Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2

Cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium (CbiA) is the first glutamine amidotransferase in the anaerobic biosynthetic pathway of vitamin B(12) and catalyzes the ATP-dependent synthesis of cobyrinic acid a,c-diamide from cobyrinic acid using either glutamine or ammonia as the nitrogen source. The cbiA gene was cloned, the overexpressed protein was purified to homogeneity, and the kinetic parameters were determined. CbiA is a monomer with K(m) values of 0.74, 2.7, 53, and 26 200 microM for cobyrinic acid, ATP, glutamine, and ammonia, respectively. Analysis of the glutaminase partial reaction demonstrated that the hydrolysis of glutamine and the synthesis of the cobyrinic acid a,c-diamide product are uncoupled. The time course for the synthesis of the diamide product and positional isotope exchange experiments demonstrate that CbiA catalyzes the sequential amidation of the c- and a-carboxylate groups of cobyrinic acid via the formation of a phosphorylated intermediate. These results support a model for the catalytic mechanism in which CbiA catalyzes the amidation of the c-carboxylate, and then the intermediate is released into solution and binds to the same catalytic site for the amidation of the a-carboxylate. Several conserved residues in the synthetase active site were mutated to address the molecular basis of the amidation order; however, no changes in the order of amidation were obtained. The mutants D45N, D48N, and E90Q have a dramatic effect on the catalytic activity, whereas no effect was found for the mutant D97N. The substitutions by alanine of L47 and Y46 residues specifically decrease the affinity of the enzyme for the c-monoamide intermediate.     

Synthesis and surface-active properties of a new class of surfactants derived from D-gluconic acid

Novel sugar-based surfactants were synthesized starting from D-gluconolactone. Three different functional groups were used to link the sugar moiety and the hydrophobic part. The physico-chemical properties for the use as adjuvant for pesticidal formulations of one of these compounds were evaluated and compared.     

Comparison of the N-Linked Oligosaccharide Structures of the Two Major Human Myelin Glycoproteins MAG and P0: Assessment and Relative Occurrence of Oligosaccharide Structures by Serial Lectin Affinity Chromatography of 14C-Glycopeptides

The N-linked oligosaccharide structures of human myelin-associated glycoprotein (MAG) and P0 have been characterized by serial lectin affinity chromatography (SLAC) of 14C-glycopeptides. 14C-Glycopeptides were prepared from purified MAG derivative and P0 by extensive proteolytic digestion and N-14C-acetylation. Assuming that all the 14C-glycopeptides were radiolabelled to the same specific radioactivity, the relative occurrence of the oligosaccharide structures was correlated to the amount of incorporated radioactivity. Sixteen and 15 fractions were generated by SLAC of MAG and P0 14C-glycopeptides, respectively. Despite this tremendous structural heterogeneity, the oligosaccharide "fingerprints" of MAG and P0 obtained by SLAC displayed similarities: (a) of the three types of N-linked oligosaccharides, the complex type accounted for 80.4% and 94.9% of MAG and P0 radioactivity, respectively; (b) biantennary complex oligosaccharides were the major structures present on MAG and P0; (c) approximately 60% of MAG and P0 oligosaccharides possessed a bisecting N-acetylglucosamine residue; and (d) large amounts of oligosaccharides with an alpha(1-6)fucose residue were found in both MAG and P0 and, noticeably, approximately 25% of the tri- and/or tetraantennary and approximately 90% of the bisected biantennary oligosaccharides of both glycoproteins contained alpha(1-6)fucose residues in the core. This study demonstrates that MAG and P0, both belonging to the immunoglobulin superfamily, display structural similarities in their N-linked oligosaccharide contents.     

Secondary response on in vitro primed human lymphocytes to allogeneic cells

In vitro primed human cells have been shown to proliferate and to generate cytotoxic effector cells only when triggered by MLR-S determinants; they do not respond to HL-A antigens alone (i.e., they behave in this respect as unprimed cells). In contrast, in vivo-primed mouse spleen cells acquire the ability to proliferate and to generate cytotoxic effector cells even when triggered by cells artifically depleted by physical means of MLR-S activity or by cells, such as fibroblasts, normally devoid of MLR-S activity. For this reason, peripheral blood lymphocytes (PBL) from immunized volunteers were studied and the immunogenetic requirements of such in vivo-primed cells were compared to those of the in vitro-primed cells.Both in vivo- and in vitro-primed PBL were found to obey the same Laws: (a) proliferation is induced only by MLR-S disparities and is not induced by HL-A disparities alone; (b) proliferation appears to be specific for a given MLR-S; (c) specific cytotoxic effectors are generated by either a specific MLR-S stimulus or a third party-cell stimulus; (d) nonspecific mitogens can also, generate memory cytotoxic effector cells from a preimmunized cell population. However, the expression of such an immune status by PBL is short-lived, suggesting homing in privileged sites of the immune memory cells.     

