studies confirm that CUF-1 is not required to generate the circadian clock- or phytochrome-responsive CAB2 expression pattern but rather functions as a positive factor to increase CAB2 expression levels. CGF-1 interaction with the CAB2 promoter mediates the acute increase in CAB2 expression in response to phytochrome activation and contributes to the light-induced high-amplitude circadian oscillation in CAB2 expression.

Domain analysis of the plant DNA-binding protein GT1a: requirement of four putative alpha-helices for DNA binding and identification of a novel oligomerization region

Light is an important environmental signal that can influence diverse developmental processes in plants. Many plant nuclear genes respond to light at the level of transcription initiation. GT-1 and GT2 are nuclear factors which interact with DNA sequences in many light-responsive gene promoters. cDNA clones which encode proteins with sequence binding specificities similar to those of these two factors have been isolated. They show significant amino acid sequence similarities within three closely spaced, putative alpha-helices that were predicted by secondary structure analysis but do not show significant homologies with any other reported DNA-binding protein. In this work, N- and C-terminal deletions of tobacco GT1a were generated by in vitro transcription and translation, and their DNA-binding activities and subunit structures were studied. The results suggest that the C-terminal domain of GT1a is critical for protein oligomerization, while a region predicted to contain four closely spaced alpha-helices is required for DNA binding. Direct chemical cross-linking and gel filtration analyses of full-length and truncated derivatives of GT1a suggest that this factor can exist in solution as a homotetramer and that oligomerization is independent of DNA binding. This study thus establishes two independent functional domains in this class of eukaryotic trans-acting factors. Possible implications of the multimeric nature of GT1a in relation to the known characteristics of light-responsive promoter architecture are discussed.

Identification of potential regulatory elements in the far-upstream region of the Arabidopsis thaliana plastocyanin promoter

The far-upstream region of the Arabidopsis thaliana plastocyanin (Pc) promoter acts positively on transcription. This -1580 to -710 region (relative to the translation start site) has enhancer-like properties since it is also functional when situated downstream of the gene. Using tobacco nuclear extracts, this region was tested for protein-binding sites. Two short binding sequences were identified. The AT-rich sequence separating these binding sites shows extensive homology to the sequences separating the paired GT-1-binding sites of the pea rbcS-3A promoter. The requirements for complex formation strongly suggest that a GT-1-like protein binds to the two identified boxes in the Pc promoter. Sequence comparisons revealed that both boxes fit within the moderate consensus sequence needed for GT-1-binding. This GT-1-like DNA-binding activity is present in light-grown as well as in dark-adapted plants. Therefore, the possible role for GT-1 in light regulation of transcription does not depend upon its de novo synthesis. In some of the gel mobility shift assays, an additional DNA-protein complex was formed. The formation of this complex was only observed if the heteropolymer poly(dAdT).poly(dAdT) was used as a non-specific competitor and was dependent on the CpG density of the probe used.

Two distinct cis-acting elements are involved in light-dependent activation of the pea elip promoter

Light activation of the pea (Pisum sativum) elip gene promoter was analysed in transgenic plants and in transiently transfected plant protoplasts. A series of promoter deletions fused to the gusA reporter was tested, and the results obtained by the two experimental approaches were in good agreement. We identified two nucleotide sequence elements involved in light-regulated expression of the elip gene. One element is similar to the GT1 binding site of the rbcS-3A gene, and the other resembles a G-box-like ACGT element. The region containing both elements was able to confer light responsiveness on a heterologous basic promoter. Electrophoretic mobility shift assays demonstrated that each element is specifically recognized by DNA-binding proteins present in nuclear extracts from pea seedlings. The G-box-like ACGT element is necessary but not sufficient for light inducibility, indicating that the two elements act together in confering light responsiveness.

