Purification and characterization of sinapoylglucose:malate sinapoyltransferase from Raphanus sativus L.

1-O-Sinapoyl--glucose:l-malate O-sinapoyltransferase (SMT; EC 2.3.1.) from cotyledons of red radish (Raphanus sativus L. var. sativus) was purified to apparent homogeneity with a 2100-fold enrichment and a 4% recovery. Apparent M_rs of 52 and 51, respectively, were determined by gel filtration and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). On isoelectric focusing, the SMT resolved into two isoforms which, on SDS-PAGE, showed, slightly different M_rs (SMT I: M_r/isoelectric point = 51/5.75; SMT II: M_r/isoelectric point = 51.5/5.9). The highest activity of SMT was found at pH 6.0 (50% at pH 5.5 and pH 6.5). The temperature maxima in the presence of 10, 50, 100 and 250 mM malate were 22, 30, 35 and 37° C, respectively, with energies of activation of 55, 81, 96 and 121 kJ · mol^-1. The enzyme accepted all the hydroxycinnamic acid-glucose esters tested with relative ratios of initial velocity values of 1008545262.6 of 1-O-sinapoyl-, 1-O-feruloyl-, 1-O-caffeoyl-, 1,2-di-O-sinapoyl-, and 1-O-(4-coumaroyl)--glucose. It showed an absolute acceptor specificity for l-malate. d-Malate as second acceptor molecule in standard assays with l-malate inhibited the reaction velocity noncompetitively (K _i = 215 mM). The substrate saturation curves were not hyperbolic. The data for sinapoylglucose indicated substrate activation; those for l-malate, substrate inhibition. Kinetic analysis suggests a random bi bi mechanism within two ranges of substrate concentrations, with a kinetically preferred pathway via the enzyme-sinapoylglucose complex indicating a slow-transition mechanism. This may be interpreted as hysteretic cooperativity with sinapoylglucose.Abbreviations IEF isoelectric focusing - Mal l-malate - pI isoelectric point - SinGlc 1-O-sinapoyl--glucose - SinMal O-sinapoyl-l-malate - SMT 1-O-sinapoyl--glucose: l-malate sinapoyltransferase - SMT I and SMT II SMT isoforms isolated after isoelectric focusing We thank H. Bisswanger (Physiologisch-chemisches Institut, Universität (Tübingen, FRG) for help on the interpretation of substrate kinetic data and B.E. Ellis (Department of Plant Science, The University of British Columbia, Vancouver, B.C., Canada) for linguistic advice. Support by the Deutsche Forschungsgemeinschaft (Bonn, FRG) and the Fonds der Chemischen Industrie (Frankfurt, FRG) is gratefully acknowledged.     

SIMPLE METHOD FOR RNA PREPARATION FROM CYANOBACTERIA1

A simple and rapid method is presented for the preparation of RNA from various cyanobacteria. Unlike other methods that require a lysis solution, lysozymes, or proteinase K, the proposed method, called the bead–phenol–chloroform (BPC) method, uses silica/zirconia beads, phenol, and chloroform to break the cells and extract RNA more efficiently. Experiments confirm that the BPC method can successfully isolate total RNA from various cyanobacterial strains without DNA contamination, and the extracted RNA samples have a relatively high purity, concentration, and yield. Furthermore, the BPC method is more rapid, simple, and economical when compared with previously reported methods.     

Biotin biochemistry and human requirements

Human biotin turnover and requirements can be estimated on the basis of (1) concentrations of biotin and metabolites in body fluids, (2) activities of biotin-dependent carboxylases, and (3) the urinary excretion of organic acids that are formed at increased rates if carboxylase activities are reduced. Recent studies suggest that the urinary excretions of biotin and its metabolite bisnorbiotin, activities of propionyl-CoA carboxylase and beta-methylcrotonyl-CoA carboxylase in lymphocytes, and urinary excretion of 3-hydroxyisovaleric acid are good indicators of marginal biotin deficiency. On the basis of studies using these indicators of biotin deficiency, an adequate intake of 30 microg (123 nmoles) of biotin per day is currently recommended for adults. The dietary biotin intake in Western populations has been estimated to be 35 to 70 microg/d (143-287 nmol/d). Recent studies suggest that humans absorb biotin nearly completely. Conditions that may increase biotin requirements in humans include pregnancy, lactation, and therapy with anticonvulsants or lipoic acid.     

