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Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Although two such methods have been developed for mammalian tissues, they have a low signal-noise ratio and/or poor resolution at the single-cell level. To overcome these drawbacks, we develop a method that uses sequence-specific miRNA-locked nucleic acid (LNA) and mRNA-LNA probes. Moreover, it augments the detection signal by rolling circle amplification, achieving a high signal-noise ratio at the single-cell level. Dot signals are counted for determining the expression levels of mRNA and miRNA molecules in specific cells. We show a high sequence specificity of our miRNA-LNA probe, revealing that it can discriminate single-base mismatches. Numerical quantification by our method is tested in transgenic rice lines with different gene expression levels. We conduct several applications. First, the spatial expression profiling of osa-miR156 and OsSPL12 in rice leaves reveals their specific expression in mesophyll cells. Second, studying rice and its mutant lines with our method reveals opposite expression patterns of miRNA and its target mRNA in tissues. Third, the dynamic expression profiles of ZmGRF8 and zma-miR396 during maize leaf development provide evidence that zma-miR396 regulates the preferential spatial expression of ZmGRF8 in bundle sheath cells. Finally, our method can be scaled up to simultaneously detect multiple miRNAs and mRNAs in a tissue. Thus, it is a sensitive and versatile technique for studying miRNA regulation of plant tissue development.

Brown planthopper (BPH), a monophagous phloem feeder, consumes a large amount of photoassimilates in rice and causes wilting. A near-isogenic line ‘TNG71-Bph45’ was developed from the Oryza sativajaponica variety ‘Tainung 71 (TNG71) carrying a dominant BPH-resistance locus derived from Oryza nivara (IRGC 102165) near the centromere of chromosome 4. We compared the NIL (TNG71-Bph45) and the recurrent parent to explore how the Bph45 gene confers BPH resistance. We found that TNG71-Bph45 is less attractive to BPH at least partially because it produces less limonene. Chiral analysis revealed that the major form of limonene in both rice lines was the L-form. However, both L- and D-limonene attracted BPH when applied exogenously to TNG71-Bph45 rice. The transcript amounts of limonene synthase were significantly higher in TNG71 than in TNG71-Bph45 and were induced by BPH infestation only in the former. Introgression of the Bph45 gene into another japonica variety, Tainan 11, also resulted in a low limonene content. Moreover, several dominantly acting BPH resistance genes introduced into the BPH-sensitive IR24 line compromised its limonene-producing ability and concurrently decreased its attractiveness to BPH. These observations suggest that reducing limonene production may be a common resistance strategy against BPH in rice.

Background: Lactoferrin (LF) exhibits multiple beneficial biological activities and thus has been used as a health food and additive. To broaden its application in the food industry, the porcine LF (pLF) gene has been engineered into rice to produce recombinant LF (rpLF) for use as a food additive. The iron-binding and antimicrobial activities of rpLF and its positive effects on early weaned piglets have been previously evaluated, yet several features, such as the signal peptide removal, glycosylation sites and antioxidant activity of rpLF, have not been fully characterized. Objective: In this work, the rice-produced rpLF was purified and its biochemical structure and antioxidant activities characterized. Methods: HPLC, Western blot, PAS/VVL/PNA staining, Edman degradation assay, MALDI-TOF, LC-MS/MS and antioxidant activity assays were performed. Results: The results showed that this purified rpLF is a mature form of LF; its signal peptide was correctly removed, and two N-glycosylation sites located at N365 and N472 were identified. The molecular mass heterogeneity of rpLF could be eliminated by treatment with PNGase glycosidase, suggesting that different degrees of N-glycosylation occur in rpLF. A series of assays including the iron chelating activity, reducing power assay, lipid peroxidase activity and radical-scavenging activity showed that the antioxidant activity of rice-produced rpLF was equivalent to that of bovine LF. Conclusion: Rice-produced rpLF was correctly processed post-translationally and displayed antioxidant activity equivalent to that of bovine LF; thus, rice-produced rpLF can be recognized as a plant-based antioxidant to be used as a functional additive in animal feed and for the food industry.

