Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase is a zinc-metalloenzyme

3-Deoxy-D-manno-2-octulosonate-8-phosphate (KDO-8-P) synthase catalyzes the aldol-type condensation of phosphoenolpyruvate and D-arabinose-5-phosphate (A-5-P) to produce KDO-8-P and inorganic phosphate. All KDO-8-P synthases, as exemplified by the enzyme from Escherichia coli, were believed not to require a metal cofactor for catalytic activity. However, recent studies have demonstrated that the KDO-8-P synthase from Aquifex aeolicus is a metalloenzyme. Moreover, sequence alignments and phylogenetic analysis of KDO-8-P synthase protein sequences strongly suggested that there is a whole subfamily of KDO-8-P synthases that are also metalloenzymes. One of these putative metalloenzymes is the ortholog from the human pathogen Helicobacter pylori. In order to test this model, we have cloned the kdsa gene encoding H. pylori KDO-8-P synthase, and overexpressed and purified the protein. This enzyme was found to bind one mol Zn/mol monomer, and the removal of this metal by treatment with 2,6-pyridine dicarboxylic acid abolished enzymatic activity. The Zn(2+) in the enzyme could be quantitatively replaced by Cd(2+), which increased the observed k(cat) by approximately 2-fold, and decreased the apparent K(m)(A-5-P) by approximately 6.5-fold. Furthermore, removal of the Zn(2+) from the enzyme did not greatly perturb its circular dichroism spectra. Thus, the divalent metal most likely serves as cofactor directly involved in catalysis.     

Subnetwork hierarchies of biochemical pathways

MOTIVATION: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied. RESULTS: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks. AVAILABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/     

Validation of a method for quantification of ketobemidone in human plasma with liquid chromatography-tandem mass spectrometry

A liquid chromatography tandem mass spectrometry (LC-MS-MS) method for determination of the analgesic aminophenol ketobemidone in human plasma is presented. Two preparation methods for plasma samples containing ketobemidone were compared, liquid-liquid extraction (LLE) and solid-phase extraction (SPE). Both methods showed good precision (n=10), 1.7% and 2.9%, respectively (0.04 micro M) and 1.1% and 2.5%, respectively (0.14 micro M). The accuracy was 98% and 103%, respectively (0.04 micro M) and 105% and 99%, respectively (0.14 micro M). Ketobemidone could be quantified at 0.43 nM, with a relative standard deviation of 17.5% (n=19) using LLE and 18.6% (n=10) using SPE. This level was an order of magnitude lower than earlier reported quantification limits. Quantitative data from plasma samples analyzed with LC-MS-MS were in good agreement with those obtained by gas chromatography with chemical ionization mass spectrometry (GC-CI/MS). This indicates that LC-MS-MS is a good alternative method to GC-MS as it is more sensitive and time-consuming derivatization can be avoided.     

Fragmentation of dihydroxyacetone kinase 1 from Saccharomyces cerevisiae indicates a two-domain structure

Global protein expression in Saccharomyces cerevisiae strains either deleted for both yeast dihydroxyacetone kinases (DAK1 and DAK2) or overexpressing DAK1, was characterized by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). We found protein expression in the double deletion strain to be highly similar to wild-type. In the strain overexpressing Dak1p, nine spots representing fragments of the Dak1p protein in the size range 40-20 kDa and amounting to approximately 30% of total Dak1p, were discovered (native size Dak1p migrates at roughly 60 kDa). Fragments were characterized by matrix-assisted laser desorption/ionization mass spectrometry and electrospray mass spectrometry analyses to represent either the N- or the C-terminal part of the DAK1 protein. Cleavage points, predicted from mass spectrometry and 2-D PAGE data, mapped almost exclusively in the middle region showing low sequence conservation between Dak1p and its closest homologues. We hypothesize that observed Dak1p fragments represent stable structural domains shielded from access by native endoproteases. Furthermore, overexpressing Dak1p with the non-native N-terminus (M)A-, resulted in native size Dak1p and N-terminal Dak1p fragments appearing in two major 2-D PAGE forms of approximately equal size and abundance, but with slightly different isoelectric points. However, when overexpressing Dak1p with the native N-terminus (M)S-, only the more acidic 2-D PAGE form appeared. In the N-terminal acetyltransferase mutant nat1delta, (M)A-Dak1p species were converted into the basic form, arguing twin spots to represent forms with acetylated and deacetylated N-termini. Data thus indicated that (M)A-N-termini, in the Dak1p context, were NatA substrates recognized with 50% lower efficiency than (M)S-N-termini.     

Condition and coalition formation by brood-rearing common eider females

Partner choice is important in nature, and partnerships or coalitionswithin which reproduction is shared are the subject of growinginterest. However, little attention has been given to questionsof which individuals are suitable partners and why. Common eider(Somateria mollissima) females sometimes pool their broods andshare brood-rearing duties, and body condition affects caredecisions. We constructed a model in which females, based ontheir body condition and the structure of the joint brood, assessthe fitness consequences of joining a coalition versus tendingfor young alone. We tested the model's predictions by comparingdata on the condition of females in enduring and transient coalitions.Our model showed that the range of acceptable brood arrays ina female coalition decreases with increasing condition of thefemale, so females tending alone should be in better conditionthan multifemale tenders. This prediction is in agreement withprevious data. The model also predicts that females in goodcondition should join coalitions with females in poor conditionand not with other females in good condition. This predictionwas also supported by data: in enduring two-female coalitions,the positive correlation between the better female's conditionand the difference in condition between the two females wasstronger than would be expected by random grouping of females.In contrast, in transient coalitions of females, this correlationdid not differ from the correlation expected under random grouping.Model assumptions seem to fit with eider natural history, andthe model may prove to be a useful way to study brood amalgamationbehavior of waterfowl in general.     

