Functional characterization of the EMCV IRES in plants.

The translation of eukaryotic messenger RNA is typically dependent upon the presence of an m7GpppN cap structure at the 5' end of the transcript. However, several animal viruses, including the Picorna viruses, have been shown to exhibit cap-independent translation through the presence of an internal ribosome entry site or IRES. This IRES-mediated cap-independent internal translation initiation has been exploited to generate bicistronic transcripts that function in animal cells. Recently IRES elements have also been identified in a small number of vertebrate, insect and yeast cellular messenger RNAs although no such sequences have been identified in endogenous plant genes and there are no reports of animal virus derived IRES activity in plant cells. Here we have constructed a bicistronic gene containing both green fluorescent protein and luciferase open-reading frames separated by the encephalomyocarditis IRES element under the control of the CaMV 35S promoter. Northern analysis reveals expression of the bicistronic transcript and in vivo imaging of GFP and luciferase activities demonstrates the functional presence of both proteins. Western blot analysis confirms the independent translation of both reporter proteins. These data suggest that insertion of the encephalomyocarditis virus (EMCV) IRES element between two open-reading frames of a plant bicistronic transcript can mediate translation of the second open-reading frame. This activity is more apparent in the leaves, than in the roots, of transgenic seedlings carrying the bicistronic reporter gene construct.

Cell wall antibodies without immunization: generation and use of de-esterified homogalacturonan block-specific antibodies from a naive phage display library.

Homogalacturonan (HG) is a multi-functional pectic polysaccharide of primary cell walls involved in calcium cross-linking and gel formation, and the regulation of ionic status and porosity of the cell wall matrix, and is a source of oligosaccharins functioning in development and defence. Phase display monoclonal antibodies with specificity for de-esterified stretches ('blocks') of pectic HG have been isolated from a naive phage display library without the need for immunization of animals or conjugation of an oligosaccharide to protein. These antibodies, designated PAM1 and PAM2, bind specifically to de-esterified and un-substituted HG. Assays with a series of pectins de-esterified by the action of plant or fungal pectin methyl esterases indicated that the antibodies were specific to de-esterified blocks resulting from the blockwise action of plant pectin methyl esterases. Analysis of antibody binding to a series of oligogalacturonides indicated that optimal binding required in the region of 30 de-esterified GalA residues. The recognition of such a large epitope by these antibodies allows the HG block architecture of primary cell walls to be identified and localized for the first time. Furthermore, we have demonstrated that monoclonal antibodies with high specificity and avidity to cell wall epitopes can be generated using a 'single pot' phage display approach.

Hgm1, a novel male-specific gene from Heterodera glycines identified by differential mRNA display.

The plant parasitic nematode Heterodera glycines is amphimictic: populations consist of both male and female individuals that reproduce sexually. However, under conditions of environmental stress, unbalanced male and female sex ratios are found. This observation requires an explanation of how sexual fate is determined in these nematodes. As a step towards identifying genes that are differentially regulated between male and female nematodes we have used cDNA differential display to screen for male-specific cDNA sequences. These studies have led to the isolation of a full-length male specific cDNA, Hgm1, that is up regulated in H. glycines males. Sequence analysis of this cDNA reveals that it represents a novel gene which encodes a 49.5 kDa acidic protein with a pI of 4.72 and a predicted 21 amino acid leader sequence. Neither the nucleotide nor the predicted amino acid sequence of this gene show any homology to sequences in the databases suggesting that Hgm1 is a previously uncharacterised gene. Here we report the isolation, molecular characterisation and expression profile of Hgm1.

Laser isolation of plant sex chromosomes: studies on the DNA composition of the X and Y sex chromosomes of Silene latifolia.

X and Y sex chromosomes from the dioecious plant Silene latifolia (white campion) were isolated from mitotic metaphase chromosome preparations on polyester membranes. Autosomes were ablated using an argon ion laser microbeam and isolated sex chromosomes were then recovered on excised fragments of polyester membrane. Sex chromosome associated DNA sequences were amplified using the degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and pools of DOP-PCR products were used to investigate the genomic organization of the S. latifolia sex chromosomes. The chromosomal locations of cloned sex chromosome repeat sequences were analysed by fluorescence in situ hybridization and data complementary to laser ablation studies were obtained by genomic in situ hybridization. In combination, these studies demonstrate that the X and Y sex chromosomes of S. latifolia are of very similar DNA composition and also that they share a significant repetitive DNA content with the autosomes. The evolution of sex chromosomes in Silene is discussed and compared with that in another dioecious species, Rumex acetosa.

