Search

Microglial activation in the central nervous system is a key event in the neuroinflammation that accompanies neurodegenerative diseases such as Alzheimer's disease (AD). Among cytokines involved in microglial activation, amyloid β (Aβ) peptide is known to be a key molecule in the induction of diverse inflammatory products, which may lead to chronic inflammation in AD. However, proteomic studies of microglia in AD are limited due to lack of proper cell or animal model systems. In this study, we performed a proteomic analysis of Aβ-stimulated human microglial cells using SILAC (stable isotope labeling with amino acids in cell culture) combined with LC-MS/MS. Results showed that 60 proteins increased or decreased their abundance by 1.5 fold or greater. Among these, ER-resident proteins such as SERPINH1, PDIA6, PDIA3, and PPIB were revealed to be key molecular biomarkers of human microglial activation by validation of the proteomic results by immunostaining, PCR, ELISA, and Western blot. Taken together, our data suggest that ER proteins play an essential role in human microglial activation by Aβ and may be important molecular therapeutic targets for treatment of AD.

We analyzed the effects of inactivating the pteridine glycosyltransferase gene (pgtA) on the photomovement of the cyanobacterium Synechocystis sp. PCC 6803 under different light conditions. The pgtA mutant displayed abnormal photomovement under UV-A/blue light. In particular, the pgtA mutant showed a negative phototactic response under UV-A (315-400 nm), whereas the wild-type did not show any photomovement. Inhibition of pterin biosynthesis by N-acetylserotonin (NAS), an inhibitor of sepiapterin reductase, also inhibited a positive phototactic response of the wild-type under white and blue light. In addition, negative phototaxis of the pgtA mutant was observed under UV-A/blue light in the presence of NAS. These results indicated that the product of the PgtA enzyme, cyanopterin, is involved in the inhibition of the negative phototaxis of the wild-type by sensing the UV-A. However, 2,4-diamino-6-hydroxypyrimidine-mediated inhibition of GTP cyclohydrolase I, the rate-limiting enzyme for pterin biosynthesis, significantly increased the positive phototaxis toward UV-A in the wild-type and the pgtA mutant. Furthermore, we measured the action spectrum of phototaxis in vivo for the wild-type and pgtA mutant. Maximal activity of the wild-type was at 300, 380 and 440 nm, indicating absorption by pterins and flavin. In particular, the UV-A/ blue peak at 380 and 440 nm obtained from the action spectrum of phototaxis was found to be closely correlated with the in vitro absorption spectrum previously reported for the cyanobacterial cryptochrome DASH. By investigating the photomovement of the wild-type and pgtA mutant to UV and blue light, we suggest that pterin can function as the chromophore of putative UV/blue photoreceptor(s) in cyanobacterial phototaxis.

Ecotypes are geographic variants of plants. Using two-dimensional gel electrophoresis, we performed a comparative analysis of intra-species proteome variation in Arabidopsis ecotypes. The effect of single gene mutations on parental ecotype proteome patterns was also examined. Three Arabidopsis ecotypes, Col-0, Ler-0 and Ws-0, were compared to identify characteristic proteome patterns. From the protein expression profile of whole seedling protein extracts, 13 differentially expressed group of proteins were distinguished by self-organizing map clustering analysis. Proteins in each cluster were identified by peptide mass fingerprinting. These isolated clusters were used as a molecular phenotype for comparison of Col-0, Ler-0, and Ws-0 with genetically close or distant ecotypes, as well as several single locus mutants. Comparison of protein patterns with other ecotypes showed that the genetic diversity of the ecotypes was reflected in quantitative differences in the protein expression patterns. Single locus mutations usually did not alter the parental protein pattern significantly, although a few mutations did cause a dramatic change relative to the parental pattern.

A binary vector devoid of a plant selection-marker gene (designated as pSSA-F) was constructed to overcome bio-safety concerns about genetically modified plants. This vector carried chloroplast-targeted superoxide dismutase (SOD) and ascorbate peroxidase (APX) genes under the control of an oxidative stress-inducible(SWPA2) promoter, and was utilized to transform potato (Solanum tuberosum L.). Integration of these foreign genes into transgenic plants was primarily performed via PCR with genomic DNA. Twelve marker-free transgenic lines were obtained by inoculating stem explants. The maximum transformation efficiency was 6.25% and averaged 2.2%. Successful integration of the SOD and APX genes rendered transgenic plants tolerant to methyl viologen-mediated oxidative stress at the leaf-disc and whole-plant levels. Our findings suggest that this technique for developing selection marker-free transgenic plants is feasible and can be employed with other crop species.

