Functional analysis of cis-regulatory elements within the promoter of the tobacco late pollen gene g10

Effect of wide variation of the Waxy gene on starch properties in hull-less barley from Qinghai-Tibet plateau in China

Granule-bound starch synthase I (GBSS I) plays an important role in the synthesis of amylose and in the determination of starch properties in barley grains. Genomic DNAs for the Waxy gene encoding GBSS I protein were sequenced from 34 barley accessions or lines from Qinghai-Tibet plateau in China, to identify Waxy gene nucleotide variations and study the roles of polymorphic sites of the Waxy gene on expression levels of Waxy transcripts and GBSS I proteins and on resulting starch properties. A total of 116 DNA polymorphic sites were identified within the barley Waxy gene, which divided the studied accessions into 11 haplotypes. Among 33 nucleotide polymorphic sites in coding regions, 5 SNPs in three exons were found to play different roles on the expression level of the Waxy transcript and the GBSS I protein and on the amylose content and starch properties. One SNP G(3935)-to-T substitution in the 10th exon in the accession Z999 (HP II-2) caused a high expression level of the Waxy transcript and the GBSS I protein and the amylose free phenotype. The other SNP alteration was a C(2453)-to-T in the fifth exon in the accession Z1191 (HP I-5), which drastically reduced the expression level of the Waxy transcript and the GBSS I protein and, finally, produced the amylose free phenotype. Three SNPs in the seventh exon in the accession Z1337 (HP I-6) did not significantly change the level of Waxy transcript, the GBSS I protein, and starch properties, except obviously reducing the breakdown value of starch viscosity and extending the peak time. A total of 84 DNA polymorphic sites were found in the noncoding regions. A 403 bp deletion at 5'UTR in the accession Z1979 (HP I-3) had low transcript level, low GBSS I protein level, and low amylose content due to the deletion of cis-acting DNA regulatory elements. A 191 bp insertion and a 15 bp insertion in the first intron and second exons, respectively, may be closely related to a higher transcript level of the Waxy gene and significant differences in some starch properties of the Waxy I DNA group as compared to the Waxy II DNA group. This study indicates the specific variations of the Waxy gene have a great effect on amylose synthesis and starch properties of hull-less barley, which could be very useful to produce new barley with variable starch properties.

Intergenic sequence between Arabidopsis caseinolytic protease B-cytoplasmic/heat shock protein100 and choline kinase genes functions as a heat-inducible bidirectional promoter

In Arabidopsis (Arabidopsis thaliana), the At1g74310 locus encodes for caseinolytic protease B-cytoplasmic (ClpB-C)/heat shock protein100 protein (AtClpB-C), which is critical for the acquisition of thermotolerance, and At1g74320 encodes for choline kinase (AtCK2) that catalyzes the first reaction in the Kennedy pathway for phosphatidylcholine biosynthesis. Previous work has established that the knockout mutants of these genes display heat-sensitive phenotypes. While analyzing the AtClpB-C promoter and upstream genomic regions in this study, we noted that AtClpB-C and AtCK2 genes are head-to-head oriented on chromosome 1 of the Arabidopsis genome. Expression analysis showed that transcripts of these genes are rapidly induced in response to heat stress treatment. In stably transformed Arabidopsis plants harboring this intergenic sequence between head-to-head oriented green fluorescent protein and β-glucuronidase reporter genes, both transcripts and proteins of the two reporters were up-regulated upon heat stress. Four heat shock elements were noted in the intergenic region by in silico analysis. In the homozygous transfer DNA insertion mutant Salk_014505, 4,393-bp transfer DNA is inserted at position -517 upstream of ATG of the AtClpB-C gene. As a result, AtCk2 loses proximity to three of the four heat shock elements in the mutant line. Heat-inducible expression of the AtCK2 transcript was completely lost, whereas the expression of AtClpB-C was not affected in the mutant plants. Our results suggest that the 1,329-bp intergenic fragment functions as a heat-inducible bidirectional promoter and the region governing the heat inducibility is possibly shared between the two genes. We propose a model in which AtClpB-C shares its regulatory region with heat-induced choline kinase, which has a possible role in heat signaling.

Comparative analysis of synthetic DNA promoters for high-level gene expression in plants

MAIN CONCLUSION

We have designed two near- constitutive and stress-inducible promoters (CmYLCV9.11 and CmYLCV4); those are highly efficient in both dicot and monocot plants and have prospective to substitute the CaMV 35S promoter. We performed structural and functional studies of the full-length transcript promoter from Cestrum yellow leaf curling virus (CmYLCV) employing promoter/leader deletion and activating cis-sequence analysis. We designed a 465-bp long CmYLCV9.11 promoter fragment (-329 to +137 from transcription start site) that showed enhanced promoter activity and was highly responsive to both biotic and abiotic stresses. The CmYLCV9.11 promoter was about 28-fold stronger than the CaMV35S promoter in transient and stable transgenic assays using β-glucuronidase (GUS) reporter gene. The CmYLCV9.11 promoter also demonstrated stronger activity than the previously reported CmYLCV promoter fragments, CmpC (-341 to +5) and CmpS (-349 to +59) in transient systems like maize protoplasts and onion epidermal cells as well as transgenic systems. A good correlation between CmYLCV9.11 promoter-driven GUS-accumulation/enzymatic activities with corresponding uidA-mRNA level in transgenic tobacco plants was shown. Histochemical (X-Gluc) staining of transgenic seedlings, root and floral parts expressing the GUS under the control of CmYLCV9.11, CaMV35S, CmpC and CmpS promoters also support the above findings. The CmYLCV9.11 promoter is a constitutive promoter and the expression level in tissues of transgenic tobacco plants was in the following order: root > leaf > stem. The tobacco transcription factor TGA1a was found to bind strongly to the CmYLCV9.11 promoter region, as shown by Gel-shift assay and South-Western blot analysis. In addition, the CmYLCV9.11 promoter was regulated by a number of abiotic and biotic stresses as studied in transgenic Arabidopsis and tobacco plants. The newly derived CmYLCV9.11 promoter is an efficient tool for biotechnological applications.

GmPRP2 promoter drives root-preferential expression in transgenic Arabidopsis and soybean hairy roots

BACKGROUND

Promoters play important roles in gene expression and function. There are three basic types of promoters: constitutive, specific, and inducible. Constitutive promoters are widely used in genetic engineering, but these promoters have limitations. Inducible promoters are activated by specific inducers. Tissue-specific promoters are a type of specific promoters that drive gene expression in specific tissues or organs. Here, we cloned and characterized the GmPRP2 promoter from soybean. The expression pattern indicated that this promoter is root-preferential in transgenic Arabidopsis and the hairy roots of soybean. It can be used to improve the root resistance or tolerance to pathogens, pests, malnutrition and other abiotic stresses which cause extensive annual losses in soybean production.

RESULTS

The GmPRP2 promoter (GmPRP2p-1062) was isolated from soybean cv. Williams 82. Sequence analysis revealed that this promoter contains many cis-acting elements, including root-specific motifs. The GmPRP2p-1062 and its 5'-deletion fragments were fused with the GUS reporter gene and introduced into Arabidopsis and the hairy roots of soybean to further determine promoter activity. Histochemical analysis in transgenic Arabidopsis showed that GUS activity was mainly detected in roots and hypocotyls in all deletion fragments except GmPRP2p-471 (a 5'-deletion fragment of GmPRP2p-1062 with 471 bp length). GUS activity was higher in transgenic Arabidopsis and hairy roots with GmPRP2p-1062 and GmPRP2p-852 (a 5'-deletion fragment of GmPRP2p-1062 with 852 bp length) constructs than the other two constructs. GUS activity was enhanced by NaCl, PEG, IAA and JM treatments and decreased by SA, ABA and GA treatments in transgenic Arabidopsis.

CONCLUSIONS

GmPRP2p-1062 is a root-preferential promoter, and its core fragment for root-preferential expression might lie between -369 and +1. GmPRP2p-852 may be useful in the genetic engineering of novel soybean cultivars in the future.

