Thermodynamics of a protein acylation: activation of Escherichia coli hemolysin toxin

HlyC, hemolysin-activating lysine-acyltransferase, catalyses the acylation (from acyl-acyl carrier protein [ACP]) of Escherichia coli prohemolysin (proHlyA) on the epsilon-amino groups of specific lysine residues, 564 and 690 of the 1024 amino acid primary structure, to form hemolysin (HlyA). Isothermal titration calorimetry was used to measure the thermodynamic properties of the protein acylation of proHlyA-derived structures, altered by substantial deletions and separation of the acylation sites into two different peptides and site directed mutation analyses of acylation sites. Acylation of proHlyA-derived proteins catalyzed by HlyC was overall an exothermic reaction driven by a negative enthalpy. The reaction, whose kinetics are compatible to a ping-pong mechanism, is composed of two partial reactions. The first, the formation of an acyl-HlyC intermediate, was entropically driven, most likely by noncovalent complex formation between acyl-ACP and HlyC; enthalpy-driven acyl transfer followed, resulting in acyl-HlyC and ACPSH product formation. The second partial reaction was an energetically unfavorable acyl transfer from acyl-enzyme intermediate to the final acyl acceptor, a proHlyA derivative. Overall the acylation of proHlyA-derived proteins catalyzed by HlyC was driven by the energetics of the acyl enzyme intermediate reaction. Of the two acylation sites, intactness of the site equivalent to proHlyA K564 was more important for acylation reaction thermodynamic stability.     

2-Deoxyglucose Enhances 1-Methyl-4-Phenyl-1, 2, 3, 6-Tetrahydropyridine-Induced ATP Loss in the Mouse Brain

Abstract: The effects of 2-deoxyglucose (2-DG), an inhibitor of the uptake and use of glucose, on ATP loss caused by the neurotoxicant 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP) were determined in the mouse brain. 2-DG alone had no effect on brain ATP levels, but when administered 30 min before MPTP exposure, 2-DG significantly enhanced MPTP-induced ATP reduction. This was reflected as an increase in ATP loss in the striatum (from 15 to 27%) as well as a significant decrease in ATP in the cerebellar cortex, an area of the brain that was not affected after exposure to MPTP alone. In mice pretreated with 2-DG, striatal ATP levels remained significantly decreased for >8 h after MPTP administration. In contrast, ATP levels in the cerebellar cortex returned to normal values within 4 h from MPTP exposure. Mazindol, a catecholamine uptake blocker, completely protected against MPTP-induced loss of striatal ATP in the absence of 2-DG, but it only partially prevented striatal ATP decrease after administration of both 2-DG and MPTP; mazindol was also ineffective in protecting against ATP loss caused by 2-DG and MPTP in the cerebellar cortex. 2-DG/MPTP-induced ATP loss appeared to be associated with the presence of the 1 -methyl-4-phenylpyridinium (MPP⁺) metabolite because (1) the pattern of ATP recovery in the striatum and cerebellar cortex appeared to reflect the pattern of MPP⁺clearance from these areas of the brain (i.e., significant MPP⁺ levels persisted longer in the striatum than in the cerebellar cortex), and (2) ATP decrease was completely prevented by blocking the conversion of MPTP to MPP⁺with the monoamine oxidase B inhibitor deprenyl. Data indicate that impairment of glucose metabolism dramatically enhances the effects of MPTP/MPP⁺ on cerebral energy supplies, making these effects relatively nonselective for dopaminergic neurons of the nigrostriatal pathway.     

The breeding status of the Ring Ouzel Turdus torquatus in the UK in 1999

Capsule The first co-ordinated census of breeding Ring Ouzels across the UK reports a minimum of 6157 (95% CI, 3586–9372) and a maximum of 7549 (95% CI, 4459–11197) territories.

Aims To set a baseline for the future monitoring of breeding Ring Ouzels and to provide a systematically based estimate of the population size.

Methods A random sample of tetrads (2 × 2 km squares) was surveyed from the known breeding range (as defined from the two national breeding bird atlases of 1968–72 and 1988–91). The survey method used tape playback and observation and involved walking four parallel transects in each tetrad.

Results Tape playback accounted for one-third of the territories located. Of the tetrads surveyed that were known to be occupied during the 1988–91 breeding bird atlas, 39–43% were unoccupied in 1999.

Conclusion The survey highlights a continuing contraction in range.     

Beneficial effect of fluorocarbon emulsion media on the function of neuromuscular preparations in vitro

The effects of liquid fluorocarbons as bathing media were determined by use of in vitro neuromuscular preparations. Rat hemidiaphragms were bathed in either oxygenated fluorocarbon (FC) emulsion or standard oxygenated Krebs solution. Contractile force in response to simple supramaximal nerve stimuli as well as to high frequency stimulation was greater, while twitch:tetanus ratio was smaller in FC emulsion. With such medium, post-tetanic potentiation of contraction was also more consistently observed. Indirectly stimulated diaphragms survived longer in FC emulsion. After cessation of oxygenation, oxygen tension (ρO(2)) of the medium declined more rapidly with Krebs than with FC emulsion; ρO(2) directly correlated with force of contraction. Similarly, in the chick biventer cervicis preparation, FC emulsion enhanced nerve-stimulated force of contraction; returning the preparation to standard Krebs solution reversed this phenomenon. Dose-resonse curves of muscle contraction in response to acetycholine and KCl administration were shifted upward during FC emulsion superfusion. Frequency of miniature endplate potentials was lower in FC emulsion than that observed in Krebs solution, measured from the same cell of the rat diaphragm. Resting membrane potentials were also greater in muscle cells sampled from FC emulsion-bathed preparations. These data suggest that FC emulsion is superior to standard Krebs solution as a bathing medium for in vitro neuromuscular preparations by virtue of the high solubility of oxygen in it.     

Efficient prediction of human protein-protein interactions at a global scale

Background

Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

Results

On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments.

Conclusions

The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0383-1) contains supplementary material, which is available to authorized users.     

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.     

A Linkage Map of the Canine Genome

A genetic linkage map of the canine genome has been developed by typing 150 microsatellite markers using 17 three-generation pedigrees, composed of 163 F₂individuals. One hundred and thirty-nine markers were linked to at least one other marker with a lod score ≥ 3.0, identifying 30 linkage groups. The largest chromosome had 9 markers spanning 106.1 cM. The average distance between markers was 14.03 cM, and the map covers an estimated 2073 cM. Eleven markers were informative on the mapping panel, but were unlinked to any other marker. These likely represent single markers located on small, distinct canine chromosomes. This map will be the initial resource for mapping canine traits of interest and serve as a foundation for development of a comprehensive canine genetic map.