The gene encoding a thermostable l-aminoacylase (LAA) from Deinococcus radiodurans BCRC12827 was isolated and expressed in transgenic rice under the control of a rice actin gene promoter or a seed-specific promoter, Ose705. The recombinant LAA in the transgenic line Ose705:LAA was specifically detected in rice grains, but not in leaves, and its identity was confirmed by a LC/MS/MS assay. Furthermore, was efficiently purified via affinity chromatography using a nickel column. Enzymatic activity of this rice-produced LAA was determined by HPLC and a maximum activity at pH 8.0 and 45 °C in a phosphate buffer supplemented with the divalent metal ion Co2+ using NAc-l-HPA as a substrate was obtained, similar to its host counterpart. This rice-produced LAA maintained approximately 50% enzyme activity after 48 h of incubation under 45 °C and maintained approximately 90% activity compared to a freshly prepared sample after being stored in rice seeds for 4 years. The present study indicated that seed-specific protein production in transgenic rice is a good and safe source for mass production of LAA, and this system can be useful for the production of other biomedical proteins as well.

Background GA 2-oxidases (GA2oxs) are involved in regulating GA homeostasis in plants by inactivating bioactive GAs through 2β-hydroxylation. Rice GA2oxs are encoded by a family of 10 genes; some of them have been characterized, but no comprehensive comparisons for all these genes have been conducted. Results Rice plants with nine functional GA2oxs were demonstrated in the present study, and these genes not only were differentially expressed but also revealed various capabilities for GA deactivation based on their height-reducing effects in transgenic plants. Compared to that of wild-type plants, the relative plant height (RPH) of transgenic plants was scored to estimate their reducing effects, and 8.3% to 59.5% RPH was observed. Phylogenetic analysis of class I GA2ox genes revealed two functionally distinct clades in the Poaceae. The OsGA2ox3, 4, and 8 genes belonging to clade A showed the most severe effect (8.3% to 8.7% RPH) on plant height reduction, whereas the OsGA2ox7 gene belonging to clade B showed the least severe effect (59.5% RPH). The clade A OsGA2ox3 gene contained two conserved C186/C194 amino acids that were crucial for enzymatic activity. In the present study, these amino acids were replaced with OsGA2ox7-conserved arginine (C186R) and proline (C194P), respectively, or simultaneously (C186R/C194P) to demonstrate their importance in planta. Another two amino acids, Q220 and Y274, conserved in OsGA2ox3 were substituted with glutamic acid (E) and phenylalanine (F), respectively, or simultaneously to show their significance in planta. In addition, through sequence divergence, RNA expression profile and GA deactivation capability analyses, we proposed that OsGA2ox1, OsGA2ox3 and OsGA2ox6 function as the predominant paralogs in each of their respective classes. Conclusions This study demonstrates rice has nine functional GA2oxs and the class I GA2ox genes are divided into two functionally distinct clades. Among them, the OsGA2ox7 of clade B is a functional attenuated gene and the OsGA2ox1, OsGA2ox3 and OsGA2ox6 are the three predominant paralogs in the family.

BackgroundPhalaenopsis orchids are one of the most common potted orchids sold worldwide. Most Phalaenopsis cultivars have long inflorescences that cause shipping problems and increase handling costs. Miniaturization of Phalaenopsis orchids not only reduces overall production costs but also can expand the appeal of the orchids to a different group of consumers who prefer to keep flowers on desks or tabletops. Although some miniature Phalaenopsis plants can be obtained via hybridization or mutation, they are unpredictable and limited in variety. We therefore used the transgenic approach of overexpressing gibberellin 2-oxidase 6 (OsGA2ox6), a rice GA deactivation gene, to investigate its functional effect in miniaturizing Phalaenopsis and to create a stable miniaturization platform to facilitate a supply for the potential demands of the miniature flower market.ResultsA commercial moth orchid,PhalaenopsisSogo Yukidian ‘SPM313’, was transformed with the plasmid vectorUbi:OsGA2ox6and successfully overexpressed theOsGA2ox6genein planta. The transgenic lines displayed darker-green, shorter, and wider leaves, thicker roots and much shorter flower spikes (10 cm vs 33 cm) than thenontransgenicline with a normal flower size and blooming ability and are therefore an ideal miniaturized form of Phalaenopsis orchids.ConclusionsWe demonstrated that the ectopic expression ofOsGA2ox6can miniaturizePhalaenopsisSogo Yukidian ‘SPM313’ while preserving its blooming ability, providing an alternative, useful method for miniaturizing Phalaenopsis species. This miniaturization by a transgenic approach can be further expanded by using GA2ox genes from different plant species or different gene variants, thereby expanding the technical platform for miniaturizing Phalaenopsis species to meet the potential demands of the miniature Phalaenopsis flower market.

