The 5'-flanking regions of three pea legumin genes: comparison of the DNA sequences

Temporal and spatial control of gene expression in horticultural crops

Biotechnology provides plant breeders an additional tool to improve various traits desired by growers and consumers of horticultural crops. It also provides genetic solutions to major problems affecting horticultural crops and can be a means for rapid improvement of a cultivar. With the availability of a number of horticultural genome sequences, it has become relatively easier to utilize these resources to identify DNA sequences for both basic and applied research. Promoters play a key role in plant gene expression and the regulation of gene expression. In recent years, rapid progress has been made on the isolation and evaluation of plant-derived promoters and their use in horticultural crops, as more and more species become amenable to genetic transformation. Our understanding of the tools and techniques of horticultural plant biotechnology has now evolved from a discovery phase to an implementation phase. The availability of a large number of promoters derived from horticultural plants opens up the field for utilization of native sequences and improving crops using precision breeding. In this review, we look at the temporal and spatial control of gene expression in horticultural crops and the usage of a variety of promoters either isolated from horticultural crops or used in horticultural crop improvement.

Functional regions of the cauliflower mosaic virus 35S RNA promoter determined by use of the firefly luciferase gene as a reporter of promoter activity

The cauliflower mosaic virus (CaMV) 35S RNA promoter has been dissected and examined in a transient expression system using the firefly luciferase gene as a reporter of promoter activity. Deletion analysis has shown that the 35S RNA promoter is composed of at least three regions-distal, medial, and proximal-which are essential for activity. The distal region contains three smaller elements homologous to the simian virus 40 "core" enhancer element, the medial region possesses a CCAAT-like box, and the proximal region contains a TATA box. A DNA segment encompassing the distal region is capable of activating the CaMV 35S core promoter in an orientation-independent, but not position-independent, fashion. The distal region can also activate a heterologous weak promoter, the CaMV 19S RNA promoter, albeit not to the high levels of the 35S RNA promoter. Multimers of the distal region are able to activate the 35S RNA promoter core to even greater levels of expression than the native 35S promoter. These experiments demonstrate that elements outside the boundaries of the core promoter (composed of proximal and medial elements) are recognized in a plant cell transient expression system.

Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum

Here, we describe two nearly identical expressed genes for cytosolic glutamine synthetase (GS3A and GS3B) in Pisum sativum L. RFLP mapping data indicates that the GS3A and GS3B genes are separate loci located on different chromosomes. DNA sequencing of the GS3A and GS3B genes revealed that the coding regions are 99% identical with only simple nucleotide substitutions resulting in three amino acid differences. Surprisingly, the non-coding regions (5' non-coding leader, the 11 introns, and 3' non-coding tail) all showed a high degree of identity (96%). In these non-coding regions, 25% of the observed differences between the GS3A and GS3B genes were deletions or duplications. The single difference in the 3' non-coding regions of the GS3A and GS3B genes was a 25 bp duplication of an AU-rich element in the GS3B gene. As the GS3B mRNA accumulates to lower levels than the GS3A gene, we tested whether this sequence which resembles an mRNA instability determinant functioned as such in the context of the GS mRNA. Using the GS3B 3' tail as part of a chimeric gene in transgenic plants, we showed that this AU-rich sequence has little effect on transgene mRNA levels. To determine whether the GS3A/GS3B genes represent a recent duplication, we examined GS3-like genes in genomic DNA of ancient relatives of P. sativum. We observed that several members of the Viceae each contain two genomic DNA fragments homologous to the GS3B gene, suggesting that this is an ancient duplication event. Gene conversion has been invoked as a possible mechanism for maintaining the high level of nucleotide similarity found between GS3A and GS3B genes. Possible evolutionary reasons for the maintenance of these 'twin' GS genes in pea, and the general duplication of genes for cytosolic GS in all plant species are discussed.

Evolution of seed storage protein genes: legumin genes of Ginkgo biloba

Legumin-like seed storage proteins have been intensively studied in crop plants. However, little is known about the molecular evolution of these proteins and their genes and it was assumed that they originated from an ancestral gene that already existed at the beginning of angiosperm evolution. We have evidence for the ubiquitous occurrence of homologous proteins in gymnosperms as well. We have characterized the major seed storage globulin from Ginkgo biloba by amino acid sequencing, which reveals clear homology to legumin-like proteins from angiosperms. The Ginkgo legumin is encoded by a gene family; we describe two of its members. The promoter regions contain sequence motifs which are known to function as regulatory elements involved in seed-specific expression of angiosperm legumins, although the tissues concerned are different in gymnosperms and angiosperms. The Ginkgo legumin gene structure is divergent from that of angiosperms and suggests that the evolution of legumin genes implicated loss of introns. From our data and from functional approaches recently described it becomes obvious that the posttranslational processing site of legumin precursors is less conserved than hitherto assumed. Finally, we present a phylogenetic analysis of legumin encoding sequences and discuss their utility as molecular markers for the reconstruction of seed plant evolution.