Expression of recombinant Pseudomonas stutzeri di-heme cytochrome c4 by high-cell-density fed-batch cultivation of Pseudomonas putida

The gene of the di-heme protein cytochrome c(4) from Pseudomonas stutzeri was expressed in Pseudomonas putida. High-yield expression of the protein was achieved by high-cell-density fed-batch cultivation using an exponential glucose feeding strategy. The recombinant cytochrome c(4) protein was purified to apparent homogeneity and analyzed by electronic absorption spectroscopy, nanoflow electrospray ionization time-of-flight mass spectrometry, and electrochemistry. Cyclic voltammograms and UV-vis electronic absorption spectra were indistinguishable from the equivalent data of native P. stutzeri cytochrome c(4). Furthermore, the calculated and experimentally determined molecular masses of recombinant cytochrome c(4) were identical. Biochemical characterization of both wild-type and mutant derivatives of the protein will be greatly enhanced and facilitated by the described high-yield fermentation and rapid isolation procedure.     

Glibenclamide inhibits islet carnitine palmitoyltransferase 1 activity,leading to PKC-dependent insulin exocytosis

Hypoglycemic sulfonylureas such as glibenclamide have been widely used to treat type 2 diabetic patients for 40 yr, but controversy remains about their mode of action. The widely held view is that they promote rapid insulin exocytosis by binding to and blocking pancreatic beta-cell ATP-dependent K+ (KATP) channels in the plasma membrane. This event stimulates Ca2+ influx and sets in motion the exocytotic release of insulin. However, recent reports show that >90% of glibenclamide-binding sites are localized intracellularly and that the drug can stimulate insulin release independently of changes in KATP channels and cytoplasmic free Ca2+. Also, glibenclamide specifically and progressively accumulates in islets in association with secretory granules and mitochondria and causes long-lasting insulin secretion. It has been proposed that nutrient insulin secretagogues stimulate insulin release by increasing formation of malonyl-CoA, which, by blocking carnitine palmitoyltransferase 1 (CPT-1), switches fatty acid (FA) catabolism to synthesis of PKC-activating lipids. We show that glibenclamide dose-dependently inhibits beta-cell CPT-1 activity, consequently suppressing FA oxidation to the same extent as glucose in cultured fetal rat islets. This is associated with enhanced diacylglycerol (DAG) formation, PKC activation, and KATP-independent glibenclamide-stimulated insulin exocytosis. The fat oxidation inhibitor etomoxir stimulated KATP-independent insulin secretion to the same extent as glibenclamide, and the action of both drugs was not additive. We propose a mechanism in which inhibition of CPT-1 activity by glibenclamide switches beta-cell FA metabolism to DAG synthesis and subsequent PKC-dependent and KATP-independent insulin exocytosis. We suggest that chronic CPT inhibition, through the progressive islet accumulation of glibenclamide, may explain the prolonged stimulation of insulin secretion in some diabetic patients even after drug removal that contributes to the sustained hypoglycemia of the sulfonylurea.     

RimM and RbfA Are Essential for Efficient Processing of 16S rRNA in Escherichia coli

The trmD operon is located at 56.7 min on the genetic map of the Escherichia coli chromosome and contains the genes for ribosomal protein (r-protein) S16, a 21-kDa protein (RimM, formerly called 21K), the tRNA (m¹G37)methyltransferase (TrmD), and r-protein L19, in that order. Previously, we have shown that strains from which the rimM gene has been deleted have a sevenfold-reduced growth rate and a reduced translational efficiency. The slow growth and translational deficiency were found to be partly suppressed by mutations in rpsM, which encodes r-protein S13. Further, the RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. Here we have isolated several new suppressor mutations, most of which seem to be located close to or within the nusA operon at 68.9 min on the chromosome. For at least one of these mutations, increased expression of the ribosome binding factor RbfA is responsible for the suppression of the slow growth and translational deficiency of a ΔrimM mutant. Further, the RimM and RbfA proteins were found to be essential for efficient processing of 16S rRNA.     

Allozyme differentiation between lowland and alpine populations of Pseudorchis albida s.lat. (Orchidaceae) in Sweden

Two taxa are usually recognized in Scandinavian Pseudorchis albida s.1. (Orchidaceae), the lowland to subalpine P. albida s.s., and the alpine P. straminea . We used allozymes to study the genetical differentiation within and among populations and taxa. Four populations of P. albida s.s. and two populations of P. straminea , all from Sweden, were included in the study. Eighteen loci of thirteen different enzyme systems were analyzed. Five loci were variable within, or between, the taxa. The taxa had different alleles at one of the five variable loci, whereas there was overlap at four loci. In all, 22 different alleles were found. Two of these alleles were confined to P. albida s.s., while four alleles were confined to P. straminea . In P. albida s.s., one locus out of 15 (6.7 %) was polymorphic. In P. straminea , three loci out of 18 (16.7 %) were polymorphic. In both taxa, the average number of alleles per polymorphic locus was 2.0 (each polymorphic locus had two alleles). Nei's genetic identity was 0.81 between taxa, and about 1 among populations of P. albida s.s., while the identity between the two populations of P. straminea was 0.98. Although the differentiation is small, present-day distributions of taxa suggest that the divergence probably started before the Weichselian glaciation. The low within-taxon and within-population variation in Scandinavia may be due to ancient founder events. The association of P. albida s.s. with anthropogenic hay-meadows and open woodland and the association of P. straminea with open mountain habitats suggest that taxa may have immigrated into Scandinavia at different times.