The broad-specificity amino acid racemase (Bsar) from Pseudomonas putida catalyzes the racemization of various amino acids, offering a flexible and feasible platform to develop a new non-antibiotic selectable marker system for plant transformation. In the present study, we demonstrated that a Bsar variant, Bsar-R174K, that is useful as a selectable marker gene in Arabidopsis and rice that were susceptible to l-lysine and D-alanine. The introduction of wild-type Bsar, Bsar-R174K or Bsar-R174A into E. coli lysine or asparagine auxotrophs was able to rescue the growth of these microorganisms in minimal media supplemented with selectable amino acid enantiomers. The transformation of Arabidopsis with Bsar or Bsar variants based on d-alanine selection revealed that Bsar-R174K had the greatest efficiency (2.40%), superior to kanamycin selection-based transformation (1.10%). Whereas, l-lysine-based selection exhibited lower efficiency for Bsar-R174K (0.17%). The progenies of selected Bsar-R174K transgenic Arabidopsis revealed normal growth properties. In addition, Bsar-R174K transgenic rice was obtained on l-lysine medium with an efficiency of 0.9%, and the progenies of the transgenic rice revealed morphologically normal phenotypes comparable with their wild-type counterparts. This study presents the first report of broad range amino acid racemase Bsar-R174K as a non-antibiotic selectable marker system applied in transgenic plants.

Summary A major challenge of modern agricultural biotechnology is the optimization of plant architecture for enhanced productivity, stress tolerance and water use efficiency (WUE). To optimize plant height and tillering that directly link to grain yield in cereals and are known to be tightly regulated by gibberellins (GAs), we attenuated the endogenous levels of GAs in rice via its degradation. GA 2‐oxidase (GA2ox) is a key enzyme that inactivates endogenous GAs and their precursors. We identified three conserved domains in a unique class of C20 GA2ox, GA2ox6, which is known to regulate the architecture and function of rice plants. We mutated nine specific amino acids in these conserved domains and observed a gradient of effects on plant height. Ectopic expression of some of these GA2ox6 mutants moderately lowered GA levels and reprogrammed transcriptional networks, leading to reduced plant height, more productive tillers, expanded root system, higher WUE and photosynthesis rate, and elevated abiotic and biotic stress tolerance in transgenic rice. Combinations of these beneficial traits conferred not only drought and disease tolerance but also increased grain yield by 10–30% in field trials. Our studies hold the promise of manipulating GA levels to substantially improve plant architecture, stress tolerance and grain yield in rice and possibly in other major crops.

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.

Forkhead box C1 (FOXC1) is a member of the forkhead family of transcription factors that are characterized by a DNA-binding forkhead domain. Increasing evidence indicates that FOXC1 is involved in tumor progression. However, the role of tumor hypoxia in FOXC1 regulation and its impact on lung cancer progression are unclear. Here, we report that FOXC1 was upregulated in hypoxic areas of lung cancer tissues from rodents or humans. Hypoxic stresses significantly induced FOXC1 expression. Moreover, hypoxia activated FOXC1 transcription via direct binding of hypoxia-inducible factor-1α (HIF-1α) to the hypoxia-responsive element (HRE) in the FOXC1 promoter. FOXC1 gain-of-function in lung cancer cells promoted cell proliferation, migration, invasion, angiogenesis, and epithelial-mesenchymal transition in vitro. However, a knockdown of FOXC1 in lung cancer cells inhibited these effects. Notably, knockdown of tumor hypoxia-induced FOXC1 expression via HIF-1-mediated FOXC1 shRNAs in lung cancer xenograft models suppressed tumor growth and angiogenesis. Finally, systemic delivery of FOXC1 siRNA encapsulated in lipid nanoparticles inhibited tumor growth and increased survival time in lung cancer-bearing mice. Taken together, these data indicate that FOXC1 is a novel hypoxia-induced transcription factor and plays a critical role in tumor microenvironment-promoted lung cancer progression. Systemic FOXC1 blockade therapy may be an effective therapeutic strategy for lung cancer.