Transgenic potato plants (Solanum tuberosum L. cv. Superior) with the ability to synthesize glycinebetaine (GB) in chloroplasts (referred to as SC plants) were developed via the introduction of the bacterial choline oxidase (codA) gene under the control of an oxidative stress-inducible SWPA2 promoter. SC1 and SC2 plants were selected via the evaluation of methyl viologen (MV)-mediated oxidative stress tolerance, using leaf discs for further characterization. The GB contents in the leaves of SC1 and SC2 plants following MV treatment were found to be 0.9 and 1.43 micromol/g fresh weight by HPLC analysis, respectively. In addition to reduced membrane damage after oxidative stress, the SC plants evidenced enhanced tolerance to NaCl and drought stress on the whole plant level. When the SC plants were subjected to two weeks of 150 mM NaCl stress, the photosynthetic activity of the SC1 and SC2 plants was attenuated by 38 and 27%, respectively, whereas that of non-transgenic (NT) plants was decreased by 58%. Under drought stress conditions, the SC plants maintained higher water contents and accumulated higher levels of vegetative biomass than was observed in the NT plants. These results indicate that stress-induced GB production in the chloroplasts of GB non-accumulating plants may prove useful in the development of industrial transgenic plants with increased tolerance to a variety of environmental stresses for sustainable agriculture applications.

To modulate the soluble sugar content of strawberry fruits, we generated transgenic plants that incorporated an antisense cDNA of ADP-glucose pyrophosphorylase (AGPase) small subunit (FagpS) under the control of the strawberry fruit-dominant ascorbate peroxidase (APX) promoter (cv. Anther). Several independent transgenic lines were obtained and grown in the greenhouse for analysis of agronomic traits. Most transgenic fruit did not show significant differences in weight and hardness compared to control fruit. However, the starch content in fruit was decreased to 27–47% and the total soluble sugar content was increased to 16–37% in transgenic plants (analyzed by the HPLC of sugar composition at four different stages of fruit development). The sugar contents of fruits in transgenic lines were particularly higher than control fruits at the red stage. The results were consistent with northern analysis, which showed that the levels of AGPase mRNA drastically were reduced in the red stage of fruits in all the transgenic plants. In other tissues of transgenic plants, the FagpS mRNA expression level was similar to control plants. Our studies indicate that fruit-specific down-regulation of the AGPase gene might be an effective strategy for increasing sugar and decreasing starch content in strawberry.

Anthocyanins are major color pigments in plants. Their biosynthetic pathways are well established, and the majority of these biosynthetic enzymes have been identified in model plants such asArabidopsis, maize, and petunia. One exception inArabidopsis is UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT). This enzyme is known as Bronze-1 (Bz1 ) in maize, where it converts anthocyanidins to anthocyanins. Phylogenetic sequence analysis of theArabidopsis thaliana UDP-glycosyltransferase (UGT) family previously indicated that UGT78D1, UGT78D2, and UGT78D3 cluster together with UF3GTs from other species. Here, we report thatUGT78D2 encodes a cytosolic UGT that is functionally consistent with maize Bz-1. Biochemically, UGT78D2 catalyzes the glucosylation of both flavonols and anthocyanidins at the 3-OH position. A T-DNA-insertedugt78d2 mutant accumulates very little anthocyanin and lacks 3-O-glucosylated quercetin. Expression analysis indicated thatUGT78D2, in opposite toBANYULS, is highly expressed in anthocyanin-accumulating seedlings but repressed in condensed tannin-accumulating seed coats. This suggests that the reciprocal regulation of these two genes is important in directing the metabolic flux to either anthocyanins or condensed tannins. Consistent with this, the ectopic expression of UGT78D2 produces purple-colored seed coats due to the accumulation of anthocyanins. Taken together, our data indicate thatUGT78D2 encodes an enzyme equivalent to maize Bz1, and that the reciprocal regulation of UGT78D2 and BANYULS is critical for the regulation of metabolic flux of anthocyanidins inArabidopsis.

A negative selectable marker gene, codA, was successfully co-transformed with a GUS reporter gene to develop selectable marker gene-free transgenic plants. The pNC binary vector contained a T-DNA harboring the codA gene next to the nptII gene, while a second binary vector, pHG, contained a GUS reporter gene. Tobacco plants ( Nicotiana tabacum cv. Samsun NN) were co-transformed via the mixture method with Agrobacterium tumefaciens LBA4404 strains harboring pNC and pHG, respectively. Seeds harvested from the co-transformants were sown on germination media containing 5-fluorocytosine (5-FC). Analysis of the progeny by GUS staining and PCR amplification revealed that all of the 5-FC-resistant R(1) plants were codA free, and that the codA gene segregated independently of the GUS gene. Because codA-free seedlings developed normally on 5-FC-containing medium, we suggest that co-transformation with negatively selectable markers is a viable method for the production of easily distinguished, selectable marker gene-free transgenic plants.

Plant photoreceptors regulate various developmental processes. Among the photoreceptors, phytochromes, red and far-red light receptors, regulate light responses through many signaling components, including phytochrome-interacting proteins. The functional relationships among phytochromes and their interacting proteins, however, have not been clearly established. Here, we sought to identify a functional relationship between phytochromes and phytochrome interacting factor 3 (PIF3). We demonstrate that PIF3 is polyubiquitinated rapidly and subsequently degraded in PHYA and PHYB-mediated light signaling. We also show that the degradation of PIF3 is mediated by the 26S proteasome. Our data indicate that light-stimulated phytochromes cause the degradation of their interacting protein, PIF3, by the 26S proteasome.

