Nuclear proteins binding to a cauliflower mosaic virus 35S truncated promoter

Development of a salicylic acid inducible minimal sub-genomic transcript promoter from Figwort mosaic virus with enhanced root- and leaf-activity using TGACG motif rearrangement

In Figwort mosaic virus sub-genomic transcript promoter (F-Sgt), function of the TGACG-regulatory motif, was investigated in the background of artificially designed promoter sequences. The 131bp (FS, -100 to +31) long F-Sgt promoter sequence containing one TGACG motif [FS-(TGACG)] was engineered to generate a set of three modified promoter constructs: [FS-(TGACG)(2), containing one additional TGACG motif at 7 nucleotides upstream of the original one], [FS-(TGACG)(3), containing two additional TGACG motifs at 7 nucleotides upstream and two nucleotides downstream of the original one] and [FS-(TGCTG)(mu), having a mutated TGACG motif]. EMSA and foot-printing analysis confirmed binding of tobacco nuclear factors with modified TGACG motif/s. The transcription-activation of the GUS gene by the TGACG motif/s in above promoter constructs was examined in transgenic tobacco and Arabidopsis plants and observed that the transcription activation was affected by the spacing/s and number/s of the TGACG motif/s. The FS-(TGACG)(2) promoter showed strongest root-activity compared to other modified and CaMV35S promoters. Also under salicylic acid (SA) stress, the leaf-activity of the said promoter was further enhanced. All above findings were confirmed by real-time and semi-qRT PCR analysis. Taken together, these results clearly demonstrated that the TGACG motif plays an important role in inducing the root-specific expression of the F-Sgt promoter. This study advocates the importance of genetic manipulation of functional cis-motif for amending the tissue specificity of a plant promoter. SA inducible FS-(TGACG)(2) promoter with enhanced activity could be a useful candidate promoter for developing plants with enhanced crop productivity.

Transient expression in mammalian cells of transgenes transcribed from theCauliflower mosaic virus35S promoter

Gene constructs containing the Cauliflower mosaic virus (CaMV) 35S promoter and a sequence coding either for a green fluorescent protein (GFP) or for firefly luciferase were transfected into Chinese hamster ovary (CHO) cells. Both reporter genes were expressed to significant levels. The 35S promoter was 40 times less active than the human eF1 alpha promoter, which is known to be one of the most potent promoters in mammalian cells. The 35S promoter must therefore be considered to be a promoter of significant potency in mammalian cells. RT-PCR analysis suggested that transcription initiation in CHO cells occurred between the TATA box and the transcription start site of the 35S promoter that function in plant cells. Further analysis by 5'RACE confirmed that transcription was initiated in CHO cells at different sites located essentially between the TATA box and the plant transcription start site, showing that 35S promoter activity in animal cells is due to the presence of promoter elements that are functional in mammalian cells, but that are not those used in plants. The data reported here raise the possibility that genes controlled by the 35S promoter, which is commonly used in transgenic plants, have the potential for expression in animal cells.

Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential

In higher plants, activation sequence-1 (as-1) of the cauliflower mosaic virus 35S promoter mediates both salicylic acid- and auxin-inducible transcriptional activation. Originally found in viral and T-DNA promoters, as-1-like elements are also functional elements of plant promoters activated in the course of a defence response upon pathogen attack. as-1-like elements are characterised by two imperfect palindromes with the palindromic centres being spaced by 12 bp. They are recognised by plant nuclear as-1-binding factor ASF-1, the major component of which is basic/leucine zipper (bZIP) protein TGA2.2 (approximately 80%) in Nicotiana tabacum. In electrophoretic mobility shift assays, ASF-1 as well as bZIP proteins TGA2.2, TGA2.1 and TGA1a showed a 3-10-fold reduced binding affinity to mutant as-1 elements encoding insertions of 2, 4, 6, 8 or 10 bp between the palindromes, respectively. This correlated with a 5-10-fold reduction in transcriptional activation from these elements in transient expression assays. Although ASF-1 and TGA factors bound efficiently to a mutant element carrying a 2 bp deletion between the palindromes [as-1/(-2)], the latter was strongly compromised with respect to mediating gene expression in vivo. A fusion protein consisting of TGA2.2 and a constitutive activation domain mediated transactivation from as-1/(-2) demonstrating binding of TGA factors in vivo. We therefore conclude that both DNA binding and transactivation require optimal positioning of TGA factors on the as-1 element.

