Interaction of a nodule specific, trans -acting factor with distinct DNA elements in the soybean leghaemoglobin Ibc 3 5′ upstream region

Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants

Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs that function in the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells carrying thousands of intracellular bacteria without signs of immune responses, and the integration of symbiont and host metabolism. The early stages of nodulation are governed by a few well-defined functions, which together constitute the common symbiosis-signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in symbiotic cells. Many of these genes are only active in symbiotic cells, reflecting the unique nature of nodules as plant structures. Although how the nodule-specific transcriptome is activated and connected to early CSSP-signaling is poorly understood, candidate TFs have been identified using transcriptomic approaches, and the importance of epigenetic and chromatin-based regulation has been demonstrated. We discuss how gene regulation analyses have advanced our understanding of nodule organogenesis, the functioning of symbiotic cells, and the evolution of symbiosis in the NFC.

Pathogen and Circadian Controlled 1 (PCC1) regulates polar lipid content, ABA-related responses, and pathogen defence in Arabidopsis thaliana

Pathogen and Circadian Controlled 1 (PCC1) was previously characterized as a regulator of defence against pathogens and stress-activated transition to flowering. Plants expressing an RNA interference construct for the PCC1 gene (iPCC1 plants) showed a pleiotropic phenotype. They were hypersensitive to abscisic acid (ABA) as shown by reduced germination potential and seedling establishment, as well as reduced stomatal aperture and main root length in ABA-supplemented media. In addition, iPCC1 plants displayed alterations in polar lipid contents and their corresponding fatty acids. Importantly, a significant reduction in the content of phosphatidylinositol (PI) was observed in iPCC1 leaves when compared with wild-type plants. A trend in reduced levels of 18:0 and increased levels of 18:2 and particularly 18:3 was also detected in several classes of polar lipids. The enhanced ABA-mediated responses and the reduced content of PI might be responsible for iPCC1 plants displaying a complex pattern of defence against pathogens of different lifestyles. iPCC1 plants were more susceptible to the hemi-biotrophic oomycete pathogen Phytophthora brassicae and more resistant to the necrotrophic fungal pathogen Botrytis cinerea compared with wild-type plants.

Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago truncatula

Root nodules are the symbiotic organ of legumes that house nitrogen-fixing bacteria. Many genes are specifically induced in nodules during the interactions between the host plant and symbiotic rhizobia. Information regarding the regulation of expression for most of these genes is lacking. One of the largest gene families expressed in the nodules of the model legume Medicago truncatula is the nodule cysteine-rich (NCR) group of defensin-like (DEFL) genes. We used a custom Affymetrix microarray to catalog the expression changes of 566 NCRs at different stages of nodule development. Additionally, bacterial mutants were used to understand the importance of the rhizobial partners in induction of NCRs. Expression of early NCRs was detected during the initial infection of rhizobia in nodules and expression continued as nodules became mature. Late NCRs were induced concomitantly with bacteroid development in the nodules. The induction of early and late NCRs was correlated with the number and morphology of rhizobia in the nodule. Conserved 41 to 50 bp motifs identified in the upstream 1,000 bp promoter regions of NCRs were required for promoter activity. These cis-element motifs were found to be unique to the NCR family among all annotated genes in the M. truncatula genome, although they contain sub-regions with clear similarity to known regulatory motifs involved in nodule-specific expression and temporal gene regulation.

Regulated genes in transgenic plants

Transgenic plants are an effective system for the study of regulated gene expression. Developmental control of expression can be monitored by assaying different tissues or by assaying a plant at different developmental stages. Analysis of the petunia 5-enolpyruvylshikimate-3-phosphate synthase gene, which is highly expressed in flowers, allowed identification of an upstream region that confers tissue-specific and developmentally regulated expression. The cell specificity of expression in floral tissues has been defined by histochemical localization. This expression is contrasted to that of the 35S promoter of cauliflower mosaic virus, a nominally constitutive promoter that shows a definite specificity of expression in floral tissues. Moreover, this expression differs in transgenic hosts of different species.

Genomic structures and characterization of the 5'-flanking regions of acyl carrier protein and Delta4-palmitoyl-ACP desaturase genes from Coriandrum sativum

The seed-specific or seed-predominant promoters of acyl carrier protein (Cs-ACP1) and Delta4-palmitoyl-acyl carrier protein desaturase (Cs-4PAD) genes, which are involved in the biosynthesis of petroselinic acid, were isolated from coriander (Coriandrum sativum) and analyzed in coriander endosperms and transgenic Arabidopsis. The expression of Cs-ACP1 and Cs-4PAD genes was coordinately regulated during seed development.

A new rice zinc-finger protein binds to the O2S box of the α-amylase gene promoter

A putative transcription factor, named RAMY, that binds to the 20-bp O2S sequences of the regulatory region of the Amy2 gene promoter has been identified using the yeast one-hybrid system from a rice library. The full length RAMY cDNA clone encodes a 218-amino acid protein and is homologous to the late embryogenesis-abundant protein (LEA5). In vitro mutagenesis and electrophoretic mobility shift assays confirmed that RAMY can bind with O2S specifically through an unusual zinc finger with a CXCX(4)CX(2)H consensus sequence. Low levels of RAMY mRNAs were detected in rice leaves and roots by Northern blot hybridization. The plant hormone gibberellin (GA) induces expression of both RAMY and Amy2 genes, as performed by Northern blot hybridization, but the increase in RAMY mRNA level occurs prior to that of the Amy2 mRNA level in the GA-treated aleurone tissues. These data suggest that RAMY may act as a trans-acting protein and is probably involved in the GA-induced expression of the rice alpha-amylase gene.

A Promoter from Pea Gene DRR206 Is Suitable to Regulate an Elicitor-Coding Gene and Develop Disease Resistance

ABSTRACT Plant nonhost disease resistance is characterized by the induction of multiple defense genes. The pea DRR206 gene is induced following inoculation with pathogens and treatment with abiotic agents, and moderately induced by wounding. A deletion series of DRR206 promoter segments was fused with the beta-glucuronidase (GUS) reporter gene and transiently transferred to tobacco, potato, and pea. GUS activity revealed that two upstream regions of the DRR206 promoter were particularly important for activation in the three plant species. Putative cis regulatory elements within the DRR206 promoter included a wound/pathogen- inducible box (W/P-box) and a WRKY box (W-box). Gel shift assays with nuclear extracts from treated and untreated tissue with the W/P-box revealed both similar and unique protein-DNA complexes from pea, potato, and tobacco. Tobacco was stably transformed with gene constructs of the DRR206 promoter fused with a DNase elicitor gene from Fusarium solani f. sp. phaseoli, FsphDNase. Pathogenicity tests indicated that the FsphDNase elicitor conferred resistance against Pseudomonas syringae pv. tabaci and Alternaria alternata in tobacco. Transgenic potatoes showed some sensitivity to the FsphDNase gene providing less protection against Phytophthora infestans. Thus, the elicitor-coding gene, FsphDNase, is capable of generating resistance in a heterologous plant system (tobacco) when fused with defined regions of the pea DRR206 promoter.