Characterization of putative cis-regulatory elements in genes preferentially expressed in Arabidopsis male meiocytes

Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs) with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs) associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb) of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.

Evaluation of rice promoters conferring pollen-specific expression in a heterologous system, Arabidopsis

Promoters can direct gene expression specifically to targeted tissues or cells. Effective with both crop species and model plant systems, these tools can help researchers overcome the practical obstacles associated with transgenic protocols. Here, we identified promoters that allow one to target the manipulation of gene expression during pollen development. Utilizing published transcriptomic databases for rice, we investigated the promoter activity of selected genes in Arabidopsis. From various microarray datasets, including those for anthers and pollen grains at different developmental stages, we selected nine candidate genes that showed high levels of expression in the late stages of rice pollen development. We named these Oryza sativa late pollen-specific genes. Their promoter regions contained various cis-acting elements that could be responsible for anther-/pollen-specific expression. Promoter::GUS-GFP reporters were constructed and introduced into Arabidopsis plants. Histochemical GUS staining revealed that six of the nine rice promoters conferred strong GUS expression that was restricted to the anthers in Arabidopsis. Further analysis showed that although the GUS signals were not detected at the unicellular stage, they strengthened in the bicellular or tricellular stages, peaking at the mature pollen stage. This paralleled their transcriptomic profiles in rice. Based on our results, we proposed that these six rice promoters, which are active in the late stages of pollen formation in the dicot Arabidopsis, can aid molecular breeders in generating new varieties of a monocot plant, rice.

Identification of the tapetum/microspore-specific promoter of the pathogenesis-related 10 gene and its regulation in the anther of Lilium longiflorum

A tapetum/microspore-specific pathogenesis-related (PR) 10 gene was previously identified in lily (Lilium longiflorum Thunb.) anthers. In situ hybridization and RNA blot analysis indicated that the lily PR10 genes are expressed specifically and differentially in the tapetum of the anther wall and in microspores during anther development. The accumulation of PR10 transcripts was exogenously induced by gibberellic acid (GA) and was suppressed by ethylene. Studies using inhibitors of GA and ethylene revealed that the lily PR10 is modulated by an antagonistic interaction between GA and ethylene. The treatment of norbornadien, an ethylene inhibitor, caused the tapetum to become densely cytoplasmic and highly polarized, whereas uniconazole, an inhibitor of GA biosynthesis, arrested tapetal development to a status close to that of control. The expression of the lily PR10g promoter in transgenic Arabidopsis was determined using the β-glucuronidase (GUS) reporter gene indicated that the decisive fragment required for anther specificity is located -1183 bp to -880 bp upstream of the transcription start site. The PR10gPro::barnase transgenic lines exhibited complete male sterility because of the disruption of the tapetum and the deformation of microspore/pollen. The anther specificity of lily PR10 highlights the importance of the tapetum/microspore-specific PR10g promoter for future biotechnological and agricultural applications.

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L

BACKGROUND

Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary.

METHODOLOGY/PRINCIPAL FINDING

In this study, a total of 63 putative BrnsLtp genes were identified through a comprehensive in silico analysis of the whole genome of B. rapa. Based on the sequence similarities, these BrnsLtps was grouped into nine types (I, II, III, IV, V, VI, VIII, IX, and XI). There is no type VII nsLtps in B. rapa, and a new type, XI nsLtps, was identified in B. rapa. Furthermore, nine type II AtLtps have no homologous genes in B. rapa. Gene duplication analysis demonstrated that the conserved collinear block of each BrnsLtp is highly identical to those in Arabidopsis and that both segmental duplications and tandem duplications seem to play equal roles in the diversification of this gene family. Expression analysis indicated that 29 out of the 63 BrnsLtps showed specific expression patterns. After careful comparison and analysis, we hypothesize that some of the type I BrnsLtps may function like Arabidopsis pathogenesis-related-14 (PR-14) proteins to protect the plant from phytopathogen attack. Eleven BrnsLtps with inflorescence-specific expression may play important roles in sexual reproduction. Additionally, BrnsLtpI.3 may have functions similar to Arabidopsis LTP1.

CONCLUSIONS/SIGNIFICANCE

The genome-wide identification, bioinformatic analysis and expression analysis of BrnsLtp genes should facilitate research of this gene family and polyploidy evolution and provide new insight towards elucidating their biological functions in plants.

Upregulation of the AT-hook DNA binding gene BoMF2 in OguCMS anthers of Brassica oleracea suggests that it encodes a transcriptional regulatory factor for anther development

Ogura cytoplasmic male sterility (OguCMS) is the most important CMS system used for F1 hybrid cabbage production worldwide. The anther abortion and defective pollen development exhibited in OguCMS are coordinately regulated by the mitochondrial male sterile gene orf138 and many nuclear transcriptional regulatory factors. AT-hook DNA binding proteins regulate cell-specific gene expression. In this study, we cloned the gene encoding the AT-hook DNA binding protein BoMF2 using the cDNA-AFLP TDF sequence, which was upregulated in OguCMS cabbage flower buds, as a querying probe. BoMF2 contains a 783-nt continuous complete open reading frame encoding a 260 amino-acid polypeptide. In vivo transient expression assays using GFP fusions showed that BoMF2 protein was located in the nucleus. BoMF2 was preferentially expressed in cabbage stamens, with a short expression window at anther development stage 7-8. However, in OguCMS flowers, BoMF2 expression continued into the mature pollen stage and was concomitant with the continued proliferation of tapetum cells exhibited in this mutant. Arabidopsis plants overexpressing BoMF2 showed significantly shorter siliques than the wild type, as well as decrease of pollen viability. These results suggest that BoMF2, a transcriptional regulatory factor, might regulate tapetum proliferation during anther development.

An intergenic region shared by At4g35985 and At4g35987 in Arabidopsis thaliana is a tissue specific and stress inducible bidirectional promoter analyzed in transgenic arabidopsis and tobacco plants

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.

The rice OsLTP6 gene promoter directs anther-specific expression by a combination of positive and negative regulatory elements

Characterization of tissue-specific plant gene promoters will benefit genetic improvement in crops. Here, we isolated a novel rice anther-specific plant lipid transfer protein (OsLTP6) gene through high through-put expressional profiling. The promoter of OsLTP6 was introduced to the upstream of the uidA gene, which encodes β-glucuronidase (GUS), and transformed into rice plants for functional analysis. Histochemical and fluorometric GUS assay showed that GUS was specifically expressed in the anthers and pollens in OsLTP6 promoter::uidA transgenic plants. Transverse section of the rice anther further indicated that the OsLTP6 promoter directed the reporter gene specifically expressed in anther tapetum. To identify regulatory elements within OsLTP6 promoter region, four progressive deletions of the OsLTP6 promoter were constructed. The results indicated that the OsLTP6 promoter achieved anther-specific expression through a combination of positive and negative regulatory elements. A 26-bp motif upstream of TATA box was a key transcriptional activator for OsLTP6 gene. CAAT box and GTGA box were the putative motifs to increase the transcription level to full expression. Two negative regulatory elements were also found in two distinct regions within this promoter. They repressed the expression in leaf and stem, respectively. These results revealed the regulating complexity of anther-specific expression.