Characterization of cis-acting elements in light regulation of the nuclear gene encoding the A subunit of chloroplast isozymes of glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana

We have characterized cis-acting elements involved in light regulation of the nuclear gene (GapA) encoding the A subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in Arabidopsis thaliana. Our results show that a 1.1-kb promoter fragment of the GapA gene is sufficient to confer light inducibility and organ specificity in transgenic Nicotiana tabacum (tobacco) plants, using the beta-glucuronidase gene of Escherichia coli as the reporter gene. Deletion analysis indicates that the -359 to -110 bp region of the GapA gene is necessary for light responsiveness. Within this region there are three copies of a decamer repeat (termed the Gap box) having the consensus sequence 5'-CAAATGAA(A/G)A-3', which has not been characterized in the promoter regions of other light-regulated genes. A deletion (to -247) producing loss of one copy of these elements from the GapA promoter reduces light induction by two- to threefold compared with a promoter deletion (to -359) with all three Gap boxes present, while deletion of all three Gap boxes (to -110) abolishes light induction completely. Gel mobility shift experiments using tobacco nuclei as the source of nuclear proteins show that GapA promoter fragments that contain these repeats bind strongly to a factor in the nuclear extract and that binding can be abolished by synthetic competitors consisting only of a monomer or dimer of the Gap box. Furthermore, a trimer, dimer, and monomer of the Gap box show binding activity and, like the authentic GapA promoter-derived probes, show binding activities that are correlated with Gap box copy number. These results strongly suggest that these repeats play important roles in light regulation of the GapA gene of A. thaliana.

Characterization of cis-acting elements in light regulation of the nuclear gene encoding the A subunit of chloroplast isozymes of glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana

We have characterized cis-acting elements involved in light regulation of the nuclear gene (GapA) encoding the A subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in Arabidopsis thaliana. Our results show that a 1.1-kb promoter fragment of the GapA gene is sufficient to confer light inducibility and organ specificity in transgenic Nicotiana tabacum (tobacco) plants, using the beta-glucuronidase gene of Escherichia coli as the reporter gene. Deletion analysis indicates that the -359 to -110 bp region of the GapA gene is necessary for light responsiveness. Within this region there are three copies of a decamer repeat (termed the Gap box) having the consensus sequence 5'-CAAATGAA(A/G)A-3', which has not been characterized in the promoter regions of other light-regulated genes. A deletion (to -247) producing loss of one copy of these elements from the GapA promoter reduces light induction by two- to threefold compared with a promoter deletion (to -359) with all three Gap boxes present, while deletion of all three Gap boxes (to -110) abolishes light induction completely. Gel mobility shift experiments using tobacco nuclei as the source of nuclear proteins show that GapA promoter fragments that contain these repeats bind strongly to a factor in the nuclear extract and that binding can be abolished by synthetic competitors consisting only of a monomer or dimer of the Gap box. Furthermore, a trimer, dimer, and monomer of the Gap box show binding activity and, like the authentic GapA promoter-derived probes, show binding activities that are correlated with Gap box copy number. These results strongly suggest that these repeats play important roles in light regulation of the GapA gene of A. thaliana.

Localization of light-inducible and tissue-specific regions of the spinach ribulose bisphosphate carboxylase/oxygenase (rubisco) activase promoter in transgenic tobacco plants

Deletions in the spinach rubisco activase (Rca) promoter in transgenic tobacco were analyzed to define the regions necessary for conferring light-inducible and tissue-specific expression. Transgenic plants were constructed with Bal 31 deletions of the Rca promoter fused to the coding region of the bacterial reporter gene beta-glucuronidase (GUS). Analysis of the Rca deletion mutants localized the region conferring normal expression downstream from -294 relative to the Rca transcription start site. A second set of transgenic plants containing the cauliflower mosaic virus (CaMV) 35S enhancer fused to the 3' end of the Rca/GUS constructs demonstrated the presence of a light-responsive element between -150 and -78 active in leaves. Regions 10 bp long within the light-responsive region, which included putative G box and GT elements, were removed by recombinant polymerase chain reaction. Deletion of the G box element resulted in a loss of gene expression in the leaves of transgenic tobacco, while deletion of the GT motif caused a 10-100-fold increase in expression in roots. However, site-directed mutagenesis of the GT motif resulted in expression patterns identical to the normal promoter. These experiments demonstrated that light-inducible and tissue-specific expression of the Rca promoter involves multiple cis elements proximal to the transcription start site, and that interactions between these elements are essential for regulating expression.