High-stringency subtraction for the identification of differentially regulated cDNA clones.

The technique of high-stringency subtraction described here facilitates subtractive hybridizations between directional cDNA libraries constructed in lambda ZAP II cloning vectors and represents an improvement on earlier methods for the subtraction of entire cDNA libraries. High-stringency subtraction is designed to eliminates the subtraction of differentially expressed cDNAs, which show similarity to constitutive sequences by the incorporation of a novel high-stringency wash step. This method also allows the size-selection of target cDNAs and incorporates an improved procedure for the synthesis of driver DNA used in subtractions.

Sex determination in dioecious Silene latifolia. Effects of the Y chromosome and the parasitic smut fungus (Ustilago violacea) on gene expression during flower development.

We have embarked on a molecular cloning approach to the investigation of sex determination in Silene latifolia Poiret, a dioecious plant species with morphologically distinguishable sex chromosomes. One of our key objectives was to define a range of genes that are up-regulated in male plants in response to Y chromosome sex-determination genes. Here we present the characterization of eight male-specific cDNA sequences and classify these according to their expression dynamics to provide a range of molecular markers for dioecious male flower development. Genetically female S. latifolia plants undergo a partial sex reversal in response to infection by the parasitic smut fungus Ustilago violacea. This phenomenon has been exploited in these studies; male-specific cDNAs have been further categorized as inducible or noninducible in female plants by smut fungus infection. Analysis of the organ-specific expression of male-specific probes in male and female flowers has also identified a gene that is regulated in a sex-specific manner in nonreproductive floral tissues common to both male and female plants. This observation provides, to our knowledge, the first molecular marker for dominant effect of the Y chromosome in nonreproductive floral organs.

Spatial expression dynamics of Men-9 delineate the third floral whorl in male and female flowers of dioecious Silene latifolia.

Sex determination in Silene latifolia is controlled by heteromorphic sex chromosomes. Female flowers have five fused carpels and ten arrested stamen primordia. The male-determining Y chromosome overrides female development to suppress carpel formation and promote stamen development. The isolation and characterization of two S. latifolia. Male enhanced cDNAs, Men-9a and Men-9b, which probably represent different alleles of a novel gene are reported here. Men-9a and Men-9b share 91.8% coding sequence nucleotide identity, yet only 85.4% amino acid identity. The Men-9 cDNAs are related to the previously reported MROS3 cDNA from S. latifolia. However, MROS3 is not present in the S. latifolia population used in these studies and the expression dynamics of Men-9a and Men-9b contrast dramatically with those reported for MROS3. Men-9 cDNAs are expressed primarily in anthers of young male flowers, with highest expression in 1-2 mm buds. Men-9 expression is also observed at a low level in female flowers. In situ hybridization analysis reveals two phases of Men-9 expression. The first phase is during a common stage of early stamen development in male and female flowers prior to stamen arrest in female flowers. The second phase of Men-9 expression is maximal in the epidermis and endothecium of Y chromosome- and Ustilago violacea-induced stamens; expression in male and female flowers extends to the epidermis of the staminal nectaries with strict boundaries at the second and fourth whorls, Men-9 gene expression therefore delineates the boundaries of the third floral whorl in S. latifolia flowers.

Characterization of a gene encoding a DNA binding protein with specificity for a light-responsive element.

The sequence element of box II (GTGTGGTTAATATG) is a regulatory component of a light-responsive element present within the upstream region of pea rbcS-3A. The nuclear protein GT-1 was defined previously as a DNA binding activity that interacts with box II. Here, we describe the isolation and characterization of cDNA sequences that encode a DNA binding protein with specificity for this element. The recombinant protein, tobacco GT-1a, shows similar sequence requirements for DNA binding to nuclear GT-1, as assayed by its ability to interact with previously defined 2-bp scanning mutations of box II, and is shown to be immunologically related to nuclear GT-1. The predicted structure of the 43-kD protein derived from the cDNA sequence suggests the presence of a novel helix-helix-turn-helix (HHTH) motif. Comparison between the predicted protein sequence encoded by the tobacco GT-1a cDNA and that of another GT binding protein, rice GT-2, reveals strong amino acid conservation over the HHTH region; this motif appears to be involved in the interaction between the recombinant protein and box II. Genomic DNA gel blot analysis indicated the presence of a small gene family of related sequences within the tobacco nuclear genome. RNA gel blot analysis of tobacco mRNA using the isolated cDNA as a probe showed that transcripts are present in several tissues, including both light-grown and dark-adapted leaves.