Using cotyledonary explants excised from seedlings germinated in vitro, efficient plant regeneration via organogenesis was established for two winter squash (Cucurbita maxima Duch.) cultivars. To establish optimal conditions for adventitious shoot induction, a variety of explants were prepared from seedlings of different ages and these were cultured using media containing different concentrations of 6-benzylaminopurine (BA). For both cultivars, plant regeneration was optimal when the proximal parts of cotyledons from 4-day-old seedlings were cultured on induction medium composed of Murashige and Skoog (MS) medium with 1 mg/l BA. After 3 weeks of culture in induction medium, 82 and 92% of explants from the two cultivars regenerated shoots. Adventitious shoots were subcultured on elongation medium composed of MS medium with 0.1 mg/l BA and the elongated shoots were successfully rooted in MS medium without growth regulators for 2 weeks. Flow cytometric analysis revealed that most of the regenerated plants were diploid.

The leaf explants of Ostericum koreanum were cultured on MS medium supplemented with 5.37 μM NAA and 0.44 μM BA and did not need transfer to growth regulator–free medium for somatic embryogenesis. The pH level of medium dropped after autoclaving and at the beginning of explant culture, then rose back to the normal pH level of medium. The low pH level of medium, pH 4.0 or 4.3, before autoclaving rose to pH 5.2 or 5.3 and pH 6.1 or 6.2 after the 1 and 8 weeks from culture initiation, respectively, and this level was variable around pH 5–pH 6 during culture period. The explants were exposed to low pH for only several days at the early period of culture. On medium of pH 4.3, the production of somatic embryos was enhanced to six times in comparison with that on medium of pH 5.8. The average regeneration rate of total somatic embryos produced on medium of low pH was over 10% higher than that at pH 5.8. The regeneration of cup-shaped embryos was improved from 33% on medium of pH 5.8 to 67% on medium of pH 4.3. Therefore, the production and regeneration of somatic embryos were enhanced by the temporary exposure of leaf explant to medium of low pH, even though somatic embryogenesis substantially occurred on medium of nearly routine pH.

Using Arabidopsis thaliana, we identified the cis-element involved in the plant unfolded protein response (UPR). In transgenic plants, tunicamycin stimulated expression of a reporter gene under the control of the BiP promoter and promoter analysis identified a 24 bp sequence crucial to this induction. When fused with a minimal promoter, a hexamer of this sequence was sufficient for induction of a reporter gene in protoplasts treated with tunicamycin or dithiothreitol. Induction rate equivalent to original promoter was observed when the assay was conducted in transgenic plants. This 24 bp sequence contained two elements also responsible for the UPR in animals. Either of these elements was sufficient for the plant UPR, indicating conservation between animals and plants of cis-elements involved in the UPR.

The superior gate stack was fabricated by employing novel high vacuum annealing followed by in-situ metal capping method to suppress GeO x regrowth. Less GeO volatilization induces less Ta diffusion into gate oxide which reduces leakage current and enables further scaling. With ZrO 2 /Zr-cap stack, highly scaled Ge (100) pMOSFETs have been demonstrated which shows extremely low EOT (6.06 A), low gate leakage current of 250 nA/cm 2 @|V g -V FB |=1V, superior SS of 70 mV/dec, and 110 cm 2 /Vs of peak hole mobility.

Citrus ( Citrus unshiu Marc.) contains high contents (0.45–5.26 mg%) of β-cryptoxanthin. cDNA clones ( CHX1 and CHX2 ) encoding β-carotene hydroxylase (Chx) were isolated from Citrus fruit and leaf cDNA libraries. Sequence analyses indicated that the clones show polymorphism and that cDNA contains an open reading frame encoding 311 amino acids (34 kDa). Phylogenetic dendrogram suggested the evolutionary link among the fruit-producing plants. RNA blot analysis showed that its expression is ubiquitous in three tissues examined — fruits, leaves, and flowers — and that it is detected as a single band. Also, during the development of fruits and leaves, the expression of CHX1 and CHX2 transcripts was consistent in all stages, which indicated that CHX1 and CHX2 genes are not regulated during fruit ripening at the transcriptional level and revealed that their expression varies with plant species, even having the same type of fruit. Our results suggest that the expression of Chx at the transcriptional level does not contribute to the changes of carotenoids biosynthesis in ripening fruit of Citrus .

Little is known about differential gene expression at the molecular level in polyploid plants. Here, we describe the molecular analysis of ApxSC (cytosolic ascorbate peroxidase from a polyploid strawberry) genes. Fifty-three cDNAs encoding ApxSC were isolated from a strawberry fruit cDNA library. These clones were categorized (i) into nine homologous (95 to 99%) gene groups on the basis of their nucleotide sequences and (ii) into four groups of similar (> 98%) polypeptides on the basis of their deduced amino acid sequences. Sequence variation among the gene groups was dispersed throughout the gene, while differences among the polypeptide groups were observed only at three amino acid positions (9, 63, and 233). These results imply that the ApxSC genes show co-dominant expression resulting from multiple alleles. This hypothesis is supported by genomic blots and primer extension analyses.