DNA binding factor GT-2 from Arabidopsis

Complementary DNA clones encoding a DNA-binding factor have been obtained from Arabidopsis by DNA hybridization with a GT-2 factor cDNA clone from rice. The GT-2 gene appears to be present as a single copy in the Arabidopsis genome and is transcribed as a 2.1 kb mRNA which is not light-regulated. The longest open reading frame in the sequenced clones predicts a protein of 65 kDa, beginning with the first in-frame methionine. The protein contains basic, acidic, and proline/glutamine-rich motifs and has significant amino acid sequence homology to the rice GT-2 factor, including three regions of 50-75 amino acids each of greater than 60% identity. Two of these regions are predicted to form similar trihelix structures postulated to be involved in selective binding to specific variations of a GT-box motif DNA sequence found in the promoter regions of several plant genes. Except for weak similarity to a tobacco GT-box binding factor, GT-1a/B2F, Arabidopsis GT-2 has no similarity to other sequences in the databases. DNA-binding studies show that Arabidopsis GT-2 has binding characteristics similar to those of the rice GT-2 factor, but dissimilar to those of the tobacco GT-1a/B2F factor. The data indicate that a DNA-binding factor containing domains of similar structure and target-sequence specificity has been conserved between monocots and dicots.

Structure and expression of a nuclear gene for the PSI-D subunit of photosystem I in Nicotiana sylvestris

The PSI-D subunit is the ferredoxin-binding site of photosystem I, and is encoded by the nuclear gene psaD. We isolated a psaD genomic clone from Nicotiana sylvestris, by screening a genomic library with a psaD cDNA which we previously cloned from N. sylvestris (Yamamoto et al., Plant Mol Biol 17: 1251, 1991). Nucleotide sequence analysis revealed that this genomic clone contains a psaD gene, which does not correspond to the psaD cDNA, so we designated these genes psaDb and psaDa, respectively. The psaDb clone encodes a protein of 214 amino acids uninterrupted by introns. The N-terminal sequence determined for the N. sylvestris PSI-D protein encoded by psaDb begins at the 49th residue. The products of psaDa and psaDb share 82.7% and 79.5% identity at the amino acid and nucleotide levels, respectively. Genomic Southern analysis showed that two copies of psaD are present in the N. sylvestris genome. Ribonuclease protection assays and immunoblot analysis in N. sylvestris indicate that both genes are expressed in leaves, stems and flower buds, but neither is expressed in roots. During leaf development, the ratio of psaDb to psaDa mRNA increases from 0.12 in leaf buds to 0.36 in mature leaves. The relative abundance of the corresponding proteins decreased over the same developmental period. These results indicate that differential regulation mechanisms control psaDa and psaDb expression at both the mRNA and protein levels during leaf development.

Regulation of gene expression by light

The past year has seen significant advances in the biochemical, genetic and molecular dissection of the light signal transduction and developmental pathways that lead to photoregulated gene expression in higher plants. A major part of recent research has focused on the assignment of biological functions to the various photoreceptors, the genetic dissection of the photoreceptor action pathways, and the identification of the cis-acting sequences and trans-acting factors that regulate the downstream light-regulated genes.

The six genes of the Rubisco small subunit multigene family from Mesembryanthemum crystallinum, a facultative CAM plant

The nucleotide sequences of the entire gene family, comprising six genes, that encodes the Rubisco small subunit (rbcS) multigene family in Mesembryanthemum crystallinum (common ice plant), were determined. Five of the genes are arranged in a tandem array spanning 20 kb, while the sixth gene is not closely linked to this array. The mature small subunit coding regions are highly conserved and encode four distinct polypeptides of equal lengths with up to five amino acid differences distinguishing individual genes. The transit peptide coding regions are more divergent in both amino acid sequence and length, encoding five distinct peptide sequences that range from 55 to 61 amino acids in length. Each of the genes has two introns located at conserved sites within the mature peptide-coding regions. The first introns are diverse in sequence and length ranging from 122 bp to 1092 bp. Five of the six second introns are highly conserved in sequence and length. Two genes, rbcS-4 and rbcS-5, are identical at the nucleotide level starting from 121 bp upstream of the ATG initiation codon to 9 bp downstream of the stop codon including the sequences of both introns, indicating recent gene duplication and/or gene conversion. Functionally important regulatory elements identified in rbcS promoters of other species are absent from the upstream regions of all but one of the ice plant rbcS genes. Relative expression levels were determined for the rbcS genes and indicate that they are differentially expressed in leaves.

