Metabolite profiling and assessment of metabolome compartmentation of soybean leaves using non-aqueous fractionation and GC-MS analysis

In the present study, non-aqueous fractionation (NAQF) and GC-MS were used to obtain a spatially resolved view of metabolism in mature leaves of soybean (Glycine max Merr.). NAQF of lyophilized soybean leaves was performed using CCl₄-n-heptane and ultracentrifugation that yielded a gradient comprised of six fractions. Chlorophyll content, and marker enzyme activities, phosphoenolpyruvate carboxylase (PEPC) and α-mannosidase, were utilized as stroma, cytosol and vacuole markers, respectively. GC-MS analyses of each fraction resulted in the identification of around 100 different metabolites. The distribution of these identified compounds showed a decreasing order from the vacuole to cytosol to chloroplast stroma. In other words, a greater number of identified compounds were found in the vacuole when compared to the cytosol or stroma. Levels of sugars, organic acids and fatty acids showed greater relative abundances in the vacuole with 50, 55, and 50% of the respective pools. A greater relative abundance of amino acids was observed in the cytosol where 45% of the total of amino acids content was recorded. The relatively large pool of sugars and phenolic acids in the vacuole compartment implies high levels of starch metabolism and phenylpropanoid biosynthesis. The low amino acids pool, on the other hand, suggests low nitrogen accumulation in the leaves of soybean. Hierarchical cluster analysis on the most abundant metabolites revealed three clusters containing 10, 20, and 2 of the 32 selected metabolites. The data were discussed in term of NAQF and GC-MS analysis of soybean mature leaves, and also in term of distribution and compartmentation of metabolites at subcellular levels.     

Evapotranspiration of tropical peat swamp forests

In Southeast Asia, peatland is widely distributed and has accumulated a massive amount of soil carbon, coexisting with peat swamp forest (PSF). The peatland, however, has been rapidly degraded by deforestation, fires, and drainage for the last two decades. Such disturbances change hydrological conditions, typically groundwater level (GWL), and accelerate oxidative peat decomposition. Evapotranspiration (ET) is a major determinant of GWL, whereas information on the ET of PSF is limited. Therefore, we measured ET using the eddy covariance technique for 4–6 years between 2002 and 2009, including El Niño and La Niña events, at three sites in Central Kalimantan, Indonesia. The sites were different in disturbance degree: a PSF with little drainage (UF), a heavily drained PSF (DF), and a drained burnt ex‐PSF (DB); GWL was significantly lowered at DF, especially in the dry season. The ET showed a clear seasonal variation with a peak in the mid‐dry season and a large decrease in the late dry season, mainly following seasonal variation in net radiation (R_n). The R_n drastically decreased with dense smoke from peat fires in the late dry season. Annual ET forced to close energy balance for 4 years was 1636 ± 53, 1553 ± 117, and 1374 ± 75 mm yr^?1 (mean ± 1 standard deviation), respectively, at UF, DF, and DB. The undrained PSF (UF) had high and rather stable annual ET, independently of El Niño and La Niña events, in comparison with other tropical rainforests. The minimum monthly‐mean GWL explained 80% of interannual variation in ET for the forest sites (UF and DF); the positive relationship between ET and GWL indicates that drainage by a canal decreased ET at DF through lowering GWL. In addition, ET was decreased by 16% at DB in comparison with UF chiefly because of vegetation loss through fires.     

Overexpression of lalA, a paralog of labA, is capable of affecting both circadian gene expression and cell growth in the cyanobacterium Synechococcus elongatus PCC 7942

In the cyanobacterium Synechococcus elongatus, LabA negatively regulates circadian gene expression under the control of Kai-protein-based clock. Here we conducted a molecular genetic analysis of lalA, a paralog of labA. Although a lalA loss of function mutant did not exhibit any apparent phenotype under our experimental conditions, lalA overexpression inhibited cell growth and decreased cell viability. Moderate lalA overexpression brought about abnormalities in circadian gene expression: reduced amplitude of kaiBC expression rhythm, and altered peak and trough timing of psbAI and kaiA expression rhythms. These results imply that lalA is capable of affecting circadian gene expression and cell growth.     