The molecular basis for N-glycosylation in the 11S globulin (legumin) of lupin seed

Ion exchange-HPLC under denaturing conditions was used to purify to homogeneity the major M(r) 44,000 alpha subunit of lupin seed (Lupinus albus, L.) 11S storage globulin (legumin). The carboxymethylated subunit was digested with trypsin and the peptide fragments separated by reverse phase HPLC. Only one glycosylated peptide reacting with concanavalin A was identified by dot-blotting. Its amino acid sequence allowed the location of this peptide within a highly conserved region in proximity to the N-terminus of the alpha subunits of the 11S globulins from other seeds. The unique presence of a serine residue in a sequence N-X-S of lupin 11S globulin, compared with all other 11S proteins, allows it to be the only protein of this class to bear covalently linked carbohydrate.

The glycinin box: a soybean embryo factor binding motif within the quantitative regulatory region of the 11S seed storage globulin promoter

The soybean embryo factor binding sequence in the glycinin A2B1a gene promoter was delimited to an A/T-rich 9 bp sequence, 5'-TAATAATTT-3', designated as the glycinin box, by DNA footprinting and gel mobility shift assay using synthetic oligonucleotides. It was shown that the interaction with the factor takes place at a defined DNA sequence rather than at random A/T-rich sequence blocks in the glycinin 5' flanking region. There are four glycinin boxes in the quantitative regulatory region between positions -545 and -378 of the glycinin A2B1a promoter. Multiple nonamer motifs similar to the glycinin box were also found in the equivalent regions of other glycinin and legumin promoters, suggesting that they must be conserved as a binding site for the embryo factor that activates the differential and stage-specific expression of seed 11S globulin genes in leguminous plants.

cis-acting regulatory regions of the soybean seed storage 11S globulin gene and their interactions with seed embryo factors

A 2.2 kb fragment containing the 5'-flanking region of the soybean glycinin A2B1a gene and its successive deletions with a shorter 5'-flanking sequence were fused, in frame, to the beta-glucuronidase (GUS) reporter gene. The resultant fusions were introduced into tobacco plants via Agrobacterium tumefaciens. Assays of the GUS activity in seeds of transgenic tobacco showed that the upstream region, -657 to -327 (relative to the transcription initiation site [+1]), of the glycinin gene is required for optimal expression of the transformed gene. Interactions between embryo nuclear factors and DNA fragments covering the downstream region of -326, in which are included the TATA box and legumin boxes, were not apparent. The embryo factors capable of binding specifically to three subregions, -653 to -527, -526 to -422, and -427 to -321, of the upstream regulatory region were detected. Such factors appeared to be organ-specific and could be found solely in developing seeds at the early middle stage of embryogenesis (around 24 days after flowering). Evidence obtained by characterizing the nature of the binding proteins and by gel mobility shift assays established that the same factor does interact with a consensus motif 5'-ATA/TATTTCN-/CTA-3' which occurs four times in the cis-acting regulatory region between -657 and -327. Moreover, this conserved motif could also be found in the 5' regulatory region of another glycinin A1aB1b gene. Thus it is likely that the observed interaction between the nuclear factor and the conserved motifs would lead to activation of transcription from the glycinin genes in maturing soybean seeds.

Sequences flanking the hexameric G-box core CACGTG affect the specificity of protein binding

The CACGTG G-box motif is a highly conserved DNA sequence that has been identified in the 5' upstream region of plant genes exhibiting regulation by a variety of environmental signals and physiological cues. Gel mobility shift assays using a panel of G-box oligonucleotides differing in their flanking sequences identified two types of binding activity (A and B) in a cauliflower nuclear extract. Competition gel retardation assays demonstrated that the two types of binding activity were distinct. Type A binding activity interacted with oligonucleotides designated as class I elements, whereas type B binding activity interacted strongly with class II elements and weakly with class I elements. A third class of elements, null elements, did not exhibit any detectable binding under our assay conditions. Gel retardation analysis of nonpalindromic hybrid G-box oligonucleotides indicated that hybrid elements of the same class exhibited binding affinity commensurate with the affinity of the weaker element, hybrid class I/II elements exhibited only type B binding, and hybrid class I/null and class II/null elements did not show any detectable binding activity. These binding activities can be explained by the affinity of bZip G-box binding homo- or heterodimer subunits for G-box half sites. These experiments led to a set of classification rules that can predict the binding activity of all reported plant G-box motifs containing the consensus hexameric core. Tissue- and/or development-specific expression of genes containing G-box motifs may be regulated by the affinity of G-box proteins for the different classes of G-box elements.