Summary A cDNA clone (Psy1) encoding phytoene synthase was isolated from the fruit cDNA library ofCitrus (Citrus unshiuMarc.). Sequence analyses and phylogenetic dendrogram revealed that the cDNA contains an open reading frame encoding 437 amino acids (47 kDa), which showed significant similarity to those of phytoene synthases of fruit-producing plants. RNA blot analysis showed that the mRNA is expressed in the edible parts and peels of fruits, leaves, and flowers, as a single transcript. Also, during the ripening of fruits, thePsy1 transcripts were detected in all stages and its expression markedly increased to the maximum level in the latest stage. A similar pattern was also detected in peels. Also, the level ofPsy1 transcripts is changed in the process of leaf development. Our results suggested that Psy1 is an important regulatory enzyme in carotenoid accumulation during fruit ripening. This is the first report to characterize the relationship between the expression ofPsy and fruit development in a woody plant.

A fruit-specific and pathogenesis-related 5/thaumatin-like (PR5/TL), 31-kDa protein was isolated by 2D-PAGE from fully-grown apples (Malus domestica cv. Fuji) and named Mdtl1 (Malus domestica thaumatin-like protein 1). Using the N-terminal sequence of the protein, the full-length cDNA encoding Mdtll was isolated. The cDNA clone (Mdtl1) consists of 944 bp with an open reading frame (ORF) of 744 bp encoding a protein of 247 amino acids. The deduced amino acid sequence of Mdtl1 shows high similarity to the sequences of PR5/TL proteins. Mdtl1 is a slightly acidic protein with a putative signal peptide and a putative N-glycosylation site, and lacks a C-terminal extension. This suggests that Mdtl1 is an apoplastic glycoprotein. Results of northern blotting indicated that expressions of Mdtl1 are developmentally regulated. Southern blot analysis showed that Mdtl1 may be present as a single copy, and there exist other genes closely related to Mdtl1 in the apple genome.

The suppression subtractive hybridization (SSH) method was used to isolate developmentally regulated genes during carnation flower maturation. Carnation flower maturation-related clones obtained by the SSH were serially assigned as CFMI (carnation flower maturation-induced) clones. Northern blot analysis showed that several CFMI clones were differentially expressed during flower development. One of the clones, CFMI-3, showed similarity to various animal secretory phospholipases A2 (PLA2). Since little is known about PLA2 gene sequence in plant species, the CFMI-3 clone was selected for further characterization by sequence analysis. Full sequence analysis reveals that the CFMI-3 contains a Ca2+ binding domain, a PLA2 active site, and 12 conserved Cys residues, which is a distinct characteristic of PLA2. Amino acid sequence alignment of CFMI-3 to various putative plant PLA2 confirmed that the CFMI-3 cDNA is the full-length putative PLA2 cDNA identified in plant species.

The 5′ untranslated region (UTR) of cucumber mosaic virus (CMV) RNA 4 confers a highly competitive translational advantage on a heterologous luciferase open reading frame. Here we investigated whether secondary structure in the 5′ UTR contributes to this translational advantage. Stabilization of the 5′ UTR RNA secondary structure inhibited competitive translational activity. Alteration of a potential single-stranded loop to a stem by substitution mutations greatly inhibited the competitive translational activity. Tobacco plants infected with wild type virus showed a 2.5-fold higher accumulation of maximal coat protein than did plants infected with a loop-mutant virus. Amplification of viral RNA in these plants could not explain the difference in accumulation of coat protein. Phylogenetic comparison showed that potential single-stranded loops of 12–23 nucleotides in length exist widely in subgroups of CMV.

We isolated a cytosolic ascorbate peroxidase (APX-c) from strawberry fruit at the turning (1/2 red) stage and determined its N-terminal amino acid sequence. Using degenerate oligonucleotides corresponding to a part of the N-terminal sequence and two sequences corresponding to conserved regions in previously reported plant ascorbate peroxidases, two RT-PCR products of 730 bp and 630 bp were synthesized. Screening of a strawberry fruit cDNA library with the PCR-amplified DNA fragments as probes resulted in a cDNA which encodes a cytosolic APX isoform. DNA sequencing revealed that the cDNA contains an open reading frame of 250 amino acids (27.3 kDa). The lack of a transit peptide in the deduced amino acid sequence implies that it encodes a cytosolic isoform. RNA blot analysis showed that the mRNA is strongly expressed in fruit and weakly in leaf, root, and petiole, but not in seed. Also, during ripening, the expression of the mRNA increased to the maximum level at the turning stage. This is the first report to identify a specific cytosolic APX isoform from multi-isoforms and characterize it at the molecular level in a nonclimacteric fruit.

