Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function

Structural genomics is a new approach in functional assignment of proteins identified via whole-genome sequencing programs. Its rationale is that nonhomologous proteins performing similar or related biological functions might have similar tertiary structure. We used dye pseudoaffinity chromatography, two-dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide-binding proteins, YnaF and YajQ. YnaF exhibited significant sequence identity with MJ0577, an ATP-binding protein from a hyperthermophile (Methanococcus jannaschii), and with UspA, a protein from Haemophilus influenzae that belongs to the Universal Stress Protein family. YnaF conserves the ATP-binding site and the dimeric structure observed in the crystal of MJ0577. The protein YajQ, present in many bacterial genomes, is missing in eukaryotes. In the absence of significant similarities of YajQ to any solved structure, we determined its structural and ligand-binding properties by NMR and isothermal titration calorimetry. We demonstrate that YajQ is composed of two domains, each centered on a beta-sheet, that are connected by two helical segments. NMR studies, corroborated with local sequence conservation among YajQ homologs in various bacteria, indicate that one of the beta-sheets is mostly involved in biological activity.

Feedback inhibition and product complexes of recombinant mouse muscle adenylosuccinate synthetase

Adenylosuccinate synthetase governs the committed step of AMP biosynthesis, the generation of 6-phosphoryl-IMP from GTP and IMP followed by the formation of adenylosuccinate from 6-phosphoryl-IMP and l-aspartate. The enzyme is subject to feedback inhibition by AMP and adenylosuccinate, but crystallographic complexes of the mouse muscle synthetase presented here infer mechanisms of inhibition that involve potentially synergistic ligand combinations. AMP alone adopts the productive binding mode of IMP and yet stabilizes the active site in a conformation that favors the binding of Mg(2+)-IMP to the GTP pocket. On the other hand, AMP, in the presence of GDP, orthophosphate, and Mg(2+), adopts the binding mode of adenylosuccinate. Depending on circumstances then, AMP behaves as an analogue of IMP or as an analogue of adenylosuccinate. The complex of adenylosuccinate.GDP.Mg(2+).sulfate, the first structure of an adenylosuccinate-bound synthetase, reveals significant geometric distortions and tight nonbonded contacts relevant to the proposed catalytic mechanism. Adenylosuccinate forms from 6-phosphoryl-IMP and l-aspartate by the movement of the purine ring into the alpha-amino group of l-aspartate.

IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase

Prokaryotes have a single form of adenylosuccinate synthetase that controls the committed step of AMP biosynthesis, but vertebrates have two isozymes of the synthetase. The basic isozyme, which predominates in muscle, participates in the purine nucleotide cycle, has an active site conformation different from that of the Escherichia coli enzyme, and exhibits significant differences in ligand recognition. Crystalline complexes presented here of the recombinant basic isozyme from mouse show the following. GTP alone binds to the active site without inducing a conformational change. IMP in combination with an acetate anion induces major conformational changes and organizes the active site for catalysis. IMP, in the absence of GTP, binds to the GTP pocket of the synthetase. The combination of GTP and IMP results in the formation of a stable complex of 6-phosphoryl-IMP and GDP in the presence or absence of hadacidin. The response of the basic isozyme to GTP alone differs from that of synthetases from plants, and yet the conformation of the mouse basic and E. coli synthetases in their complexes with GDP, 6-phosphoryl-IMP, and hadacidin are nearly identical. Hence, reported differences in ligand recognition among synthetases probably arise from conformational variations observed in partially ligated enzymes.

[Spanish flu in Norway 1918-19]

The Spanish flu pandemic killed between 50-100 million people worldwide in 1918-19. This article discusses Spanish flu in Norway between 1918-19 from three different approaches. How did Spanish flu affect Norway? Spanish flu was probably imported to Norway across the North Sea from Britain. From the middle of June 1918, Spanish flu swept across the country in three different waves: the summer epidemic of 1918, the autumn epidemic of 1918 and the winter epidemic of 1918-19. In Norway 13,000-15,000 died, most of them during the autumn of 1918 and mostly from pneumonia or pulmonary complications. What were the consequences? Most deaths occurred in young adults; many families experienced tragedies. Spanish flu is considered the worst demographic crisis of the twentieth century. The additional costs to the public purse were huge after the epidemic. Why was it that Spanish flu had such devastating effects? The virus causing the pandemic was very virulent and resulted in a higher mortality rate than that experienced during other pandemics. These characteristics may be explained by genetic features of the 1918 virus. This article points at conditions in Norway at the time of Spanish flu that may have contributed to the severity of the outbreak.

Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure

Vertebrates possess two isozymes of adenylosuccinate synthetase. The acidic isozyme is similar to the synthetase from bacteria and plants, being involved in the de novo biosynthesis of AMP, whereas the basic isozyme participates in the purine nucleotide cycle. Reported here is the first instance of overexpression and crystal structure determination of a basic isozyme of adenylosuccinate synthetase. The recombinant mouse muscle enzyme purified to homogeneity in milligram quantities exhibits a specific activity comparable with that of the rat muscle enzyme isolated from tissue and K(m) parameters for GTP, IMP, and l-aspartate (12, 45, and 140 microm, respectively) similar to those of the enzyme from Escherichia coli. The mouse muscle and E. coli enzymes have similar polypeptide folds, differing primarily in the conformation of loops, involved in substrate recognition and stabilization of the transition state. Residues 65-68 of the muscle isozyme adopt a conformation not observed in any previous synthetase structure. In its new conformation, segment 65-68 forms intramolecular hydrogen bonds with residues essential for the recognition of IMP and, in fact, sterically excludes IMP from the active site. Observed differences in ligand recognition among adenylosuccinate synthetases may be due in part to conformational variations in the IMP pocket of the ligand-free enzymes.

Plasmid profile analysis and antibiotic resistance of Salmonella strains from clinical isolates in Cluj-Napoca

Resistance patterns, plasmid profiles and the genetic resistance determinants were investigated in 38 isolates of Salmonella enterica serotype Typhimurium and 19 isolates of Salmonella enterica serovar Enteritidis derived from children hospitalized in two clinics in Cluj-Napoca, during the period of 1995-1997. Incidence of plasmid and antibiotic resistance was very high in Salmonella typhimurium isolates. All strains were resistant to almost all antibiotics tested but susceptible to the third generation cephalosporines and fluoroquinolones. We identified three resistance patterns and six plasmid profiles. Each plasmid profile was characterized by the presence of two large plasmids of 150-180 Kbp. Approximately 60% of strains harbored three or four small plasmids of 1.3 to 9.5 Kbp. The plasmids of 8.5 Kbp encoded resistance to beta-lactam antibiotics and were non-conjugative. The other small plasmids were cryptic and also non-conjugative. Salmonella enteritidis isolates were susceptible to many antibiotics, except Tetracycline and Trimethoprim-Sulfamethoxazole. We identified three different resistance patterns but nine plasmid profiles. All plasmid profiles were characterized by the presence of a large plasmid (> 100 Kbp). The number and the diversity of small plasmids were higher than in S. typhimurium strains. There was no parallelism between resistance and plasmid profile: for the same resistance pattern a number of two or three plasmid profiles were found. Our conclusions are that Salmonella typhimurium strains were multiresistant to antibiotics and that many genetically different strains of Salmonella typhimurium and Salmonella enteritidis were responsible for gastroenteritis in children from Cluj County. The increasing antibiotic resistance highlights the need for more refined methods in genetic and epidemiological characterization of bacteria involved in gastrointestinal infections.

Plasmid profile analysis and restriction enzyme analysis in characterizing Shigella flexneri isolates from an outbreak

Shigella flexneri strains which are multiply resistant to antimicrobial agents were isolated from 11 children from an orphanage in Cluj-Napoca during an epidemiological investigation initiated by the Department of Epidemiology. Plasmid profile analysis and restriction endonuclease analysis were used in conjunction with biotyping, serotyping and antimicrobial susceptibility testing for identifying epidemiological related isolates. All strains were serotype 2a and with one exception all of them showed the same resistotype. Plasmid profile analysis differentiated S. flexneri isolate into four patterns, with two common plasmids of 3.5 and 1.9 kb. This study indicates that this outbreak was caused by at least two different strains of S. flexneri which were not differentiated by the classical technique-biotyping, serotyping and antimicrobial susceptibility pattern.