The trans-acting protein interacting with the DNA motif proximal to the transcriptional start site of plant L-asparaginase is bacterial sarcosine oxidase

A trans-acting protein interacting with a specific sequence motif proximal to the transcriptional start site of the L-asparaginase promoter has been observed previously (E. Vincze, J. M. Reeves, E. Lamping, K. J. F. Farnden, and P. H. S. Reynolds, Plant Mol. Biol. 26:303-311, 1994). Gel retardation experiments in which protein extracts of Mesorhizobium loti and developing nodules were used suggested a bacterial origin for the repressor binding protein (rep2037). Nodulation tests were performed by using different Fix(-) Tn5 mutants of M. loti. Analyses of these mutants revealed a correlation between the presence of Mesorhizobium in the nodule-like structures and the ability of nodule protein extracts to bind the repressor binding domain (RBD). Through the use of mutated RBD sequences, the RBD sequence was identified as CTAAAAT. The repressor protein was isolated from M. loti NZP2037 by multiple chromatographic procedures and affinity separation by using concatemers of RBD attached to magnetic beads. Sequencing of the recovered protein resulted in identification of the repressor protein as the sarcosine oxidase alpha subunit. This was confirmed by expression of the gene encoding the M. loti alpha subunit of sarcosine oxidase in Escherichia coli. When the expressed peptide was bound to RBD, the gel retardation result was identical to the result obtained with rep2037 from M. loti strain NZP2037.

Regulatory regions and nuclear factors involved in nodule-enhanced expression of a soybean phosphoenolpyruvate carboxylase gene: implications for molecular evolution

We have determined the genomic organization of two closely related phosphoenolpyruvate carboxylase genes in soybean, GmPEPC7, which is expressed at high levels in root nodules, and the housekeeping gene GmPEPC15. Their nucleotide sequences, including most introns and 5;-flanking regions within 600 bp upstream from the transcription start sites, are well conserved, suggesting that they were duplicated quite recently. To gain insights into the process of evolution of the tissue-specifically expressed GmPEPC7gene, we produced chimeric constructs carrying either the GmPEPC7or GmPEPC15promoter fused to the beta-glucuronidase gene. The expression patterns of the reporter observed in nodules that developed on transgenic hairy roots reflected the levels of mRNA levels produced by the genes in wild-type soybean plants, indicating that the GmPEPC7promoter directs nodule-specific expression. Loss-of-function experiments showed that the segment of GmPEPC7between -466 and -400, designated as the "switch region" (SR), was necessary for expression in nodules, although proteins that bind to SR were not detectable in a gel-retardation assay. Another gel-retardation assay indicated that putative nodule nuclear proteins bind specifically to the region of GmPEPC7between -400 and -318, designated as the "amplifier region" (AR). Both SR and AR have characteristic sequences that are not found in the GmPEPC15promoter. Furthermore, experiments using hybrid promoters derived from GmPEPC15demonstrated that AR confers high-level expression in nodules only in combination with SR. When wild-type soybean plants were subjected to prolonged darkness and subsequently illuminated, the level of GmPEPC7mRNA in nodules decreased and then recovered. This study suggests that the acquisition of two interdependent cis-acting elements resulted in molecular evolution of the nodule-enhanced GmPEPC7gene.

A novel HMG A-like protein binds differentially to the AT-rich regions located in the far distal and proximal parts of a soybean glutamine synthetase gene (GS15) promoter

In soybean (Glycine max L.) ammonium provided externally or as the result of symbiotic nitrogen fixation stimulates the transcription of GS15, a gene encoding cytosolic glutamine synthetase. Strong constitutive positive expression (SCPE), silencer-like and organ-specific elements, located respectively in the distal, the central and the proximal region of the promoter are required to control the ammonium responsiveness of the gene expression [Tercé-Laforgue et al. (1999) Plant Mol. Biol. 39: 551]. It was hypothesized that the correct spatial conformation of the promoter permitted the cooperative action of these three cis-acting elements. Further investigations were therefore required to ascertain this hypothesis. A nodule nuclear protein, binding to a 66 bp AT-rich DNA fragment containing a 13 bp AT-rich repeated sequence (AT-1) and located just downstream of the SCPE element, was identified using a gel retardation assay. A cDNA clone likely to code for this protein was isolated using the yeast one-hybrid system. It encodes a novel DNA binding protein (AT-1SNBP) similar to HMG A proteins but exhibiting a higher molecular weight. AT-1SNBP appears to be encoded by a single gene that is expressed in roots, root nodules and leaves of soybean. Since two other 13 bp AT-rich repeated sequences (AT-2 and AT-3) were localized in the organ-specific element, we have quantified the binding affinity of AT-1SNBP to these sequences. We demonstrate that AT-1SNBP binds differentially to DNA fragments containing AT-1, AT-2 and AT-3 and that its binding affinity depends on the presence of adjacent sequences. This result suggests that AT-1SNBP may be an architectural protein involved in maintaining the spatial conformation of the GS15 promoter, thus facilitating the interaction between the distal and proximal regulatory elements.

In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato

We generated transgenic tomato plants with altered expression of heat stress transcription factor HsfA1. Plants with 10-fold overexpression of HsfA1 (OE plants) were characterized by a single HsfA1 transgene cassette, whereas plants harboring a tandem inverted repeat of the cassette showed cosuppression (CS plants) by posttranscriptional silencing of the HsfA1 gene connected with formation of small interfering RNAs. Under normal growth conditions, major developmental parameters were similar for wild-type (WT), OE, and CS plants. However, CS plants and fruits were extremely sensitive to elevated temperatures, because heat stress-induced synthesis of chaperones and Hsfs was strongly reduced or lacking. Despite the complexity of the plant Hsf family with at least 17 members in tomato, HsfA1 has a unique function as master regulator for induced thermotolerance. Using transient reporter assays with mesophyll protoplasts from WT tomato, we demonstrated that plasmid-encoded HsfA1 and HsfA2 were well expressed. However, in CS protoplasts the cosuppression phenomenon was faithfully reproduced. Only transformation with HsfA2 expression plasmid led to normal expression of the transcription factor and reporter gene activation, whereas even high amounts of HsfA1 expression plasmids were silenced. Thermotolerance in CS protoplasts was restored by plasmid-borne HsfA2, resulting in expression of chaperones, thermoprotection of firefly luciferase, and assembly of heat stress granules.