Tobacco transcription factor TGA2.2 is the main component of as-1-binding factor ASF-1 and is involved in salicylic acid- and auxin-inducible expression of as-1-containing target promoters

In higher plants, activating sequence-1 (as-1) of the cauliflower mosaic virus 35 S promoter mediates both salicylic acid (SA)- and auxin-inducible transcriptional activation. Originally found in promoters of several viral and bacterial plant pathogens, as-1-like elements are also functional elements of plant promoters activated in the course of a defense response upon pathogen attack. Nuclear as-1-binding factor (ASF-1) and cellular salicylic acid response protein (SARP) bind specifically to as-1. Four different tobacco bZIP transcription factors (TGA1a, PG13, TGA2.1, and TGA2.2) are potential components of either ASF-1 or SARP. Here we show that ASF-1 and SARP are very similar in their composition. TGA2.2 is a major component of either complex, as shown by supershift analysis and Western blot analysis of DNA affinity-purified SARP. Minor amounts of a protein immunologically related to TGA2.1 were detected, whereas TGA1a was not detectable. Overexpression of either TGA2.2 or a dominant negative TGA2.2 mutant affected both SA and auxin (2, 4D) inducibility of various target promoters encoding as-1-like elements, albeit to different extents. This indicates that TGA2.2 is a component of the enhancosome assembling on these target promoters, both under elevated SA and 2,4D concentrations. However, the effect of altered TGA2.2 levels on gene expression was more pronounced upon SA treatment than upon 2,4D treatment.

Characterization of two divergent endo-beta-1,4-glucanase cDNA clones highly expressed in the nonclimacteric strawberry fruit

Two cDNAs clones (Cel1 and Cel2) encoding divergent endo-beta-1, 4-glucanases (EGases) have been isolated from a cDNA library obtained from ripe strawberry (Fragaria x ananassa Duch) fruit. The analysis of the amino acid sequence suggests that Cel1 and Cel2 EGases have different secondary and tertiary structures and that they differ in the presence of potential N-glycosylation sites. By in vitro translation we show that Cel1 and Cel2 bear a functional signal peptide, the cleavage of which yields mature proteins of 52 and 60 kD, respectively. Phylogenetic analysis revealed that the Cel2 EGase diverged early in evolution from other plant EGases. Northern analysis showed that both EGases are highly expressed in fruit and that they have different temporal patterns of accumulation. The Cel2 EGase was expressed in green fruit, accumulating as the fruit turned from green to white and remaining at an elevated, constant level throughout fruit ripening. In contrast, the Cel1 transcript was not detected in green fruit and only a low level of expression was observed in white fruit. The level of Cel1 mRNA increased gradually during ripening, reaching a maximum in fully ripe fruit. The high levels of Cel1 and Cel2 mRNA in ripe fruit and their overlapping patterns of expression suggest that these EGases play an important role in softening during ripening. In addition, the early expression of Cel2 in green fruit, well before significant softening begins, suggests that the product of this gene may also be involved in processes other than fruit softening, e.g. cell wall expansion.

Roles of the 35S promoter and multiple overlapping domains in the pathogenicity of the pararetrovirus cauliflower mosaic virus

Elements associated with the 35S promoter involved in generating the pregenomic RNA (35S RNA) of the pararetrovirus cauliflower mosaic virus have been extensively studied in heterologous systems, but little is known about their role in viral pathogenicity. To investigate these elements, premature termination codons were progressively inserted into the 3' end of the adjacent gene VI to dissect it from colinear 35S enhancer sequences. The ability to cause a systemic infection in plants was retained with loss of up to 40 amino acids from the gene VI polypeptide, but truncations into a putative zinc finger proved lethal. In the 35S promoter, removal of the TATA box also abolished infectivity. However, upstream deletions encompassing the 35S enhancer showed that the sequence between -207 and -56 from the cap site comprised nonessential elements, although complete removal of this fragment caused loss of infectivity even when domain spacing was restored by linker insertion. Two separate enhancer domains (-207 to - 150 and -95 to -56) were identified, of which either one or the other, but not both, was required for infectivity. Some mutations affected the cellular levels of viral RNAs in unexpected ways, as with removal of the as-1 enhancer element causing an increase in 35S RNA. Others altered the relative abundance of nuclear and cytoplasmic viral DNAs. Mutations in promoter domains thought to be involved in regulating tissue-specific expression did not significantly affect virus accumulation in leaves versus roots, whereas gene VI mutants showed reduced root accumulation. We conclude that elements associated with the cauliflower mosaic virus 35S promoter contain extensive nonessential regions that can behave differently in their proper context than as isolated elements.