A 61 bp enhancer element of the tobacco beta-1,3-glucanase B gene interacts with one or more regulated nuclear proteins

We show that a 61 bp fragment derived from the promoter region of the tobacco class I beta-1,3-glucanase GLB gene enhances transcription in Nicotiana plumbaginifolia protoplasts independent of orientation relative to the start of transcription. This fragment leads to a cooperative stimulation of transcription when combined with the cauliflower mosaic virus 35S as-1 enhancer element. The GLB enhancer contains two copies of the sequence AGCCGCC, which is conserved in several genes showing expression patterns similar to the GLB gene, as well as a sequence identical at 6 of 7 bp. Point mutations in these three sequences eliminate the enhancer activity of the 61 bp fragment. Nuclear extracts prepared from leaves of tobacco plants contain one or more putative transcription factors that interact specifically with the GLB enhancer. This factor was much less abundant in nuclear extracts prepared from upper leaves of untreated tobacco plants than in nuclear extracts prepared from upper leaves of ethylene-treated plants or from lower leaves. Since beta-1,3-glucanase genes are expressed at very low levels in upper leaves of tobacco plants, at higher levels in lower leaves, and are induced in all leaves after treatment of plants with the stress hormone ethylene, we conclude that the enhancer element interacts with one or more transcription factors whose binding activity is correlated with gene expression in vivo.

Developmental and organ-specific changes in DNA-protein interactions in the tomato rbcS3B and rbcS3C promoter regions

Sites of DNA-protein interaction were mapped in the promoter regions of two of the five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) in tomato. The two genes, designated rbcS3B and -3C, are actively transcribed in cotyledons of light-grown seedlings and in leaves, but are transcriptionally inactive cotyledons of dark-grown seedlings, in young and mature tomato fruit, and in roots. The combination and order of conserved DNA sequence elements in the promoter regions of the two genes are essentially identical, but differ considerably from that found in the promoters of the other three tomato rbcS genes, which show different transcription patterns. Nuclear extracts from cotyledons of 7-day-old tomato seedlings, and from leaves and young tomato fruit of mature plants defined multiple DNase I-protected sites in the promoter regions of both genes. The protection patterns were organ-specific, and encompassed previously identified conserved DNA sequence motifs as well as uncharacterized sequences. In contrast, nuclear extracts from mature tomato fruit and roots of 7-day-old seedlings failed to protect any of the promoter sequences, implying that DNA-binding proteins required for transcription of rbcS3B and -3C are inactive in these organs. These results are somewhat surprising since DNA-binding proteins from cotyledons of dark-grown seedlings and young fruit interact with the two promoters, although rbcS3B and -3C are not transcribed in these organs. The basis for transcriptional regulation of these two genes is discussed and the detailed pattern of DNase I protection in the promoter regions of the two genes is presented.

Developmental and organ-specific changes in DNA-protein interactions in the tomato rbcS1, rbcS2 and rbcS3A promoter regions

DNase I footprinting assays were used to map sites of DNA-protein interaction in the promoter regions of three of the five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) in tomato. Organ-specific differences in DNase I protection patterns were observed using nuclear extracts derived from cotyledons, leaves, young fruit, mature fruit, and roots of tomato, implying that organ-specific transcription of these genes is controlled at the level of DNA-protein interaction. The three genes, designated rbcS1, -2 and -3A are similarly expressed in cotyledons of dark-grown seedlings, in immature tomato fruit, and in leaves under conditions of water stress. These three genes share at least three DNA sequence motifs, including the G-box sequence, which are apparently not present in the other two tomato rbcS genes. We find protection of one or more of these sequences in the aforementioned organs, indicating that the corresponding DNA-binding proteins could function in directing differential expression of the genes, although functional studies would be required to establish this point. While most of the DNase I protections encompass previously identified conserved sequence motifs and their flanking sequence, we also observe protection of additional sequences, many of which occur in the region of the transcription start site.