The promoter of the carotenoid cleavage dioxygenase 4a-5 gene of Chrysanthemum morifolium (CmCCD4a-5) drives petal-specific transcription of a conjugated gene in the developing flower

Carotenoids comprise one of the major groups of pigments in flowers. Because carotenoids are physiologically indispensable pigments for all photosynthetic plants, their catabolism must be discretely regulated in photosynthetic organs and non-photosynthetic organs such as petals or fruits. In the chrysanthemum, carotenoid cleavage dioxygenase 4a (CmCCD4a), which is dominantly expressed in petals, cleaves carotenoid, leading to a white flower. CmCCD4a-5 was recently identified as a new member of the CmCCD4a family, but its detailed expression profile in plant tissues has not yet been established. In this study, we sequenced a 1094-bp region upstream of CmCCD4a-5 and assessed its petal-specific promoter activity. To evaluate the activity of this gene, we constructed two types of transgenic Arabidopsis thaliana that possessed, respectively, a fusion gene of a 1090-bp or 505-bp segment of the upstream region plus the β-d-glucuronidase (GUS) gene (1090bUR::GUS and 505bUR::GUS). GUS activity in the 505bUR::GUS strain was observed mainly in the anthers/pollen in flower buds, whereas GUS activity of the 1090bUR::GUS strain was observed in immature petals of the flower buds. Among the cis-acting elements located between positions -505 and -1090, no elements that have previously been reported to enhance the expression in petals or to suppress it in anthers/pollen were detected by PLACE analysis, indicating the existence of unknown cis-element(s). A semiquantitative reverse transcription-polymerase chain reaction analysis revealed that CmCCD4a-5 transcription was prominent in petals but was undetectable in roots, stems and leaves.

Characterization of a Pollen-Specific and Desiccation-Associated AP2/ERF Type Transcription Factor Gene from Castor Bean (Ricinus communis L.)

DREB transcription factors (TF) belong to the superfamily of AP2/ERF and their involvement in protein-protein interactions and DNA binding has been proposed. AP2/ERF proteins have important functions in the transcriptional regulation of a variety of biological processes related to growth and development, as well as various responses to environmental stimuli, regulating expression of plant biotic and abiotic stress-responsive genes. In this study an AP2/ERF TF gene (named RcDREB1) was isolated from castor bean (Ricinus communis L.) and its expression was analyzed in developing seeds, leaves, ovules, stems and petals of plants cultivated under field conditions. Transcripts were only observed in pollen grains, peaking during anthesis. The RcDREB1 deduced amino acid sequence was compared to other AP2/ERF TF proteins and presented 38–78% identity. Phylogenetic analysis classified it as a member of the CBF/DREB subfamily, rooting with the subgroup A-5. The RcDREB1 promoter was fused to the gus reporter gene and used to transform tobacco. Transgenic plants were exposed to various abiotic stress treatments (low and high tempera- tures, drought, salinity and exogenous ABA) and no detectable GUS expression was observed, suggesting that the RcDREB1 promoter is not active under tested conditions. In silico analyses revealed the presence of three copies of the regulatory late pollen-specific element (AGAAA) in the RcDREB1 5′-region. Interestingly, GUS expression was only observed in pollen grains, starting when the flower opened and initiating the senescence process; at this point, desiccated mature pollen grains are released from anthers. In addition, dehydrated developing pollen grains also expressed the gus gene. This is the first study on a DREB gene presenting pollen-specific expression.

5' Regulatory region of ubiquitin 2 gene from Porteresia coarctata makes efficient promoters for transgene expression in monocots and dicots

KEY MESSAGE

Porteresia ubiquitin 5' regulatory region drives transgene expression in monocots and dicots. Ubiquitin promoters are promising candidates for constitutive transgene expression in plants. In this study, we isolated and characterized a novel 5' regulatory sequence of a ubiquitin gene from Porteresia coarctata, a stress-tolerant wild grass species. Through functional analysis in heterologous plant systems, we have demonstrated that full length (Port Ubi2.3) or truncated sequence (PD2) of the isolated regulatory fragment can drive constitutive expression of GUS in monocots and/or dicots. In silico analysis of Port Ubi2.3 has revealed the presence of a 640 bp core promoter region followed by two exons and two introns with numerous putative cis-acting sites scattered throughout the regulatory region. Transformation and expression studies of six different deletion constructs in rice, tobacco and sugarcane revealed that the proximal intron has an enhancing effect on the activity of the core promoter in both monocots and dicots, whereas, Port Ubi2.3 was able to render strong expression only in monocots. This regulatory sequence is quite distinct from the other reported ubiquitin promoters in structure and performs better in monocots compared to other commonly used promoters-maize Ubi1 and Cauliflower Mosaic Virus 35S.

Epigenetic repression of male gametophyte-specific genes in the Arabidopsis sporophyte

Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pollen are not expressed in the sporophyte. How pollen-specific genes are down-regulated in the sporophyte has yet to be established. In this study, we have performed a bioinformatics analysis of publicly available genome-wide epigenetics data of several sporophytic tissues. By combining this analysis with DNase I footprinting data, we assessed means by which the repression of pollen-specific genes in the Arabidopsis sporophyte is conferred. Our findings show that, in seedlings, the majority of pollen-specific genes are associated with histone-3 marked by mono- or trimethylation of Lys-27 (H3K27me1/H3K27me3), both of which are repressive markers for gene expression in the sporophyte. Analysis of DNase footprint profiles of pollen-specific genes in the sporophyte displayed closed chromatin proximal to the start codon. We describe a model of two-staged gene regulation in which a lack of nucleosome-free regions in promoters and histone modifications in open reading frames repress pollen-specific genes in the sporophyte.

Characterization and expression analysis of waxy alleles in barley accessions

Granule Bound Starch Synthase I (GBSS I) encoded by the waxy gene plays an important role in accumulating amylose during the development of starch granules in barley. In this study, we isolated and characterized waxy alleles of three waxy (GSHO 908, GSHO 1828 and NA 40) and two non-waxy barley accessions (PI 483237 and CIho 15773), estimated the expression patterns of waxy genes via Real-time quantitative PCR (RT-qPCR), investigated promoter activity by analyzing promoter-GUS expression, and examined possible effects of waxy alleles on starch granule morphology in barley accessions by scanning electron microscopy (SEM). A 193-bp insertion in intron 1, a 15-bp insertion in the coding region, and some single nucleotide polymorphic sites were detected in the waxy barley accessions. In addition, a 397-bp deletion containing the TATA box, transcription starting point, exon 1 and partial intron 1 were also identified in the waxy barley accessions. RT-qPCR analysis showed that waxy accessions had lower waxy expression levels than those of non-waxy accessions. Transient expression assays showed that GUS activity driven by the 1,029-bp promoter of the non-waxy accessions was stronger than that driven by the 822-bp promoter of the waxy accessions. SEM revealed no apparent differences of starch granule morphology between waxy and non-waxy accessions. Our results showed that the 397-bp deletion identified in the waxy barley accessions is likely responsible for the reduction of waxy transcript, leading to lower concentrations of GBSS I protein thus lower amylose content.

Characterization of the sporophyte-preferential gene promoter from the red alga Porphyra yezoensis using transient gene expression

The life cycle of plants entails an alternation of generations, the diploid sporophyte and haploid gametophyte stages. There is little information about the characteristics of gene expression during each phase of marine macroalgae. Promoter analysis is a useful method for understanding transcriptional regulation; however, there is no report of promoter analyses in marine macroalgae. In this study, with the aim of elucidating the differences in the transcriptional regulatory mechanisms between the gametophyte and sporophyte stages in the marine red alga Porphyra yezoensis, we isolated the promoter from the sporophyte preferentially expressed gene PyKPA1, which encodes a sodium pump, and analyzed its promoter using a transient gene expression system with a synthetic β-glucuronidase (PyGUS) reporter. The deletion of -1432 to -768 relative to the transcription start site resulted in decreased GUS activity in sporophytes. In contrast, deletion from -767 to -527 increased GUS activity in gametophytes. Gain-of-function analyses showed that the -1432 to -760 region enhanced the GUS activity of a heterologous promoter in sporophytes, whereas the -767 to -510 region repressed it in gametophytes. Further mutation and gain-of-function analyses of the -767 to -510 region revealed that a 20-bp GC-rich sequence (-633 to -614) is responsible for the gametophyte-specific repressed expression. These results showed that the sporophyte-specific positive regulatory region and gametophyte-specific negative regulatory sequence play a crucial role in the preferential expression of PyKPA1 in P. yezoensis sporophytes.

