Development of a novel data mining tool to find <Emphasis Type="Italic">cis</Emphasis>-elements in rice gene promoter regions

Background  

Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions.     

γ-Radiation Induces Leaf Trichome Formation in Arabidopsis

We observed induction of additional trichome formation on the adaxial surface of mature leaves of Arabidopsis after massive doses (1-3 kilograys) of gamma-radiation from cobalt-60. A typical increase in trichome number was observed in the seventh leaf when the full expansion of the fifth leaf was irradiated. Under normal growth conditions, trichome numbers on the adaxial surface of seventh leaf of the Arabidopsis ecotypes Columbia (Col) and Landsberg erecta (Ler) were 122.5 +/- 22.7 and 57.5 +/- 14.5, respectively. However, gamma-radiation induced additional trichome formation and the numbers rose to 207.9 +/- 43.7 and 95.0 +/- 27.1 in Col and Ler, respectively. In Col the shape of new trichomes was intact and their formation was spatially maintained at equal distances from other trichomes. In Ler trichome morphology was aberrant and the formation was relatively random. Treatment with antioxidants before gamma-irradiation suppressed the increase in trichome number, and treatment with methyl viologen and light induced small trichomes. These results suggest that gamma-radiation-induced trichome formation is mediated by active oxygen species generated by water radiolysis. gamma-Radiation-induced trichome formation was blocked in the trichome mutants ttg-1, gl1-1, and gl2-1. These results suggest that gamma-radiation-induced trichome formation is mediated by the normal trichome developmental pathway.     

Activation of 40-kDa Protein Kinases in Response to Hypo- and Hyperosmotic Shock in the Halotolerant Green Alga Dunaliella tertiolecta

Changes in protein kinase activities in Dunaliella tertiolectain response to hypo- and hyperosmotic shocks were assessed byassays of protein kinase activities on SDS-polyacrylamide gelsthat contained protein substrates, Hypoosmotic shock (transferfrom 0.5 to 0.2 M Nacl) transiently activated a 40-kDa proteinkinase (low osmotic pressure-activated protein kinase, LAP kinase)that phosphorylated myelin basic protein (MBP) and histone H1but not casein. By contrast, hyperosmotic shock (transfer from0.5 to 1.1 M NACl) rapidly activated another 40-kDa proteinkinase (high osmotic pressure-activated protein kinase, HAPkinase) that phosphorylated casein and histone H1 but not MBP.Inhibitors of protein kinases, namely, K-252a and staurosporine,suppressed the activation of both LAP kinase and HAP kinase.The protein kinase activities in extracts of osmotically shockedcells disappeared completely after treatment with calf intestinalalkaline phosphatase. Anti-phosphotyrosine monoclonal antibodiesdid not cross-react with either LAP kinase or HAP kinase. Theseresults indicate that at least two 40-kDa protein kinases, LAPkinase and HAP kinase, are activated by hyper- and hypoosmoticshock, respectively, and that their activities are regulatedvia phosphorylation by putative protein kinase(s) that act atan upstream position in the signaling cascade(s) that followsosmotic shock. (Received July 24, 1995; Accepted October 20, 1995)     

Cell death suppressor Arabidopsis bax inhibitor-1 is associated with calmodulin binding and ion homeostasis

Cell death suppressor Bax inhibitor-1 (BI-1), an endoplasmic reticulum membrane protein, exists in a wide range of organisms. The split-ubiquitin system, overlay assay, and bimolecular fluorescence complementation analysis demonstrated that Arabidopsis (Arabidopsis thaliana) BI-1 (AtBI-1) interacted with calmodulin in yeast (Saccharomyces cerevisiae) and in plant cells. Furthermore, AtBI-1 failed to rescue yeast mutants lacking Ca2+ ATPase (Pmr1 or Spf1) from Bax-induced cell death. Pmr1 and Spf1, p-type ATPases localized at the inner membrane, are believed to be involved in transmembrane movement of calcium ions in yeast. Thus, the presence of intact Ca2+ ATPases was essential for AtBI-1-mediated cell death suppression in yeast. To investigate the effect of AtBI-1 on calcium homeostasis, we evaluated sensitivity against cyclopiazonic acid (CPA), an inhibitor of sarcoplasmic/endoplasmic reticulum Ca2+ ATPase in AtBI-1-overexpressing or knock-down transgenic Arabidopsis plants. These plants demonstrated altered CPA or ion stress sensitivity. Furthermore, AtBI-1-overexpressing cells demonstrated an attenuated rise in cytosolic calcium following CPA or H2O2 treatment, suggesting that AtBI-1 affects ion homeostasis in plant cell death regulation.     

