Purification and biochemical characterization of ovine alpha-1-proteinase inhibitor: mechanistic adaptations and role of Phe350 and Met356

The glycoprotein alpha-1-proteinase inhibitor (alpha-1-PI) is a member of the serpin super family that causes rapid and irreversible inhibition of redundant serine protease activity. A homogenous preparation of ovine alpha-1-PI, a 60 kDa protein was obtained by serially subjecting ovine serum to 40-70% (NH(4))(2)SO(4) precipitation, Blue Sepharose, size-exclusion, and concanavalin-A chromatography. Extensive insights into the trypsin, chymotrypsin, and elastase interaction with ovine alpha-1-PI, point towards the involvement of Phe(350) besides the largely conserved Met(356) in serine protease recognition and consequent inhibition. The N-terminal of C-terminal peptides cleaved on interaction with elastase, trypsin, and chymotrypsin prove the presence of diffused sub-sites in the vicinity of Met(356) and the strategically positioned Pro anchored peptide stretch. Further, human alpha-1-PI is more thermolabile compared to ovine alpha-1-PI, higher thermolability is mainly attributed to poorer glycosylation. The enzymatic deglycosylation of human and ovine alpha-1-PI results in diminished thermostability of the inhibitors, with sharp decrease in thermal transition temperatures but retaining their inhibitory potency. Homology modeling of the deduced amino acid sequence of ovine alpha-1-PI using the human alpha-1-PI template has been used to explain the observed inhibitor-protease interactions.     

Protein S3 fragments neighboring mRNA during elongation and termination of translation on the human ribosome

Protein S3 fragments were determined that crosslink to modified mRNA analogues in positions +5 to +12 relative to the first nucleotide in the P-site bound codon in model complexes mimicking states of ribosomes at the elongation and translation termination steps. The mRNA analogues contained a Phe codon UUU/UUC at the 5′-termini that could predetermine the position of the tRNA^Phe on the ribosome by the P-site binding and perfluorophenylazidobenzoyl group at a nucleotide in various positions 3′ of the UUU/UUC codon. The crosslinked S3 protein was isolated from 80S ribosomal complexes irradiated with mild UV light and subjected to cyanogen bromide—induced cleavage at methionine residues with subsequent identification of the crosslinked oligopeptides. An analysis of the positions of modified oligopeptides resulting from the cleavage showed that, in dependence on the positions of modified nucleotides in the mRNA analogue, the crosslinking sites were found in the N-terminal half of the protein (fragment 2–217) and/or in the C-terminal fragment 190–236; the latter reflects a new peculiarity in the structure of the mRNA binding center in the ribosome, unknown to date. The results of crosslinking did not depend on the type of A-site codon or on the presence of translation termination factor eRF1.     

Comparative hydrocarbon utilization by hydrophobic and hydrophilic variants of Pseudomonas aeruginosa

Aims: To investigate hydrocarbon degradation by hydrophobic, hydrophilic and parental strains of Pseudomonas aeruginosa. Methods and Results: Partitioning of hydrocarbon‐degrading P. aeruginosa strain in a solvent/aqueous system yielded hydrophobic and hydrophilic fractions. Exhaustive partitioning of aqueous‐phase cells yielded the hydrophilic variants (L), while sequential fractionation of the hydrophobic phase cells yielded successive fractions exhibiting increasing cell‐surface hydrophobicity (CSH). In hydrocarbon adherence assays (bacterial attachment to hydrocarbon), L had a value of 20%, which increased from 61·7% in first hydrophobic fraction (H₁) to 72·2% in the third (H₃). Crude oil degradation by L was 70%, but increased from 82% in H₁ to 93% in H₃. L variant produced most exopolysaccharides and reduced surface tension from about 73 to 49 mN m^?1. Rhamnolipid production was highest in L, but was not detected in all crude oil cultures. Conclusions: Hydrophobic subpopulations of hydrocarbon‐degrading P. aeruginosa exhibited greater hydrocarbon‐utilizing ability than hydrophilic ones, or the parental strain. Significance and Impact of the Study: Results demonstrate that a population of P. aeruginosa consists of cells with different CSH which affect hydrocarbon utilization. This potentially provides the population with the capacity to utilize different hydrophobic substrates found in petroleum. Judicious selection of such hydrophobic subpopulations can enhance hydrocarbon pollution bioremediation.     