The purpose of this study is to determine the growth performance and immune characteristics of early weaned piglets receiving rice bran expressing porcine lactoferrin as a feed additive. Full-length cDNA encoding porcine lactoferrin (LF) driven by a rice actin promoter was transformed into rice plants, and its integration into the rice genome was verified by Southern blot analysis. The expression of recombinant LF (rLF) in whole grains and rice bran was also confirmed, and the amount of rLF accumulated in rice bran was estimated by immunoblot assay to be approximately 0.1% of rice bran weight. An iron-binding assay showed that the rLF retained iron-binding activity and the binding capacity of 1 mg/mL rLF would be saturated by 100 microM of FeCl(3). Thirty-six early weaned piglets at 21 days old were randomly selected into two groups and fed a diet containing 5% transgenic rice bran containing 50 mg/kg rLF (rLF group) and 5% rice bran (control group) to investigate the piglets' growth performance and immune characteristics. The results showed no significant difference in growth performance between the groups during the feeding period. However, the aerobic bacteria, anaerobic bacteria, and coliform counts in the cecal contents of the rLF-fed group were significantly lower than those of the control group. Additional immune characteristics such as the IgG concentration in the rLF group was higher than the control group at the 28th day, but leukocyte counts and the peripheral lymphocyte ratio remained similar. In summary, porcine LF expressed in rice bran, a byproduct of rice, can be used as a functional additive to improve antimicrobial capabilities and IgG concentration of early weaned piglets.

Echinacea purpurea L. (EP) is a plant originally used by native Americans to treat respiratory infections and have long been used to aid in wound healing and to enhance the immune system. The purpose of this study was to demonstrate the ability of EP extracts to stimulate the production of nitric oxide (NO) and TNF-α as well as to evaluate the cell viability by the use of chicken peripheral blood mononuclear cells (PBMCs) and RAW 264.7 macrophages in vitro. The polysaccharides content of EP was 162.2±8.4 mg/g dry weight (DW)The EP extracted with a 55% ethanol at 55℃ contained 22.3 ±1.0 mg gallic acid equivalent/g DW of total phenolic compounds and 86.0 ± 4.6 mg quercetin equivalent/g of flavonoid content. The result of cell viability assay showed that 89% and 81% of chicken PBMCs and RAW 264.7 macrophages, respectively, were survived under the treatment of 3.2 mg/ml of EP extracts by microculture tetrazolium assays (MTAs). Moreover, the cell inhibitory activity did not show the 50% cyto-toxicity effect (IC50). In addition, NO production by stimulated chicken PBMCs and RAW 264.7 macrophages exhibited individually the linear relations with the concentration of EP extracts, and they were approximately 70 and 60 μM in 800 μg/ml, respectively. The tendency with the release of TNF-α by RAW 264.7 macrophages also corresponded with EP extracts concentration. It is concluded, EP extracts act as an immunostimulant for both tested cells but have no serious effect on inhibiting chicken PBMCs viability.

Understanding the evolution of the maize B chromosome requires insight into the molecular organization of a large number of B clones, which can be potentially obtained by microdissection of the chromosome. Yet, the microdissection protocols currently available are ineffective for a large-scale isolation. In an attempt to improve its efficiency, a protocol was adopted to screen a microdissected B library with probes prepared from the degenerate oligonucleotide primed-PCR product of genomic DNA. This protocol resulted in 59 new B clones, most of which were highly repetitive sequences located in various B regions but mostly in the heterochromatic blocks of the long arm. They also appeared in A chromosomes. Twenty-four of these were retrotransposons, ten knob, 18 noncoding sequences, and seven unknown sequences. The implication of the new B sequences on the B evolution is discussed.

