The transcriptional activator Opaque2 recognizes two different target sequences in the 22-kD-like alpha-prolamin genes

Gain-of-function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice

XPB2 and SEN1 helicases were identified through activation tagging as potential candidate genes in rice for inducing high water-use efficiency (WUE) and maintaining sustainable yield under drought stress. As a follow-up on the high-water-use-efficiency screening and physiological analyses of the activation-tagged gain-of-function mutant lines that were developed in an indica rice variety, BPT-5204 (Moin et al. in Plant Cell Environ 39:2440-2459, 2016a, https://doi.org/10.1111/pce.12796 ), we have identified two gain-of-function mutant lines (XM3 and SM4), which evidenced the activation of two helicases, ATP-dependent DNA helicase (XPB2) and RNA helicase (SEN1), respectively. We performed the transcript profiling of XPB2 and SEN1 upon exposure to various stress conditions and found their significant upregulation, particularly in ABA and PEG treatments. Extensive morpho-physiological and biochemical analyses based on 24 metrics were performed under dehydration stress (PEG) and phytohormone (ABA) treatments for the wild-type and the two mutant lines. Principal component analysis (PCA) performed on the dataset captured 72.73% of the cumulative variance using the parameters influencing the first two principal components. The tagged mutants exhibited reduced leaf wilting, improved revival efficiency, constant amylose:amylopectin ratio, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits with respect to their controls. These observations were further validated under greenhouse conditions by the periodic withdrawal of water at the pot level. Germination of the seeds of these mutant lines indicated their insensitivity to high ABA concentration. The associated upregulation of stress-specific genes further suggests that their drought tolerance might be because of the coordinated expression of several stress-responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.

Expression pattern of the alpha-kafirin promoter coupled with a signal peptide from Sorghum bicolor L. Moench

Regulatory sequences with endosperm specificity are essential for foreign gene expression in the desired tissue for both grain quality improvement and molecular pharming. In this study, promoters of seed storage α-kafirin genes coupled with signal sequence (ss) were isolated from Sorghum bicolor L. Moench genomic DNA by PCR. The α-kafirin promoter (α-kaf) contains endosperm specificity-determining motifs, prolamin-box, the O2-box 1, CATC, and TATA boxes required for α-kafirin gene expression in sorghum seeds. The constructs pMB-Ubi-gfp and pMB-kaf-gfp were microprojectile bombarded into various sorghum and sweet corn explants. GFP expression was detected on all explants using the Ubi promoter but only in seeds for the α-kaf promoter. This shows that the α-kaf promoter isolated was functional and demonstrated seed-specific GFP expression. The constructs pMB-Ubi-ss-gfp and pMB-kaf-ss-gfp were also bombarded into the same explants. Detection of GFP expression showed that the signal peptide (SP)::GFP fusion can assemble and fold properly, preserving the fluorescent properties of GFP.

Spatial distribution pattern analysis of Dof1 transcription factor in different tissues of three Eleusine coracana genotypes differing in their grain colour, yield and photosynthetic efficiency

In the present study Dof1 gene of finger millet was cloned and sequenced. In silico analysis reveals 61% identity with the Sorghum bicolor and 57% identity with the Oryza sativa Dof1 sequence. A comparative analysis of gene sequences from different crops and three finger millet genotypes {Brown (PRM-1), Golden (PRM-701) and White (PRM-801)} differing in grain colour, yield and photosynthetic efficiency showed a high degree of sequence identity of Dof1 sequence gene ranging from 22 to 70% as evident from distance matrix of the built phylogenetic tree showing two major clusters. A total of five conserved motifs were observed in Dof1 sequences of different cereals. Motif 1 with multilevel consensus sequence CKNCRRYWTKGGAMRNVPVG contains zinc finger Dof domain. Motif 3 and motif 5 contains protein kinase phosphorylation site. Motif 2 contains Dof domain and zinc finger N-glycosylation site while motif 4 is involved in Zinc finger type profiling. Further, we studied the spatial distribution of Dof1 gene in three vegetative tissues (root, stem and flag leaf) as well as four stages of developing spikes (S1, S2, S3 and S4) of the three finger millet genotypes using qualitative and quantitative PCR based approaches. Physiological parameters (plant height, leaf area, chlorophyll content, SPAD value and photosynthetic efficiency) at the time of flowering was found to be highest in white (PRM-801) genotype followed by golden (PRM-701) and brown (PRM-1) genotype. Semi-quantitative RT-PCR and quantitative real-time PCR analysis revealed that the expression of Dof1 is highest in leaves and lowest in roots, which suggests its role in regulation of photosynthesis-related genes and carbon skeleton synthesis. Also at grain maturity stage, expression of Dof1 was higher in white (PRM-801) genotype followed by golden (PRM-701) and brown (PRM-1) genotype. The result is suggestive of Dof1 role in the accumulation of grain protein and yield attribute through regulation of key enzymes involved in source to sink relationship during grain filling stage.