Yellow lupine cyclophilin transcripts are highly accumulated in the nodule meristem zone

Cyclophilin (CyP) is one of the enzymes that act as peptidylprolyl cis-trans isomerases (EC 5.2.1.8). The cDNA and an intronless gene coding for cytosolic CyP have been isolated from yellow lupine. The deduced amino acid sequence of the characterized open reading frame shows approximately 80% homology with cytosolic CyP from other organisms. Southern blots of genomic DNA indicate that there is a small family of genes for CyP-related genes in the yellow lupine genome. RNA blot analyses demonstrate that CyP genes are expressed in all plant organs. The amount of CyP transcripts is dramatically increased in root nodules. In situ hybridization experiments indicate that CyP transcripts are localized mainly in meristematic tissues, with the highest level observed in the nodule meristem zone. The promoter of the sequenced gene contains 5' AAAGAT 3' and AT-rich motifs that are characteristic for some nodulin promoters.

CPP1, a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene

Nodulin genes are specifically expressed in the nitrogen-fixing root nodules. We have identified a novel type of DNA-binding protein (CPP1) interacting with the promoter of the soybean leghemoglobin gene Gmlbc3. The DNA-binding domain of CPP1 contains two similar Cys-rich domains with 9 and 10 Cys, respectively. Genes encoding similar domains have been identified in Arabidopsis thaliana, Caenorhabditis elegans, the mouse, and human. The domains also have some homology to a Cys-rich region present in some polycomb proteins. The cpp1 gene is induced late in nodule development and the expression is confined to the distal part of the central infected tissue of the nodule. A constitutively expressed cpp1 gene reduces the expression of a Gmlbc3 promoter-gusA reporter construct in Vicia hirsuta roots. These data therefore suggest that CPP1 might be involved in the regulation of the leghemoglobin genes in the symbiotic root nodule.

Identification of cis-acting elements important for expression of the starch-branching enzyme I gene in maize endosperm

The genes encoding the starch-branching enzymes (SBE) SBEI, SBEIIa, and SBEIIb in maize (Zea mays) are differentially regulated in tissue specificity and during kernel development. To gain insight into the regulatory mechanisms controlling their expression, we analyzed the 5'-flanking sequences of Sbe1 using a transient gene expression system. Although the 2.2-kb 5'-flanking sequence between -2,190 and +27 relative to the transcription initiation site was sufficient to promote transcription, the addition of the transcribed region between +28 and +228 containing the first exon and intron resulted in high-level expression in suspension-cultured maize endosperm cells. A series of 5' deletion and linker-substitution mutants identified two critical positive cis elements, -314 to -295 and -284 to -255. An electrophoretic mobility-shift assay showed that nuclear proteins prepared from maize kernels interact with the 60-bp fragment containing these two elements. Expression of the Sbe1 gene is regulated by sugar concentration in suspension-cultured maize endosperm cells, and the region -314 to -145 is essential for this effect. Interestingly, the expression of mEmBP-1, a bZIP transcription activator, in suspension-cultured maize endosperm cells resulted in a 5-fold decrease in Sbe1 promoter activity, suggesting a possible regulatory role of the G-box present in the Sbe1 promoter from -227 to -220.

The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue light-dependent post-transcriptional mechanism

Cryptochrome 2 is a flavin-type blue light receptor mediating floral induction in response to photoperiod and a blue light-induced hypocotyl growth inhibition. cry2 is required for the elevated expression of the flowering-time gene CO in response to long-day photoperiods, but the molecular mechanism underlying the function of cry2 is not clear. The carboxyl domain of cry2 bears a basic bipartite nuclear localization signal, and the cry2 protein was co-fractionated with the nucleus. Analysis of transgenic plants expressing a fusion protein of CRY2 and the reporter enzyme GUS (GUS-CRY2) indicated that the GUS-CRY2 fusion protein accumulated in the nucleus of transgenic plants grown in dark or light. The C-terminal domain of cry2 that contains the basic bipartite nuclear localization signal was sufficient to confer nuclear localization of the fusion protein. Phenotypic analysis of transgenic plants expressing the fusion protein GUS-CRY2 demonstrated that GUS-CRY2 acts as a functional photoreceptor in vivo, mediating the blue light-induced inhibition of hypocotyl elongation. These results strongly suggest that cry2 is a nuclear protein. Although no obvious light regulation was found for the nuclear compartmentation of GUS-CRY2 fusion protein, the abundance of GUS-CRY2 was regulated by blue light in a way similar to that of cry2.

VsENBP1 regulates the expression of the early nodulin PsENOD12B

A DNA-binding protein, VsENBP1, previously isolated from Vicia sativa was shown to bind in a sequence-specific manner to the early nodulin ENOD12 gene promoter from Pisum sativum. Here, the functional importance of the VsENBP1 binding sites on the PsENOD12B promoter has been studied in vivo. A promoter-gusA fusion in which a mutation was introduced at the putative target sequence, AATAA, was inactive in nodules of transgenic Vicia hirsuta roots. Gel retardation assays showed that VsENBP1 does not bind to the mutated promoter segment, suggesting that VsENBP1 activates the PsENOD12B expression in nodules through its interaction with its target sequence. In the presence of the 35S enhancer, an ENOD12 promoter-GUS construct gave expression in root vascular tissue in addition to the root nodules. Overexpression of Vsenbp1 in transgenic V. hirsuta roots reduced the leaky expression in root vascular tissue in contrast to nodules in which a small increase in GUS expression was observed. The results indicate that VsENBP1 acts as a repressor of ENOD12 expression in root tissue.

NADH-glutamate synthase in alfalfa root nodules. Genetic regulation and cellular expression

NADH-dependent glutamate synthase (NADH-GOGAT; EC 1.4.1.14) is a key enzyme in primary nitrogen assimilation in alfalfa (Medicago sativa L.) root nodules. Here we report that in alfalfa, a single gene, probably with multiple alleles, encodes for NADH-GOGAT. In situ hybridizations were performed to assess the location of NADH-GOGAT transcript in alfalfa root nodules. In wild-type cv Saranac nodules the NADH-GOGAT gene is predominantly expressed in infected cells. Nodules devoid of bacteroids (empty) induced by Sinorhizobium meliloti 7154 had no NADH-GOGAT transcript detectable by in situ hybridization, suggesting that the presence of the bacteroid may be important for NADH-GOGAT expression. The pattern of expression of NADH-GOGAT shifted during root nodule development. Until d 9 after planting, all infected cells appeared to express NADH-GOGAT. By d 19, a gradient of expression from high in the early symbiotic zone to low in the late symbiotic zone was observed. In 33-d-old nodules expression was seen in only a few cell layers in the early symbiotic zone. This pattern of expression was also observed for the nifH transcript but not for leghemoglobin. The promoter of NADH-GOGAT was evaluated in transgenic alfalfa plants carrying chimeric beta-glucuronidase promoter fusions. The results suggest that there are at least four regulatory elements. The region responsible for expression in the infected cell zone contains an 88-bp direct repeat.

