Functions of OsDof25 in regulation of OsC4PPDK.

Relative little is known about the functions of the so-called Dof zinc factors in plants. Here we report on the analysis of OsDof25 and show a function in regulation of the important C4 photosynthesis gene, OsC4PPDK in rice. Over-expression of OsDof25 enhanced the expression of OsC4PPDK in transient expression experiments by binding in a specific way to a conserved Dof binding site which was confirmed by yeast and in vitro binding studies. Expression studies using promoter GUS plants as well as qPCR experiments showed that OsDof25 expressed in different tissues including both photosynthetic and non-photosynthetic organs and that expression of OsDof25 was partially overlapping with the OsC4PPDK gene. Conclusive evidence for a role of OsDof25 in regulation of C4PPDK came from loss-of-function and gain-of-function experiments with transgenic rice, which showed that down-regulation or over-expression of OsDof25 correlated with OsC4PPDK expression and that OsDof25 has functions as transcriptional activator.

Transcription and somatic transposition of the maize En/Spm transposon system in rice.

Transposition of the maize En/Spm system in rice was investigated using a two-component construct consisting of an immobilised transposase source driven by the CaMV 35S-promoter, and a modified I/dSpm transposon. Mobilization of I/dSpm in somatic sectors was demonstrated by sequencing of excision products and isolation of flanking genomic sequences in T0 and T1 progeny plants. Since the transposition efficiency appeared to be considerably lower than that observed in maize or in other heterologous systems like Arabidopsis, we examined En/Spm transcription and splicing in the transgenic rice plants. Northern analysis revealed the presence of transcripts encoding the active TnpA and TnpD transposases, with the latter predominating; this is the reverse of what is seen in maize and Arabidopsis. RT-PCR analysis confirmed the occurrence of correct splicing and the formation of the two other alternatively spliced transcripts (TnpB and TnpC), as previously described for maize. Two alternative splice donor sites at the end of exon 1 were identified in maize at positions 578 and 704. We observe that rice is similar to maize in that TnpA is preferentially spliced at position 578. We also show that in Arabidopsis splicing occurs preferentially at position 704, as in other dicots like tobacco. These observations indicate differences in the splicing of transcripts of the maize En/Spm element between dicot and monocot hosts. Nevertheless, the ratio in which the transcripts for the active transposases are produced seems to determine the efficiency of transposition, irrespective of the host considered. A limiting amount of TnpA might therefore be responsible for the lower transposition activity of En/Spm in rice. Alternatively, reduced mobility of the modified I/dSpm element used may have resulted from the absence of critical sequences necessary for transposition. The influence of endogenous, autonomous, En/Spm -related elements present in the rice genome on the transposition behaviour of the exogenous maize element is also considered.

Transpositional behaviour of an Ac/Ds system for reverse genetics in rice.

A collection of transposon Ac/ Ds enhancer trap lines is being developed in rice that will contribute to the development of a rice mutation machine for the functional analysis of rice genes. Molecular analyses revealed high transpositional activity in early generations, with 62% of the T0 primary transformants and more than 90% of their T1 progeny lines showing ongoing active transposition. About 10% of the lines displayed amplification of the Ds copy number. However, inactivation of Ds seemed to occur in about 70% of the T2 families and in the T3 generation. Southern blot analyses revealed a high frequency of germinal insertions inherited in the T1 progeny plants, and transmitted preferentially over the many other somatic inserts to later generations. The sequencing of Ds flanking sites in subsets of T1 plants indicated the independence of insertions in different T1 families originating from the same T0 line. Almost 80% of the insertion sites isolated showing homology to the sequenced genome, resided in genes or within a range at which neighbouring genes could be revealed by enhancer trapping. A strategy involving the propagation of a large number of T0 and T1 independent lines is being pursued to ensure the recovery of a maximum number of independent insertions in later generations. The inactive T2 and T3 lines produced will then provide a collection of stable insertions to be used in reverse genetics experiments. The preferential insertion of Ds in gene-rich regions and the use of lines containing multiple Ds transposons will enable the production of a large population of inserts in a smaller number of plants. Additional features provided by the presence of lox sites for site-specific recombination, or the use of different transposase sources and selectable markers, are discussed.