Compositional and transcriptional analyses of reduced zein kernels derived from the opaque2 mutation and RNAi suppression

Corn protein is largely made up of a group of nutritionally limited storage proteins known as zein. The reduction of zein can be achieved by a transcriptional mutation, opaque2 (o2), or a transgene targeting zein through RNA interference (RNAi). Zein reduction results in an increase of more nutritionally balanced non-zein proteins, and therefore enhance the overall quality of corn protein. In this study, the composition of mature kernels and the transcriptional profile of developing kernels of these two types of zein reduced kernels were compared. Both zein reduced kernels contained higher levels of lysine and tryptophan and free amino acids were 10-20-folds more abundant than the wild-type counterpart. We also found that free lysine contributed partially to the increased lysine in o2 kernels while protein-bound lysine was mainly responsible for the increased lysine in transgenic zein reduction (TZR) kernels. Although they had relatively similar gene expression patterns in developing endosperm, o2 kernels had greater transcriptional changes than TZR kernels in general. A number of transcripts that were specifically down-regulated in o2 were identified. Many promoter sequences of these transcripts contain putative O2 binding motifs, suggesting that their expression is directly regulated by O2.

Amplification of prolamin storage protein genes in different subfamilies of the Poaceae

Prolamins are seed storage proteins in cereals and represent an important source of essential amino acids for feed and food. Genes encoding these proteins resulted from dispersed and tandem amplification. While previous studies have concentrated on protein sequences from different grass species, we now can add a new perspective to their relationships by asking how their genes are shared by ancestry and copied in different lineages of the same family of species. These differences are derived from alignment of chromosomal regions, where collinearity is used to identify prolamin genes in syntenic positions, also called orthologous gene copies. New or paralogous gene copies are inserted in tandem or new locations of the same genome. More importantly, one can detect the loss of older genes. We analyzed chromosomal intervals containing prolamin genes from rice, sorghum, wheat, barley, and Brachypodium, representing different subfamilies of the Poaceae. The Poaceae commonly known as the grasses includes three major subfamilies, the Ehrhartoideae (rice), Pooideae (wheat, barley, and Brachypodium), and Panicoideae (millets, maize, sorghum, and switchgrass). Based on chromosomal position and sequence divergence, it becomes possible to infer the order of gene amplification events. Furthermore, the loss of older genes in different subfamilies seems to permit a faster pace of divergence of paralogous genes. Change in protein structure affects their physical properties, subcellular location, and amino acid composition. On the other hand, regulatory sequence elements and corresponding transcriptional activators of new gene copies are more conserved than coding sequences, consistent with the tissue-specific expression of these genes.

Wild-type opaque2 and defective opaque2 polypeptides form complexes in maize endosperm cells and bind the opaque2-zein target site

The Opaque2 (O2) basic leucine (Leu)-zipper transcriptional activator controls the expression of several genes in maize (Zea mays). We investigated the phosphorylation extent of wild-type O2 and mutant-defective or mutant-truncated o2 polypeptides in endosperm cells, their subcellular localization, participation in complex formation, and involvement in functional activity. Besides wild type, four mutant alleles (o2T, o2-52, o2It, and o2-676) producing o2 polypeptides and a null transcript allele (o2R) were considered. Observing the effects of these mutations, multiphosphorylation events in O2 or o2 proteins were confirmed and further investigated, and the involvement of both the nuclear localization signal (NLS)-B and Leu-zipper domains in proper targeting to the nucleus was ascertained. The absence of these domains in the o2T and o2It-S mutant-truncated forms holds them within the cytoplasm, where they are partially phosphorylated, whereas the presence of NLS-B and a partial Leu-zipper domain in o2-52 distributes this mutant-truncated form in both cytoplasm and nucleus. Although mutated in the NLS-B domain, the o2It-L and o2-676 mutant-defective forms are, respectively, partially or completely distributed into the nucleus. Only wild-type O2 and mutant-defective o2 polypeptides bearing the Leu-zipper are able to form complexes whose components were proven to bind the O2-zein target site by in vitro analyses. The transcription of a subset of H-zein genes as well as H-zein polypeptide accumulation in several o2-mutant-defective genotypes indicate the in vivo involvement of o2-mutant-defective proteins in O2-zein target site recognition. The gathered information broadens our knowledge on O2 functional activity and our view on possible quality protein maize trait manipulation or plant transformation via the utilization of cisgenic elements.

Molecular evolution of the Opaque-2 gene in Zea mays L

The Opaque-2 gene (O2) in maize encodes a transcriptional activator that controls the expression of various genes during kernel development, particularly some of the most abundant endosperm storage protein genes. Compared to its wild relative teosinte, maize has bigger and heavier kernels, with an increased proportion of starch and an altered distribution of the various storage protein categories. The molecular evolution of the O2 gene was investigated in connection with its possible involvement in the domestication process. Most of the coding sequence and parts of introns, 5'UTR, and 3' noncoding regions were sequenced in a set of cultivated and teosinte accessions. One hundred six polymorphic sites (5.4%) and 72 insertions/deletions, located mostly in noncoding regions, were found. Molecular diversity was quite high (pi = 0.0138, theta = 0.0167) compared to that of other transcription factors in maize. The synonymous and nonsynonymous diversity patterns along the coding sequence suggested that different regions are submitted to different functional constraints. Such an evolution would probably be favored by the observed rapid decay of linkage disequilibrium with distance. Cultivated accessions retained about 70% of the diversity observed in teosintes. Purifying selection was detected in both maize and teosintes. No conclusive evidence was obtained for a role of the O2 gene in the domestication process.