Identification of sequences required for AL2-mediated activation of the tomato golden mosaic virus-yellow vein BR1 promoter

A 108 bp sequence has been identified in the tomato golden mosaic virus-yellow vein (yvTGMV) B component that is necessary and sufficient for AL2-mediated activation of the BR1 promoter. The sequence appears to have a bipartite arrangement, with elements located between -144 to -77 and -59 to -36 from the transcription start site, with both being required for activation by AL2. These sequences are located upstream of a TATA box and bind nuclear proteins from spinach, tomato and Arabidopsis. These sequences are also capable of binding Arabidopsis PPD2, which has been shown previously to interact with the yvTGMV coat protein (CP) promoter. We have identified two putative transcription factor-binding sites (CCAAT and GTGANTG10) that are conserved in sequences necessary for activation of the yvTGMV BR1, as well as the yvTGMV and cabbage leaf curl virus (CabLCV) CP promoters, which are all activated by AL2. The yvTGMV BR1 promoter exhibits AL2-independent expression in vascular tissue, similar to the yvTGMV, CabLCV and spinach curly top virus CP promoters. Together, this further confirms a common regulatory mechanism for AL2-mediated activation of bipartite begomovirus promoters.

The promoter of an A9 homolog from the conifer Cryptomeria japonica imparts male strobilus-dominant expression in transgenic trees

KEY MESSAGE : GUS analysis in Cryptomeria japonica revealed that the CjMALE1 promoter is activated in the male strobilus of C. japonica. Toward the development of male sterile technology for Cryptomeria japonica, a male strobilus-dominant promoter of C. japonica was isolated. The CjMALE1 gene was isolated from a male strobilus-specific suppression subtractive hybridization (SSH) library, and the promoter was isolated by the TAIL-PCR method. To characterize the CjMALE1 promoter, β-glucuronidase (GUS)-fused genes were constructed and introduced into C. japonica using Agrobacterium tumefaciens. GUS expression from CjMALE1-2.5 K (2,718 bp fragment)::GUS C. japonica and CjMALE1-1 K (1,029 bp fragment)::GUS C. japonica was detected in the tapetum and microspore mother cells. These promoter fragments were comparably active in the pre-meiotic stage of the male strobilus of C. japonica. Our analysis showed that the 1,029 bp promoter had all the cis-elements necessary for male strobilus-dominant expression of CjMALE1. When CjMALE1-1 K::GUS was introduced into Arabidopsis, GUS expression was detected in the same spatiotemporal pattern as in C. japonica. These results suggest that the CjMALE1 promoter is subject to transcriptional regulatory systems consisting of cis- and trans-elements that have been highly conserved during evolution.

A 286 bp upstream regulatory region of a rice anther-specific gene, OSIPP3, confers pollen-specific expression in Arabidopsis

OSIPP3 gene (coding for pectin methylesterase inhibitor protein) was isolated from a pre-pollinated inflorescence-specific cDNA library by differential screening of stage-specific libraries from Oryza sativa. OSIPP3 is present in the genome of rice as a single copy gene. OSIPP3 gene was expressed exclusively in the pre-pollinated spikelets of rice. Upstream regulatory region (URR) of OSIPP3 was isolated and a series of 5'-deletions were cloned upstream of GUS reporter gene and were used to transform Arabidopsis. OSIPP3_del1 and del2 transgenic plants showed GUS expression in root, anther and silique, while OSIPP3_del3 showed GUS activity only in anthers and siliques. Pollen-specific expression was observed in case of plants harboring OSIPP3_del4 construct. It can, therefore, be concluded that the OSIPP3 URR between -178 and +108 bp is necessary for conferring pollen-specific expression in Arabidopsis.

Spatial and temporal activity of upstream regulatory regions of rice anther-specific genes in transgenic rice and Arabidopsis

Upstream regulatory regions (URRs) of rice anther-specific genes, namely OSbHLH (coding for basic helix-loop-helix-containing protein) and OSFbox (F-box protein encoding gene), selected from the microarray data have been cloned to control expression of GUS and GFP reporter genes in stably transformed rice. Quantitative real time PCR analysis shows maximum transcript accumulation of these two genes in the meiotic anthers. Analysis of OSbHLH and OSFbox URRs by PLACE database reveal the presence of known pollen-specific cis elements. The URRs of both OSbHLH and OSFbox genes have maximum activity in the meiotic anther stage in rice, but confer constitutive expression in the heterologous dicot system, Arabidopsis, indicative of monocot specificity. Another rice gene (OSIPK; with homology to genes encoding calcium-dependent protein kinases) URR already reported to have anther-specific activity in Arabidopsis and tobacco also confers anther-specific expression in rice and is active in the pollen tubes, suggesting it belongs to the category of late expressed genes. The spatial activity of three URRs has also been analysed by histochemical evaluation of GUS activity in different anther cells/tissues. The activity of OSIPK URR in rice is strongest among the three URRs.

Sequence characterization and expression pattern of BcMF21, a novel gene related to pollen development in Brassica campestris ssp. chinensis

In this report a full length cDNA, Brassica campestris Male Fertile 21 (BcMF21) was successfully isolated from one of the cDNA-amplified fragment length polymorphism (cDNA-AFLP) transcript-derived fragments (TDFs), BBP10, that was found down-regulated in the flower buds of sterile plants in Brassica campestris L. ssp. chinensis Makino genic male sterile (GMS) AB line system (Bcajh 97-01A/B). BcMF21 protein structure analysis showed a signal peptide at the N-terminus; two protein kinase C phosphorylation sites, five N-myristoylation sites and one casein kinase II phosphorylation site. The promoter region of BcMF21, a 779 bp upstream of ATG was isolated by thermal asymmetric interlaced-PCR (TAIL-PCR). Bioinformatics analysis revealed that the promoter of BcMF21 contained several classical cis-acting elements and three pollen specific elements. Transient expression analysis showed that the promoter could drive green fluorescence protein (GFP) expression. Quantitative reverse transcript-PCR analysis revealed that BcMF21 was specifically expressed in flower buds. The transcript level of BcMF21 was much lower in the sterile flower buds than in the fertile flower buds in 'Bcajh 97-01A/B' system. In situ hybridization further showed that BcMF21 was only expressed in the tetrads and the microspores at the tetrad stage and the uninucleate stage. In addition, phylogenetic analysis demonstrated that the BcMF21 was relative conserved within family Crucifereae and might be originated from the ancestor diploid B. campestris within genus Brassica according to the Triangle of U theory.

MYB80, a regulator of tapetal and pollen development, is functionally conserved in crops

The Arabidopsis AtMYB80 transcription factor (formerly AtMYB103) regulate genes essential for tapetal and pollen development. One of these genes, coding for an aspartic protease (UNDEAD), may control the timing of tapetal programmed cell death (PCD). In crop plants such as rice and wheat, abiotic stresses lead to abnormal tapetal development resulting in delayed PCD. Manipulation of AtMYB80 function has been used to develop a reversible male sterility system applicable to hybrid crop production. MYB80 homologs were cloned from wheat, rice, canola and cotton. The promoters of the homologs drove temporal and spatial expression patterns of the GUS reporter gene in the tapetum and microspores of Arabidopsis anthers identical to the AtMYB80 promoter. A short region is conserved in all five MYB80 promoters. The MYB80 homolog genes, driven by the AtMYB80 or their respective promoters, rescued the atmyb80 mutant, completely restoring male fertility. The canola MYB80 was fused to the EAR (ERF-associated amphiphilic repression) repressor and canola plants transgenic for the construct exhibited premature tapetal degradation and subsequent pollen abortion. The five MYB80 homologs all shared a 44 amino acid sequence immediately adjacent to the R2R3 domain which appears to be necessary for MYB80 function.