An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm

A cDNA encoding a DNA-binding protein of the DOF class of transcription factors was isolated from a barley endosperm library. The deduced amino acid sequence for the corresponding protein is 94% identical through the DOF domain to the prolamin-box (P-box) binding factor PBF from maize. The gene encoding the barley PBF (BPBF) maps to chromosome 7H, and its expression is restricted to the endosperm where it precedes that of the hordein genes. The BPBF expressed in bacteria as a GST-fusion binds a P-box 5'-TGTAAAG-3' containing oligonucleotide derived from the promoter region of an Hor2 gene. Binding was prevented when the P-box motif was mutated to 5'-TGTAgAc-3'. A P-box binding activity, present in barley and wheat endosperm nuclei, interacted similarly to BPBF with this synthetic oligonucleotide, and the binding was abolished by 1,10-phenanthroline. Transient expression experiments in developing barley endosperms demonstrate that BPBF transactivates transcription from the P-box element of a native Hor2 promoter and that direct binding of BPBF to its target site is essential for transactivation since mutations in the DOF DNA-binding domain or in the P-box motif of this promoter abolished both binding and transactivation. Evidence was also obtained for the presence in wheat of a Pbf homologue having similar DNA-binding properties to that of BPBF. These results strongly implicate this endosperm-specific DOF protein from barley as an important activator of hordein gene expression and suggest the evolutionary conservation of the Pbf gene function among small grain cereals.

Specific interaction of the tomato bZIP transcription factor VSF-1 with a non-palindromic DNA sequence that controls vascular gene expression

The grp1.8 gene of French bean (Phaseolus vulgaris) is specifically expressed in vascular tissue and encodes a glycine-rich structural protein (GRP1.8) of the cell wall. Earlier promoter analysis had shown that a 28 bp fragment of the grp1.8 promoter (vs-1) confers vascular expression to heterologous minimal promoters and is bound by the tomato bZIP transcription factor VSF-1. Here, we analysed the interaction of VSF-1 with fragments of the vs-1 element and studied the molecular basis of specific binding both in the DNA sequence of the promoter element as well as in the protein. The minimal binding site of VSF-1 is a 9 bp, non-palindromic sequence with two non-identical half-sites and a central nucleotide which separates them. The amino acid sequence of the VSF-1 DNA-binding basic domain has a Lys at position -10 instead of a conserved Arg found in the other bZIP factors isolated so far. This lysine was found to be required for specific recognition of the non-palindromic binding site: a mutant VSF-1 with a Lys-to-Arg substitution at position -10 bound with higher affinity to a palindromic sequence than the wild-type protein. The minimal binding site of VSF-1 was sufficient and necessary to confer vascular-specific expression to a heterologous promoter in vivo. The vsf-1 promoter also showed vascular-specific expression in transgenic tobacco. The close similarity of these expression patterns suggests that VSF-1 is specifically involved in vascular expression of the grp1.8 gene in plants.

A novel type of DNA-binding protein interacts with a conserved sequence in an early nodulin ENOD12 promoter

The pea genes PsENOD12A and PsENOD12B are expressed in the root hairs shortly after infection with the nitrogen-fixing bacterium Rhizobium leguminosarum bv. viciae or after application of purified Nod factors. A 199 bp promoter fragment of the PsENOD12B gene contains sufficient information for Nod factor-induced tissue-specific expression. We have isolated a Vicia sativa cDNA encoding a 1641 amino acid protein, ENBP1, that interacts with the 199 bp ENOD12 promoter. Two different DNA-binding domains were identified in ENBP1. A domain containing six AT-hooks interacts specifically with an AT-rich sequence located between positions -95 and -77 in the PsENOD12B promoter. A second domain in ENBP1 is a cysteine-rich region that binds to the ENOD12 promoter in a sequence non-specific but metal-dependent way. ENBP1 is expressed in the same cell types as ENOD12. However, additional expression is observed in the nodule parenchyma and meristem. The presence of three small overlapping ORFs in the 5'-untranslated region of the ENBP1 cDNA indicates that ENBP1 expression might be regulated at the translational level. The interaction of ENBP1 with a conserved AT-rich element within the ENOD12 promoter and the presence of the ENBP1 transcript in cells expressing ENOD12 strongly suggest that ENBP1 is a transcription factor involved in the regulation of ENOD12. Finally, the C-terminal region of ENBP1 shows strong homology to a protein from rat that is specifically expressed in testis tissue.

Isolation and promoter characterization of barley gene Itr1 encoding trypsin inhibitor BTI-CMe: differential activity in wild-type and mutant lys3a endosperm

The gene Itr1, encoding trypsin inhibitor BTI-CMe, has been obtained from a genomic library of Hordeum vulgare L. The gene has no introns and presents in its 5'-upstream region 605 bp that are homologous to the long terminal repeats (LTR) of the 'copia-like' retro-transposon Bare-1. Functional analysis of the Itr1 promoter by transient expression in protoplasts derived from different barley tissues, has shown that in this system the Itr1 promoter retains its endosperm specifity and the trans-regulation mediated by the Lys3a gene. The proximal promoter extending 343 bp upstream of the translation initiation ATG codon is sufficient to confer full GUS expression and for endosperm specifity. In protoplasts derived from the lys3a mutant, Risø 1508, GUS activity was less than 5% of that obtained with the same constructs in the protoplasts of wild-type Bomi from which it derives. Gel retardation experiments, after incubation with proteins obtained from both types of endosperm nuclei, also show differential patterns. Possible reasons for these differences are discussed.

Identification of tissue-specific, dehydration-responsive elements in the Trg-31 promoter

Trg-31 is a pea gene which is rapidly induced in response to dehydration stress. Trg-31 belongs to a family of membrane intrinsic proteins that play a role in facilitating inter-membrane transport. In order to understand the mechanism of regulation of Trg-31 expression we defined the cis-acting elements of the Trg-31 promoter and the trans-acting factors that interact with them. Deletion analysis of the Trg-31 promoter in transgenic tobacco plants indicated the presence of two positive regulatory region: (1) between the -1412 to -1066 nucleotides and (2) between the -559 to -391 nucleotides, with respect to the transcription initiation site. A negative regulatory element was also identified between -1066 and -559 nucleotides. All three regulatory regions specifically regulated Trg-31 induction in leaf tissue and had little or no effect on Trg-31 induction in root tissue. Gel-mobility shift assays indicated the presence of leaf nuclear proteins that interacted with the -1412 to -1066 and -1066 to -559 regions and an 'ABRE-like' sequence at -74 in the 5' promoter region of Trg-31.