Diffusional water permeability of mammalian red blood cells

An extensive programme of comparative nuclear magnetic resonance measurements of the membrane diffusional permeability for water (Pd) and of the activation energy (Ea,d) of this process in red blood cells (RBCs) from 21 mammalian species was carried out. On the basis of Pd, these species could be divided into three groups. First, the RBC's from humans, cow, sheep and "large" kangaroos (Macropus giganteus and Macropus rufus) had Pd values approximately 5 x 10(-3) cm/s at 25 degrees and 7 x 10(-3) cm/s at 37 degrees C. The RBCs from other marsupial species, mouse, rat, guinea pig and rabbit, had Pd values roughly twice higher, whereas echidna RBCs were twice lower than human RBCs. The value of Ea,d was in most cases correlated with the values of Pd. A value of Ea,d approximately 26 kJ/mol was found for the RBCs from humans and the species having similar Pd values. Low values of Ea,d (ranging from 15 to 22 kJ/mol) appeared to be associated with relatively high values of Pd. The highest values of Ea,d (33 kJ/mol) was found in echidna RBCs. This points to specialized channels for water diffusion incorporated in membrane proteins; a relatively high water permeability of the RBC membrane could be due to a greater number of channel proteins. There are, however, situations where a very high water permeability of RBCs is associated with a high value of Ea,d (above 25 kJ/mol) as in the case of RBCs from mouse, rat and tree kangaroo. Moreover, it was found that Pd in different species was positively correlated to the RBC membrane phosphatidylcholine and negatively correlated to the sphingomyelin content. This suggests that in addition to the number of channel proteins, other factors are involved in the water permeability of the RBC membrane.

Comparative nuclear magnetic resonance studies of diffusional water permeability of red blood cells from different species. V--Rabbit (Oryctolagus cuniculus)

1. The diffusional water permeability (Pd) of rabbit red blood cell (RBC) membrane has been monitored by a doping nuclear magnetic resonance (NMR) technique on control cells and following inhibition with p-chloromercuribenzene sulfonate (PCMBS). 2. The values of Pd were around 6.3 x 10(-3) cm/sec at 15 degrees C, 7.0 x 10(-3) cm/sec at 20 degrees C, 8.0 x 10(-3) cm/sec at 25 degrees C, 9.1 x 10(-3) cm/sec at 30 degrees C and 10.7 x 10(-3) cm/sec at 37 degrees C. 3. Systematic studies on the effects of PCMBS on water diffusion indicated that the maximal inhibition was reached in 15 min at 37 degrees C with 0.5 mM PCMBS. 4. The values of maximal inhibition were around 71-74% at all temperatures. 5. The basal permeability to water was estimated as 1.6 x 10(-3) cm/sec at 15 degrees C, 2.0 x 10(-3) cm/sec at 20 degrees C, 2.4 x 10(-3) cm/sec at 25 degrees C, 2.6 x 10(-3) cm/sec at 30 degrees C, and 3.1 x 10(-3) cm/sec at 37 degrees C. 6. The activation energy of water diffusion was around 18 kJ/mol and increased to 27 kcal/mol after incubation with PCMBS in conditions of maximal inhibition of water diffusion. 7. The membrane polypeptide electrophoretic pattern of rabbit RBCs has been compared with its human counterpart. 8. The rabbit membrane contained a higher amount of spectrin (bands 1 and 2), while the band 6 (glyceraldehyde-3-phosphate dehydrogenase) was markedly less intense.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparative nuclear magnetic resonance studies of diffusional water permeability of red blood cells from sheep and cow