Interaction of seed nuclear proteins with transcriptionally-enhancing regions of the pea (Pisum sativum L.) legA gene promoter

An 873-basepairs promoter fragment (-833 to +40), of the legA (legumin seed storage protein) gene of pea is known to be fully functional in transgenic plants. This fragment has been enzymically cleaved, and the products examined for the ability to interact specifically with nuclear proteins. Use of DNA-binding and mobility-shift assays has shown that promoter sequences between -316 and +40 do not form stable complexes with seed nuclear extracts. Fragments from -549 to -316 and -833 to -582, however, did interact strongly with seed, but not leaf, nuclear proteins. Each probe reacted similarly to form three distinct and stable complexes, although only the complex with least mobility appeared to be specific when challenged with competitor DNA fragments. Competitor studies also indicate that a single factor (designated LABF1) forms these specific low-mobility complexes with both probes. Fractionation of seed nuclear proteins by sodium dodecyl sulphate polyacrylamide gel electrophoresis, followed by elution and renaturation, shows that LABF1 activity resides in the 84 000- to 116 000-Mr size range of polypeptides. The tissue-specific activity of LABF1 is temporally correlated with legumin gene expression, a relationship consistent with suggestions that this factor may act as a transcriptional enhancer.

Developmental and environmental regulation of pea legumin genes in transgenic tobacco

Two distinct legumin genes (LegA1 and LegA2) which encode a major class of seed storage protein in pea were isolated from a genomic library. The cloned fragments were introduced into tobacco via Agrobacterium-mediated transformation and the regenerated plants were used to study the expression characteristics of the genes in a heterologous host. It was found that both LegA1 and LegA2 were functional members of the pea legumin gene family and that their expression was similar in both pea and transgenic tobacco. Legumin was detected only in the seed of tobacco where the primary translation products were processed in a manner analogous to that which occurs in pea. Legumin gene expression was also shown to be temporally regulated during seed development. Legumin polypeptides and mRNA began to accumulate 16 days after flowering (DAF), in contrast to the endogenous tobacco storage proteins which were apparent at 13 DAF. It was also demonstrated that the legumin genes in tobacco were environmentally regulated to the nutritional status of the plant. As has been previously shown in pea, legumin accumulation in transgenic tobacco seed was progressively reduced when the plants were grown under conditions of increasing severity of sulphur-nutrient stress. The reduced accumulation of protein was correlated with lower levels of legumin mRNA in the developing seed. Despite encoding nearly identical subunits, nucleotide sequence data for LegA1 and LegA2 showed that the similarity of their respective 5'-flanking regions was restricted to several short elements mostly within 240 bp from the start of transcription. However, a deletion series using the LegA1 gene demonstrated that 237 bp of 5'-flanking sequence was insufficient to permit the expression of the legumin gene in tobacco. The data indicated that an as yet unidentified sequence element(s) located between positions -668 and -237 was essential in re-establishing the high level of regulated gene expression observed with the full-length LegA1 gene.

Molecular cloning, genomic organization, expression and evolution of 12S seed storage protein genes of Arabidopsis thaliana

We have identified a number of genes of the flowering plant Arabidopsis thaliana that are abundantly expressed during embryogenesis. In this paper we discuss four of these genes, which comprise a gene family: complete genomic nucleotide sequence of two of the genes and partial sequence of the other two shows that they are all homologous to the 12S globulin seed storage protein genes of other angiosperms. The four genes fall into three subfamilies, as defined by cross-hybridization. One subfamily contains two genes in the Landsberg erecta strain, but only a single gene in the Columbia strain of Arabidopsis. The other two of these 12S gene subfamilies contain only single genes in both strains. Thus, the seed storage protein gene family in Arabidopsis appears much simpler than that in other higher plants.These genes are expressed during the latter half of embryogenesis, a period in which abscisic acid (ABA) is thought to play a role in gene regulation, and known to play a role in seed physiology. We observed no significant difference in the expression profiles of these four genes in ABA-deficient and ABA-insensitive mutants of Arabidopsis, except that the onset of detectable expression of all of the transcripts is slightly delayed in both types of mutants.