Highly efficient production and characterization of T-DNA plants for rice ( Oryza sativa L.) functional genomics.

We investigated the potential of an improved Agrobacterium tumefaciens-mediated transformation procedure of japonica rice ( Oryza sativa L.) for generating large numbers of T-DNA plants that are required for functional analysis of this model genome. Using a T-DNA construct bearing the hygromycin resistance ( hpt), green fluorescent protein ( gfp) and beta-glucuronidase ( gusA) genes, each individually driven by a CaMV 35S promoter, we established a highly efficient seed-embryo callus transformation procedure that results both in a high frequency (75-95%) of co-cultured calli yielding resistant cell lines and the generation of multiple (10 to more than 20) resistant cell lines per co-cultured callus. Efficiencies ranged from four to ten independent transformants per co-cultivated callus in various japonica cultivars. We further analysed the T-DNA integration patterns within a population of more than 200 transgenic plants. In the three cultivars studied, 30-40% of the T(0) plants were found to have integrated a single T-DNA copy. Analyses of segregation for hygromycin resistance in T(1) progenies showed that 30-50% of the lines harbouring multiple T-DNA insertions exhibited hpt gene silencing, whereas only 10% of lines harbouring a single T-DNA insertion was prone to silencing. Most of the lines silenced for hpt also exhibited apparent silencing of the gus and gfp genes borne by the T-DNA. The genomic regions flanking the left border of T-DNA insertion points were recovered in 477 plants and sequenced. Adapter-ligation Polymerase chain reaction analysis proved to be an efficient and reliable method to identify these sequences. By homology search, 77 T-DNA insertion sites were localized on BAC/PAC rice Nipponbare sequences. The influence of the organization of T-DNA integration on subsequent identification of T-DNA insertion sites and gene expression detection systems is discussed.

Glucocorticoid-inducible gene expression in rice.

We have studied the use of a glucocorticoid receptor-based inducible gene expression system in the monocotyledonous model plant rice (Oryza sativa L.). This system, originally developed by T. Aoyama and N.-H. Chua [(1997) Plant J 11: 605-612], is based on the chimaeric transcriptional activator GVG, consisting of the yeast Gal4 DNA-binding domain, the VP16 activation domain and the glucocorticoid receptor domain. For application in rice, we designed an optimized binary vector series (pINDEX) and tested this with the beta-glucuronidase (gusA) reporter gene. GUS expression was tightly controlled and relatively low concentrations (1-10 microM) of the glucocorticoid hormone dexamethasone (DEX) were able to induce GUS activities to levels comparable to those conferred by the strong cauliflower mosaic virus (CaMV) 35S promoter. DEX was taken up efficiently by the roots of tissue-cultured plantlets or mature plants in hydroponic culture, and induced GUS activity throughout the whole plant. DEX-induced GUS expression patterns were consistent in all lines and their T1 progeny. The phenotype of tissue-cultured rice plantlets was not affected when inductions with 10-100 microM DEX were limited to 1-4 days or when 2-week inductions were performed with 1 microM DEX, which was already sufficient to reach near-maximal GUS activity. However, 2-week inductions with 10 microM DEX caused growth retardation and developmental defects. As the severity of these effects varied between different lines, we could select lines with a mild phenotype for future use as activator lines in crosses with 'target' plants.

Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis.

A GFP excision assay was developed to monitor the excision of Ac introduced into rice by Agrobacterium-mediated transformation. The presence of a strong double enhancer element of the CaMV 35S promoter adjacent to the Ac promoter induced very early excision, directly after transformation into the plant cell, exemplified by the absence of Ac in the T-DNA loci. Excision fingerprint analysis and characterization of transposition events from related regenerants revealed an inverse correlation between the number of excision events and transposed Ac copies, with single early excisions after transformation generating Ac amplification. New transpositions were generated at a frequency of 15-50% in different lines, yielding genotypes bearing multiple insertions, many of which were inherited in the progeny. The sequence of DNA flanking Ac in three representative lines provided a database of insertion tagged sites suitable for the identification of mutants of sequenced genes that can be examined for phenotypes in a reverse genetics strategy to elucidate gene function. Remarkably, two-thirds of Ac tagged sites showing homology to sequences in public databases were in predicted genes. A clear preference of transposon insertions in genes that are either predicted by protein coding capacity or by similarity to ESTs suggests that the efficiency of recovering knockout mutants of genes could be about three times higher than random. Linked Ac transposition, suitable for targeted tagging, was documented by segregation analysis of a crippled Ac element and by recovery of a set of six insertions in a contiguous sequence of 70 kb from chromosome 6 of rice.