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.

Minimal sequence requirements for the regulated expression of rbcS-3A from Pisum sativum in transgenic tobacco plants.

RbcS-3A, the most highly expressed member of the pea multigene family encoding the small subunit of ribulose 1,5-bisphosphate carboxylase, is expressed in a light-dependent and organ-specific manner. In order to further delineate the sequences which mediate this complex pattern of regulation, putative regulatory sequences were assayed for function in transgenic tobacco plants in the context of an inactive 5' deleted rbcS-3A test gene. We have identified a minimal functional unit of 58 bp which is able to confer organ-specific transcriptional activity. It contains two sequences conserved among the pea rbcS family members, namely box II (-151 to -138; GTGTGGTTAATATG) and box III (-125 to -114; ATCATTTTCACT). These sequences bind the nuclear factor termed GT-1 in vitro. Substitution mutations within this 58 bp element have demonstrated that sequences upstream of, or located between, boxes II and III are not required for the transcriptional activity conferred by this element. Distance and orientation of these sequences from the gene are not critical for activity within the limits tested. DNA fragments upstream of nucleotide -170 of rbcS-3A that contain other GT-1 binding sites can also confer regulated expression upon the rbcS-3A promoter deleted to -50. Multimers of individual motifs, namely four tandem copies of boxes II and III, are unable to drive expression of the deleted promoter. These observations suggest that while GT-1 binding is necessary for promoter activity it is by itself not sufficient.

Spacing between GT-1 binding sites within a light-responsive element is critical for transcriptional activity.

Dissection of the light-responsive element (LRE) located between -166 and -50 of rbcS-3A from pea has revealed critical spacing requirements between the two GT-1 binding sites for light-responsive transcription. An increase in spacing between the two sites by as little as 2 bp reduces dramatically the rbcS-3A transcript levels in vivo. Mutation of the 10 bp between the binding sites leads to slightly lower transcript levels, as do deletions of either 3 bp or 8 bp. Deletions of 5 bp or 7 bp from between the GT-1 binding sites do not affect rbcS-3A transcript levels; however, a deletion of 10 bp virtually abolishes the activity of this element. These spacing changes within the light-responsive element similarly affect transcription of a divergently oriented and truncated nopaline synthase promoter. Most spacing changes between the two GT-1 binding sites, however, do not impair the binding of GT-1 to this element in vitro. Together with previous observations, these results suggest that the nuclear factor GT-1 may interact with the binding sites in either a productive or nonproductive manner and that GT-1 binding is necessary but not sufficient for light-responsive transcription. We also discuss our results in relation to the observed spacing of similar sequence elements present within other light-responsive promoters.

Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants.

The 35S promoter of cauliflower mosaic virus (CaMV) is able to confer high-level gene expression in most organs of transgenic plants. A cellular factor from pea and tobacco leaf tissue, which recognizes nucleotides in a tandemly repeated TGACG motif at the -75 region of this promoter, has been detected by DNase I footprinting and gel retardation assays. This factor is named activation sequence factor 1 (ASF-1). A cellular factor binding to the two TGACG motifs can also be detected in tobacco root extracts. Mutations at these motifs inhibit binding of ASF-1 to the 35S promoter in vitro. When examined in transgenic tobacco, these mutations cause a 50% drop in leaf expression of the 35S promoter. In addition, these same mutations attenuate stem and root expression of the 35S promoter about 5- to 10-fold when compared to the level of expression in leaf. In contrast, mutations at two adjacent CCAAT-box-like sequences have no dramatic effect on promoter activity in vivo. A 21-base-pair element containing the two TGACG motifs is sufficient for binding of ASF-1 in vitro when inserted in a green-tissue-specific promoter. In vivo, the insertion of an ASF-1 binding site caused high levels of expression in root. Thus, a single factor binding site that is defined by site-specific mutations is shown to be sufficient to alter the expression pattern of promoters in vivo.