A very large repetitive element (StarkB, 22.8 kb) is present in the maize B chromosome, presumably not organized as tandem arrays. Results of the current study are contrary to this notion. Out of eighteen StarkB-carrying sequences, nine were the expected internal fragment of StarkB, and nine others were fragments spanning two StarkB elements. One of the two StarkB components, GrandeB, was flanked in all clones with identical target sequences, as opposed to other Grandes that are associated with different target sequences. Also observed was a prominent Southern signal associated with a fragment representing the junction of two adjacent StarkB units. A clone possessing a structure inverse to that of the second component of StarkB is proposed to be the initial element into which a GrandeB inserted to derive StarkB. Most, if not all, isolated StarkB arrays were not the original form, being disrupted by the invasion of various mobile elements intertwined with various stages of amplification.

Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs). Two classes of GA2oxs inactivate GAs through 2β-hydroxylation: a larger class of C19 GA2oxs and a smaller class of C20 GA2oxs. In this study, we show that members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination. Using mutant and transgenic analysis, C20 GA2oxs were shown to play pleiotropic roles regulating rice growth and architecture. In particular, rice overexpressing these GA2oxs exhibited early and increased tillering and adventitious root growth. GA negatively regulated expression of two transcription factors, O. sativa homeobox 1 and TEOSINTE BRANCHED1, which control meristem initiation and axillary bud outgrowth, respectively, and that in turn inhibited tillering. One of three conserved motifs unique to the C20 GA2oxs (motif III) was found to be important for activity of these GA2oxs. Moreover, C20 GA2oxs were found to cause less severe GA-defective phenotypes than C19 GA2oxs. Our studies demonstrate that improvements in plant architecture, such as semidwarfism, increased root systems and higher tiller numbers, could be induced by overexpression of wild-type or modified C20 GA2oxs.

Rice oil bodies enclosed by unique structural proteins, oleosins, are found in the embryo and the aleurone layer, but not the starchy endosperm where starch and storage proteins are accumulated. To examine oleosin promoter specificity, a sesame storage protein, 2S albumin, was expressed in transgenic rice seeds under the control of a rice oleosin promoter. In all transgenic rice seeds, the sesame 2S albumin was found exclusively in the bran fraction after milling. Immunological staining revealed that the sesame 2S albumin was also located in the embryo and the outermost cells of the starchy endosperm. Furthermore, immunogold labeling showed that the transgenic 2S albumin was deposited in both type-I and type-II protein bodies of the outermost cells of the endosperm as well as in the type-II protein bodies of the embryo. The methionine and cysteine contents in the bran from four homozygous transgenic lines were elevated by 24–38 and 50–62%, respectively, compared with those of wild-type plants. The results suggest that the rice oleosin promoter is bran-specific and could be used to add value to rice bran, an abundant by-product of rice polishing, by genetic engineering.

An in vitro system was established to study the transcription and processing of threonine tRNA using spinach chloroplast enzyme extract. Experiments using a series of 5' deletion mutants demonstrated that the transcription of trnT gene required no 5' upstream promoter elements. Four plasmid DNA templates containing trnT were constructed for tRNA processing assay. The processing reaction was carried out either with exogenously added precursor-tRNAs made by T7 RNA polymerase or with RNAs synthesized by the transcription activity in the same processing enzyme extract. Both assays demonstrated that the 5' and 3' ends of mature tRNA were processed endonucleolytically and the processing of the 5' end preceded the maturation of the 3' end. The activity of nucleotidyl transferase that adds CCA nucleotides to the 3' end of tRNA was also observed. The use of a coupled transcription and processing system provides us with a better insight to the tRNA processing mechanism of the chloroplast.