A 45-bp proximal region containing AACA and GCN4 motif is sufficient to confer endosperm-specific expression of the rice storage protein glutelin gene, GluA-3

A 45-bp proximal region of the rice glutelin promoter (-104/-60) containing two putative cis-elements, the AACA motif and GCN4 motifs, was fused to a truncated CaMV 35S promoter (-90/+9; -90 delta 35S)/GUS. The 45-bp fragment specifically enhanced the promoter activity in endosperm tissue of transformed tobacco. A substitution mutation of the GCN4 motif reduced the promoter activity, whereas mutation of the AACA motif increased the activity in the embryo as well as in the endosperm. These results suggest that the GCN4 motif generally enhances the promoter activity but that the combination of the two motifs confers the endosperm specificity. Furthermore, the function of the two motifs was dependent on the orientation and/or distance from a G-box element in -90 delta 35S, suggesting that synergistic interaction between the factors that recognize those motifs and the G-box element is important for transcriptional regulation.

Characterisation of LTR sequences involved in the protoplast specific expression of the tobacco Tnt1 retrotransposon

The tobacco Tnt1 retrotransposon is the only plant retrotransposon that has been shown to be transcriptionally active, and its transcription is strongly induced when preparing leaf-derived protoplasts. We have analysed in this paper the LTR sequences important for Tnt1 expression in tobacco protoplasts. We show that LTR sequences upstream of the TATA box are sufficient to confer protoplast-dependent induction to a heterologous promoter. We also show that this region contains two short activator elements, and that one of these sequences, BII, interacts with protoplast-specific nuclear factors.

The cauliflower mosaic virus 35S promoter is regulated by cAMP in Saccharomyces cerevisiae

The cauliflower mosaic virus 35S promoter confers strong gene expression in plants, animals and fission yeast, but not in budding yeast. On investigating this paradox, we found that in budding yeast the promoter acts through two domains. Whereas the upstream domain acts as a silencer, the downstream domain couples expression to the nutritional state of the cells via the RAS/cAMP pathway. Point mutations indicate that two boxes with similarity to the cAMP regulated element (CRE) of mammalian cells mediate this response. Gel retardation assays show that, in both yeast and plant protein extracts, factors bind to this promoter element. Therefore, transcriptional activation appears to be highly conserved at the level of transcription factors and specific DNA target elements in eukaryotes. This offers new ways to investigate gene regulation mechanisms of higher eukaryotes, which are not as amenable to genetic analysis as yeast.

MNF1, a leaf tissue-specific DNA-binding protein of maize, interacts with the cauliflower mosaic virus 35S promoter as well as the C4 photosynthetic phosphoenolpyruvate carboxylase gene promoter

When gel shift assays were performed with maize nuclear extract and a DNA fragment containing the cauliflower mosaic virus (CaMV) 35S promoter, three DNA-protein complexes were observed. Analyses with nuclear extracts prepared from green leaves, etiolated leaves, stems and roots showed that the complexes resulted from the existence of at least two nuclear factors. One of them is presumably a constitutive nuclear factor found in all tissues tested, and another is a leaf-specific factor present both in green and etiolated leaves. This leaf-specific nuclear factor seemed to be identical to MNF1, previously identified as a factor interacting with the promoter of the maize gene for phosphoenolpyruvate carboxylase involved in the C4 photosynthesis. Deletion analysis revealed that MNF1 binds to the sequence from -281 to -235 relative to the transcription start site of the CaMV 35S promoter. MNF1-like nuclear protein was also found in tobacco nuclear extracts. The possibility that MNF1 participates as a positive trans-acting factor in the expression of genes in maize leaves is discussed.

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.

Repression of the CaMV 35S promoter by the octopine synthase enhancer element

A 16 base-pair palindrome upstream of the Agrobacterium tumefaciens octopine synthase (ocs) gene functions as a positive regulatory element in plant cells (Ellis et al. (1987) EMBO J. 6, 3203-3208; Fromm et al. (1989) Plant Cell 1, 977-984). We have converted it into a negative element by locating two copies flanking the TATA-box of the constitutively expressed CaMV 35S promoter. The reduced promoter activity is very likely due to sterical hindrance of the ocs binding protein (OCSTF) x ocs complex with the transcription initiation complex. We propose that this type of constructs can be used for the identification of recognition sites for DNA-binding proteins which are labile in vitro as well as for determining the DNA-binding activity of a trans-acting factor in vivo.