The regulator of MAT2 (ROM2) protein binds to early maturation promoters and represses PvALF-activated transcription

The regulation of maturation (MAT)- and late embryogenesis (LEA)-specific gene expression in dicots involves factors related to ABI3, a seed-specific component of the abscisic acid signal transduction pathways from Arabidopsis. In French bean (Phaseolus vulgaris), the ABI3-like factor, PvALF, activates transcription from MAT promoters of phytohemagglutinin (DLEC2) and beta-phaseolin (PHS beta) genes. We describe the regulator of MAT2 (ROM2) as a basic leucine zipper (bZIP) DNA binding protein that recognizes motifs with symmetric (ACGT) and asymmetric (ACCT) core elements present in both MAT promoters. ROM2 antagonizes trans-activation of the DLEC2 promoter by PvALF in transient expression assays. Repression was abolished by mutations that prevented binding of ROM2 to the DLEC2 seed enhancer region. Moreover, a hybrid protein composed of a PvALF activation domain and the DNA binding and dimerization domain of ROM2 activated gene expression, indicating that ROM2 recognizes the DLEC2 enhancer in vivo; consequently, ROM2 functions as a DNA binding site-dependent repressor. Supershift analysis of nuclear proteins, using a ROM2-specific antibody, revealed an increase in ROM2 DNA binding activity during seed desiccation. A corresponding increase in ROM2 mRNA coincided with the period when DLEC2 mRNA levels declined in embryos. These results demonstrate developmental regulation of the ROM2 repressor and point to a role for this factor in silencing DLEC2 transcription during late embryogenesis.

gsa1 is a universal tetrapyrrole synthesis gene in soybean and is regulated by a GAGA element

Expression of plant tetrapyrroles is high in photosynthetic tissues and in legume root nodules in the form of chlorophyll and heme, respectively. The universal tetrapyrrole precursor delta-aminolevulinic acid (ALA) is synthesized from glutamate 1-semialdehyde (GSA) by GSA aminotransferase in plants, which is encoded by gsa. Immunoblot analysis showed that GSA aminotransferase was expressed in soybean leaves and nodules, but not in roots, and that protein correlated with enzyme activity. These observations indicate that GSA aminotransferase expression is controlled in tetrapyrrole formation and argue against significant activity of an enzyme other than the well described aminotransferase for GSA-dependent ALA formation. gas mRNA and protein were induced in soybean nodules, and their activation was temporally intermediate between those of the respective early and late genes endo2 and lb. A GSA aminotransferase gene, designated gsa1, was isolated and appears to be one of two gsa genes in the soybean genome. gsa1 mRNA accumulated to high levels in leaves and nodules, but not in uninfected roots as discerned with a gsa1-specific probe. Message levels were higher in leaves from etiolated plantlets than in mature plants, and expression in the former was slightly elevated by light. The expression pattern of gsa1 mRNA was qualitatively similar to that of total gsa. The data strongly suggest that gsa1 is a universal tetrapyrrole synthesis gene and that a gsa gene specific for a tissue, tetrapyrrole, or light condition is unlikely. The gsa1 promoter contained a genetic element found in numerous Drosophila melanogaster genes; the so-called GAGA element displayed single-stranded character in vitro and formed a complex with nuclear factors from nodules and leaves but not from roots. From these observations we infer that the GAGA element is involved in the transcriptional control of gsa1.

A plant basal in vitro system supporting accurate transcription of both RNA polymerase II- and III-dependent genes: supplement of green leaf component(s) drives accurate transcription of a light-responsive rbcS gene

An in vitro transcription initiation system has been developed from nuclei of rapidly growing, non-green tobacco (Nicotiana tabacum) cultured (BY-2) cells. Conditions for nuclear extraction and in vitro transcription reaction have been optimized with a tobacco beta-1,3-glucanase gene, a constitutively expressed gene in BY-2 cells. The in vitro system supports accurate transcription of RNA polymerase II-dependent promoters from not only plant genes (tobacco beta-1,3-glucanase gene, cauliflower mosaic virus 35S promoter) but also animal genes (adenovirus 2 major late promoter, simian virus 40 early major promoter). In addition, this system drives accurate transcription of an RNA polymerase III-dependent Arabidopsis thaliana U6 snRNA gene. As BY-2 cells do not differentiate in response to light or any other stimuli, they would provide a basal transcription system which lacks tissue-specific and light-responsive nuclear signals as well as chloroplast-derived signals. Consequently, the BY-2 cell-free system is unable to transcribe the tomato gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS3C) whose expression is tissue-specific and light-inducible. However, the transcription of rbcS3C was obtained by supplementing the BY-2 system with a nuclear extract of light-grown tomato seedlings. The promoter regions necessary for rbcS transcription was mapped in vitro using a series of 5' deletion mutants. The 351 bp upstream sequence is essential and the further upstream region from -351 to -441 enhances its transcription. The in vitro basal system will be useful to identify specific signals from both the nucleus and chloroplast in green leaves and other organs/tissues.

Analysis of the lupin Nodulin-45 promoter: conserved regulatory sequences are important for promoter activity

The promoter from the Lupinus angustifolius late nodulin gene, Nodulin-45, has been analysed to identify cis-elements and trans-acting factors. Various regions of the Nodulin-45 promoter, fused to the luciferase reporter gene, were introduced into Lotus roots using an Agrobacterium rhizogenes, transformation procedure. The transgenic roots were then nodulated. The promoter region A (-172 to +13, relative to the transcription start site) was capable of directing low-level expression of the reporter gene and in a nodule-enhanced manner when compared to roots. The addition of region C (-676 to -345) resulted in a significant increase in the expression within the nodule, whilst a low level of root expression was maintained. The C region, which confers this high-level nodule expression, contains the nodule consensus motifs AAAGAT and CTCTT. When region C was ligated to a minimal promoter element from the unrelated asparaginase gene rather than the Nodulin-45 A region, nodule-enhanced expression was still apparent, but at a much lower level. Mutation of the AAAGAT element in this construct resulted in a further significant decrease of expression. Gel retardation assays revealed that a factor from lupin nodule nuclear extracts interacted with two sequences of the C region. The binding of the factor to both of these regions could be removed by the addition of an oligonucleotide containing the AT-rich binding site for the soybean factor NAT2. This suggests that the lupin factor identified here is a NAT2 homologue. No factor binding was observed to the AAAGAT or CTCTT elements present in the C region.