Homologous genes for the C4 isoform of phosphoenolpyruvate carboxylase in a C3 and a C4 Flaveria species

The C4 isoform of phosphoenolpyruvate carboxylase (PEPCase) in Flaveria trinervia is encoded by the ppcA subgroup of the PEPCase gene family and is abundantly expressed in the mesophyll cells of leaves. The homologous ppcA genes in the C3 plant F pringlei are only weakly expressed and their transcripts do not show the strictly leaf-specific accumulation pattern observed for the F. trinervia genes. Two representative members of the ppcA subfamilies of F. trinervia (C4) and F. pringeli (C3)-named ppcA1-were characterized by Southern blotting, nucleotide sequencing and primer extension analysis. Comparison of the deduced amino acid sequences reveals a close similarity between C4 and C3 isoforms. Only few C4-specific positions can be detected when all known plant PEPCases are included in the comparison. A regulatory domain involved in light-dependent phosphorylation/dephosphorylation of the C4 and crassulacean acid metabolism (CAM) isoforms is present in the ppcA1 gene products of both the C3 and C4 Flaveria. The 5' flanking regions are essentially homologous. The putative promoter regions share several identical sequence motifs (CCAAT, AT-1 and GT-1 box III/III* elements). Additionally, alterations in elements that could contribute to differences in expression rates and light regulation are found. The significance of these findings is discussed with respect to the molecular evolution of C4 photosynthesis in Flaveria.

Plant transcription factors: present knowledge and future challenges

By the use of three different experimental approaches, more than 40 cDNA clones encoding putative transcription factors have been isolated from plants. In this review, we compare the relative advantages and disadvantages of each approach, suggest methods for investigating the activity of the factors in vitro and in vivo, and discuss strategies to elucidate their physiological functions during plant growth and development.

Characterization of the interaction of plant transcription factors using a bacterial repressor protein

Transcription initiation from a eukaryotic polymerase II promoter requires a functional interaction of regulatory transcriptional activators with at least one of the basal transcription factors binding in the vicinity of the TATA box. To characterize this type of interaction in vivo, we have inserted the bacterial Tet repressor-operator complex in nine different positions between an enhancer element (as-1) and the TATA box of the cauliflower mosaic virus (CaMV) 35S RNA promoter. A direct contact between the transcriptional activator ASF-1, which binds to as-1, and the transcriptional machinery should be affected by a repressor protein bound between them, as the spacing of only 34 base pairs (bp) between as-1 and the TATA box is too short to allow looping of the DNA around the repressor. In each construct, the distance of 34 bp was kept constant, while the position of the 19-bp tet operator relative to the TATA box differed by 2 bp. Thus, the position of the Tet repressor relative to the plant transcription factors was consecutively changed by 72 degrees, which allowed us to investigate whether repression depended on the stereospecific alignment of the repressor with the transcription factors. Binding of the Tet repressor to the operator blocked transcription only when the operator was inserted less tha 5 bp from the TATA box. In all other promoter derivatives, no inhibitory effect of the repressor was observed, which suggests that ASF-1 does not directly interact with the general transcription machinery.

Deletion analysis of a phytochrome-regulated monocot rbcS promoter in a transient assay system

We have developed a transient gene expression assay system in the aquatic monocot Lemna gibba in which DNA was introduced into intact tissue by particle bombardment. Constructs based on the Lemna rbcS gene SSU5B, which is positively regulated by phytochrome in vivo, also showed phytochrome regulation in the transient assay system. Reporter gene expression increased 12-fold over dark levels in response to a single treatment with red light. This increase was not observed if far-red light was immediately followed by the red light. A 5' deletion analysis of the promoter defined a region from position -205 to position -83 relative to the start of transcription as necessary to observe the phytochrome response. This region contains the binding site for the light-induced binding activity (LRF-1) found in Lemna nuclear extracts. Upstream of position -205, we found evidence for the presence of at least two upstream activating sequences and a silencer.