Yeast one-hybrid screening for DNA-protein interactions.

One-hybrid screening in yeast is a powerful method to rapidly identify heterologous transcription factors that can interact with a specific regulatory DNA sequence of interest (the bait sequence). In this technique, the interaction between two proteins (bait and prey) is detected via in vivo reconstitution of a transcriptional activator that turns on expression of a reporter gene. Detection is based on the interaction of a transcription factor (prey) with a bait DNA sequence upstream of a reporter gene. To ensure that DNA binding results in reporter-gene activation, cDNA expression libraries are used to produce hybrids between the prey and a strong trans-activating domain. The advantage of cloning transcription factors or other DNA-binding proteins via one-hybrid screenings, compared to biochemical techniques, is that the procedure does not require specific optimization of in vitro conditions.

Identification of UV-B light-responsive regions in the promoter of the tryptophan decarboxylase gene from Catharanthus roseus.

The tryptophan decarboxylase (Tdc) gene encodes a key enzyme in the biosynthesis of terpenoid indole alkaloids (TIAs) in Catharanthus roseus. TIAs absorb ultraviolet light (UV) and putative functions in plants include a role as UV protectants. In support of this possible function we demonstrate here that UV light induces accumulation of several TIAs as well as expression of the Tdc gene in C. roseus. In addition, in tobacco a Tdc-gusA construct was found to be specifically induced by UV-B light. Lack of induction by UV-A or other wavelengths of light indicate that Tdc expression is regulated by a specific UV-B receptor and corresponding signal transduction pathway. To identify UV-responsive Tdc promoter elements, a loss-of-function analysis was performed, in which deletion derivatives were fused to the gusA reporter gene and analysed in transgenic tobacco plants. Truncation of the Tdc promoter from -1818 (relative to the start of transcription) to -160 reduced expression levels two-fold without affecting the qualitative UV response. Deletion to -37 further reduced expression levels five-fold, but the delta37 promoter also remained UV-responsive. Subsequently, the -160 to -37 region was further studied by gain-of-function experiments, in which the transcriptional activities of tetramerized subfragments fused to truncated promoters were analysed. Combination of the data identified several functional regions in the -160 to +198 promoter. The - 160 to -99 region acts as the main transcriptional enhancer. UV-responsive elements appeared to be redundant in the -160 Tdc promoter and to reside between -99 and -37 and between -37 and + 198.

Nuclear factors GT-1 and 3AF1 interact with multiple sequences within the promoter of the Tdc gene from Madagascar periwinkle: GT-1 is involved in UV light-induced expression.

Plant secondary metabolites of the terpenoid indole alkaloid (TIA) class comprise several compounds with pharmaceutical applications. A key step in the TIA biosynthetic pathway is catalysed by the enzyme tryptophan decarboxylase (TDC), which channels the primary metabolite tryptophan into TIA metabolism. In Catharanthus roseus (Madagascar periwinkle), the Tdc gene is expressed throughout plant development. Moreover, Tdc gene expression is induced by external stress signals, such as fungal elicitor and UV light. In a previous study of Tdc promoter architecture in transgenic tobacco it was shown that the -538 to -112 region is a quantitative determinant for the expression level in different plant organs. Within this sequence one particular region (-160 to -99) was identified as the major contributor to basal expression and another region (-99 to -37) was shown to be required for induction by fungal elicitor. Here, the in vitro binding of nuclear factors to the -572 to -37 region is described. In extracts from tobacco and C. roseus, two binding activities were detected that could be identified as the previously described nuclear factors GT-1 and 3AF1, based on their mobility and binding characteristics. Both factors appeared to interact with multiple regions in the Tdc promoter. Mutagenesis of GT-1 binding sites in the Tdc promoter did not affect the basal or elicitor-induced expression levels. However, induction of the Tdc promoter constructs by UV light was significantly lower, thereby demonstrating a functional role for GT-1 in the induction of Tdc expression by UV light.