Characterization of a chalcone synthase (CHS) flower-specific promoter from Lilium orential 'Sorbonne'

The first enzyme in the flavonoid pathway, chalcone synthase, is encoded by a gene (CHS) whose expression is normally under developmental control. In our previous studies, an 896-bp promoter region of a flower-specific CHS gene was isolated from Lilium orential 'Sorbonne', and designated as PLoCHS. Here, the PLoCHS promoter was fused to the β-glucuronidase (GUS) gene to characterize its spatial and temporal expression in Petunia hybrida 'Dreams Midnight' using an Agrobacterium-mediated leaf disc transformation method. Our results demonstrated that GUS expression was present in flowers, but reduced or absent in the other tissues (leaf and stem) examined. In petals, GUS activity reached its peak at flower developmental stage 4, and decreased at later stages. Deletion analysis indicated that even a 307-bp fragment of the PLoCHS promoter could still direct flower-specific expression. Further deletion of the region from -261 to -72 bp resulted in weak expression in different organs, including flowers, leaves and stems. This evidence combined with prediction of cis-acting elements in the PLoCHS promoter suggests that the TACPyAT box located in this promoter plays a key role in the regulation of organ-specific expression.

Functional analysis of a rice late pollen-abundant UDP-glucose pyrophosphorylase (OsUgp2) promoter

OsUgp2, a rice UDP-glucose pyrophosphorylase gene, has previously been shown to preferentially express in maturing pollens and plays an important role in pollen starch accumulation. Here, a 1943 bp promoter fragment (P1943) of OsUgp2 was characterized by 5' deletion and gain-of-function experiments. P1943 and its 5' deletion derivatives (P1495, P1005, P665 and P159) were fused to GUS reporter gene and stably introduced into rice plants. Histochemical analyses of different tissues and pollens at different developmental stages of the transgenic plants showed that P1943 could only direct GUS expression in binucleate pollens. P1495 and P1005 could still drive GUS expression in binucleate pollens but at a lower level. On the other hand, neither P665 nor P159 transformant exhibited any GUS activity in pollens. Gain-of-function analyses showed that the region (-1005 to -665 relative to translation start site) combined with a minimal CaMV 35S promoter could direct GUS expression in pollens. Further analysis of 5' deletion truncated at -952, -847 and -740 delimited a 53 bp region (-1005 to -952) essential for pollen-specific expression. The 53 bp sequence contains two motifs of TTTCT and TTTC, which were known to be pollen-specific cis-elements. In addition, the same P1943-GUS fusion construct was introduced into tobacco to analyze its specificity in dicotyledon. Interestingly, the GUS expression pattern in transgenic tobacco was quite different from that in rice. High level of GUS expression was detected in mature pollens as well as leaves, roots, sepals and stigmas. These findings suggested a complicated transcriptional regulation of OsUgp2.

Putative cis-regulatory elements in genes highly expressed in rice sperm cells

Background

The male germ line in flowering plants is initiated within developing pollen grains via asymmetric division. The smaller cell then becomes totally encased within a much larger vegetative cell, forming a unique "cell within a cell structure". The generative cell subsequently divides to give rise to two non-motile diminutive sperm cells, which take part in double fertilization and lead to the seed set. Sperm cells are difficult to investigate because of their presence within the confines of the larger vegetative cell. However, recently developed techniques for the isolation of rice sperm cells and the fully annotated rice genome sequence have allowed for the characterization of the transcriptional repertoire of sperm cells. Microarray gene expression data has identified a subset of rice genes that show unique or highly preferential expression in sperm cells. This information has led to the identification of cis-regulatory elements (CREs), which are conserved in sperm-expressed genes and are putatively associated with the control of cell-specific expression.

Findings

We aimed to identify the CREs associated with rice sperm cell-specific gene expression data using in silico prediction tools. We analyzed 1-kb upstream regions of the top 40 sperm cell co-expressed genes for over-represented conserved and novel motifs. Analysis of upstream regions with the SIGNALSCAN program with the PLACE database, MEME and the Mclip tool helped to find combinatorial sets of known transcriptional factor-binding sites along with two novel motifs putatively associated with the co-expression of sperm cell-specific genes.

Conclusions

Our data shows the occurrence of novel motifs, which are putative CREs and are likely targets of transcriptional factors regulating sperm cell gene expression. These motifs can be used to design the experimental verification of regulatory elements and the identification of transcriptional factors that regulate sperm cell-specific gene expression.

Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress

Plants respond to heat stress by enhancing the expression of genes encoding heat shock protein (HSPs) genes through activation of heat shock factors (HSFs) which interact with heat shock elements present in the promoter of HSP genes. Plant HSFs have been divided into three conserved classes viz A, B and C. In the present study, a detailed analysis has been done of all rice HSFs, along with their spliced variants. Their chromosomal localization reveals that six HSFs are segmentally duplicated and four pairs of these segmentally duplicated HSF encoding genes show pseudo-functionalization. Expression profiling through microarray and quantitative real-time PCR showed that eight OsHsfs express at a higher level during seed development, while six HSFs are up-regulated in all the abiotic stresses studied. The expression of OsHsfA2a gene in particular was greatly stimulated by heat stress in both root and shoot tissues and also during panicle and seed development. OsHsfA3 was found more responsive to cold and drought stress, while OsHsfA7 and OsHsfA9 showed developing seed-specific expression. This study also revealed that spliced variants generally accumulated at a higher level in all the tissues examined. Different hormones/elicitors like ABA, brassinosteroids and salicylic acid also alter OsHsf gene expression. Calcium in combination with heat stress elevated further the level of HSF transcripts. Expression analysis by both microarray and real-time RT-PCR revealed a unique stable constitutive expression of OsHsfA1 across all the tissues and stresses. A detailed in silico analysis involving identification of unidentified domains has been done by MEME-motif tool in their full-length proteins as well as in DNA-binding domains. Analysis of 1 kb putative promoter region revealed presence of tissue-specific, abiotic stress and hormone-related cis-acting elements, correlating with expression under stress conditions.

Genome-wide identification of antioxidant component biosynthetic enzymes: comprehensive analysis of ascorbic acid and tocochromanols biosynthetic genes in rice

During the last two decades, several exciting reports have provided many advances in the role and biosynthesis of l-ascorbic acid (AsA) and tocochromanols, including tocopherols and tocotrienols, in higher plants. There are increasing bodies of experimental evidence that demonstrate that AsA and tocochromanols (especially tocopherols) play an important role as antioxidants and nutrients in mammals and photosynthetic organisms and are also involved in plant responses to stimuli. Although AsA and tocochromanol biosynthesis pathways have been well characterized using Arabidopsis, these pathways are still poorly understood in rice, which is an economically important monocot cereal crop. In this study using computational analysis of sequenced rice genome, we identified eight and seven potential non-redundant members involved in AsA and tocochromanol biosynthetic pathways, respectively. The results reveal that the common feature of these gene promoters is the combination of light-responsive, hormone-responsive, and stress-responsive elements. These findings, together with expression analysis in the MPSS database, indicate that AsA and tocochromanols might be co-related with the complex signaling pathways involved in plant responses.

Pollen-specific expression of Oryza sativa indica pollen allergen gene (OSIPA) promoter in rice and Arabidopsis transgenic systems

Earlier, a pollen-specific Oryza sativa indica pollen allergen gene (OSIPA), coding for expansins/pollen allergens, was isolated from rice, and its promoter--upon expression in tobacco and Arabidopsis--was found active during the late stages of pollen development. In this investigation, to analyze the effects of different putative regulatory motifs of OSIPA promoter, a series of 5' deletions were fused to β-glucuronidase gene (GUS) which were stably introduced into rice and Arabidopsis. Histochemical GUS analysis of the transgenic plants revealed that a 1631 bp promoter fragment mediates maximum GUS expression at different stages of anther/pollen development. Promoter deletions to -1272, -966, -617, and -199 bp did not change the expression profile of the pollen specificity. However, the activity of promoter was reduced as the length of promoter decreased. The region between -1567 and -199 bp was found adequate to confer pollen-specific expression in both rice and Arabidopsis systems. An approximate 4-fold increase in the GUS activity was observed in the pollen of rice when compared to that of Arabidopsis. As such, the OSIPA promoter seems promising for generation of stable male-sterile lines required for the production of hybrids in rice and other crop plants.

Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

Background

Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS) and sequencing-by-synthesis (SBS). Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield), LaGrue (low milling yield), Ilpumbyeo (high eating quality), YR15965 (low eating quality), and Nipponbare (control).

Results

The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved cis regulatory elements were identified. Numerous specifically expressed transcription factor (TF) genes were identified in Cypress (282), LaGrue (312), Ilpumbyeo (363), YR15965 (260), and Nipponbare (357). Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation) that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase) and granule bound starch synthase I (GBSS I) in Cypress than that in LaGrue during early seed development.

Conclusion

This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved in the biosynthesis of starch, aspartate family amino acids, and storage proteins. Some of the differentially expressed genes could be useful for the development of molecular markers if they are located in a known QTL region for milling yield or eating quality in the rice genome. Therefore, our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars has provided a rich genomic resource for further elucidating the molecular basis of grain quality in rice.

A rice β-1,3-glucanase gene Osg1 is required for callose degradation in pollen development

Plant β-1,3-glucanases are involved in plant defense and development. In rice (Oryza sativa), 14 genes encoding putative β-1,3-glucanases have been isolated and sequenced. However, only limited information is available on the function of these β-1,3-glucanase genes. In this study, we report a detailed functional characterization of one of these genes, Osg1. Osg1 encodes a glucanase carrying no C-terminal extension. Osg1 was found to be expressed throughout the plant and highly expressed in florets, leaf sheaths, and leaf blades. Investigations using real-time PCR, immunocytochemical analysis, and a GUS-reporter gene driven by the Osg1 promoter indicated that Osg1 was mainly expressed at the late meiosis, early microspore, and middle microspore stages in the florets. To elucidate the role of Osg1, we suppressed expression of the Osg1 gene by RNA interference in transgenic rice. The silencing of Osg1 resulted in male sterility. The pollen mother cells appeared to be normal in Osg1-RI plants, but callose degradation was disrupted around the microspores in the anther locules of the Osg1-RI plants at the early microspore stage. Consequently, the release of the young microspores into the anther locules was delayed, and the microspores began to degenerate later. These results provide evidence that Osg1 is essential for timely callose degradation in the process of tetrad dissolution.

The fasciclin-like arabinogalactan protein gene, FLA3, is involved in microspore development of Arabidopsis

Arabinogalactan proteins are widely distributed in plant tissues and cells, and may function in the growth and development of higher plants. To our knowledge, there is currently no direct evidence concerning the involvement of fasciclin-like arabinogalactan proteins (FLA) in sexual reproduction in Arabidopsis. In this study, Arabidopsis FLA3 was found to be specifically expressed in pollen grains and tubes. Subcellular localization showed that FLA3 anchors tightly to the plasma membrane, and its glycosylphosphatidylinositol anchor may affect its localization. FLA3-RNA interference transgenic plants had approximately 50% abnormal pollen grains (including shrunken and wrinkled phenotypes) which lacked viability. Cytological observations revealed that pollen abortion occurred during the transition from uninucleate microspores to bicellular pollens, with abnormal cellulose distribution seen by calcofluor white staining. Transmission electron microscopy showed that the basic structure of the exine layer in aberrant pollen was normal, but the intine layer appeared to have some abnormalities. Taken together, these results suggest that FLA3 is involved in microspore development and may affect pollen intine formation, possibly by participating in cellulose deposition. In FLA3-overexpressing transgenic plants, defective elongation of the stamen filament and reduced female fertility led to short siliques with low seed set, which suggested that ectopic expression of FLA3 in tissues may reduce or disrupt cell growth and then result in defects throughout the plant.

BoPMEI1, a pollen-specific pectin methylesterase inhibitor, has an essential role in pollen tube growth

Pectin methylesterase (PME) is known to have important roles in pollen development and pollen tube growth. As pivotal regulatory factors in PME activity modulation, PME inhibitors (PMEIs) are thought to be key regulators of cell wall stability at the tip of the pollen tube. We report on the cloning and characterization of a novel B. oleracea PMEI gene, BoPMEI1. Heterologously expressed BoPMEI1 showed PMEI activity. RT-PCR studies of different tissues and promoter-GUS fusions confirmed that BoPMEI1 was specifically expressed in mature pollen grains and pollen tubes. Based on in vivo transient assays, we found that BoPMEI1 appears to be largely localized to the plasma membrane. Transgenic Arabidopsis plants expressing antisense BoPMEI1 under the control of the CaMV 35S promoter suppressed the expression of the orthologous gene At1g10770, which led to partial male sterility and decreased seed set by inhibition of pollen tube growth. Our study demonstrates the involvement of BoPMEI1 in pollen tube growth.

Several cis-elements including a palindrome involved in pollen-specific activity of SBgLR promoter

SBgLR (Solanum tuberosum genomic lysine-rich) is a pollen-specific gene cloned from potato (Solanum tuberosum L.). The region from -269 to -9 (The A of translation start site "ATG" as +1) of the SBgLR promoter was identified as critical for gene specific expression in pollen grains. Sequence analysis indicates a palindromic sequence "TTTCTATTATAATAGAAA" in the -227 to -209 region, in which two pollen-specific motifs TTTCT and AGAAA surround a unique putative TATA box. Moreover, nine putative pollen-specific motifs are located in the region between the TATA box and ATG. We placed the -227 to -9 region (reserving the palindrome) and the -222 to -9 region (breaking the palindrome) downstream of the CaMV35S enhancer, respectively, to construct two fusion promoters. Histochemical assays in transgenic plants demonstrated that the region from -222 to -9 is necessary and sufficient for pollen-specific expression of the uidA gene. However, the region of -227 to -9 is incapable of driving GUS expression in pollen grains and parts of vegetative tissues. A series of 5' deletions from -269 to -9 of SBgLR promoter were constructed. A transient expression assay indicated that the region from the -227 to -9 suppressed gfp gene expression in pollen, and a positive regulatory element was present in the region of -253 to -227. The function of the palindromic sequence as a repressor inhibiting gene expression in pollen was further confirmed by the mutated promoter, breaking the palindrome by substituting its 3'-flanking five base pairs, which resumes the reporter gene expression in mature pollen.

Molecular analysis and expression of a floral organ-specific polygalacturonase gene isolated from rapeseed (Brassica napus L.)

High throughput screening of stage-specific differentially expressed genes in a Brassica napus two-line Rs1046A/B subtractive library was used to identify the BnQRT3 gene associated with cell wall metabolism. Phylogenetic analysis indicates the protein product of BnQRT3 is polygalacturonase. According to cytological comparisons of Rs1046 sterile and fertile anthers, RT-PCR studies and in situ hybridizations, BnQRT3 is expressed most strongly in floral organs and may play an essential role in pollen maturation. Analysis of the histological staining pattern of BnQRT3 promoter-GUS constructs in transgenic Arabidopsis and Brassica napus revealed that proximal part of 5'-flanking region directed expression in the vascular tissue of filaments, veins in sepal and petals, stigma, branch connective and the floral organ abscission zone during the open flower stage. In the meanwhile, Activity of BnQRT3 was detected in the anthers, which commences at the microsporocyte stage and persists as anther approaches dehiscence. Strong GUS expression also can be observed in the vascular tissue of leaves and stem by compression with forceps or excision, suggesting that the BnQRT3 promoter is responsive to wounding.

Isolation and heterologous transformation analysis of a pollen-specific promoter from wheat (Triticum aestivum L.)