We isolated a genomic DNA harboring a cytosolic ascorbate peroxidase gene (ApxSC) from a genomic library of the strawberry (Fragaria x ananassa). Restriction mapping and sequence analyses showed that the DNA is composed of 2.5 kb of the full-length ApxSC gene, 3.7 kb of the 5'-upstream region, and 0.5 kb of the 3'-downstream region. The ApxSC genomic DNA contains 10 exons and 9 introns, which is similar to the structure of pea ApxI. A primer extension analysis suggested that the transcription of ApxSC gene was started at three start sites with different degrees. The promoter region of ApxSC gene contains a sequence or structure distinct from other reported plant ascorbate peroxidase genes, though with several known functional elements such as a TATA box.

We studied the sintering process of sol-gel-prepared monodisperse submicrometer CeO2 spheres by examining the microstructural changes of single spherical particles after successive heat treatment in oxygen up to 850°C using transmission electron microscopy. Steps of organic phase removal, CeO2 crystallization, grain growth, and particle condensation were clearly illustrated. Grain-size and sphere-diameter changes were measured quantitatively using this technique. CeO2 particles were found to be highly porous until collapse, which occurred at~850°C.

Induction of cell death is an important component of plant defense against pathogens. There have been many reports on the role of phytohormones in pathogen-induced cell death, but jasmonic acid (JA) has not been implicated as a regulator of the response. Here, we report the function of NbHB1, Nicotiana benthamiana homeobox1, in pathogen-induced cell death in connection with JA signaling. Involvement of NbHB1 in cell death was analysed by gain- and loss-of-function studies using Agrobacterium-mediated transient overexpression and virus-induced gene silencing, respectively. Expression of NbHB1 following pathogen inoculations and various treatments was monitored by reverse transcription polymerase chain reaction. Transcript levels of NbHB1 were upregulated by infection with virulent and avirulent bacterial pathogens. Ectopic expression of NbHB1 accelerated cell death following treatment with darkness, methyl jasmonate, or pathogen inoculation. Conversely, when NbHB1 was silenced, pathogen-induced cell death was delayed. NbHB1-induced cell death was also delayed by silencing of NbCOI1, indicating a requirement for JA-mediated signaling. Overexpression of the domain-deleted proteins of NbHB1 revealed that the homeodomain, leucine zipper, and part of the variable N-terminal region were necessary for NbHB1 functionality. These results strongly suggest the role of NbHB1 in pathogen-induced plant cell death via the JA-mediated signaling pathway.

Trimethylation of histone H3 at lysine 27 (H3K27me3) is a histone marker that is present in inactive gene loci in both plants and animals. Transcription of some of the genes with H3K27me3 should be induced by internal or external cues, yet the dynamic fate of H3K27me3 in these genes during transcriptional regulation is poorly understood in plants. Here we show that H3K27me3 in two cold-responsive genes, COR15A and ATGOLS3, decreases gradually in Arabidopsis during exposure to cold temperatures. We found that removal of H3K27me3 can occur by both histone occupancy-dependent and -independent mechanisms. Upon cold exposure, histone H3 levels decreased in the promoter regions of COR15A and ATGOLS3 but not in their transcribed regions. When we returned cold-exposed plants to normal growth conditions, transcription of COR15A and ATGOLS3 was completely repressed to the initial level before cold exposure in 1 day. In contrast, plants still maintained the cold-triggered decrease in H3K27me3 at COR15A and ATGOLS3, but this decrease did not enhance transcriptional induction of the two genes upon re-exposure to cold. Taken together, these results indicate that gene activation is not inhibited by H3K27me3 itself but rather leads to removal of H3K27me3, and that H3K27me3 can be inherited at a quantitative level, thereby serving as a memory marker for recent transcriptional activity in Arabidopsis.

In yeast and animals, tri- and dimethylation of histone H3 at lysine 4 (H3K4me3/2) are markers of transcriptionally active genes that have recently been shown to be primary ligands for the plant homeodomain (PHD) finger. However, PHD fingers able to bind to H3K4me3/2 have not been identified in plants. Here, we identify 83 canonical PHD fingers in the Arabidopsis proteome database that are supported by both SMART and Pfam prediction. Among these, we focus on PHD fingers in ING (inhibitor of growth) homologues (AtING) and Alfin1-like (AL) proteins, which are highly similar to those in human ING2 and bromodomain PHD finger transcription factor (BPTF), based on predicted tertiary structures. ING proteins are found in yeast, animals and plants, whereas AL proteins exist only in plants. In vitro binding experiments indicated that PHD fingers in AtING and AL proteins in Arabidopsis can bind to H3K4me3, and, to a lesser extent, to H3K4me2. In addition, mutational analysis confirmed that a predicted aromatic cage and a specific conserved acidic residue are both crucial for binding to H3K4me3/2. Finally, we demonstrate that AtING and AL proteins are nuclear proteins that are expressed in various tissues of the Arabidopsis plant. Thus, we propose that ING and AL proteins are nuclear proteins that are involved in chromatin regulation by binding to H3K4me3/2, the active histone markers, in plants.