1. The diffusional water permeability (p) of sheep and cow red blood cell (RBC) membrane has been monitored by a doping nuclear magnetic resonance (NMR) technique on control cells and following inhibition with p-chloromercuribenzene sulfonate (PCMBS). 2. There were no significant differences in the water permeability of sheep and cow RBCs, the values of p being around 3 x 10(-3) cm/sec at 20 degrees C and 5 x 10(-3) cm/sec at 37 degrees C. 3. Systematic studies of the effects of PCMBS on water diffusion indicated that in both species the maximal inhibition is reached in 60-90 min at 37 degrees C with 1 mM PCMBS. 4. The degree of inhibition increased as the temperature of measurement decreased, regardless of PCMBS concentration and incubation time. 5. The values of maximal inhibition ranged from 60-70% at 20 degrees C to 50-60% at 37 degrees C in the case of sheep RBCs, and from 45-55% at 20 degrees C to 40-50% at 37 degrees C in the case of cow RBCs. 6. The basal permeability to water of sheep RBCs was estimated as 1.0 x 10(-3) cm/sec at 20 degrees C and 2.2 x 10(-3) cm/sec at 37 degrees C, and that of cow RBCs as 1.6 x 10(-3) cm/sec at 20 degrees C and 2.7 x 10(-3) cm/sec at 37 degrees C. 7. In both species the activation energy of water diffusion was around 23 kJ/mol in control cells and reached values of around 30 kJ/mol after incubation with PCMBS in conditions of maximal inhibition of water diffusion.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparative nuclear magnetic resonance studies on water diffusional permeability of red blood cells from mice and rats

1. The diffusional water permeability (P) of mouse and rat red blood cell (RBC) membrane has been monitored by a doping nuclear magnetic resonance (NMR) technique on control cells and following exposure to various concentrations of p-chloromercuribenzene sulfonate (PCMBS). 2. There were no significant differences in the water permeability of mouse and rat RBCs, the values of P being around 6 x 10(-3)/sec at 20 degrees C and 11 x 10(-3) cm/sec at 37 degrees C. 3. Systematic studies of the effects of PCMBS on water diffusion indicated that the maximal inhibition is reached in 60 min at 20 degrees C with 1 mM PCMBS for the mouse RBCs and with 2 mM PCMBS for the rat RBCs. 4. The values of maximal inhibition ranged from 55-57% at 37 degrees C and reached values around 70% at 10 degrees C. 5. The degree of inhibition increased as the temperature of measurement decreased, regardless of PCMBS concentration and incubation time. 6. The basal permeability to water of mouse RBCs was estimated as 1.8 x 10(-3) cm/sec at 20 degrees C and 4.6 x 10(-3) cm/sec at 37 degrees C, and that of rat RBCs as 2.2 x 10(-3) cm/sec at 20 degrees C and 4.2 x 10(-3) cm/sec at 37 degrees C. 7. In both species the activation energy was around 27 kJ/mol and reached values over 40 kJ/mol after incubation with PCMBS in the conditions of maximal inhibition of water diffusion.

Effects on water diffusion of inhibitors affecting various transport processes in human red blood cells

The water permeability of human red blood cells has been monitored by nuclear magnetic resonance (NMR) following exposure to inhibitors of various transport processes across their membranes. No significant inhibition of water diffusion could be detected after the treatment of red blood cells with the anion exchange transport inhibitor dihydro-4,4'-diisothiocyano-stilbene-2,2'-disulfonate (H2DIDS) or the glucose transport inhibitors diallyl-diethyl-stilbestrol (DADES), cytochalasin B, or 30 mM iodoacetamide. It is for the first time that the effects of glucose transport inhibitors has been studied in detail by the NMR approach. A special case proved to be phloretin, an inhibitor of anion, nonelectrolyte and glucose permeability. A small but statistically significant inhibition of water permeability (around 12% at 20 degrees C) was induced by exposure to 2 mM phloretin (for 60 min at 37 degrees C); after a pretreatment of cells with 12 mM N-ethylmaleimide (NEM), for 60 min at 37 degrees C, the degree of inhibition induced by phloretin increased (becoming 17% at 20 degrees C). None of the inhibitors prevented or potentiated the strong inhibitory effect on water diffusion of a mercurial, p-chloromercuribenzene sulfonate (PCMBS). No increase in the activation energy of water diffusion occurred by treatment with the reagents used (exception the effect of PCMBS). The present results clarify some conflicting reports concerning the effects on water permeability of inhibitors of various transport processes in red blood cells and indicate that in addition to the drastic inhibition induced by mercurials other reagents may also have inhibitory effects.