The promoter of a pollen-specific gene TaPSG719 was isolated from wheat (Triticum aestivum L.) by inverse-PCR (IPCR). Sequence analysis revealed that the promoter contains two cis-acting elements (AGAAA and GTGA) known to confer anther/pollen-specific gene expression which suggests that the promoter of TaPSG719 gene is a pollen-specific one. To ascertain the regulatory function of TaPSG719 promoter, two deleted fragments (-1,776 to -1 bp and -1,019 to -1 bp) were fused to the beta-glucuronidase (GUS) gene and transformed into tobacco plants. Similar GUS expression patterns were observed in all transformed plants and its activity was detected exclusively in pollen. No GUS activity in any other floral or vegetative tissue was observed. The results confirm that TaPSG719 promoter is pollen-specific and active during the middle stages of pollen development till anther matured, and it can drive pollen-specific gene expression across the species.

Overexpression of LEAFY in apple leads to a columnar phenotype with shorter internodes

To break the juvenile stage of apple (Malus x domestica Borkh.) we transferred the LFY gene of Arabidopsis into the genome of the apple cv. 'Pinova'. A total of five transgenic clones constitutively overexpressing the LFY gene were obtained. Approximately, 20 shoots of each clone were rooted and transferred to the glasshouse. No flowers were obtained on transgenic plants during the first 2 years of cultivation. Evaluation of the expression of possible LFY targets revealed that no transcripts could be detected for MdAP1-1 and MdAP1-2. MdTFL1 was unaffected. Based on the absence of the LFY core-binding sequence within promoter sequences of MdAP1-1 and MdAP1-2, it was concluded that LFY was not able to induce these genes. The LFY genes of apple were unaffected in transgenic plants and sequence alignments of the C-terminal amino acid sequence showed a high conservation of these proteins. A change in binding ability to DNA can therefore be excluded. Instead of early flowering, the transgenic plants showed an altered phenotype, which is similar to the columnar phenotype of the 'McIntosh Wijcik' mutant of apple. The transgenic plants showed shortened internodes and a significantly reduced length of the regrowing shoot. A negative correlation was observed between the length of the regrowing shoot and the LFY mRNA transcript level. Furthermore, the LFY transgenic apple plants showed an increased shoot diameter at node 20, which was positively correlated with the LFY mRNA transcript level. Based on our results, we assume an alternative role of LFY in apple.

Isolation and promoter analysis of anther-specific genes encoding putative arabinogalactan proteins in Malus x domestica

In this study, we searched for anther-specific genes involved in male gametophyte development in apple (Malus x domestica Borkh. cv. Fuji) by differential display-PCR. Three full-length cDNAs were isolated, and the corresponding genomic sequences were determined by genome walking. The identified genes showed intronless 228- to 264-bp open reading frames and shared 82-90% nucleotide sequence. Sequence analysis identified that they encoded a putative arabinogalactan protein (AGP) and were designated MdAGP1, MdAGP2, and MdAGP3, respectively. RT (reverse transcriptase)-PCR revealed that the MdAGP genes were selectively expressed in the stamen. Promoter analysis confirmed that the MdAGP3 promoter was capable of directing anther- or pollen-specific expression of the GUS reporter in tobacco and apple. Furthermore, expression of ribosome-inactivating protein under the control of the MdAGP3 promoter induced complete sporophytic male sterility as we had expected.

Levels and Stability of Expression of Transgenes

It is well known that in a given cell, at a particular time, only a fraction of the entire genome is expressed. Expression of a gene, nuclear, or organellar starts with the onset of transcription and ends in the synthesis of the functional protein. The regulation of gene expression is a complex process that requires the coordinated activity of different proteins and nucleic acids that ultimately determine whether a gene is transcribed, and if transcribed, whether it results in the production of a protein that develops a phenotype. The same also holds true for transgenic crops, which lie at the very core of insert design.

There are multiple checkpoints at which the expression of a gene can be regulated and controlled. Much of the emphasis of studies related to gene expression has been on regulation of gene transcription, and a number of methods are used to effect the control of gene expression. Controlling transgene expression for a commercially valuable trait is necessary to capture its value. Many gene functions are either lethal or produce severe deformity (resulting in loss of value) if over-expressed. Thus, expression of a transgene at a particular site or in response to a particular elicitor is always desirable.

Isolation and characterization of the plant glsA promoter from Alstroemeria

The differentiation of a vegetative cell and a generative cell is a critical event during pollen development. The Lilium GlsA is known to localize in pollen and is considered to be involved in development of the generative cell. Here, we cloned a glsA ortholog from Alstroemeria, a commercially important cut flower. The expression of AaglsA (Alstroemeria aurea glsA) transcripts increased gradually after pollen mitosis I (PMI) and reached a significant level when the generative cell started to elongate. Analysis of the promoter of AaglsA suggests that AaglsA expression is controlled by several cis-regulatory elements during pollen development. This is the first investigation of reproductive factors regulating male gametogenesis in Alstroemeria.

Cloning and expression analysis of a pollen preferential rapid alkalinization factor gene, BoRALF1, from broccoli flowers

Rapid alkalinization factors (RALFs) are recently reported active peptide hormones and are considered to play important roles in plant development. We previously identified a differentially expressed cDNA fragment between cabbage flower buds of sterility lines and its maintainer line, which showed significant homology to Arabidopsis RALFL9. The novel RALF cDNA (BoRALF1) was isolated from broccoli flower buds by EST assembly. The open reading frame (ORF) comprises 240 bp, encoding a small putative preprotein of 79 amino acids (molecular weight of 8.72 kDa and a pI of 7.8), which contains the mature polypeptide at its C terminus. BoRALF1 shares 70.3% identity with Arabidopsis RALFL9, but has only moderate similarity with functionally characterized RALFs (ranging from 16.2% to 38.0%). BoRALF1 shows typical features of RALFs, including the 28-aa signal peptide, typical arrangement of four position conserved cysteines, the YIXY motif and a similar secondary structure. RT-PCR studies of different tissues and promoter-GUS fusions confirmed that BoRALF1 is expressed strictly in mature pollen grains and in the anther cells around the loculi. Based on in vivo transient assays, we found that BoRALF1 appears to be largely localized in the plasma membrane. Although the function of BoRALF1 remains to be determined, our experiments confirm the presence of RALF peptide in broccoli, and suggest it could have a role in anther or pollen development.

Characterization of a pollen-preferential gene OSIAGP from rice (Oryza sativa L. subspecies indica) coding for an arabinogalactan protein homologue, and analysis of its promoter activity during pollen development and pollen tube growth

During differential screening of inflorescence-specific cDNA libraries from Oryza sativa indica, an arabinogalactan protein (OSIAGP) cDNA (586 bp) expressing preferentially in the inflorescence has been isolated. It encodes an arabinogalactan protein of 59 amino acids (6.4 kDa) with a transmembrane domain and a secretory domain at the N terminus. The protein shows homology with AGP23 from Arabidopsis, and its homologue in japonica rice is located on chromosome 6. OSIAGP transcripts also accumulate in shoots and roots of rice seedling grown in the dark, but light represses expression of the gene. Analysis of a genomic clone of OSIAGP revealed that its promoter contains several pollen-specificity and light-regulatory elements. The promoter confers pollen-preferential activity on gus, starting from the release of microspores to anther dehiscence in transgenic tobacco, and is also active during pollen tube growth. Analysis of pollen preferential activity of the promoter in the transgenic rice system revealed that even the approximately 300 bp fragment has activity in pollen and the anther wall and further deletion down to approximately 100 bp completely abolishes this activity, which is consistent with in-silico analysis of the promoter. Arabinogalactan proteins have been shown to be involved in the cell elongation process. The homology of OSIAGP with AGP23 and the fact that seedling growth in the dark and pollen tube growth are events based on cell elongation strengthen the possibility of OSIAGP performing a similar function.

Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice

BACKGROUND

Rice transcription regulator OsWRKY13 influences the functioning of more than 500 genes in multiple signalling pathways, with roles in disease resistance, redox homeostasis, abiotic stress responses, and development.