Expression of the sorghum 10-member kafirin gene cluster in maize endosperm

Functional analysis of chromosomal segments containing linked genes requires the insertion of contiguous genomic sequences from bacterial artificial chromosomes (BACs) into the genome. Therefore, we introduced a 90-kb large BAC clone carrying a 10-copy tandem array of kafirin storage protein genes from sorghum linkage group J, mixed with a selectable marker gene, directly into maize cells using the particle bombardment method. Transgenic plants were regenerated and seeds from eight different transgenic lines were produced. One such transgenic plant was selected that had the entire kafirin gene cluster on a single continuous DNA fragment spanning more than 45 kb integrated into its genome. When alcohol-soluble proteins from individual T2 and T3 seeds of this event were analyzed, significant levels of kafirin were found in addition to the endogenous zein storage proteins, demonstrating that the large exogenous DNA segment is stably integrated into the maize genome and expressed at high levels in subsequent generations. Therefore, we could provide a new utility of plant transformation by the particle bombardment method for functional genomics of multigene families and the modification of the nutritive quality of cereal grains. Despite a tandem array of highly homologous sequences at the transgenic locus, no gene silencing was observed, probably owing to the effects of co-transformed flanking sequences. The expression studies of the transgenic locus also revealed new features of storage protein gene promoters that differed from previous transient gene expression studies, thereby illustrating the significance of the concentration and configuration of DNA-protein interactions in the regulation of gene expression.

Arabidopsis ABI5 subfamily members have distinct DNA-binding and transcriptional activities

A small family of novel basic leucine zipper proteins that includes abscisic acid (ABA)-INSENSITIVE 5 (ABI5) binds to the promoter region of the lea class gene Dc3. The factors, referred to as AtDPBFs (Arabidopsis Dc3 promoter-binding factors), were isolated from an immature seed cDNA library. AtDPBFs bind to the embryo specification and ABA-responsive elements in the Dc3 promoter and are unique in that they can interact with cis-elements that do not contain the ACGT core sequence required for the binding of most other plant basic leucine zipper proteins. Analysis of full-length cDNAs showed that at least five different Dc3 promoter-binding factors are present in Arabidopsis seeds; one of these, AtDPBF-1, is identical to ABI5. As expected, AtDPBF-1/ABI5 mRNA is inducible by exogenous ABA in seedlings. Despite the near identity in their basic domains, AtDPBFs are distinct in their DNA-binding, dimerization, and transcriptional activity.

The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development

HvGAMYB, a MYB transcription factor previously shown to be expressed in barley aleurone cells in response to gibberellin during germination, also has an important role in gene regulation during endosperm development. The mRNA was detected early (10 DAF) in the seeds where it accumulates, not only in the aleurone layer, starchy endosperm, nucellar projection and vascular tissue, but also in the immature embryo as shown by in situ hybridization analysis. The HvGAMYB protein, expressed in bacteria, binds to oligonucleotides containing the 5'-TAACAAC-3' or 5'-CAACTAAC-3' sequences, derived from the promoter regions of the endosperm-specific genes Hor2 and Itr1, encoding a B-hordein and trypsin-inhibitor BTI-CMe, respectively. Binding is prevented when these motifs are mutated to 5'-TgACAAg-3' and 5'-CgACTgAC-3'. Transient expression experiments in co-bombarded developing endosperms demonstrate that HvGAMYB trans-activates transcription from native Hor2 and Itr1 promoters through binding to the intact motifs described above. Trans-activation of the Hor2 promoter also requires an intact prolamine box (PB). This suggests that HvGAMYB interacts in developing barley endosperms with the PB-binding factor BPBF, an endosperm-specific DOF transcriptional activator of the Hor2 gene. The in vivo interaction experiment between HvGAMYB and BPBF was done in the yeast two-hybrid system, where HvGAMYB potentiates the BPBF trans-activation capacity through interaction with its C-terminal domain.

Expression of the REB transcriptional activator in rice grains improves the yield of recombinant proteins whose genes are controlled by a Reb-responsive promoter

The gene encoding the rice transcription factor, REB (rice endosperm bZIP) was cloned from a bacterial artificial chromosome library of rice. The cloned 6,227-bp-long Reb gene is composed of six exons and five introns and is flanked by a 1.2-kb 5' promoter and a 1.2-kb 3' terminator region. The function of the Reb gene was explored by a transient assay by using a rice immature endosperm system. The effector constructs containing the native gene or fusion genes linking Reb to the rice actin (Act) or globulin (Glb) gene promoters and the reporter gene construct Glb-beta-glucuronidase (GUS) were used in this study. When these effector constructs were cotransferred with the reporter uidA gene encoding GUS under the control of the Glb promoter into immature rice endosperm cells, the Glb promoter was activated. The transient GUS expression was 2.0 to 2.5-fold higher with the effector construct than without. When the upstream activation sequence containing the GCCACGT(A/C)AG motifs of the Glb promoter was deleted, the activation by REB was abolished. On the other hand, a gain-of-function experiment showed that inserting the upstream activation sequence into the glutelin-1 (Gt1) promoter made it responsive to activation by REB. When cotransformed with Reb gene, mature transgenic rice grains containing the human lysozyme gene driven by the Glb promoter produced 3.7-fold more lysozyme. Accumulation of recombinant lysozyme in mature seed ranged from 30.57 to 279.61 microg.mg(-1) total soluble protein in individual transformants from 30 independent transformation events. Thus, our results show that REB is not only a transcriptional activator, it can also be used to increase the expression of recombinant protein in transgenic rice grains.