Multiple interactions between tissue-specific nuclear proteins and the promoter of the phosphoenolpyruvate carboxylase gene for C4 photosynthesis in Zea mays

The expression of the phosphoenolpyruvate carboxylase (PEPC) gene involved in C4 photosynthesis is regulated in a highly organized manner. Nuclear factors interacting with DNA fragments from the 5' flanking region (from positions -1012 to +88 relative to the transcription start site) of the maize gene were identified by gel shift assays. Among the three kinds of such nuclear proteins (MNF1, MNF2a and MNF2b) found in the extract from maize leaves, MNF2a and MNF2b, which were distinguishable by their chromatographic behavior, interacted with the same motif of the repeated sequence (RS2) in the region from -432 to -201. MNF1 interacted with the region from -905 to -818 in which two copies of another kind of repeated sequence (RS1) reside. All of these nuclear factors were found only in the extracts from green and etiolated leaves but not in those from stems and roots. The relative content of MNF1 and MNF2b was almost equal in green and etiolated leaves, while that of MNF2a was significantly higher in etiolated leaves than green leaves. It is suggested that expression of the PEPC gene is controlled by the combined effects of these nuclear factors.

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.

Techniques in plant molecular biology--progress and problems

Progress in plant molecular biology has been dependent on efficient methods of introducing foreign DNA into plant cells. Gene transfer into plant cells can be achieved by either direct uptake of DNA or the natural process of gene transfer carried out by the soil bacterium Agrobacterium. Versatile gene-transfer vectors have been developed for use with Agrobacterium and more recently vectors based on the genomes of plant viruses have become available. Using this technology the expression of foreign DNA, the functional analysis of plant DNA sequences, the investigation of the mechanism of viral DNA replication and cell to cell spread, as well as the study of transposition, can be carried out. In addition, the versatility of the gene-transfer vectors is such that they may be used to isolate genes not amenable to isolation using conventional protocols. This review concentrates on these aspects of plant molecular biology and discusses the limitations of the experimental systems that are currently available.

cis regulatory elements directing tuber-specific and sucrose-inducible expression of a chimeric class I patatin promoter/GUS-gene fusion

The 5'-upstream region of the class I patatin gene B33 directs strong expression of the beta-glucuronidase (GUS) reporter gene in potato tubers and in leaves treated with sucrose. Cis-acting elements affecting specificity and level of expression were identified by deletion analysis in transgenic potato plants. A putative tuber-specific element is located downstream from position -195. Nuclear proteins present in leaf and tuber extracts bind specifically to a conserved AT rich motif within this region. A DNA fragment between -183 and -143, including the binding site is, however, not able to enhance the expression of a truncated 35S promoter from cauliflower mosaic virus. Independent positive elements contributing to a 100-fold increase relative to the basic tuber-specific element are located between -228 and -195; -736 and -509, -930 and -736 and -1512 and -951. Sucrose inducibility is controlled by sequences downstream of position -228, indicating that the tuber-specific and sucrose-inducible elements are in close proximity.

Identification of potato nuclear proteins binding to the distal promoter region of the proteinase inhibitor II gene

Potato nuclear proteins specifically bind to a DNA sequence at the most 5' distal region of the promoter of a potato proteinase inhibitor II gene. Binding studies using the electrophoretic mobility-shift assay showed the appearance of two protein-DNA complexes in the presence of both tuber and leaf nuclear protein extracts. Mechanical wounding of the leaves had no effect on the amount of specific protein-DNA complexes formed. DNase I protection analysis and binding to synthetic oligonucleotides identified the sequence 5'-GAGGGTATTTTCGTAA-3' as the target for the noncooperative binding of two potato nuclear proteins to the upstream element. Methylation interference experiments showed that guanine nucleotides separated by one turn of the DNA helix were in close contact with the proteins. The binding ability of a series of mutated synthetic oligonucleotides further defined the sequence requirements for protein binding, which appeared to contact one side of the DNA helix.

Epigenetic changes in the expression of the maize A1 gene in Petunia hybrida: role of numbers of integrated gene copies and state of methylation

The Petunia hybrida mutant RL01 is white flowering due to a genetic block in the anthocyanin pathway. The introduction of the maize A1 cDNA under the control of the CaMV 35S RNA promoter leads to the production of pelargonidin derivatives, resulting in a brick red flower phenotype. Among the transgenic petunia plants the pigmentation of the petals exhibited different expression patterns which could be categorized into the 'red', the 'variegated', and the 'white' phenotype. This system proved to be especially suitable for the investigation of gene expression by simply looking at the pigmentation pattern of the petals. The uniformity of floral pelargonidin pigmentation is inversely correlated with the number of integrated A1 copies. Furthermore, a correlation was found between the methylation status of the 35S RNA promoter and the instability of the floral pelargonidin coloration. The status of promoter methylation controlling the expression of the A1 gene seems to be influenced by the copy number and the chromosomal position of the transferred gene.