A G-box element from the Catharanthus roseus strictosidine synthase (Str) gene promoter confers seed-specific expression in transgenic tobacco plants.

The enzyme encoded by the strictosidine synthase (Str) gene from Catharanthus roseus catalyses a key step in the biosynthesis of the pharmaceutically important terpenoid indole alkaloids. Str cDNA and genomic clones have already been isolated, allowing us to study the regulation of Str gene expression. Here we focus on the role of a putative cis-acting element, CACGTG, in the Str promoter. This sequence is known as a G-box, and functions as a transcription-regulating sequence in a number of other promoters. By means of electrophoretic mobility shift assays it was demonstrated that the Str G-box is capable of interacting with nuclear factors in tobacco and with the cloned tobacco G-box-binding factor TAF-1. Disruption of the Str G-box sequence by two single-nucleotide mutations prevented binding of factors, thereby demonstrating the specificity of the observed interactions. Functional analysis in transgenic tobacco plants demonstrated that these mutations also reduced the transcriptional activity of constructs containing tetramers of the Str G-box sequence. Expression directed by a tetramer of the Str G-box fused to a truncated promoter containing only a TATA box was confined to seeds and was found to increase during seed maturation. Thus, the Str G-box tetramer is able to direct seed-specific expression independently of other regulatory sequences. G-box-directed expression in leaves required the presence of an enhancer region from the cauliflower mosaic virus (CaMV) 35S promoter. The results indicate that the G-box needs to interact with other elements to drive expression in leaf, and that it can by itself confer seed-specific expression as a multimer. The fact that only some of the G-boxes found in different promoters serve as seed-specific elements indicates that sequences flanking the G-box determine the transcriptional activity in different tissues. Based on sequence comparisons we propose that the nucleotides at positions -4, -3, -2 and/or +4 are important in determining seed-specific expression.

The promoter of the strictosidine synthase gene from periwinkle confers elicitor-inducible expression in transgenic tobacco and binds nuclear factors GT-1 and GBF.

Strictosidine synthase (STR) is a key enzyme in the biosynthesis of terpenoid indole alkaloids. This class of secondary metabolites harbours several pharmaceutically important compounds used, among other applications, in cancer treatment. Terpenoid indole alkaloid biosynthesis and expression of biosynthetic genes including Str1 is induced by fungal elicitors. To identify elicitor-responsive regulatory promoter elements and trans-acting factors, the single-copy Str1 gene was isolated from the subtropical plant species Catharanthus roseus (Madagascar periwinkle). Str1 upstream sequences conferred elicitor-responsive expression to the beta-glucuronidase (gusA) reporter gene in transgenic tobacco plants. Main enhancer sequences within the Str1 promoter region studied were shown to be located between -339 and -145. This region and two other regions of the promoter bound the tobacco nuclear protein factor GT-1. A G-box located around position -105 bound nuclear and cloned G-box-binding factors (GBFs). A mutation that knocked out GBF binding had no measurable effect on expression, which indicates that the G-box is not essential for the elicitor responsiveness of the Str1 promoter. No obvious homologies with promoter elements identified in other elicitor-responsive genes were observed, suggesting that the Str1 gene may depend on novel regulatory mechanisms.

Elicitor-responsive promoter regions in the tryptophan decarboxylase gene from Catharanthus roseus.