Reduced susceptibility to interference in the consolidation of motor memory before adolescence

Are children superior to adults in consolidating procedural memory? This notion has been tied to "critical," early life periods of increased brain plasticity. Here, using a motor sequence learning task, we show, in experiment 1, that a) the rate of learning during a training session, b) the gains accrued, without additional practice, within a 24 hours post-training interval (delayed consolidation gains), and c) the long-term retention of these gains, were as effective in 9, 12 and 17-year-olds and comparable to those reported for adults. However, a follow-up experiment showed that the establishment of a memory trace for the trained sequence of movements was significantly more susceptible to interference by a subsequent motor learning experience (practicing a reversed movement sequence) in the 17-year-olds compared to the 9 and 12-year-olds. Unlike the 17-year-olds, the younger age-groups showed significant delayed gains even after interference training. Altogether, our results indicate the existence of an effective consolidation phase in motor learning both before and after adolescence, with no childhood advantage in the learning or retention of a motor skill. However, the ability to co-consolidate different, successive motor experiences, demonstrated in both the 9 and 12-year-olds, diminishes after puberty, suggesting that a more selective memory consolidation process takes over from the childhood one. Only the adult consolidation process is gated by a recency effect, and in situations of multiple, clashing, experiences occurring within a short time-interval, adults may less effectively establish in memory experiences superseded by newer ones.     

Carbonic Anhydrase of a Unicellular Red Alga Porphyridium cruentum R-l. II. Distribution and Role in Photosynthesis

Antibody was raised against Porphyridium carbonic anhydrase(CA) which was electrophoretically recovered from the gel afterSDS-polyacrylamide slab gel electrophoresis (SDS-PAGE) of thepartially purified enzyme. The antiserum reacted with CA ofPorphyridium, but not with that of Chlamydomonas reinhardtii.Even though the antiserum did not react with CA from P. cruentumR-l in Ouchterlony's double immunodiffusion, it blocked theenzyme activity in the presence of 1% Nonidet P-40 and 1% TritonX-100. After Western blotting and enzyme-linked immunostaining(ELIS), only one band which reacted with the antiserum was detectedin the extract of low-CO₂ cells (grown under ordinary air) ofP cruentum, while no significant band was detected in that ofhigh-CO₂ cells (grown under air enriched with 1–5% CO₂).Immunogold electron microscopy of low-CO₂ cells of P. cruentumR-l using this antibody revealed that most of the CA was localizedin the chloroplast, with some in the cytoplasm. No specificbinding of gold particles was observed in the high-CO₂ cells. ¹Present address: National Institute for Basic Biology, Myodaiji,Okazaki 444, Japan (Received May 18, 1987; Accepted September 7, 1987)     

Extracellular matrix formation by amebocytes during epithelial regeneration in the pearl oysterPinctada fucata

Summary To identify the cells which produce the extracellular matrix during bivalve wound healing, we observed epithelial regeneration inPinctada fucata and evaluated the ability of amebocytes to produce the matrix in vitro. Between days 1 and 3 after an ovary was implanted with abiotic material (a shell ball) via an incision, agranular amebocytes formed a sheath, consisting of 10–20 cell layers, between the implant and incised ovarian tissue. Extracellular matrix was deposited in the spaces between the amebocytes in the sheath. At the incised follicle, gonadal epithelial cells were attached to the newly formed matrix. When a mantle allograft (2 mm square) was implanted with abiotic material to bring them into close contact, epithelial cells emigrated from the allograft along the surface of the abiotic material where they attached to the newly formed matrix at the sheath of amebocytes. In vitro, agranular amebocytes formed a matrix composed of fibrils with a diameter of 20 nm during a 6-day culture period. Pepsin-digested extract of the cell layer forming the matrix gave protein bands with electrophoretic mobilities identical to - and -sized components of a collagen purified from this animal. The matrix exhibited immunoreaction to antiserum raised against the collagen and was stained by alcian bluc. Thus, the agranular amebocyte apparently has the ability to produce an extracellular matrix containing collagen and possibly proteoglycan(s).     

Rice has two distinct classes of protein kinase genes related to SNF1 of Saccharomyces cerevisiae , which are differently regulated in early seed development

We have isolated five cDNA clones (osk1–5) for protein kinases from rice which are related to SNF1 protein kinase of Saccharomyces cerevisiae. Based on the sequence homology, these cDNAs can be classified into two groups, group 1 (osk1) and group 2 (osk2–5). The products of these genes were demonstrated to be functional SNF1-related protein kinases by in vitro and in vivo experiments. Recombinant proteins expressed from both groups of genes were fully active as protein kinases and could phosphorylate SAMS peptide, a substrate specific for the SNF1/AMPK family, as well as themselves (autophosphorylation). Moreover, expression of osk3 cDNA in yeast snf1 mutants restored SNF1 function. Northern blot analyses showed differential expression of these two gene groups; group 1 is expressed uniformly in growing tissues (young roots, young shoots, flowers, and immature seeds), whereas group 2 is strongly expressed in immature seeds. SNF1-related protein kinases have been reported from different plant species, such as rye, barley, Arabidopsis, tobacco, and potato, while the type of gene strongly expressed in immature seeds is known only in cereals such as rye, barley, and, from our findings, in rice. Expression levels of the group 2 genes were further analyzed in seeds during seed maturation. Expression is transiently increased in the early stages of seed maturation and then decreases. The expression peak precedes those of the sbe1 and waxy genes, which are involved in starch synthesis in rice. Taken together, these findings suggest that group 2 OSK genes play important roles in the early stages of endosperm development in rice seeds. Received: 30 April 1998 / Accepted: 20 August 1998