Methylation of the Opaque2 box in zein genes is parent-dependent and affects O2 DNA binding activity in vitro

In the maize endosperm, the expression of the subfamily 4 (SF4) of the zein genes is under the transcriptional control of the Opaque2 (O2) basic leucine zipper transcriptional activator, which binds to the O2-box 5'-TCCACGTAGA-3'. Southern experiments showed that the O2-box core sequence ACGT is heavily methylated in sporophytic tissues but becomes hypomethylated in the endosperm. DNA analyses of two inbred lines and their reciprocal crosses indicate that the hypomethylation state is established on the maternal complements of the endosperm. Electrophoretic mobility shift assay (EMSA) and southwestern experiments with endosperm protein extracts and recombinant O2 using oligonucleotides with methylated and unmethylated cytosines in the O2-box indicate an inhibitory effect of modified sequences on O2-binding activity. These results suggest that DNA methylation modulates O2 activity in vivo and shed light on molecular mechanisms involved in the parent-dependent zein gene expression in maize endosperm.

Specific combinations of zein genes and genetic backgrounds influence the transcription of the heavy-chain zein genes in maize opaque-2 endosperms

The transcript levels of heavy-chain zein genes (zH1 and zH2) and the occurrence of the zH polypeptides in different opaque-2 (o2) lines were investigated by RNA-blot analyses and by sodium dodecylsulfate-polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis protein fractionations. Four mutant alleles o2R, o2T, o2It, and o2-676 introgressed into different genetic backgrounds (GBs) were considered. The mono-dimensional gel electrophoresis zein pattern can be either conserved or different among the various GBs carrying the same o2 allele. Likewise, in the identical GB carrying different o2 alleles, the zein pattern can be either conserved or differentially affected by the different mutant allele. Zein protein analysis of reciprocal crosses between lines with different o2 alleles or the same o2 showed in some case a more than additive zH pattern in respect to the o2 parent lines. Electrophoretic mobility shift assay approaches, with O2-binding oligonucleotide and endosperm extracts from the above o2 lines, failed to reveal o2-specific retarded band in any of the o2 extracts. The results suggest that the promoter of some zH1 and zH2 contains motif(s) that can respond to factors other than O2.

The DapA gene encoding the lysine biosynthetic enzyme dihydrodipicolinate synthase from Coix lacryma-jobi: cloning, characterization, and expression analysis

Dihydrodipicolinate synthase (DHPS) is the main enzyme of a specific branch of the aspartate pathway leading to lysine biosynthesis in higher plants. We have cloned and characterized the DHPS-encoding Dap)A gene from the maize-related grass Coix lacryiana-jobi. The DapA open reading frame is interrupted by two introns and encodes the 326 amino acid-long Coix DHPS protein, which is 95% identical to the maize DHPS protein. Coix DNA gel blot analysis with maize DHPS cDNA as a probe showed a single strongly hybridizing band along with faint bands. RNA gel blot analysis showed that DHPS transcripts are present in coleoptiles, embryos, endosperms, and roots but are almost undetectable in blades of young leaves of both Coix and maize. The 5'-flanking region of the DapA gene contains a TGACTC GCN4-like element located 372 bp upstream the putative translation start codon. Steady-state levels of DHPS mRNA were slightly reduced in the endosperms and embryos of the maize lysine-rich opaque2 mutants when compared with those in normal kernels. Selective binding assay with the maize Opaque2 protein (O2) showed that the GCN4-like element is not an O2 binding site, suggesting that the DHPS gene is not under the control of O2.

Transcription activation mediated by the bZIP factor SPA on the endosperm box is modulated by ESBF-1 in vitro

A modified in vitro transcription system has been used to study the function of the cloned bZIP transcription factor SPA and the binding activity ESBF I in activating transcription from the bifactorial endosperm box region of the wheat prolamin LMWG-1D1 gene. Recombinant SPA expressed in Escherichia coli activated transcription from the endosperm box motif, and this was dependent upon the binding of the nuclear protein ESBF I. ESBF I did not activate transcription independently, but potentiated SPA-mediated transcriptional activation. ESBF I is likely to be the equivalent of, or contain the recently characterised DOF class of, Zn-finger protein called WPBF. These data provide new information about the interplay of members of the bZIP and DOF transcription factor families in regulating expression from bifactorial sites found in a variety of plant promoters.