The tryptophan decarboxylase (Tdc) gene from Catharanthus roseus (Madagascar periwinkle) encodes a key enzyme in biosynthesis of terpenoid indole alkaloids. The expression of the Tdc gene is transcriptionally induced by fungal elicitors. Tdc upstream sequences from -1818 to +198 relative to the transcriptional start site were functionally analysed to identify cis-acting elements that determine basal expression or respond to elicitor. In a loss-of-function analysis promoter derivatives with 5' or internal deletions fused to the gusA reporter gene were analysed in transgenic tobacco plants. Whereas promoter activity dropped considerably following deletion down to -160, this short promoter derivative was still elicitor-responsive. Subsequently, the -160 to -37 region was further studied by gain-of-function experiments, in which subfragments were tested as tetramers cloned on two different truncated promoters. Combination of the data resulted in the identification of three functional regions in the -160 promoter. The region between -160 to -99 was shown to act as the main transcriptional enhancer. Two separable elicitor-responsive elements were found to reside between -99 and -87 and between -87 and -37. These two elements are not redundant in the Tdc promoter, since their combination gave a distinct elicitor response.

Vectors for transcription factor cloning and target site identification by means of genetic selection in yeast.

We describe the construction of a number of vectors that can be used in yeast genetic selection systems for cloning of transcription factors or other DNA-binding proteins and for identification of the target sites recognized by transcription factors. For transcription factor cloning we have designed an integration vector with two HIS3 reporter gene cassettes to stably integrate reporter gene constructs at the non-essential yeast PDC6 locus. This set of plasmids was tested in a one-hybrid assay with the rice transcription factor Oshox1, a member of the class of homeodomain leucine zipper proteins. A hybrid protein of Oshox1 and the Gal4 transcriptional activation domain was shown to specifically activate a reporter gene construct with upstream Oshox1 binding sites, which had been integrated at the PDC6 locus using the described vector system. Target site identification by genetic selection in yeast employs a transcriptional activator construct and a library of genomic or random DNA fragments upstream of a reporter gene. We have constructed two variants of a bacteriophage lambda vector which facilitates the construction of the required reporter gene library because of high cloning efficiency and easy conversion into a yeast/Escherichia coli shuttle vector library by Cre-loxP-mediated automatic subcloning. Tests with Oxhox1 as transcriptional activator demonstrated the usefulness of the deprived reporter gene vector.

Versatile transformation vectors to assay the promoter activity of DNA elements in plants.

A convenient vector system was developed to evaluate transcriptional promoter activities in plants. Two primary vectors, optionally containing the cauliflower mosaic virus (CaMV) 35S -47 or -90 minimal promoters, offer multiple sites for cloning the sequence of interest upstream from the beta-glucuronidase gene (gusA). The promoter-gusA cassette can be transferred to a binary vector containing the selectable neomycin phosphotransferase II-encoding gene (nptII) next to the left border. In addition, the transferred DNA (T-DNA) contains the chloramphenicol acetyltransferase gene (cat) driven by the CaMV 35S promoter. Activity of cat can serve as a reference for gusA expression to correct for effect of chromosomal position or T-DNA copy number.

Characterization of the Ac/Ds behaviour in transgenic tomato plants using plasmid rescue.

We describe the use of plasmid rescue to facilitate studies on the behaviour of Ds and Ac elements in transgenic tomato plants. The rescue of Ds elements relies on the presence of a plasmid origin of replication and a marker gene selective in Escherichia coli within the element. The position within the genome of modified Ds elements, rescued both before and after transposition, is assigned to the RFLP map of tomato. Alternatively to the rescue of Ds elements equipped with plasmid sequences, Ac elements are rescued by virtue of plasmid sequences flanking the element. In this way, the consequences of the presence of an (active) Ac element on the DNA structure at the original site can be studied in detail. Analysis of a library of Ac elements, rescued from the genome of a primary transformant, shows that Ac elements are, infrequently, involved in the formation of deletions. In one case the deletion refers to a 174 bp genomic DNA sequence immediately flanking Ac. In another case, a 1878 bp internal Ac sequence is deleted.

Ac-induced disruption of the double Ds structure in tomato.

The maize doubleDs element is stably maintained in the tomato genome. Upon the subsequent introduction of Ac into a plant containing doubleDs, disruption of the doubleDs structure and DNA rearrangements at the site of the doubleDs element were observed. No indications were obtained for excision of the complete doubleDs structure. The consequences of transactivation of doubleDs in these experiments are different from those described for transactivation of single Ds elements in tomato. The mechanisms by which such rearrangements could have occurred in tomato are discussed in relation to complex insertions containing doubleDs in maize.