Evaluating methods to quantify spatial variation in the velocity of biological invasions

Invading species rarely spread homogeneously through a landscape and invasion patterns typically display irregular frontal boundaries as the invasion progresses through space. Those irregular patterns are generally produced by local environmental factors that may slow or accelerate movement of the frontal boundary. While there is an abundant literature on species distribution modelling methods that quantify local suitability for species establishment, comparatively few studies have examined methods for measuring the local velocity of invasions that can then be statistically analysed in relation to spatially variable environmental factors. Previous studies have used simulations to compare different methods for estimating the overall rate of spread of an invasion. We adopted a similar approach of simulating invasions that resemble two real case‐studies, both in terms of their spatial resolution (i.e. considering the size of one cell as one km) and their spatial extent (> 600 000 km²). Simulations were sampled to compare how different methods used to measure local spread rate, namely the neighbouring, nearest distance and Delaunay methods, perform for spatio‐temporal comparisons. We varied the assessment using three levels of complexity of the spatio‐temporal pattern of invasion, three sample sizes (500, 1000 and 2000 points), three different spatial sampling patterns (stratified, random, aggregated), three interpolation methods (generalized linear model, kriging, thin plate spline regression) and two spatio‐temporal modelling structures (trend surface analysis and boundary displacement), resulting in a total of 486 different scenarios. The thin plate spline regression interpolation method, in combination with trend surface analysis, was found to provide the most robust local spread rate quantification as it was able to reliably accommodate different sampling conditions and invasion patterns. This best approach was successfully applied to two case‐studies, the invasion of France by the horse‐chestnut leafminer Cameraria ohridella and by the bluetongue virus, generally in agreement with previously published values of spread rates. Potential avenues for further research are discussed.     

Photoaffinity labeling with the activator IMP and site-directed mutagenesis of histidine 995 of carbamoyl phosphate synthetase from Escherichia coli demonstrate that the binding site for IMP overlaps with that for the inhibitor UMP

Photoaffinity labeling with IMP was used to attach covalently this activator to its binding site of Escherichia coli carbamoyl phosphate synthetase. We now identify histidine 995 of the large enzyme subunit as the amino acid that is cross-linked with IMP. The identification was carried out by comparative peptide mapping in two chromatographic systems of peptides differentially labeled with [3H]IMP and with the labeled inhibitor [14C]UMP, followed by automated Edman degradation and radiosequence analysis. Site-directed substitution of His995 by alanine confirmed His995 to be the only amino acid in the protein forming a covalent adduct with IMP. The His995Ala mutant protein was soluble and active and exhibited normal kinetics for the activator ornithine and for the substrates in the presence of ornithine. However, the mutation selectively induced changes in the activation by IMP and the inhibition by UMP, and it abolished the photolabeling of the enzyme by IMP without affecting the photolabeling by the inhibitor UMP. Since UMP is cross-linked to Lys993 [Cervera, J., et al. (1996) Biochemistry 35, 7247-7255] only two residues upstream of the site of IMP labeling, the results provide structural evidence for earlier proposals which suggested that UMP and IMP bind in a single or overlapping site. The two residues are within the region previously proposed as the binding fold for the nucleotide effectors. In the crystal structure of the enzyme, Lys993 and His995 are exposed and line a crevice where a Pi molecule was found [Thoden, J. B., et al. (1997) Biochemistry 36, 6305-6316]. UMP and IMP appear to bind in this crevice, possibly toward the C-side of the beta-sheet in a Rossman fold. Their binding in this site is consistent with the selectivity of adduct formation of UMP with Lys993 and of IMP with His995. It is also consistent with the nonessentiality of His995 for the binding, since the interactions with other residues that line the crevice must contribute a large part of the binding energy. The lack of an effect of the mutation on the activation by ornithine is consistent with the binding of this activator in a separate site in the protein.     

Molecular characterization and evolution of arthropod-pathogenic Rickettsiella bacteria

We determined the 16S rRNA gene sequences of three crustacean "Rickettsiella armadillidii" strains. Rickettsiella bacteria overall appear to form a monophyletic group that diverged from Coxiella bacteria approximately 350 million years ago. Therefore, the genus Rickettsiella as a whole (not just Rickettsiella grylli) should be classified among the Gammaproteobacteria instead of the Alphaproteobacteria.     

Partial randomization of the four sequential amidation reactions catalyzed by cobyric acid synthetase with a single point mutation

Cobyric acid synthetase (CbiP) from Salmonella typhimurium catalyzes the glutamine and ATP-dependent amidation of carboxylates b, d, e, and g within adenosyl cobyrinic acid a,c-diamide. After each round of catalysis the partially amidated intermediates are released into solution and the four carboxylates are amidated in the sequential order of e, d, b, and g for the wild type enzyme. In the presence of [gamma-18O4]-ATP and adenosyl cobyrinic a,c-diamide the enzyme will catalyze the positional isotope exchange of the betagamma-bridge oxygen with the two beta-nonbridge oxygens. These results support the proposal that ATP is used to activate the carboxylate groups via the formation of a phosphorylated intermediate. CbiP catalyzes the hydrolysis of glutamine in the absence of ATP or adenosyl cobyrinic acid a,c-diamide, but the rate of glutamine hydrolysis is enhanced by a factor of 60 in the presence of these two substrates together. This result suggests that the formation of the phosphorylated intermediate is coupled to the activation of the site utilized for the hydrolysis of glutamine. However, the rate of glutamine hydrolysis is approximately 2.5 times the rate of ADP formation, indicating that the two active sites are partially uncoupled from one another and that some of the ammonia from glutamine hydrolysis leaks into the bulk solution. The mutation of D146 to either alanine or asparagine results in a protein that is able to catalyze the formation of cobyric acid. However, the strict amidation order observed with the wild type CbiP is partially randomized with carboxylate b being amidated last. With the D146N mutant, the predominant pathway occurs in the sequence d, e, g, and b. It is proposed that this residue enforces the amidation order in the wild type enzyme via charge-charge repulsion between the side chain carboxylate and the carboxylates of the substrate.