Growth at elevated CO2 concentrations leads to modified profiles of secondary metabolites in tobacco cv. SamsunNN and to increased resistance against infection with potato virus Y

The effect of elevated CO2 concentrations on the levels of secondary metabolites was investigated in tobacco plants grown under two nitrogen supply (5 and 8 mM NH4NO3) and CO2 conditions (350 and 1000 p.p.m.) each. High CO2 resulted in a dramatic increase of phenylpropanoids in the leaves, including the major carbon-rich compound chlorogenic acid (CGA) and the coumarins scopolin and scopoletin at both nitrogen fertilizations. This was accompanied by increased PAL activity in leaves and roots, which was even higher at the lower nitrogen supply. Hardly any change was observed for the structural phenolic polymer lignin and the sesquiterpenoid capsidiol. In contrast, elevated CO2 led to clearly decreased levels of the main nitrogen-rich constituent nicotine at the lower N-supply (5 mM NH4NO3) but not when plants were grown at the higher N-supply (8 mM NH4NO3). Inoculation experiments with potato virus Y (PVY) were used to evaluate possible ecological consequences of elevated CO2. The titre of viral coat-protein was markedly reduced in leaves under these conditions at both nitrogen levels. Since PR-gene expression and free salicylic acid (SA) levels remained unchanged at elevated CO2, we suggest that the accumulation of phenylpropanoids, for example, the major compound CGA and the coumarins scopolin and scopoletin may result in an earlier confinement of the virus at high CO2. Based on our results two final conclusions emerge. First, elevated CO2 leads to a shift in secondary metabolite composition that is dependent on the availability of nitrogen. Second, changes in the pool of secondary metabolites have important consequences for plant-pathogen interactions as shown for PVY as a test organism.     

Cytochrome P-450cam and putidaredoxin interaction during electron transfer.

Cytochrome P-450cam, the bacterial hemeprotein which catalyzes the 5-exo-hydroxylation of d-camphor, requires two electrons to activate molecular oxygen for this monooxygenase reaction. These two electrons are transferred to cytochrome P-450cam in two one-electron steps by the physiological reductant, putidaredoxin. The present study of the kinetics of reduction of cytochrome P-450cam by reduced putidaredoxin has shown that the reaction obeys first order kinetics with a rate constant of 33 s-1 at 25 degrees C with respect to: 1) the appearance of the carbon monoxide complex of Fe(II) cytochrome P-450cam; 2) the disappearance of the 645 nm absorbance band of high-spin Fe(III) cytochrome P-450cam; and 3) the disappearance of the g = 1.94 EPR signal of reduced putidaredoxin. This data was interpreted as indicative of the rapid formation of a bimolecular complex between reduced putidaredoxin Fe(III) cytochrome P-450cam. The existence of the complex was first shown indirectly by kinetic analysis and secondly directly by electron paramagnetic resonance spectroscopic analysis of samples which were freeze-quenched approximately 16 ms after mixing. The direct evidence for complex formation was the loss of the EPR signal of Fe(III) cytochrome P-450cam upon formation of the complex while the EPR signal of reduced putidaredoxin decays with the same kinetics as the appearance of Fe(II) cytochrome P-450. The mechanism of the loss of the EPR signal of cytochrome P-450 upon formation of the complex is not apparent at this time but may involve a conformational change of cytochrome P-450cam following complex formation.     

A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

Background

Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.

Methodology/Principal Findings

The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO₂ fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a β-1,3-glucan) outside of the plastids. We identified various β-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes.

Conclusions/Significance

Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.     

Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis

Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here, we propose and evaluate a statistical approach for distinguishing low‐level ploidy variants (e.g. diploids, triploids and tetraploids) based on genotyping‐by‐sequencing (GBS) data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands of heterozygous SNPs (i.e. allelic ratios). Whereas the method does not require prior information on ploidy, a reference set of samples with known ploidy can be included in the analysis if it is available. We explore the power and limitations of this method using simulated data sets and GBS data from natural populations of aspen (Populus tremuloides) known to include both diploid and triploid individuals. The proposed method was able to reliably discriminate among diploids, triploids and tetraploids in simulated data sets, and this was true for different levels of genetic diversity, inbreeding and population structure. Power and accuracy were minimally affected by low coverage (i.e. 2×), but did sometimes suffer when simulated mixtures of diploids, autotetraploids and allotetraploids were analysed. Cytotype assignments based on the proposed method closely matched those from previous microsatellite and flow cytometry data when applied to GBS data from aspen. An R package (gbs2ploidy) implementing the proposed method is available from CRAN.