Critical regions within the rice metallothionein OsMT2b gene promoter are identified and the 5'-untranslated region (5'-UTR) is found essential for the high-level promoter activity in germinated transgenic rice embryos. Many metallothionein (MT) genes are highly expressed in plant tissues. A rice subfamily p2 (type 2) MT gene, OsMT2b, has been shown previously to exhibit the most abundant gene expression in young rice seedling. In the present study, transient expression assays and a transgenic approach were employed to characterize the expression of the OsMT2b gene in rice. We found that the OsMT2b gene is strongly and differentially expressed in germinated rice embryos during seed germination and seedling development. Histochemical staining analysis of transgenic rice carrying OsMT2b::GUS chimeric gene showed that high-level GUS activity was detected in germinated embryos and at the meristematic part of other tissues during germination. Deletion analysis of the OsMT2b promoter revealed that the 5'-flanking region of the OsMT2b between nucleotides -351 and -121 relative to the transcriptional initiation site is important for promoter activity in rice embryos, and this region contains the consensus sequences of G box and TA box. Our study demonstrates that the 5'-untranslated region (5'-UTR) of OsMT2b gene is not only necessary for the OsMT2b promoter activity, but also sufficient to augment the activity of a minimal promoter in both transformed cell cultures and germinated transgenic embryos in rice. We also found that addition of the maize Ubi intron 1 significantly enhanced the OsMT2b promoter activity in rice embryos. Our studies reveal that OsMT2b351-ubi(In) promoter can be applied in plant transformation and represents potential for driving high-level production of foreign proteins in transgenic rice.

Background The rice gene, OsMADS45, which belongs to the MADS-box E class gene, participates in the regulation of floral development. Previous studies have revealed that ectopic expression of OsMADS45 induces early flowering and influences reduced plant height under short-day (SD) conditions. However, the regulation mechanism of OsMADS45 overexpression remains unknown. We introduce an OsMADS45 overexpression construct Ubi:OsMADS45 into TNG67 plants (an Hd1 (Heading date 1) and Ehd1 (Early heading date 1) defective rice cultivar grown in Taiwan), and we analyzed the expression patterns of various floral regulators to understand the regulation pathways affected by OsMADS45 expression. Results The transgenic rice exhibit a heading date approximately 40 days earlier than that observed in TNG67 plants, and transgenic rice display small plant size and low grain yield. OsMADS45 overexpression did not alter the oscillating rhythm of the examined floral regulatory genes but advanced (by approximately 20 days) the up-regulate of two florigens, Hd3a (Heading Date 3a) and RFT1 (RICE FLOWERING LOCUS T1) and suppressed the expression of Hd1 at the juvenile stage. The expression levels of OsMADS14 and OsMADS18, which are two well-known reproductive phase transition markers, were also increased at early developmental stages and are believed to be the major regulators responsible for early flowering in OsMADS45-overexpressing transgenic rice. OsMADS45 overexpression did not influence other floral regulator genes upstream of Hd1 and Ehd1, such as OsGI (OsGIGANTEA), Ehd2/Osld1/RID1 and OsMADS50. Conclusion These results indicate that in transgenic rice, OsMADS45 overexpressing ectopically activates the upstream genes Hd3a and RFT1 at early development stage and up-regulates the expression of OsMADS14 and OsMADS18, which induces early flowering.

We have investigated the mechanism of transcription termination in vitro by spinach chloroplast RNA polymerase using templates encoding variants of the transcription-termination structure (attenuator) of the regulatory region of the threonine (thr) operon of Escherichia coli. Fourteen sequence variants located within its d(G+C) stem-loop and d(A+T)-rich regions were studied. We found that the helix integrity in the stem-loop structure is necessary for termination but that its stability is not directly correlated with termination efficiency. The sequence of the G+C stem-loop itself also influences termination. Moreover, the dA template stretch at the 3' end of the terminator plays a major role in termination efficiency, but base pairing between the A and U tract of the transcript does not. From the studies using deletion variants and a series of mutants that alter the sequences immediately downstream from the transcription termination site, we found that termination of transcription by spinach chloroplast RNA polymerase was also modulated by downstream DNA sequences in a sequence-specific manner. The second base immediately following the poly(T) tract is crucial for determining the termination efficiency by chloroplast RNA polymerase, but not of the T7 or E.coli enzymes.