Endoribonuclease E (RNase E) is a regulator of global gene expression in Escherichia coli and is the best studied member of the RNase E/G ribonuclease family. Homologues are present in other bacteria but the roles of plant RNase E/G-like proteins are not known. Arabidopsis thaliana contains a single nuclear gene (At2g04270) encoding a product with the conserved catalytic domain of RNase E/G-like proteins. At2g04270 and the adjacent At2g04280 gene form converging transcription units with a approximately 40 base overlap at their 3' ends. Several translation products were predicted from the analyses of At2g04270 cDNAs. An antibody raised against a recombinant A. thaliana RNase E/G-like protein recognized a 125 kDa protein band in purified chloroplast preparations fractionated by SDS-PAGE. The 125 kDa RNase E/G-like protein was detected in cotyledons, rosette and cauline leaves. T-DNA insertions in exon 6 or intron 11 of At2g04270 result in loss of the 125 kDa band or truncation to a 110 kDa band. Loss of At2g04270 function resulted in the arrest of chloroplast development, loss of autotrophic growth, and reduced plastid ribosomal, psbA and rbcL RNA levels. Homozygous mutant plants were pale-green, contained smaller plastids with fewer thylakoids and shorter granal stacks than wild-type chloroplasts, and required sucrose at all growth stages following germination right up to flowering and setting seeds. Recombinant A. thaliana RNase E/G-like proteins rescued an E. coli RNase E mutant and cleaved an rbcL RNA substrate. Expression of At2g04270 was highly correlated with genes encoding plastid polyribonucleotide phosphorylase, S1 RNA-binding, and CRS1/YhbY domain proteins.

Angiosperm seeds integrate various environmental signals, such as water availability and light conditions, to make a proper decision to germinate. Once the optimal conditions are sensed, gibberellin (GA) is synthesized, triggering germination. Among environmental signals, light conditions are perceived by phytochromes. However, it is not well understood how phytochromes regulate GA biosynthesis. Here we investigated whether phytochromes regulate GA biosynthesis through PIL5, a phytochrome-interacting bHLH protein, in Arabidopsis. We found that pil5 seed germination was inhibited by paclobutrazol, the ga1 mutation was epistatic to the pil5 mutation, and the inhibitory effect of PIL5 overexpression on seed germination could be rescued by exogenous GA, collectively indicating that PIL5 regulates seed germination negatively through GA. Expression analysis revealed that PIL5 repressed the expression of GA biosynthetic genes (GA3ox1 and GA3ox2), and activated the expression of a GA catabolic gene (GA2ox) in both PHYA- and PHYB-dependent germination assays. Consistent with these gene-expression patterns, the amount of bioactive GA was higher in the pil5 mutant and lower in the PIL5 overexpression line. Lastly, we showed that red and far-red light signals trigger PIL5 protein degradation through the 26S proteasome, thus releasing the inhibition of bioactive GA biosynthesis by PIL5. Taken together, our data indicate that phytochromes promote seed germination by degrading PIL5, which leads to increased GA biosynthesis and decreased GA degradation.

Compared to mammals, little is known about the unfolded protein response (UPR) in plants. Using an oligonucleotide array comprising approximately 8200 Arabidopsis genes we investigated the effect of endoplasmic reticulum (ER) stress on gene expression. Expression of 26 genes increased, including at least nine whose products act in the ER, while their transcriptional activations were confirmed by promoter analyses. Among them, BiP-L, a novel BiP, whose expression appeared to be regulated by two promoter sequences perfectly matching mammalian ERSE. Cloning and sequencing of full-length BiP-L cDNA showed it contained a signal peptide sequence and the ER retention signal (HDEL). Interestingly, BiP-L was substantially different from the other two Arabidopsis BiP genes in genomic organization and sequence homology. Furthermore, phylogenetic analysis showed that the BiP-L protein is the most distal form among the reported plant BiP proteins. RNA levels of BiP-L were very low in various mature Arabidopsis plant organs, while significant levels of BiP-L only observed in stressed seedlings. Transcription of BiP-L during ER stress was shown to be regulated by a feedback loop.

A cDNA and genomic DNA encoding an abscisic acid responsive gene (ASR) homologue (Asr1) was isolated from an inodorus melon, Cucumis melo var. kuwata, cDNA and genomic library. The Asr1 gene showed the strongest fruit-specific expression and differential expression profiles during fruit development, which were expressed from a low copy gene. The promoter region of the Asr1 gene contained several putative functional cis-elements, which may be involved in the response to plant hormones and environmental stresses. These results suggest that Asr1 may play an important role in the regulation of melon fruit ripening.

Retrotransposons are present in multi-copy numbers that are integrated into plant genomes with considerable heterogeneous sequences within a single plant and between plant species, which allows the use of retrotransposons as additional sources of DNA polymorphism. A primer design for the sequence-tagged specific site and cleaved amplified polymorphic sequences (STS-CAPs) that are derived from retrotransposon-like sequences was developed for the molecular marker analysis in Hibiscus syriacus. This method was applied for the detection of sequence variations of intact retrotransposons that exist in plant genomes, which resulted in higher polymorphisms than in the amplified fragment length polymorphism (AFLP). Through STS-CAPs, specific fingerprinting data among H. syriacus varieties can be easily distinguished and generated with reproducible results. It could also be adapted to any species that possess multi-copy retrotransposons for varietal identification as well as the assessment of genetic relationships.