Management of calcareous grasslands for Nickerl’s fritillary (<Emphasis Type="Italic">Melitaea aurelia</Emphasis>) has to consider habitat requirements of the immature stages,isolation, and patch area

We analysed the habitat preferences of adult stages and oviposition electivity of Melitaea aurelia in calcareous grasslands in the Diemel Valley (central Germany) to assess the key factors for successful management. Egg-laying and adult habitats of M. aurelia were more or less congruent. Oviposition electivity at the host plant (Plantago media) was best explained by a combination of host plant quantity and vegetation structure. Habitat quality, isolation and patch area explained 86% of the current patch occupancy of M. aurelia. With M. aurelia preferentially inhabiting transitional vegetation types, management requires a balance between abandonment and disturbance. Disturbances provide open soil that facilitates germination of the host plant Plantago media. On the other hand, immature and adult stages of M. aurelia perform best on calcareous grasslands with a high amount of host plants and low disturbance intensity. Traditional rough grazing regimes seem to be the most favourable tool for developing the necessary spatial and temporal heterogeneity in patches. The best results may be achieved by rotational grazing where only a subset of inhabited patches is grazed intensively each year. Our analysis of patch occupancy indicates that it would be desirable to restore patches in close proximity to occupied sites.     

Cloning and characterization of an acyl-CoA-dependent diacylglycerol acyltransferase 1 (DGAT1) gene from Tropaeolum majus, and a study of the functional motifs of the DGAT protein using site-directed mutagenesis to modify enzyme activity and oil content

SUMMARY: A full-length cDNA encoding a putative diacylglycerol acyltransferase 1 (DGAT1, EC 2.3.1.20) was obtained from Tropaeolum majus (garden nasturtium). The 1557-bp open reading frame of this cDNA, designated TmDGAT1, encodes a protein of 518 amino acids showing high homology to other plant DGAT1s. The TmDGAT1 gene was expressed exclusively in developing seeds. Expression of recombinant TmDGAT1 in the yeast H1246MATalpha quadruple mutant (DGA1, LRO1, ARE1, ARE2) restored the capability of the mutant host to produce triacylglycerols (TAGs). The recombinant TmDGAT1 protein was capable of utilizing a range of (14)C-labelled fatty acyl-CoA donors and diacylglycerol acceptors, and could synthesize (14)C-trierucin. Collectively, these findings confirm that the TmDGAT1 gene encodes an acyl-CoA-dependent DGAT1. In plant transformation studies, seed-specific expression of TmDGAT1 was able to complement the low TAG/unusual fatty acid phenotype of the Arabidopsis AS11 (DGAT1) mutant. Over-expression of TmDGAT1 in wild-type Arabidopsis and high-erucic-acid rapeseed (HEAR) and canola Brassica napus resulted in an increase in oil content (3.5%-10% on a dry weight basis, or a net increase of 11%-30%). Site-directed mutagenesis was conducted on six putative functional regions/motifs of the TmDGAT1 enzyme. Mutagenesis of a serine residue in a putative SnRK1 target site resulted in a 38%-80% increase in DGAT1 activity, and over-expression of the mutated TmDGAT1 in Arabidopsis resulted in a 20%-50% increase in oil content on a per seed basis. Thus, alteration of this putative serine/threonine protein kinase site can be exploited to enhance DGAT1 activity, and expression of mutated DGAT1 can be used to enhance oil content.     