Expression of OLE16 and OLE18, two oleosin isoforms in oil bodies of rice seeds, was suppressed by RNA interference. Electron microscopy revealed a few large, irregular oil clusters in 35S::ole16i transgenic seed cells, whereas accumulated oil bodies in 35S::ole18i transgenic seed cells were comparable to or slightly larger than those in wild-type seed cells. Large and irregular oil clusters were observed in cells of double mutant seeds. These unexpected differences observed in oil bodies of 35S::ole16i and 35S::ole18i transgenic seeds were further analyzed. In comparison to wild-type plants, OLE18 levels were reduced to approximately 40% when OLE16 was completely eliminated in 35S::ole16i transgenic plants. In contrast, OLE16 was reduced to only 80% of wild-type levels when OLE18 was completely eliminated in 35S::ole18i transgenic plants. While the triacylglycerol content of crude seed extracts of 35S::ole16i and 35S::ole18i transgenic seeds was reduced to approximately 60% and 80%, respectively, triacylglycerol in isolated oil bodies was respectively reduced to 45% and 80% in accordance with the reduction of their oleosin contents. Oil bodies isolated from both 35S::ole16i and 35S::ole18i transgenic seeds were found to be of comparable size and stability to those isolated from wild-type rice seeds, although they were merely sheltered by a single oleosin isoform. The drastic difference between the triacylglycerol contents of crude seed extracts and isolated oil bodies from 35S::ole16i transgenic plants could be attributed to the presence of large, unstable oil clusters that were sheltered by insufficient amounts of oleosin and therefore could not be isolated together with stable oil bodies.

Spinach chloroplast RNA polymerase has been shown to efficiently terminate transcription at the threonine attenuator (thra) from Escherichia coli [7]. In this study, efficient transcription termination by the chloroplast RNA polymerase was observed at a second prokaryotic terminator, the histidine attenuator (hisa) from Salmonella typhimurium. Termination occurred regardless of the orientation of either attenuator. In higher-plant chloroplast DNA, the genes for the β subunit of the ATPase (atpB) and the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) are adjacent and divergently transcribed. Bidirectional transcription vectors, containing the histidine and threonine terminators, were constructed to analyze the divergently oriented atpB and rbcL promoters. One plasmid construction, pRTT7, contained two tandem copies of the threonine attenuator (pRTT7). Two additional constructs, pRHT1 and pRHT2, each contained oppositely oriented copies of thra and hisa. A DNA fragment containing the rbcL and atpB promoters was inserted between the two terminators present in the pRTT7, pRHT1, and pRHT2 plasmids. Transcription of these recombinant DNAs by spinach chloroplast RNA polymerase resulted in discretely sized rbcL and atpB transcripts. In addition, these bidirectional transcription vectors were used to identify previously uncharacterized chloroplast promoters.

Using transfer DNA (T-DNA) with functions of gene trap and gene knockout and activation tagging, a mutant population containing 55,000 lines was generated. Approximately 81% of this population carries 1-2 T-DNA copies per line, and the retrotransposon Tos17 was mostly inactive in this population during tissue culture. A total of 11,992 flanking sequence tags (FSTs) have been obtained and assigned to the rice genome. T-DNA was preferentially ( approximately 80%) integrated into genic regions. A total of 19,000 FSTs pooled from this and another T-DNA tagged population were analyzed and compared with 18,000 FSTs from a Tos17 tagged population. There was difference in preference for integrations into genic, coding, and flanking regions, as well as repetitive sequences and centromeric regions, between T-DNA and Tos17; however, T-DNA integration was more evenly distributed in the rice genome than Tos17. Our T-DNA contains an enhancer octamer next to the left border, expression of genes within genetics distances of 12.5 kb was enhanced. For example, the normal height of a severe dwarf mutant, with its gibberellin 2-oxidase (GA2ox) gene being activated by T-DNA, was restored upon GA treatment, indicating GA2ox was one of the key enzymes regulating the endogenous level of GA. Our T-DNA also contains a promoterless GUS gene next to the right border. GUS activity screening facilitated identification of genes responsive to various stresses and those regulated temporally and spatially in large scale with high frequency. Our mutant population offers a highly valuable resource for high throughput rice functional analyses using both forward and reverse genetic approaches.