Identification of cis-regulatory elements required for endosperm expression of the rice storage protein glutelin gene GluB-1

Rice storage protein glutelin genes are coordinately regulated during seed development. A previous 5' deletion analysis using transgenic tobacco revealed that the minimum 5' region necessary for endosperm specificity was within -245 bp of the transcription start site, and included the AACA and GCN4 motifs that are highly conserved in the 5'-flanking regions of all glutelin genes. In this paper, the sequence elements essential for endosperm-specific expression are characterized in stable transgenic tobacco plants by both loss-of-function and gain-of-function experiments using this minimum promoter. Base substitution analysis shows that the proximal AACA motif between -73 and -61, and the GCN4 motif between -165 and -158 act as critical elements. An ACGT motif between -81 and -75, and Skn-I-like elements between -173 and -169 also play important roles in controlling the seed-specific expression. When the distal region between -245 and -145 containing the AACA and the GCN4 motifs or the proximal region between -113 and -46 containing the ACGT and AACA motifs is fused to a truncated promoter (-90 to +9) of the CaMV 35S gene fused to the beta-glucuronidase (GUS) reporter gene, high levels of seed-specific expression are observed in these fusions, thereby indicating that either pair of motifs is sufficient to confer seed expression in these fusions. However, when substituted for by the CaMV 35S core promoter (-46 to +1), seed expression is abolished, suggesting that the sequence between -90 and -46 of the CaMV 35S promoter containing G-box-like motif (as-1 element) is required for such specific expression in addition to AACA and GCN4 motifs. Therefore, we conclude that at least three cis-regulatory elements, the AACA motif, GCN4 motif and ACGT motif, are necessary to mediate endosperm expression of the GluB-1 glutelin gene.

Identification of a DNA-binding factor that recognizes an alpha-coixin promoter and interacts with a Coix Opaque-2 like protein

Transient expression and electrophoretic mobility shift assay were used to investigate the cis elements and the DNA-binding proteins involved in the regulation of expression of a 22 kDa zein-like alpha-coixin gene. A set of unidirectional deletions was generated in a 962 bp fragment of the alpha-coixin promoter that had been previously fused to the reporter gene GUS. The constructs were assayed by transient expression in immature maize endosperm. There was no significant decrease in GUS activity as deletions progressed from -1084 to -238. However, deletion from -238 to -158, which partially deleted the O2c box, resulted in a dramatic decrease in GUS activity emphasizing the importance of the O2 box in the quantitative expression of the gene. The -238 promoter fragment interacted with Coix endosperm nuclear proteins to form 5 DNA-protein complexes, C1-C5, as detected by EMSA. The same retarded complexes were observed when the -158 promoter fragment was used in the binding reactions. Reactions with nuclear extracts isolated from Coix endosperms harvested from 6 to 35 days after pollination revealed that the 5 DNA-protein complexes that interact with the alpha-coixin promoter are differentially assembled during seed development. Deletion analysis carried out on the -238/ATG promoter fragment showed that a 35 bp region from -86 to -51 is essential for the formation of the complexes observed. When nuclear extracts were incubated with an antiserum raised against the maize Opaque-2 protein, the formation of 4 complexes, C1, C3, C4 and C5, was prevented indicating that an Opaque-2 like protein participates in the formation of those complexes. Complex C2 was not affected by the addition of the O2 antibody, suggesting the existence of a novel nuclear factor, CBF1, that binds to the promoter and makes protein-protein associations with other proteins present in Coix endosperm nuclei.

Cooperative DNA binding and sequence discrimination by the Opaque2 bZIP factor

The maize Opaque2 (O2) protein is a basic leucine zipper transcription factor that controls the expression of distinct classes of endosperm genes through the recognition of different cis-acting elements in their promoters. The O2 target region in the promoter of the alpha-coixin gene was analyzed in detail and shown to comprise two closely adjacent binding sites, named O2u and O2d, which are related in sequence to the GCN4 binding site. Quantitative DNase footprint analysis indicated that O2 binding to alpha-coixin target sites is best described by a cooperative model. Transient expression assays showed that the two adjacent sites act synergistically. This synergy is mediated in part by cooperative DNA binding. In tobacco protoplasts, O2 binding at the O2u site is more important for enhancer activity than is binding at the O2d site, suggesting that the architecture of the O2-DNA complex is important for interaction with the transcriptional machinery.

The bifactorial endosperm box of gamma-zein gene: characterisation and function of the Pb3 and GZM cis-acting elements

The proximal region of the gamma-zein promoter (gamma Z) has a functional bifactorial prolamin box element containing two cis-acting elements, a prolamin-box motif (Pb3) and a GCN4-like motif (GZM). By particle bombardment of maize endosperms with 5' deletions and internal deletions of gamma Z fused to the GUS gene, we have shown that a 135 bp region containing the bifactorial element is involved in the transcriptional activation of the gamma Z promoter. However, the 135 bp region was unable to activate the gamma Z promoter in the absence of a 84 bp downstream sequence. Using in vivo footprinting and gel mobility shift assays with 15 DAP endosperm nuclear extracts, we have demonstrated the presence of trans-acting factors that interact with Pb3 and GZM target sites. Base-substitution mutations within Pb3 and GZM decreased transcription activity of the gamma Z promoter suggesting a co-ordinated function between the two cis-acting elements. Two additional cis-motifs upstream of the bifactorial prolamin element have been identified: a motif with high homology to the AACA elements of rice glutelin genes and an AZM motif containing an ACGT core which binds nuclear proteins other than the Opaque 2 (O2).