Developmental regulation of photosynthate distribution in leaves of rice

mRNA expression patterns of genes for metabolic key enzymes sucrose phosphate synthase (SPS), phosphoenolpyruvate carboxylase (PEPC), pyruvate kinase, ribulose 1,5-bisphosphate carboxylase/oxygenase, glutamine synthetase 1, and glutamine synthetase 2 were investigated in leaves of rice plants grown at two nitrogen (N) supplies (N_0.5, N_3.0). The relative gene expression patterns were similar in all leaves except for 9^th leaf, in which mRNA levels were generally depressed. Though increased N supply prolonged the expression period of each mRNA, it did not affect the relative expression intensity of any mRNA in a given leaf. SPS V_max, SPS limiting and PEPC activities, and carbon flow were examined. The ratio between PEPC activity and SPS V_max was higher in leaves developed at the vegetative growth stage (vegetative leaves: 5^th and 7^th leaves) than in leaves developed after the ear primordia formation stage (reproductive leaves: 9^th and flag leaves). PEPC activity and SPS V_max decreased with declining leaf N content. After using ¹⁴CO₂ the ¹⁴C photosynthate distribution in the amino acid fraction was higher in vegetative than in reproductive leaves when compared for the same leaf N status. Thus, at high PEPC/SPS activities ratio, more ¹⁴C photosynthate was distributed to the amino acid pool, whereas at higher SPS activity more ¹⁴C was channelled into the saccharide fraction. Thus, leaf ontogeny was an important factor controlling photosynthate distribution to the N- or C-pool, respectively, regardless of the leaf N status.     

Screening of white rot fungi for biobleaching of <Emphasis Type="Italic">Acacia</Emphasis> oxygen-delignified kraft pulp

To reduce the levels of chlorine-based chemicals in Acacia kraft pulp, we sought to isolate white rot fungus strains that could be used for biobleaching. For this purpose, we collected 600 fungal sources from Indonesia and subjected them to a three-step screening method. The first step involved culturing the strains on Acacia mangium wood powder, guaiacol and agar (WGA) medium. Of the 600 sources, 258 strains grew on WGA medium and generated a red color. The second step revealed that 31 of the 258 strains could degrade extractive-free A. mangium wood powder. The third step examined the ability of the strains to bleach A. mangium oxygen-delignified kraft pulp (A-OKP) under various pH conditions and showed that five strains could biobleach A-OKP at pH 5, 6, and 8. In contrast, the biobleaching abilities of Trametes versicolor and Phanerochaete chrysosporium, which served as standards, were much lower than those of the five new strains, particularly at pH 8. These five strains may be useful for biobleaching of A-OKP.     

The gefitinib-sensitizing mutant epidermal growth factor receptor enables transformation of a mouse fibroblast cell line

A specific inhibitor of the Epidermal Growth Factor Receptor (EGFR), Gefitinib, displays significant antitumor effects against non-small cell lung cancers (NSCLC) that express EGFR with mutations in their tyrosine kinase domain. Although previous reports have already demonstrated that oncogenic transformation can be induced by some mutant EGFR forms, the precise differences between mutant and wild-type EGFR in terms of mechanisms of transformation have not been fully elucidated. We show here that a murine fibroblast cell line, NR6 becomes transformed by an expression level of the mutant EGFR form lacking E746-A750 that is far less than that needed with transfected wild-type EGFR. However, the mutant EGFR was unable to transform NR6 in a ligand-independent manner, as was seen with the wild-type EGFR. The consequent biological features after transformation, including DNA synthesis or cell cycle progression and biochemical characteristics such as MAPK activation mediated by the mutant EGFR are comparable and equivalent to those mediated by wild-type EGFR. These data suggest that the mutant EGFR possesses greater ligand-dependent transformation when compared with wild-type EGFR, although the exact mechanisms to account for this characteristic remain to be defined.     