Characterization of a nuclear protein that binds to three elements within the silencer region of a bean chalcone synthase gene promoter

The chalcone synthase (EC 2.3.1.74) gene promoter from the bean Phaseolus vulgaris L. contains a silencer element between positions -140 and -326 fro the transcription start site that is functional in electroporated soybean protoplasts. This element contains three binding sites for a bean nuclear factor (SBF-1) with DNA sequence recognition properties that are very similar to those of nuclear factor GT-1. By using a synthetic tetramer of one of the binding sites as probe, we have purified sequence-specific SBF-1 activity approximately 1750-fold from suspension-cell nuclei, by using a combination of ammonium sulfate precipitation, gel filtration, heparin-agarose chromatography, and sequence-specific DNA affinity chromatography. The factor exhibited an apparent molecular weight of 160,000-200,000 on the basis of gel filtration. A subunit molecular weight of approximately 95,000 was determined from SDS/polyacrylamide gel electrophoretic analysis of purified fractions, followed by Southwestern blot analysis (a protein blot probed with oligonucleotide probes), and from UV-cross-linking experiments. The factor lost DNA-binding activity on treatment with alkaline phosphatase. We discuss the properties of SBF-1 in relation to the functionality of GT-1 binding sequences in plant genes.

Multiple nuclear factors interact with upstream sequences of differentially regulated beta-conglycinin genes

The expression of the alpha' and beta subunit genes of beta-conglycinin is differentially regulated during soybean embryo development. Although both are expressed solely in developing seeds during mid to late stages of embryo development, the alpha' subunit is expressed more highly on a per gene basis, and alpha' subunit mRNA begins to accumulate three to five days earlier than beta subunit mRNA. In cultured cotyledons, beta subunit gene(s) respond to changes in methionine or abscisic acid levels, whereas expression of the alpha' subunit gene(s) is unaffected by these changes. To investigate the mechanisms by which these genes are transcriptionally regulated, we examined the interactions of nuclear proteins with upstream sequences from the alpha' and beta subunit genes. Four distinct DNA binding factors were identified in nuclear extracts from developing soybean seeds. These factors are termed Soybean Embryo Factors (SEF) 1 through 4. SEF binding sites are distributed non-uniformly between the alpha' and beta subunit genes, and the amount of protein binding is modulated over the course of embryo development. DNA footprinting revealed the sequences recognized by three of these factors. Factors which behave in a manner similar to that of SEF3 were also identified in nuclear extracts from developing tobacco and sunflower seeds.

The Cauliflower Mosaic Virus 35S Promoter: Combinatorial Regulation of Transcription in Plants

Appropriate regulation of transcription in higher plants requires specific cis elements in the regulatory regions of genes and their corresponding trans-acting proteins. Analysis of the cauliflower mosaic virus (CaMV) 35S promoter has contributed to the understanding of transcriptional regulatory mechanisms. The intact 35S promoter confers constitutive expression upon heterologous genes in most plants. Dissection into subdomains that are able to confer tissue-specific gene expression has demonstrated that the promoter has a modular organization. When selected subdomains are combined, they confer expression not detected from the isolated subdomains, suggesting that synergistic interactions occur among cis elements. The expression patterns conferred by specific combinations of 35S subdomains differ in tobacco and petunia. This indicates that a combinatorial code of cisregulatory elements may be interpreted differently in different species.

Localization of a phytochrome-responsive element within the upstream region of pea rbcS-3A

The pea rbcS-3A promoter with a 5' deletion to -166 (-166 rbcS-3A) contains two GT-1-binding sites. Mutational analyses demonstrated that a decrease in affinity for GT-1 correlates with reduced promoter activity. Transcription of -166 rbcS-3A in transgenic etiolated seedlings is induced by red light and suppressed by far-red light, indicating that it contains a phytochrome-responsive element.

Localization of a phytochrome-responsive element within the upstream region of pea rbcS-3A

The pea rbcS-3A promoter with a 5' deletion to -166 (-166 rbcS-3A) contains two GT-1-binding sites. Mutational analyses demonstrated that a decrease in affinity for GT-1 correlates with reduced promoter activity. Transcription of -166 rbcS-3A in transgenic etiolated seedlings is induced by red light and suppressed by far-red light, indicating that it contains a phytochrome-responsive element.