Promoters of nuclear-encoded respiratory chain complex I genes from Arabidopsis thaliana contain a region essential for anther/pollen-specific expression

Regulatory promoter regions responsible for the enhanced expression in anthers and pollen are defined in detail for three nuclear encoded mitochondrial Complex I (nCl) genes from Arabidopsis thaliana. Specific regulatory elements were found conserved in the 5' upstream regions between three different genes encoding the 22 kDa (PSST), 55 kDa NADH binding (55 kDa) and 28 kDa (TYKY) subunits, respectively. Northern blot analysis and transgenic Arabidopsis plants carrying progressive deletions of the promoters fused to the beta-glucuronidase (GUS) reporter gene by histochemical and fluorimetric methods showed that all three promoters drive enhanced expression of GUS specifically in anther tissues and in pollen grains. In at least two of these promoters the -200/-100 regions actively convey the pollen/anther-specific expression in gain of function experiments using CaMV 35S as a minimal promoter. These nCl promoters thus contain a specific regulatory region responding to the physiological demands on mitochondrial function during pollen maturation. Pollen-specific motifs located in these regions appear to consist of as little as seven nucleotides in the respective promoter context.

The GCN4 motif in a rice glutelin gene is essential for endosperm-specific gene expression and is activated by Opaque-2 in transgenic rice plants

The GCN4 motif is conserved in a number of seed storage protein genes, and promoter fragments containing this motif have been shown to be involved in controlling seed-specific expression of the genes studied. All genes encoding the rice seed storage protein glutelin contain the GCN4 motif at similar sites in their 5' flanking regions. Using a stable homologous transgenic system, we have analysed the promoter of the rice glutelin gene GluB-1 and demonstrated that the GCN4 motif functions as an essential cis-element for endosperm-specific gene expression. Moreover, a 21 bp GluB-1 promoter fragment spanning the GCN4 motif, as a multimer, directed GUS gene expression in endosperm of transgenic rice plants, when fused directly to the core promoter (-46) of CaMV 35S. In transiently transfected rice protoplasts, over a hundred-fold transactivation was observed from the 21 bp sequence by the bZIP type transcriptional activator Opaque-2 (O2) co-expressed under a CaMV 35S promoter. The transactivation was also evident in transgenic plants containing both O2 and the 21 bp sequence/GUS fusion. The O2-mediated activation requires binding of O2 to an intact GCN4 motif. Our results suggest that a bZIP protein functionally similar to O2 may exist in rice and participate in controlling the endosperm-specific expression of GluB-1 through the GCN4 motif.

The molecular and functional characterization of an Opaque2 homologue gene from Coix and a new classification of plant bZIP proteins

The seed storage proteins of Coix, sorghum and maize are codified by homologous genes which are coordinately expressed in the endosperm in a temporal-specific fashion. Opaque2 (O2), a bZIP protein originally isolated from maize, has been described as a transcription activator of alpha- and beta-prolamin genes. The isolation and characterization of cDNA and genomic clones encoding the Opaque2 homologue from Coix are reported here. The coding region of the Coix O2 gene is interrupted by five introns and codifies a polypeptide of 408 amino acids. Comparison of the deduced amino acid sequence with two different sequences of maize O2 protein showed that the Coix O2 protein is similar to the maize O2 isolated from W22 maize inbred line. The Coix O2 protein has the same binding specificity and expression pattern of the maize O2. The O2 proteins together with OHP1, OsBZIPPA, SPA, CPRF2 and RITA1 were assigned to one of the five bZIP plant families in an updated classification of plant bZIP according to bZIP domain similarity.

ACGT and vicilin core sequences in a promoter domain required for seed-specific expression of a 2S storage protein gene are recognized by the opaque-2 regulatory protein

The expression of Brazil nut storage albumin genes is highly regulated during seed development. Several sequences in the promoter of one of these genes show homologies with the target sites of the maize O2 bZIP regulatory protein. We therefore asked whether the O2 protein would recognize these promoter sequences. We show that the O2 protein binds to three different sequences (F1, F2 and F3). F1 and F3 are hybrid C/G and A/G boxes, respectively, that are homologous to the O2-binding site of a maize alpha-zein gene. F2 is a new O2-binding sequence related to the O2 target sites of the Coix alpha-coxin, the maize b-32 genes and the AP-1 pseudopalindrome. Molecular modelling showed that an Asn and a Ser in the 02 DNA binding domain make different base-specific contacts with each operator. 5' Promoter deletions of the be2S1 gene showed that the domain containing the O2 target sites F1 and F2 is required for detectable reporter gene expression in transgenic tobacco seeds. Moreover, the homologous coix O2 protein was shown to in situ transactivate the promoter region encompassing the three O2-binding sites F1, F2 and F3. Thus, these sites may be in vivo regulatory sequences mediating activation by bZIP regulatory proteins.