The sequence of a gene encoding convicilin from pea (Pisum sativum L.) shows that convicilin differs from vicilin by an insertion near the N-terminus

The sequence of a gene encoding convicilin, a seed storage protein in pea (Pisum sativum L.), is reported. This gene, designated cvcA, is one of a sub-family of two active genes. The transcription start of cvcA was mapped. Convicilin genes are expressed in developing pea seed cotyledons, with maximum levels of the corresponding mRNA species present at 16-18 days after flowering. The gene sequence shows that convicilin is similar to vicilin, but differs by the insertion of a 121-amino-acid sequence near the N-terminus of the protein. This inserted sequence is very hydrophilic and has a high proportion of charged and acidic residues; it is of a similar amino acid composition to the sequences found near the C-terminal of the alpha-subunit in pea legumin genes, but is not directly homologous with them. Comparison of this sequence with the 'inserted' sequence in soya-bean (Glycine max) conglycinin (a homologous vicilin-type protein) suggests that the two insertions were independent events. The 5' flanking sequence of the gene contains several putative regulatory elements, besides a consensus promoter sequence.

A transposon-like structure in the 5' flanking sequence of a legumin gene from Pisum sativum

The legumin storage proteins of Pisum sativum are coded for by a multigene family. An insertion element (Pis1) has been found integrated into the 5' flanking sequence of the legC legumin seed storage protein gene. This element contains all the sequence features of the CACTA family of insertion elements, has perfect 12 bp inverted repeats at its termini, and generates a target host site duplication upon integration. An 8 bp sequence within the left arm of the insertion element shows perfect homology to a sequence in the legC flanking region. Three stem-loop structures which can be formed within the element have the same stem sequence.

The pea lectin gene family contains only one functional gene

Molecular hybridization experiments have shown that the pea genome contains four regions which hybridize with pea lectin cDNA (Kaminski, Buffard, and Strosberg, 1986. Plant Science 46, 111-116). The complete organization of the pea lectin gene family was investigated. Four partial EcoRI genomic libraries were screened with a lectin cDNA (pPS 15-50) covering the entire coding region. Four positive recombinant phages, λI 101, λI 52, λIII 51 and λIV 22, were isolated and the DNA sequences of the subclones, designated respectively PSL1, PSL2, PSL3 and PSL4, were determined. PSL2, PSL3 and PSL4 are incomplete genes; the presence of several stop codons in the correct reading frames indicate that these genes cannot code for a functional lectin protein. The sequences of PSL1 and pPS 15-50 have identical coding regions. The pea lectin gene has no intervening sequences and is flanked at its 5' region by a sequence containing an exceptionally high A+T content (73%). Eucaryotic consensus sequences such as a TATA box and a polyadenylation signal are also found in the flanking regions of the PSL1 clone.

An inspection of the domain between putative TATA box and translation start site in 79 plant genes

Over 75 published genomic DNA sequences from several higher plants have been collected and flanking regions of the leader sequences have been analysed. In a majority of the plants, the first AUG codon on processed mRNA acted as a translation initiation site. The consensus sequence for the context was TAAACAATGGCT (on plus strand of DNA). This differed from the earlier suggestion for eukaryotic mRNAs based mainly on data from animals. Leader sequences were generally 40-80 nucleotides in length and were A+T rich. Adenine was present in a majority of the cases at the transcription start site which was flanked by pyrimidine bases. The putative TATA box was present 32 +/- 7 nucleotides upstream from the transcription initiation site. The consensus sequence for TATA box and surrounding region was TCACTATATATAG.

Functional analysis of regulatory elements in a plant embryo-specific gene

Previously we demonstrated the expression of a plant embryo-specific gene encoding the alpha' subunit of beta-conglycinin, a seed storage protein of soybean (Glycine max), in transgenic petunia plants. To examine the regulatory elements that control the expression of this embryo-specific gene (Gmg17.1), a series of deletion mutants was made that contain the alpha'-subunit gene flanked in the 5' direction from +14 nucleotides to -8.5 kilobases (kb) relative to the site of transcription initiation. Each of these deletion mutants was introduced into the genome of petunia cells with the help of Ti-plasmid-derived vectors. Petunia plants were regenerated from transformed cells and expression of the introduced soybean gene was examined. When the alpha'-subunit gene was flanked by 159 nucleotides upstream (Gmg17.1 delta-159), the gene was expressed at a low level in immature embryos. When the gene was flanked by 257 nucleotides upstream of the site of transcription initiation (Gmg17.1 delta-257), a high level of expression was obtained. An additional 8 kb of DNA sequence (which includes the sequence GTGGATAG at -560, which is identical to the core enhancer sequence of simian virus 40 and some animal genes) did not significantly increase the level of expression. The increase in expression level between the delta-159 and delta-257 mutants was at least 20-fold. Analysis of the nucleotides between delta-159 and delta-257 reveals four repeats of a 6-base-pair (G + C)-rich sequence (see formula in text). The deletion Gmg17.1 delta-159 contains a single AACCCA sequence. We suggest that the (G + C)-rich repeats play a critical role in determining the level of expression of the transgenic plants.