Identification of several soybean cytosolic glutamine synthetase transcripts highly or specifically expressed in nodules: expression studies using one of the corresponding genes in transgenic Lotus corniculatus

A DNA fragment containing sequences hybridizing to the 5' region of GS15, a gene encoding soybean cytosolic glutamine synthetase, was isolated from a soybean genomic library. Mapping and partial sequence analysis of the genomic clone revealed that it encodes a cytosolic GS gene, GS21, which is different from GS15. In parallel, a number of cDNA clones encoding cytosolic GS were isolated using the coding region of pGS20 as a probe (pGS20 is a cDNA clone which corresponds to a transcript of the GS15 gene). Two new full-length cDNAs designated pGS34 and pGS38 were isolated and sequenced. In the 5' non-coding region a strong homology was found between the two clones and the GS21 gene. However, none of these sequences were identical, which suggests that there are at least three members in this group of genes. In order to determine their relative levels of transcription, specific sequences from pGS34, pGS38 and GS21 were used in an RNAse protection assay. This experiment clearly showed that GS21 and the gene encoding pGS38 are specifically expressed in young or mature nodules, whereas the gene encoding pGS34 is highly transcribed in nodules and constitutively expressed at a lower level in other soybean organs. In order to further analyse the molecular mechanisms controlling GS21 transcription, different fragments of the promoter region were fused to the Escherichia coli reporter gene encoding beta-glucuronidase (GUS) and the constructs were introduced into Lotus corniculatus via Agrobacterium rhizogenes-mediated transformation. Analysis of GUS activity showed that the GS21 promoter-GUS constructs were expressed in the vasculature of all vegetative organs. This result is discussed in relation to species-specific metabolic and developmental characteristics of soybean and Lotus.

Narrow A/T-rich zones present at the distal 5'-flanking sequences of the zein genes Zc1 and Zc2 bind a unique 30 kDa HMG-like protein

Nuclear extracts from maize endosperm were used to investigate protein-DNA interactions in the 5'-upstream region of the Zc1 and Zc2 genes. These genes encode for zeins of apparent molecular mass (MWapp) 16 and 28 kDa, respectively, which accumulate in the endosperm during seed maturation. Binding assays revealed specific binding of a nuclear protein to three A/T-rich elements, 0.9-1.0 kbp upstream from the initiation codon. One of these elements (41 bp, 88% A/T), present in Zc1, contained a 13 nucleotide duplication. The other two (28 bp, 86% A/T; 42 bp alternating A-T) are consecutive elements in Zc2. Competition experiments strongly suggest that the three elements bind to the same protein. Protein-DNA interaction was detected in endosperm nuclear extracts of 8 to 21 days after pollination (DAP), as well as in 25 DAP embryos and in different tissues from plantlets. The protein factor has an MWapp of ca. 30 kDa. This factor has properties suggesting it is an HMG-like protein. These results are consistent with a growing accumulation of data for a number of genes indicating that A/T-rich elements, located at distal and proximal zones of the 5'-flanking sequences, interact with HMG-like proteins.

The expression of a chimeric Phaseolus vulgaris nodulin 30-GUS gene is restricted to the rhizobially infected cells in transgenic Lotus corniculatus nodules

In Phaseolus vulgaris there is a nodulin family, Npv30, of ca. 30 kDa, as detected in an in vitro translation assay [2]. We isolated a gene (npv30-1) for one of the members of this family. The nucleotide sequence of the promoter of npv30-1 contains nodule-specific motifs common to other late nodulin genes. The promoter was fused to the GUS reporter gene; this chimeric fusion was introduced into Lotus corniculatus via Agrobacterium rhizogenes transformation. GUS activity was only detected in the infected cells of the nodules of transgenic plants. By contrast, the expression of a 35S-GUS construct was restricted to the uninfected cells and the vascular tissue.

Repression of the L-asparaginase gene during nodule development in Lupinus angustifolius

Upon the establishment of an effective nitrogen-fixing symbiosis in amide-transporting plants the enzymatic activity and transcript levels of L-asparaginase are dramatically decreased. This decrease in L-asparaginase activity is essential for the correct functioning of the Rhizobium-legume symbiosis in lupin in which asparagine, synthesized from recently fixed nitrogen, is exported to aerial parts of the plant for use in growth and development. Concomitant with this decrease in L-asparaginase transcript a DNA-binding protein was detected in the nodules. This binding protein was not detectable in ineffective nodules, in nodules treated with nitrate, or in root tips, mature roots, developing flowers or developing seeds. The DNA-binding activity was shown to interact with a 59 bp sequence proximal to the transcription start site. Within this sequence a CTAAAAT direct repeat and a ACTGT/TGTCA incomplete inverted repeat were implicated in the binding of protein to the DNA by DNase I protection experiments. Competitive binding studies with synthesized binding sites were consistent with the CTAAAAT/TGTCA sequence pair proximal to the transcription start site having the highest affinity for the DNA-binding protein. We postulate that this DNA-binding protein is associated with repression of L-asparaginase gene expression in mature lupin root nodules.

In Trifolium subterraneum, chalcone synthase is encoded by a multigene family

Chalcone synthase (CHS) catalyzes the first and key regulatory step in flavonoid biosynthesis. We report the existence and characterization of a CHS multigene family present in Trifolium subterraneum L. cultivar Karridale. The CHS family consists of at least four members, which are tightly clustered in a 15-kb region. The complete sequences of two of these genes (CHS1 and CHS2) are presented. The putative promoters of these genes have sequences which are homologous to those known, or implicated, in regulation of the expression of phenylpropanoid-encoding genes.

Regulatory sequences involved in the peroxidase gene expression in Arabidopsis thaliana

Organ-specific expression of two peroxidase genes (prxCa and prxEa) from Arabidopsis thaliana was studied. The prxCa gene showed non-specific expression with relatively high levels of mRNA accumulation in the roots, stems and leaves of A. thaliana. The prxEa gene, on the other hand, accumulated high levels of mRNA only in roots. Promoter fragments from each gene were fused to the coding region of β-glucuronidase (gusA) reporter gene introduced into tobacco. Promoter/gusA contructs were transferred to tobacco (Nicotiana tabacum BY-2) protoplasts by electroporation or to N. tabacum SR-1 by Agrobacterium tumefaciens-mediated leaf disk transformation. Transient expression in tobacco protoplasts showed that the 580 fragment from prxEa (Ea-580) expressed thirteen-fold and eight-fold higher GUS activity than prxCa (Ca-622) fragment and CaMV35S promoter, respectively. Tobacco plants transformed with the gusA gene, fused to the -580 deletion (Ea-580), exhibited high GUS expression in roots. The root-specific expression of GUS gene was also observed when the -281 bp deletion end point was used. Although the GUS activity in transgenic tobacco under the control of Ca-622 was low, the activity was found in all organs examined. Histochemical analyses of stem and root tissues of Ea-580 showed that the GUS gene was expressed specifically in phloem and pith parenchyma cells. For Ca-622, high level, specific expression of the gusA gene was observed in the xylem of roots. The results of this study implicate multiple cis-elements in the control of transcription from the prxEa promoter.