The wheat transcriptional activator SPA: a seed-specific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes

The conserved bifactorial endosperm box found in the promoter of wheat storage protein genes comprises two different cis elements that are thought to be involved in regulating endosperm-specific gene expression. Endosperm nuclear extracts contain binding activities. One is called ESBF-I, which binds to the endosperm motif (EM), and the other is called ESBF-II, which binds to the GCN4-like motif(GLM). Here, we present a functional analysis of the endosperm box of a low-molecular-weight glutenin gene found on the 1D1 chromosome of hexaploid wheat (LMWG-1D1) in transgenic tobacco plants. Our analysis demonstrates the necessity of the EM and GLM for endosperm-specific gene expression and suggests the presence in tobacco of functional counterparts of wheat ESBF-I and ESBF-II. Furthermore, we describe the isolation and characterization of cDNA clones encoding SPA, a seed-specific basic leucine zipper protein from wheat that can activate transcription from the GLMs of the -326-bp LMWG-1D1 promoter in both maize and tobacco leaf protoplasts. This activation is also partially dependent on the presence of functional EMs, suggesting interactions between SPA with ESBF-I-like activities.

Analysis of kafirin promoter activity in transgenic tobacco seeds

Sequences corresponding to 855 bp of 5' promoter region and the transit peptide from lambdaGK.1,a genomic clone encoding a 22 kDa alpha-kafirin seed protein from sorghum, were translationally fused to a cloned beta-glucuronidase (GUS) coding sequence from uidA and transferred to tobacco via Agrobacterium tumefaciens-mediated transformation. No GUS expression was detectable at any stage of growth in stems or leaves of these plants. However, GUS expression was detected in both embryo and endosperm tissues of resulting tobacco seeds 10-15 days after flowering. Dissected tissues indicate endosperm expression was localized within the bulk endosperm and not within the parenchyma cell layer underlying the integument. These studies also demonstrate that within dissected tobacco embryos, expression from the kafirin promoter was restricted to the mesocotyl region.

GT-2: in vivo transcriptional activation activity and definition of novel twin DNA binding domains with reciprocal target sequence selectivity

GT-2 is a novel DNA binding protein that interacts with a triplet functionally defined, positively acting GT-box motifs (GT1-bx, GT2-bx, and GT3-bx) in the rice phytochrome A gene (PHYA) promoter. Data from a transient transfection assay used here show that recombinant GT-2 enhanced transcription from both homologous and heterologous GT-box-containing promoters, thereby indicating that this protein can function as a transcriptional activator in vivo. Previously, we have shown that GT-2 contains separate DNA binding determinants in its N- and C-terminal halves, with binding site preferences for the GT3-bx and GT2-bx promoter motifs, respectively. Here, we demonstrate that the minimal DNA binding domains reside within dual 90-amino acid polypeptide segments encompassing duplicated sequences, termed trihelix regions, in each half of the molecule, plus 15 additional immediately adjacent amino acids downstream. These minimal binding domains retained considerable target sequence selectivity for the different GT-box motifs, but this selectivity was enhanced by a separate polypeptide segment farther downstream on the C-terminal side of each trihelix region. Therefore, the data indicate that the twin DNA binding domains of GT-2 each consist of a general GT-box recognition core with intrinsic differential binding activity toward closely related target motifs and a modified sequence conferring higher resolution reciprocal selectivity between these motifs.

The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms

The maize Opaque-2 (O2) protein is a transcription factor of the basic/leucine-zipper class, involved in the regulation of endosperm proteins including the 22kDa alpha-zein storage proteins and b32 protein. In this study we have focussed our attention on the relationship between O2 and the cyPPDK1 gene, which encodes a cytoplasmic pyruvate orthophosphate dikinase (PPDK) isoform. The results of this study showed that PPDK activity is detectable in wild-type maize endosperms, while in o2 mutant endosperms, the levels of PPDK protein, mRNA and enzymatic activity are reduced, indicating that O2 is involved in the regulation of cyPPDK1 in this tissue. By employing transient expression experiments in tobacco mesophyll protoplasts, we have demonstrated that the O2 protein can activate expression of a chloramphenicol acetyl transferase reporter gene placed under the control of the cyPPDK1 promoter. An in vitro binding assay and DNaseI footprint analysis demonstrated that a specific sequence in the cyPPDK1 promoter can be recognized and protected by maize O2 protein. The regulation by the O2 locus of cyPPDK1 reported here, and control of alpha-zein synthesis by O2 suggest that the O2 protein may play a more general role in maize endosperm development than previously thought.

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.

Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds

The storage protein napin is one of the major protein components of Brassica napus L. (oilseed rape) seeds. To investigate the transcriptional regulation of the napin promoter, different constructs of the napin gene napA promoter were fused to the Escherichia coli uidA gene and transformed into B. napus. A-152-bp promoter construct directed a strong expression of the marker gene in mature seeds. The 5' deletion of an additional 8 completely abolished this activity. This deletion disrupted sequence motifs that are similar to an E-box, (CA decreases NNTG) and an ABRE (CGCCA decreases CGTGTCC) element (identify is indicated by bold face). Further, internal deletion of a segment corresponding to -133 to -121 caused an eightfold reduction in the activity of the -152 construct. This region contains an element, CAAACAC, conserved in many storage-protein gene promoters. These results imply that the E-box/ABRE-like sequence is a major motif of the napA promoter and suggest that the CAAACAC sequence is important for high activity of the napA promoter. Similar results have been obtained by analysing some of the constructs in transgenic tobacco, suggesting that many of the cis-elements in the napA promoter are conserved, at least in dicotyledonous species.