We have isolated and characterized a gene encoding cytosolic glutathione reductase from Brassica campestris (B. campestris). The gene (BcgGR1) is presented as a single copy in the B. campestris genome and is composed of 17 exons and 16 introns in the trancribed region with coding sequence beginning in the 2nd exon and ending in the 17th exon. BcgGR1 is expressed strongly in roots and calli, and moderately in stems and leaves. The transcription is strongly induced by various stress treatments including ozone, paraquat, salt, hydrogen peroxide, chilling or ABA but depressed by heat treatment. The transcript level of BcgGR1 is increased significantly at 2 h after the onset of ozone (300 ppb), paraquat (10 microM) or salt (250 mM NaCI) treatments and reached a maximum level by 10-24 h. However, the maximum induction of BcgGR1 is reached at 2-4 h after the onset of hydrogen peroxide (10 mM), chilling (10 degrees C) or ABA (1 mM) treatments. The rapid reduction of BcgGR1 transcripts after 4 h in ABA treatment is distinguished from hydrogen peroxide and chilling treatments.

The accumulation of unfolded proteins in the endoplasmic reticulum (ER) elicits an ER-to-nucleus signaling pathway known as the unfolded protein response (UPR) in eukaryotes. In yeast, Ire1p, a kinase/endoribonuclease in the ER membrane, plays a key role in the UPR signaling. We isolated two cDNA homologs of IRE1 gene from Arabidopsis (AtIre1a, AtIre1b). The two IRE1 homologs were predicted to form a type I transmembrane protein structure and contain kinase/endoribonuclease domains at their C-terminal halves. The expressions of the two genes were detected in various organ tissues of the Arabidopsis plant. The C-terminal half of the AtIre1a protein showed in vitro autophosphorylation activity. However, we could not detect endoribonuclease activity of the AtIre1a protein when we used yeast HAC1 RNA as the substrate in vivo.

Two cDNA clones (NtmybAS1 andNtmybAS2) encoding MYB-related proteins with strong sequence similarity to petunia (Petunia hybrida) PhMYB3 were isolated from a tobacco (Nicotiana tabacumcv Samsun) pollen cDNA library. Northern blot and in situ hybridization revealed that NtmybAS transcripts are specifically expressed in both sporophytic and gametophytic tissues of the anther including tapetum, stomium, vascular tissue, and developing pollen. Random binding site selection assays revealed that NtMYBAS1 bound to DNA sequences closely resembling consensus MYB binding sites MBSI and MBSIIG, with a higher affinity for MBSI. Transient expression analyses of the N-terminal MYB domain demonstrated the presence of functional nuclear localization signals, and full-length NtMYBAS1 was able to activate two different phenylalanine ammonia-lyase promoters (PALA and gPAL1) in tobacco leaf protoplasts. Similar analysis of truncated NtmybAS1cDNAs identified an essential, C-terminal trans-activation domain. Further in situ hybridization analyses demonstrated strict co-expression of NtmybAS and gPAL1 in the tapetum and stomium. Despite abundant expression ofNtmybAS transcripts in mature pollen,gPAL1 transcripts were not detectable in pollen. Our data demonstrate that NtMYBAS1 is a functional anther-specific transcription factor, which is likely to be a positive regulator ofgPAL1 expression and phenylpropanoid synthesis in sporophytic, but not in gametophytic, tissues of the anther.

Two cDNA clones encoding ADP-glucose pyrophosphorylases have been isolated from fruit and leaf cDNA libraries of Citrus ( Citrus unshiu Mac. cv. Miyagawa) in which one was designated as agpS for the small subunit and the other as agpL for the large subunit. Both cDNAs have uninterrupted open reading frames deriving 57–58 kDa polypeptides. The deduced amino acid sequence of agpS has a unique feature. That is, it lacks a cysteine residue (Cys-12) which is usually conserved in all other dicot enzymes. This is the first report of agpS lacking Cys-12 among dicot small subunits. The expression pattern of both subunits showed a different profile in which leaves synthesized both agpS and agpL more vigorously than those of fruits. During leaf development, the transcripts of agpS and agpL showed a higher expression level at younger stages. During fruit development, the expression level of both subunits was observed to be highest in the mini-green stage, but it decreased in the small green stage and it increased again towards the maturing stage. These results suggest that both subunits may play an important role in the regulation of Citrus fruit and leaf development.

RNA species of plant tripartite RNA viruses show distinct translational activities in vitro when the viral RNA concentration is high. However, it is not known what causes the differential translation of virion RNAs. Using an in vitro wheat germ translation system, we investigated the translation efficiencies and competitive activities of chimeric cucumber mosaic virus (CMV) RNAs that contained viral untranslated regions (UTRs) and a luciferase-coding sequence. The chimeric RNAs exhibited distinct translation efficiencies and competitive activities. For example, the translation of chimeric CMV RNA 4 was about 40-fold higher than that of chimeric CMV RNA 3 in a competitive environment. The distinct translation resulted mainly from differences in competitive activities rather than translation efficiencies of the chimeric RNAs. The differential competitive activities were specified by viral 5′ UTRs, but not by 3′ UTRs or viral proteins. The competitive translational activities of the 5′ UTRs were as follows: RNA 4 (coat protein)>RNAs 2 and 1 (2a and 1a protein, or replicase)>RNA 3 (3a protein).