RESULTS

To determine the putative transcriptional regulation mechanism of OsWRKY13, the putative cis-acting elements of OsWRKY13-influenced genes were analyzed using the whole genome expression profiling of OsWRKY13-activated plants generated with the Affymetrix GeneChip Rice Genome Array. At least 39 transcription factor genes were influenced by OsWRKY13, and 30 of them were downregulated. The promoters of OsWRKY13-upregulated genes were overrepresented with W-boxes for WRKY protein binding, whereas the promoters of OsWRKY13-downregulated genes were enriched with cis-elements putatively for binding of MYB and AP2/EREBP types of transcription factors. Consistent with the distinctive distribution of these cis-elements in up- and downregulated genes, nine WRKY genes were influenced by OsWRKY13 and the promoters of five of them were bound by OsWRKY13 in vitro; all seven differentially expressed AP2/EREBP genes and six of the seven differentially expressed MYB genes were suppressed by in OsWRKY13-activated plants. A subset of OsWRKY13-influenced WRKY genes were involved in host-pathogen interactions.

CONCLUSION

These results suggest that OsWRKY13-mediated signalling pathways are partitioned by different transcription factors. WRKY proteins may play important roles in the monitoring of OsWRKY13-upregulated genes and genes involved in pathogen-induced defence responses, whereas MYB and AP2/EREBP proteins may contribute most to the control of OsWRKY13-downregulated genes.

Efficient production of genetically engineered, male-sterile Arabidopsis thaliana using anther-specific promoters and genes derived from Brassica oleracea and B. rapa

Prevention of transgene flow from genetically modified crops to food crops and wild relatives is of concern in agricultural biotechnology. We used genes derived from food crops to produce complete male sterility as a strategy for gene confinement as well as to reduce the food purity concerns of consumers. Anther-specific promoters (A3, A6, A9, MS2, and MS5) were isolated from Brassica oleracea and B. rapa and fused to the beta-glucuronidase (GUS) reporter gene and candidate genes for male sterility, including the cysteine proteases BoCysP1 and BoCP3, and negative regulatory components of phytohormonal responses involved in male development. These constructs were then introduced into Arabidopsis thaliana. GUS analyses revealed that A3, A6, and A9 had tapetum-specific promoter activity from the anther meiocyte stage. Male sterility was confirmed in tested constructs with protease or gibberellin insensitive (gai) genes. In particular, constructs with BoCysP1 driven by the A3 or A9 promoter most efficiently produced plants with complete male sterility. The tapetum and middle layer cells of anthers expressing BoCysP1 were swollen and excessively vacuolated when observed in transverse section. This suggests that the ectopic expression of cysteine protease in the meiocyte stage may inhibit programmed cell death. The gai gene also induced male sterility, although at a low frequency. This is the first report to show that plant cysteine proteases and gai from food crops are available as a novel tool for the development of genetically engineered male-sterile plants.

Various spatiotemporal expression profiles of anther-expressed genes in rice

The male gametophyte and tapetum play different roles during anther development although they are differentiated from the same cell lineage, the L2 layer. Until now, it has not been possible to delineate their transcriptomes due to technical difficulties in separating the two cell types. In the present study, we characterized the separated transcriptomes of the rice microspore/pollen and tapetum using laser microdissection (LM)-mediated microarray. Spatiotemporal expression patterns of 28,141 anther-expressed genes were classified into 20 clusters, which contained 3,468 (12.3%) anther-enriched genes. In some clusters, synchronous gene expression in the microspore and tapetum at the same developmental stage was observed as a novel characteristic of the anther transcriptome. Noteworthy expression patterns are discussed in connection with gene ontology (GO) categories and gene annotations, which are related to important biological events in anther development, such as pollen maturation, pollen germination, pollen tube elongation and pollen wall formation.

A novel C2-domain phospholipid-binding protein, OsPBP1, is required for pollen fertility in rice

Pollen fertility is a crucial factor for successful pollination and essential for seed formation. Recent studies have suggested that a diverse range of internal and external factors, signaling components and their related pathways are likely involved in pollen fertility. Here, we report a single C2-domain containing protein, OsPBP1, initially identified through cDNA microarray analysis. OsPBP1 is a single copy gene and preferentially expressed in pistil and pollen but down-regulated by pollination. OsPBP1 had a calcium concentration-dependent phospholipid-binding activity and was localized mainly in cytoplasm and nucleus, but translocated onto the plasma membrane in response to an intracellular Ca(2+) increase. Pollen grains of antisense OsPBP1 transgenic lines were largely nonviable, germinated poorly in vitro and of low fertility. OsPBP1 protein was localized in a region peripheral to pollen wall and vesicles of elongating pollen tube, and its repressed expression reduced substantially this association and led to alteration of microfilament polymerization during pollen germination. Taken together, these results indicate that OsPBP1 is a novel functional C2-domain phospholipids-binding protein that is required for pollen fertility likely by regulating Ca(2+) and phospholipid signaling pathways.

Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis

In this study we analyzed transcript abundance and promoters of genes encoding mitochondrial proteins to identify signaling pathways that regulate stress-induced gene expression. We used Arabidopsis (Arabidopsis thaliana) alternative oxidase AOX1a, external NADP H-dehydrogenase NDB2, and two additional highly stress-responsive genes, At2g21640 and BCS1. As a starting point, the promoter region of AOX1a was analyzed and functional analysis identified 10 cis-acting regulatory elements (CAREs), which played a role in response to treatment with H(2)O(2), rotenone, or both. Six of these elements were also functional in the NDB2 promoter. The promoter region of At2g21640, previously defined as a hallmark of oxidative stress, shared two functional CAREs with AOX1a and was responsive to treatment with H(2)O(2) but not rotenone. Microarray analysis further supported that signaling pathways induced by H(2)O(2) and rotenone are not identical. The promoter of BCS1 was not responsive to H(2)O(2) or rotenone, but highly responsive to salicylic acid (SA), whereas the promoters of AOX1a and NDB2 were unresponsive to SA. Analysis of transcript abundance of these genes in a variety of defense signaling mutants confirmed that BCS1 expression is regulated in a different manner compared to AOX1a, NDB2, and At2g21640. These mutants also revealed a pathway associated with programmed cell death that regulated AOX1a in a manner distinct from the other genes. Thus, at least three distinctive pathways regulate mitochondrial stress response at a transcriptional level, an SA-dependent pathway represented by BCS1, a second pathway that represents a convergence point for signals generated by H(2)O(2) and rotenone on multiple CAREs, some of which are shared between responsive genes, and a third pathway that acts via EDS1 and PAD4 regulating only AOX1a. Furthermore, posttranscriptional regulation accounts for changes in transcript abundance by SA treatment for some genes.

Analysis of Arabidopsis arginase gene transcription patterns indicates specific biological functions for recently diverged paralogs

The detailed expression patterns of transcripts of two Arabidopsis arginase genes, ARGAH1 and ARGAH2, have not been previously described, and phylogenetic analysis suggests that they diverged independently of duplication events in other lineages. Therefore, we used beta-glucuronidase reporter fusions and quantitative reverse-transcriptase PCR to analyze tissue-specific expression of ARGAH1 and ARGAH2 during Arabidopsis development, and in response to the availability of nutrients and exposure to methyl jasmonate (MeJA). We demonstrated tissue-specific transcript expression and enzyme activity in pollen for ARGAH1, but not ARGAH2. Conversely, we demonstrated MeJA-inducibility of ARGAH2, but not ARGAH1. In addition, we used microarrays to identify genes for which transcript abundance following MeJA treatment differed in wild type and ARGAH2 mutants. These ARGAH2 and MeJA responsive genes included a putative pathogenesis-related protein pathogenesis response-1 (At2g14610), and a gene of unknown function (At5g03090). Interestingly, these genes had opposite responses to the loss of ARGAH2, suggesting multiple downstream effects of arginase activity, following MeJA treatment. These results, and the variety and complexity of expression patterns of ARGAH1 and ARGAH2 transcript expression and their related reporter gene fusions that we observed point to multiple functions of arginase genes in Arabidopsis, some of which have resulted through a sub-functionalization not shared by all angiosperms.