Peptidoglycan recognition proteins involved in 1,3-beta-D-glucan-dependent prophenoloxidase activation system of insect

The prophenoloxidase (proPO) cascade is a major innate immune response in invertebrates, which is triggered into its active form by elicitors, such as lipopolysaccharide, peptidoglycan, and 1,3-beta-D-glucan. A key question of the proPO system is how pattern recognition proteins recognize pathogenic microbes and subsequently activate the system. To investigate the biological function of 1,3-beta-D-glucan pattern recognition protein in the proPO cascade system, we isolated eight different 1,3-beta-D-glucan-binding proteins from the hemolymph of large beetle (Holotrichia diomphalia) larvae by using 1,3-beta-D-glucan immobilized column. Among them, a 20- and 17-kDa protein (referred to as Hd-PGRP-1 and Hd-PGRP-2) show high sequence identity with the short forms of peptidoglycan recognition proteins (PGRPs-S) from human and Drosophila melanogaster. To be able to characterize the biochemical properties of these two proteins, we expressed them in Drosophila S2 cells. Hd-PGRP-1 and Hd-PGRP-2 were found to specifically bind both 1,3-beta-D-glucan and peptidoglycan. By BIAcore analysis, the minimal 1,3-beta-D-glucan structure required for binding to Hd-PGRP-1 was found to be laminaritetraose. Hd-PGRP-1 increased serine protease activity upon binding to 1,3-beta-D-glucan and subsequently induced the phenoloxidase activity in the presence of both 1,3-beta-D-glucan and Ca(2+), but no phenoloxidase activity was elicited under the same conditions in the presence of peptidoglycan and Ca(2+). These results demonstrate that Hd-PGRP-1 can serve as a receptor for 1,3-beta-D-glucan in the insect proPO activation system.     

The structure-activity relationship of various YO compounds, novel plasmin inhibitors, in the apoptosis induction

We have previously reported that YO-2, a selective plasmin inhibitor, induces thymocyte apoptosis. To elucidate the mechanism of YO-2-induced apoptosis, other YO compounds with different plasmin inhibitory action were tested for the pro-apoptotic activity in this study. The treatment of rat thymocytes with the YO compounds which had the hydrophobic but not the hydrophilic moiety at the C-terminal increased DNA fragmentation, the number of condensed nuclei and caspase-3-like activity. All pro-apoptotic YO compounds not only were potent plasmin inhibitors but also had the hydrophobic C-terminal as the common structure. Therefore, the target molecule of the YO compounds may be located not on the cell surface but rather inside the cells.     

A presumed human nuclear autoantigen that translocates to plasma membrane blebs during apoptosis

The structure and subcellular localization of a number of molecules change during apoptosis. These molecules are recognized by the immune system, leading to the development of autoimmunity when apoptotic cells fail to be effectively cleared by phagocytosis. We searched for such molecules by analyzing sera from 12 individuals who suffered from autoimmune diseases and from 3 patients with amyotrophic lateral sclerosis. One serum sample, designated 681, detected an antigen that fulfilled the above criteria. In Western blotting of lysates of human Jurkat T cells, the 681 antigen appeared as a distinct signal with a molecular mass of 60 kDa in normal cells, and 2 additional signals with faster mobilities were detected in apoptotic cells. The results of subcellular fractionation and immunofluorescence experiments revealed this antigen to be strictly localized in the nucleus of normal cells, but to be translocated to a region near the plasma membrane, to membrane blebs in particular, after the induction of apoptosis. Under conditions in which membrane blebbing was inhibited in apoptotic cells, the antigen still moved away from the nucleus, but its accumulation at the periplasmic region was completely abolished. The apparent partial cleavage and intracellular redistribution of the 681 antigen in apoptotic cells mimics changes previously reported for the nuclear autoantigen La, but the 681 antigen was clearly distinct from La. These results suggest that cleavage-dependent exit from the nucleus during apoptosis is a phenomenon common to nuclear autoantigens.