A rice (Oryza sativa L. cv. Nakdong) cDNA clone, Oshsp26, encoding the chloroplast-localized small heat shock protein (smHSP) was isolated. Southern blot analysis of genomic DNA and the result of screening of a cDNA library indicated that the Oshsp26 gene is encoded by a single gene in the rice genome. The Oshsp26 gene was expressed following heat stress: the transcript level was highest when rice leaves were treated at high temperatures for 2h at 42 degrees C, and the transcripts became detectable after 20min and reached a maximum level after 2h. It was also found that the Oshsp26 gene was expressed following oxidative stress even in the absence of heat stress. Treatment of rice plants with methyl viologen (MV) in the light and treatment with hydrogen peroxide (H(2)O(2)), either in the light or in the dark, both caused a significant accumulation of the transcripts and the protein. Since MV treatment in the light leads to the generation of H(2)O(2) inside the chloroplast, it is likely that H(2)O(2) by itself acts to induce the expression of the Oshsp26 gene. These results suggest that the chloroplast smHSP plays an important role in protecting the chloroplast against damage caused by oxidative stress as well as by heat stress.

Three cDNA clones encoding ADP-glucose pyrophosphorylases were isolated from a full red fruit cDNA library of watermelon (Citrullus vulgaris S.). Sequence analyses indicated that one clone, wms1, corresponds to the small subunit, and two clones, wml1 and wml2 (a partial gene), are the large subunits of AGPase. The presumed AGPase proteins encoded by wms1, wml1, and wml2 have 526, 526, and 481 amino acids, respectively. The protein sequences have the conserved amino acids important for the substrate or regulator binding site, with some variation. Developmental changes in the amounts of wms1, wml1, and wml2 transcripts in fruits were measured by northern blot analysis. Their expression levels decreased from the small green to medium green stages, then increased in accordance with fruit ripening, which was different from those of tomato and oriental melon.

We isolated three cDNAs encoding different isoforms of ADP-glucose pyrophosphorylase (AGP) large submits from tomato plants. Three clones, designated AgpL1, AgpL2, and AgpL3 were 2019, 2105, and 1850bp, respectively. The clones had a long, uninterrupted open reading frame with a start codon at the 5' region and different copies of polyadenylation signal (AATAAA) at the 3' region, deriving 57-58kDa polypeptides. Sequence comparison and phylogenetic analysis revealed that the three isoforms represented different types of AGP large subunits, AgpL1 was strongly expressed in stems and weakly in roots. Accumulation of AgpL1 transcripts was found even in unpollinated ovaries and sustained at the early stages of fruit development. ApgL2 was expressed in roots and fruits. AgpL3 was exclusively expressed in leaves. The present study suggests that the three isoforms of tomato AGP large subunits are organ-specific in their expressions.

We isolated a DNA fragment (ALU1-P) encoding a protein with an activity of aluminum tolerance from an Al tolerant soil microorganism, Arthrobacter viscosus. This microorganism was isolated from acidic tea field soils. The cloned DNA is composed of 1090 nucleotides, which has one open-reading frame without any stop codon. However, when the DNA fragment was transferred into Escherichia coli, a microorganism susceptible to Al toxicity, it endowed E. coli with Al tolerance. The deduced amino acid sequence of the DNA showed 65% identity with the protein of YbaX gene in Escherichia coli, and 51.1% identity with YB91 Haein hypothetical protein of HI1191 gene in Haemophilus influenzae. The ALU1-P gene in the expression vector produced a protein of 192 amino acids deriving a molecular weight of 21.3 kDa by using the stop codon in vector. The ALU1-P gene is a new one that has the characteristic of Al tolerance.

We have isolated a genomic clone encoding trichobakin (TBK), a type I ribosome-inactivating protein from the plant Trichosanthes sp. Bac Kan 8-98 (family Cucurbitaceae), by PCR using specific primers designed from the cDNA sequences of alpha-trichosanthin. The sequence encoding mature TBK was constructed in the pET-21d(+) vector for overexpression in Escherichia coli strain BL21(DE3). The recombinant protein was purified to homogeneity by CM-Sepharose chromatography on FPLC with a final yield of about 55 mg/l of culture. The protein has a molecular mass of about 27 kDa, as shown by SDS/PAGE and matrix-assisted laser-desorption ionization MS. It was found that the protein inhibited luciferase mRNA translation in the rabbit reticulocyte cell-free system with an IC(50) value (that which causes a 50% reduction of residual translational activity) of about 3.5 pM. The rRNA N-glycosidase activity of the protein was also proved at the above-mentioned concentration after rRNAs were treated with acid aniline.