The maize transcription factor Opaque-2 activates a wheat glutenin promoter in plant and yeast cells

The promoter of the wheat low-molecular-weight glutenin (LMWG1D1) gene contains a cis element called the GCN4 like motif (GLM) which has low homology to one class of binding site for the maize endosperm-specific b-ZIP transcription factor Opaque-2 (O2). Previous work has shown that the GLM element interacts with the nuclear factor ESBFII during wheat endosperm development at the time of maximum transcription of the LMWG1D1 gene. In this paper we demonstrate that O2 binds to the GLM element and can activate high levels of transcription from the wheat GLM in transient assays in plant protoplasts and in yeast cells. Lower levels of O2 activation through the GLM element in yeast containing a defective GCN4 gene showed that GCN4 was necessary for high levels of O2 transcriptional activation, indicating that O2 may need to heterodimerise with GCN4 to activate transcription in yeast. These observations provide evidence that the GLM represents a new type of O2 DNA-binding site, and support a postulate that an O2 homologue may activate endosperm-specific expression of wheat storage protein genes.

A maize DNA-binding factor with a bZIP motif is induced by low temperature

We have isolated a low temperature-induced maize gene, mlip15, via cross hybridization using rice lip19. The longest cDNA isolated comprised 1179 bp and coded for a 135 amino acid bZIP (basic region/leucine zipper) protein. The gene showed 61.4% and 68.9% identity with the rice gene at the DNA and amino acid sequence levels, respectively, and is distinct from other maize genes that code for bZIP proteins. The level of mlip15 transcript was positively regulated by low temperature in the same way as the lip19 transcript. The levels of the transcript were also strongly increased by salt stress and exogenous abscisic acid, and slightly increased by anaerobiosis, but were not affected by heat shock and drought. The mLIP15 protein and truncated derivatives, produced in rabbit reticulocyte lysates or in an Escherichia coli expression system, were able to bind to a fragment of the wheat histone H3 gene promoter. This binding was diminished by addition of a molar excess of the hexamer sequence 5'-ACGTCA-3' found in the promoter and of the G-box-like sequence, but not by the addition of the ocs sequence or a mutated hexamer sequence. The factor bound to a promoter region of the maize Adh1 gene, expression of which is also induced by low temperature. These results lead to the conclusion that mlip15 is a strong candidate for a low temperature-induced transcription factor in maize.

Pollen specificity elements reside in 30 bp of the proximal promoters of two pollen-expressed genes

Functional analyses previously identified minimal promoter regions required for maintaining high-level expression of the late anther tomato LAT52 and LAT59 genes in tomato pollen. Here, we now define elements that direct pollen specificity. We used a transient assay system consisting of two cell types that differentially express the LAT genes and both "loss-of-function" and "gain-of-function" approaches. Linker substitution mutants analyzed in the transient assay and in transgenic plants identified 30-bp proximal promoter regions of LAT52 and LAT59 that are essential for their expression in pollen and that confer pollen specificity when fused to the heterologous cauliflower mosaic virus 35S core promoter. In vivo competition experiments demonstrated that a common trans-acting factor interacts with the pollen specificity region of both LAT gene promoters and suggested that a common mechanism regulates their coordinate expression. Adjacent upstream elements, the 52/56 box in LAT52 and the 56/59 box in LAT59, are involved in modulating the level of expression in pollen. The 52/56 box may be a target for the binding of a member of the GT-1 transcription factor family.

The involvement of Opaque 2 on beta-prolamin gene regulation in maize and Coix suggests a more general role for this transcriptional activator

The maize opaque 2 (o2) mutation is known to have numerous pleiotropic effects. Some polypeptides have their expression depressed while others are enhanced. The best characterized effects of the o2 mutation are those exerted on endosperm genes encoding the storage protein class of the 22 kDa alpha-zeins and the ribosome inactivating protein b-32. The Opaque 2 (O2) locus encodes a basic domain-leucine zipper DNA-binding factor, O2, which transcriptionally regulates these genes. In the maize-related grass Coix lacryma-jobi, an O2-homologous protein regulates the 25 kDa alpha-coixin family. We show in this paper that O2 transcriptionally regulates the structurally and developmentally different class of the beta-prolamins. A new O2-binding box was identified in beta-prolamin genes from maize and Coix that, together with the boxes previously identified in other endosperm expressed genes, forms a curious collection of O2 cis elements. This may have regulatory implications on the role of O2 in the mechanism that controls coordinated gene expression in the developing endosperm. Considering that the O2 locus controls at least three distinct classes of genes in maize endosperm, we propose that the O2 protein may play a more general role in maize endosperm development than previously conceived.

Transcription factors in plant growth and development

The target DNA sequences of several classes of plant transcription factors, including basic leucine zipper (bZIP) proteins and Myb-related factors, have been characterized in vivo as well as in vitro. The bZIP proteins, for example, act at ACGT elements, the flanking nucleotides determining their binding specificities. Overexpression, co-suppression, and antisense technology studies of factor genes in transgenic plants have uncovered the roles of bZIP, homeodomain, and MADS box factors in plant growth and development; for example, ectopic expression of pMADS1 alone in early Petunia development is sufficient for homeotic conversion of sepals into petaloid organs.