Cloning and characterization of a nodule-enhanced glutamine synthetase-encoding gene from Lupinus luteus

Glutamine synthetase (GS)-encoding genes in Lupinus luteus constitute a small family of genes showing different expression patterns [Boroń et al., Acta Biochim. Polon. 36 (1989) 295-301]. One member of this family, the LlNGS1 gene, is strongly induced in root nodules close to the onset of nitrogen fixation and is referred to as a nodule-enhanced GS gene. We present here the structure of the nodule-enhanced LlNGS1 gene, the first gene of this class which has been sequenced. LlNGS1 is composed of twelve exons and shows structural similarity to the GS gene from Medicago sativa, indicating structure conservation of GS genes in legumes. Comparison of protein coding regions, as well as 5'-untranslated regions derived from LlNGS1 and a Lupinus angustifolius pGS5 GS cDNA clone [Grant et al., Plant Mol. Biol. 13 (1989) 481-490], revealed a high degree of shared identity between both genes, indicating that they are orthologous. The sequence of the LlNGS1 5'-flanking region (2.3 kb) contains several elements implicated in regulation of nodulin genes, as well as other characteristic DNA motifs. RNA blot hybridization analysis carried out using a probe corresponding to the LlNGS1 3'-untranslated region revealed that this gene is also transcribed in leaves, but at a barely detectable level.

In vitro binding of nuclear proteins to the barley plastocyanin gene promoter region

Plastocyanin is a nuclear-encoded chloroplast protein participating in electron transport during photosynthesis. The plastocyanin gene is expressed in photosynthetic tissue in a developmentally regulated manner and the expression is stimulated by light. A genomic clone encoding the plastocyanin precursor was isolated from a barley (Hordeum vulgare) lambda library using a barley cDNA clone as a probe and the sequence of a 1.9-kb DNA fragment containing the plastocyanin gene was determined. TATA and CCAAT boxes are located 34-bp and 68-bp, respectively, upstream of the transcription start site, the 5'-untranslated leader is 78 nucleotides long, and the intronless gene has at least two different polyadenylation sites. DNA sites in the plastocyanin gene that mediate binding of barley nuclear proteins were mapped by mobility-shift assays with fragments of the promoter/upstream region. Two of the three specific binding sites characterised in more detail were found to form complexes with the same factor in cross-competition experiments. One of these sites, narrowed down to a 17-bp sequence at position -512, contains the consensus binding site for Myb-like transcription factors. The third specific binding site, located at position -622, contains the sequence CACGTG which is a high-affinity-binding site for transcription factors of the basic-region leucine-zipper family.

Minimal enhancer elements of the leghemoglobin lba and lbc3 gene promoters from Glycine max L. have different properties

The characteristics of the soybean leghemoglobin lba gene promoter were analyzed and important promoter elements from the lba and lbc3 promoters were compared using transgenic Lotus corniculatus plants. A 5' deletion analysis of the lba promoter delimited two cis-acting elements controlling expression: a distal positive element (-1254, -884) required for expression and a proximal element (-285, -60) essential for full-level activity. In contrast to the corresponding region of the lbc3 promoter, the lba proximal element is unable to control expression from the heterologous CaMV 35S enhancer. The upstream positive element of the lba gene contains a position- and orientation-independent enhancer between positions (-1091, -788). The sequence of this enhancer region is conserved in the lbc3 gene upstream (-1333, -1132) of the previously assigned strong positive element (SPE; -1090, -947). The present analysis revealed some of the properties of this extended lbc3 SPE element. The extended element (-1364, -947) functions in both orientations from 5' locations whereas the SPE2 subcomponent (-1364, -1154) containing the conserved sequence is only active in the correct orientation. Removal of the SPE2 by internal deletion demonstrates that the SPE2 subcomponent is indispensable for the activity of the lbc3 upstream positive element. These results indicate that the upstream positive elements of the lba and lbc3 genes possess different properties although their conserved minimal enhancer sequence has similar function. This may reflect the differential expression of the two lb genes of Glycine max L.

Comparative sequence analysis of cis elements present in Glycine max L. leghemoglobin lba and lbc3 genes

The soybean leghemoglobin lba gene promoter sequence was determined and aligned with the promoter sequence of the soybean lbc3 gene from the same gene family. Five highly conserved regions were found. There are two large conserved regions, one of which overlaps the basic promoter while the other defines a minimal enhancer in the upstream positive elements. Within the minimal enhancer, an inverted repeat with similarity to the binding site of a yeast transcription factor, GCN4, was found. This particular repeat is conserved in the promoters of all functional soybean lb genes as well as in lb gene promoters from other legumes. This suggests that the inverted repeat is important for leghemoglobin gene expression.

Analysis of nuclear proteins interacting with a wheat alpha/beta-gliadin seed storage protein gene

The promoter region (-524 to -46) of the wheat alpha/beta-gliadin seed storage protein gene was analyzed for interactions with nuclear proteins from developing wheat seeds. Six complexes were detected within the first 165 bp upstream of the transcriptional start site. One of the proteins was a non-sequence specific AT-binding protein. The remaining five proteins bound in a sequence specific manner. One (CABP) mapped to a conserved CA-rich element at -134 to -112 while another (PalBP) mapped to an adjacent, palindromic sequence at -112 to -106. Three proteins (CTBPs 1-3) formed complexes at two, independent homologous sites. The activities of four of the binding proteins, CTBPs 1-3 and CABP, exhibited similar patterns of expression during seed development: they first appeared at early to mid stages, reached a maximum at mid stage and subsequently decreased, paralleling the pattern of gliadin mRNA accumulation. The non-specific AT-binding protein was detected at relatively high levels only at mid development. PalBP activity, on the other hand, first appeared at mid stage and was present at a constant level throughout later stages of development. The results suggest that the binding proteins may regulate gliadin expression in an antagonistic manner.

Isolation and characterization of fruit vacuolar invertase genes from two tomato species and temporal differences in mRNA levels during fruit ripening

To determine the relationship between invertase gene expression and glucose and fructose accumulation in ripening tomato fruit, fruit vacuolar invertase cDNA and genomic clones from the cultivated species, Lycopersicon esculentum cv. UC82B, and a wild species, Lycopersicon pimpinellifolium, were isolated and characterized. The coding sequences of all cDNA clones examined are identical. By comparison to the known amino acid sequence of mature L. esculentum fruit vacuolar invertase, a putative signal sequence and putative amino-terminal and carboxy-terminal propeptides were identified in the derived amino acid sequence. Of the residues 42% are identical with those of carrot cell wall invertase. A putative catalytic site and a five-residue motif found in carrot, yeast, and bacterial invertases are also present in the tomato sequence. Minor differences between the nucleotide sequences of the genomic clones from the two tomato species were found in one intron and in the putative regulatory region. The gene appears to be present in one copy per haploid genome. Northern analysis suggests a different temporal pattern of vacuolar invertase mRNA levels during fruit development in the two species, with the invertase mRNA appearing at an earlier stage of fruit development in the wild species. Nucleotide differences found in the putative regulatory regions may be involved in species differences in temporal regulation of this gene, which in turn may contribute to observed differences in hexose accumulation in ripening fruit.