A chimeric gene encoding a precursor polypeptide of sesame 2S albumin, a sulfur-rich seed storage protein, was expressed in transgenic rice plants under the control of the glutelin promoter with the aim of improving the nutritive value of rice. Rice grains harvested from the first generation of ten different transformed lines inherited the transgene, and the accumulated sesame 2S albumin was presumably processed correctly as its mature form in sesame seed. This transgene was specifically expressed in maturing rice seeds with its encoded sesame 2S albumin exclusively accumulated in the seeds. The crude protein content in rice grains from five putative homozygous lines was increased by 0.64-3.54%, and the methionine and cysteine contents of these transgenic rice grains were respectively elevated by 29-76% and 31-75% compared with those of wild-type rice grains.

Deleting part of the 3′ end of the spinach chloroplast serine tRNA coding region, which destroyed the proper folding of its RNA transcript and resulted in the inhibition of tRNA processing, allowed the detection of a serine tRNA primary transcript. The transcription start site for this primary transcript, synthesized from the internal promoter, was mapped to −12 upstream from the mature tRNA coding region. Transcription analysis with various 5′ deletion mutants suggested that the AT-rich region between −31 and −11, immediately upstream of the serine tRNA transcription start site, affects the transcription efficiency, and possibly the selection of transcription start site. Identification of the transcription start site for the spinach chloroplast serine tRNA gene in this study represents the first example of 5′ end mapping of a tRNA precursor transcribed from chloroplast tRNA genes containing an internal promoter.

A fifth, previously undetected transcript for the plastid gene encoding the beta subunit of spinach chloroplast ATPase (atpB) has recently been identified in vitro. In this report we show that this transcript is present in vivo and its 5' end is at the translation start codon. When synthesized in vitro using spinach chloroplast RNA polymerase, the 5' end of this novel transcript is located at the beginning of the second codon of the atpB coding sequence. Although this atpB transcript lacks an untranslated leader region, it is an abundant RNA in vivo and is associated with crude polysomal fractions, as are the four larger atpB transcripts. In vitro synthesis of the leaderless transcript does not occur for a plasmid DNA in which the "-35' region of the promoter is deleted.

The in vivo transcripts of the tobacco chloroplast gene for the beta subunit of the ATPase (atpB) were examined. In tobacco, like spinach, the atpB gene encodes multiple transcripts. Six tobacco atpB transcripts are present in vivo, with 5' ends at positions "-90", "-255", "-290", "-490", "-500" and "-610" relative to the translation initiation site. The 5' end of the atpB gene ("-610" position) is 20 base pairs from the 5' end of the rbcL gene, coded for on the complementary strand. The "-255", "-490" and "-610" regions are recognized as promoters in vitro by spinach chloroplast and E. coli RNA polymerases.

When rice ( Oryza sativa L.) embryos were cultured on Murashige-Skoog medium containing 2,4-dichlorophenoxyacetic acid and kinetin, both embryogenic (E) and non-embryogenic (NE) calli were formed. One and two-dimensional electrophoresis indicated that there were some qualititative differences between the proteins present in E and NE calli, and in rice embryos. Several E and NE-specific and embryo-specific polypeptides were evident. Two of the E-specific polypeptides of 54 and 24 kD corresponded to the major polypeptides in rice embryo extracts. One polypeptide of 22.7 kD was consistently present in the extracts from NE calli, but was present in much lower amounts in E calli, and was absent from embryo extracts. When E and NE calli were placed on regeneration medium for 12 days there were few changes in the polypeptide patterns of the two cell types, except for an increase in the amount of a 45 kD polypeptide in the NE calli.

To determine whether chloroplast RNA polymerase will accurately terminate transcription in vitro, we have fused the spinach chloroplast rbcL promoter to the 3' end of the rbcL gene as well as to various factor independent transcription terminators from E. coli. Transcription of the rbcL minigene did not result in production of the expected 265 nucleotide RNA. However, the spinach chloroplast RNA polymerase did terminate transcription with varying efficiency at the thra, rrnB, rrnC and gene 32 terminators. The most efficient transcription termination was observed for the threonine attenuator. For each of the prokaryotic terminators, the chloroplast enzyme ceased transcription at essentially the same position as the E. coli RNA polymerase. These data indicate that the transcription termination process in chloroplasts has some features in common with the mechanism used in prokaryotes.