Screening of Australian Native Grasses for Rhizoremediation of Aliphatic Hydrocarbon-Contaminated Soil

Rhizoremediation involves the breakdown of contaminants in soil resulting from microbial activity that is enhanced in the plant root zone. The objective of this study was to identify Australian native grass species as suitable candidates for rhizoremediation application. Seeds of nine perennial Australian native grasses were sown in soil from a mine site and artificially contaminated with a 60:40 diesel/oil mixture at concentrations of 1% (w/w), 0.5% (w/w), and 0% (control). Seedling emergence was not adversely affected by the presence of hydrocarbon contamination for all but one grass species. Three promising species (Brachiaria decumbens, Cymbopogon ambiguus, and Microlaena stipoides var. Griffin) were assessed for growth characterization in contaminated and uncontaminated soils. The evaluated species survived for 120 days in the contaminated soil and, in some instances, produced considerably more root biomass in the presence of contamination. C. ambiguus showed growth stimulation in the presence of contamination (1% and 0.5% w/w) with significantly increased root biomass production compared with the control (p = 0.0001). B. decumbens and M. stipoides showed tolerance, without adverse growth effects in the presence of diesel/oil at the exposed concentrations. Stimulation of the rhizosphere microbial population that is capable of degrading diesel/oil was found for all of the species tested, using a most probable number method for enumeration. This investigation has identified suitable candidates for further investigation of their rhizoremediation potential.     

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

Theoretical microscopic titration curves (THEMATICS) is a computational method for the identification of active sites in proteins through deviations in computed titration behavior of ionizable residues. While the sensitivity to catalytic sites is high, the previously reported sensitivity to catalytic residues was not as high, about 50%. Here THEMATICS is combined with support vector machines (SVM) to improve sensitivity for catalytic residue prediction from protein 3D structure alone. For a test set of 64 proteins taken from the Catalytic Site Atlas (CSA), the average recall rate for annotated catalytic residues is 61%; good precision is maintained selecting only 4% of all residues. The average false positive rate, using the CSA annotations is only 3.2%, far lower than other 3D-structure-based methods. THEMATICS-SVM returns higher precision, lower false positive rate, and better overall performance, compared with other 3D-structure-based methods. Comparison is also made with the latest machine learning methods that are based on both sequence alignments and 3D structures. For annotated sets of well-characterized enzymes, THEMATICS-SVM performance compares very favorably with methods that utilize sequence homology. However, since THEMATICS depends only on the 3D structure of the query protein, no decline in performance is expected when applied to novel folds, proteins with few sequence homologues, or even orphan sequences. An extension of the method to predict non-ionizable catalytic residues is also presented. THEMATICS-SVM predicts a local network of ionizable residues with strong interactions between protonation events; this appears to be a special feature of enzyme active sites.     

Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site

Bacterioferritins, also known as cytochrome b (1), are oligomeric iron-storage proteins consisting of 24 identical amino acid chains, which form spherical particles consisting of 24 subunits and exhibiting 432 point-group symmetry. They contain one haem b molecule at the interface between two subunits and a di-nuclear metal binding center. The X-ray structure of bacterioferritin from Mycobacterium smegmatis (Ms-Bfr) was determined to a resolution of 2.7 A in the monoclinic space group C2. The asymmetric unit of the crystals contains 12 protein molecules: five dimers and two half-dimers located along the crystallographic twofold axis. Unexpectedly, the di-nuclear metal binding center contains zinc ions instead of the typically observed iron ions in other bacterioferritins.     

Chemical and biological investigation of N-hydroxy-valdecoxib: An active metabolite of valdecoxib

The inhibition of cyclooxygenase enzymes plays an important role in the treatment of inflammatory diseases. N-Hydroxy-4-(5-methyl-3-phenylisoxazol-4-yl)benzenesulfonamide (3)—a primary metabolite of the highly selective COX-2 inhibitor valdecoxib—was synthesized and stabilized as its monohydrate (3a·H₂O). The anti-inflammatory properties of 3a·H₂O were investigated in carrageenan-induced edema and in acute and chronic pain models. Based on our biological investigation, we conclude that N-hydroxy-valdecoxib 3a is an active metabolite of valdecoxib.