Deletion analysis and localization of SbPRP1, a soybean cell wall protein gene, in roots of transgenic tobacco and cowpea

SbPRP1 is a member of the soybean (Glycine max L. Merr) proline-rich cell wall protein family and is expressed at high levels in root tissue. To characterize the sequences required for this expression, we have fused 1.1 kb of upstream flanking DNA sequence from an SbPRP1 genomic clone to a gene encoding beta-glucuronidase (GUS). This construct was introduced into tobacco using Agrobacterium tumefaciens-mediated transformation. Histochemical staining of GUS activity in transgenic tobacco indicated that SbPRP1 is expressed in the apical and elongating region of both primary and lateral roots, most strongly in the epidermis. A similar localization pattern was found in transformed hairy roots when this construct was introduced into cowpea (Vigna aconitifolia) using Agrobacterium rhizogenes-mediated transformation. Nested 5'-deletion analysis of the SbPRP1 promoter indicated that a minimal promoter for SbPRP1 expression in roots is located within the first 262 bases of upstream flanking DNA and that the region between -1080 and -262 is required for maximal expression of this gene. Gel retardation assays showed that nuclear factors can be detected in soybean roots which specifically bind to sequences located between -1080 and -623, a region which is needed for maximal expression of the SbPRP1 promoter. Northern hybridization analysis was also used to show that little SbPRP1 mRNA was present in roots during the first 24 h after imbibition. These studies indicate that SbPRP1 expression is localized to the actively growing region of the root and that this expression is temporally regulated during very early stages of seedling growth.

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.

Organization of non-vertebrate globin genes

The organization of non-vertebrate globin genes exhibits substantially more variability than the three-exon, two-intron structure of the vertebrate globin genes. (1) The structures of genes of the single-domain globin chains of the annelid Lumbricus and the mollusc Anadara, and the globin gene coding for the two-domain chains of the clam Barbatia, are similar to the vertebrate plan. (2) Genes for single-domain chains exist in bacteria and protozoa. Although the globin gene is highly expressed in the bacterium Vitreoscilla, the putative globin gene hmp in E. coli, which codes for a chimeric protein whose N-terminal moiety of 139 residues contains 67 residues identical to the Vitreoscilla globin, may be either unexpressed or expressed at very low levels, despite the presence of normal regulatory sequences. The DNA sequence of the globin gene of the protozoan Paramecium, determined recently by Yamauchi and collaborators, appears to consist of two exons separated by a short intron. (3) Among the lower eukaryotes, the yeasts Saccharomyces and Candida have chimeric proteins consisting of N-terminal globin and C-terminal flavoprotein moieties of about the same size. The structure of the gene for the chimeric protein of Saccharomyces exhibits no introns. According to Riggs, the presence of chimeric proteins in E. coli and other prokaryotes, such as Alcaligenes and Rhizobium, as well as in yeasts, suggests a previously unrecognized evolutionary pathway for hemoglobin, namely that of a multipurpose heme-binding domain attached to a variety of unrelated proteins with diverse functions. (4) The published globin gene sequences of the insect larva Chironomus have an intron-less structure and are present as clusters of multiple copies; the expression of the globin genes is tissue and developmental stage-specific. Furthermore, the expression of many of these genes has not yet been demonstrated despite the presence of apparently normal regulatory sequences in the two flanking regions. Unexpectedly, Bergtrom and collaborators have recently shown that at least three Ctt globin II beta genes contain putative introns. (5) Pohajdak and collaborators have found a seven-exon and six-intron structure for the globin gene of the nematode Pseudoterranova which codes for a two-domain globin chain. Although the second and fourth introns of the N-terminal domain correspond to the two introns found in vertebrate globin genes, the position of the third intron is close to that of the central intron in plant hemoglobins.(ABSTRACT TRUNCATED AT 400 WORDS)

Single-stranded DNA of 5'-upstream region of the rolC gene interacts with nuclear proteins of carrot cell cultures

Using the gel retardation assay, proteins of carrot cells capable of binding to a single-stranded DNA of 5'-upstream region of the rolC gene were found. From competition experiments, these DNA-protein interactions were specific to single-stranded nucleotide sequence of Ava S fragment (from -94 bp to +23 bp relative to the transcription initiation site). Methylation interference experiments showed that G residue at the position of -41 bases on the bottom strand was important for DNA-protein binding. This residue was located between CAAT box and TATAA box. Such specific interaction between single-stranded DNA and nuclear proteins may play a role in transcription by RNA polymerase II.

AT-rich promoter elements of soybean heat shock gene Gmhsp17.5E bind two distinct sets of nuclear proteins in vitro

A 33 bp double-stranded oligonucleotide homologous to two AT-rich sequences located upstream (-907 to -889 and -843 to -826) to the start of transcription of heat shock gene Gmhsp17.5E of soybean stimulated transcription when placed 5' to a truncated (-140) maize Adh1 promoter. The chimeric promoter was assayed in vivo utilizing anaerobically stressed sunflower tumors transformed by a pTi-based vector of Agrobacterium tumefaciens. Nuclear proteins extracted from soybean plumules were shown to bind double-stranded oligonucleotides homologous to AT-rich sequences in the 5' flanking regions of soybean beta-conglycinin, lectin, leghemoglobin and heat shock genes. These proteins were also shown to bind AT-rich probes homologous to homeobox protein binding sites from the Antennapedia and engrailed/fushi tarazu genes of Drosophila. Binding activity specific for AT-rich sequences showed a wide distribution among various plant organs and species. Preliminary characterization indicated that two sets of nuclear proteins from soybean bind AT-rich DNA sequences: a diverse high-molecular-weight (ca. 46-69 kDa) group, and a low-molecular-weight (23 and 32 kDa) group of proteins. The latter meets the operational criteria for high-mobility group proteins (HMGs).

Synergistic effect of upstream sequences, CCAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco

The thermoregulated expression of the soybean heat shock (hs) gene Gmhsp17.3-B is regulated via the heat shock promoter elements (HSEs), but full promoter activity requires additional sequences located upstream of the HSE-containing region. Structural features within this putative enhancer region include a run of simple sequences which are also present upstream of HSE-like sequences of other soybean hs genes, and three perfect CCAAT box sequences located immediately upstream from the most distal HSE of the promoter. A series of heterologous and homologous promoter fusions linked to the chloramphenicol acetyl transferase (CAT) gene was constructed and examined in transgenic tobacco plants. The region containing the AT-rich domain of the 5' flanking region was unable to direct transcription from the TATA box of a truncated delta CaMV35S promoter. Heat-inducible CAT activity was detectable when additional sequences from the native promoter containing three CCAAT boxes and a single HSE were present in the constructions. Complete reconstitution of the native hs promoter/enhancer region increased hs specific CAT activities only very little, but deletion of CCAAT box sequences reduced CAT expression five-fold. Our results suggest that AT-rich sequences have a moderate effect on thermoinducible expression levels of the soybean heat shock gene and that CCAAT box sequences act cooperatively with HSEs to increase the hs promoter activity.