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PubMed1989

Selectivity in solute transport: binding sites and channel structure in maltoporin and other bacterial sugar transport proteins.

A stereospecific binding site is not the only determinant governing the selectivity of transport proteins. An understanding of transport across cellular membranes requires a description of the different compartments within a transmembrane channel; evidence for the existence of these compartments comes from the selectivity properties of genetically modified maltoporin. Such compartments may also be of significance in determining the specificity of other transport proteins.

Bacterial Outer Membrane Proteins↗
PubMed1990

Preparative separation of pyrogens from proteins by isoelectric focusing using a multicompartment electrolyser with Immobiline membranes.

Due to the nature of lipopolysaccharide endotoxin structures of bacterial pyrogens, their removal from solutions containing therapeutic proteins is often a problem in the pharmaceutical industry. In this report we describe the application of electromotive force to dislodge lipopolysaccharide endotoxins from proteins. This was performed by employing a multicompartment electrolyzer fitted with Immobiline membranes of specified pIs. A thousand-fold reduction of endotoxin could be achieved in the model test system described. This contribution describes the use of a new recycling isoelectric focusing approach without the use of carrier ampholytes.

Isoelectric Focusing↗
PubMed1991

The Drosophila neurogenic gene neuralized encodes a novel protein and is expressed in precursors of larval and adult neurons.

Neuralized belongs to a group of genes involved in neurogenesis in Drosophila. Loss of function mutations lead to an overproduction of neurons at the expense of epidermal tissues. We have cloned the neuralized locus and examined its expression pattern during development. Expression is initially observed during embryogenesis in the neurogenic ectoderm and later in neuroblasts. In addition, transcripts are also found in sensory precursor cells during imaginal disc development. Other tissues that express neuralized include the embryonic mesoderm and specific follicle cells in the ovary. The predicted neuralized gene product is a highly basic protein with a novel motif that bears some resemblance to those found in nucleic acid-binding proteins. The first half of this motif has sequence similarity to the first half of a homeobox whereas the second half is similar to the helix-turn-helix structure of bacterial repressors.

Amino Acid Sequence↗
PubMed2006

Biodegradable polyurethane cytocompatibility to fibroblasts and staphylococci.

Biodegradable polyurethanes have potential for use as implantable devices (orthopedic, maxillofacial, cardiovascular, wound dressing and plastic surgery) because of their controllable elasticity, and the possibility of changing their chemistry and structure. Studying bacterial and cell adhesion to polyurethanes helps to determine surface cytocompatibility and suitability for in vivo trials. Staphylococcus aureus, Staphylococcus epidermidis and hTERT human fibroblast cells were used to determine the cytocompatibility of experimental biodegradable polyurethanes (PUs) with different hydrophobic-to-hydrophilic (pho:phi) content ratios (100% pho, 70% pho, and 30% pho). Poly(L/DL-lactide) 70/30% (PLDL) and Thermanox were used as control surfaces. Surface characterization using noncontact profilometry, contact angles, and scanning electron microscopy (SEM) showed that the three PU surfaces, PLDL, and Thermanox have different properties. On the 100% PU and 30% PU surfaces, hTERT cells spread less in comparison to the 70% PU, PLDL, and Thermanox surfaces. The adsorption of fibronectin to the surfaces had no effect on the adhesion and spreading of hTERT cells when compared to the uncoated surfaces. The trend for S. aureus was the most adhered on the 70% PU and 30% PU, then Thermanox, followed by 100% PU and PLDL, respectively. The amount of S. epidermidis adhesion followed the trend of the most on 70% PU, then 100% PU, then 30% PU and PLDL, and the least on Thermanox. These results suggest that the 70% PU surface is cytocompatible to hTERT fibroblasts, while the 100% PU and 30% PU were not. All surfaces encouraged S. aureus and S. epidermidis colonization, particularly the 70% PU.

Bacterial Adhesion↗
PubMed1995

Superoxide dismutase protects Escherichia coli against killing by human serum.

To assess the role of superoxide dismutase in protecting Escherichia coli from killing by human serum and neutrophils, we constructed isogenic, smooth-lipopolysaccharide K-12 strains, either sod wild-type, delta sodA, or delta sodA delta sodB. The delta sodA delta sodB strain was killed by serum much more readily than either the wild-type or delta sodA strain. After allowing for this serum sensitivity difference, the delta sodA delta sodB strain also showed increased susceptibility to phagocytic killing by human neutrophils. These results indicate that superoxide dismutase protects E. coli from killing by serum (complement system) and by human neutrophils, possibly by a role in maintaining bacterial membrane structure.

Complement System Proteins↗
PubMed1999

Heterobifunctional photoaffinity probes for cytochrome P450 2B.

Three heterobifunctional photoaffinity probes, N-(p-azidobenzyl)-N-methyl-p-aminobenzylamine (I), N-(p-azidobenzyl)-N-methyl-p-aminophenethylamine (II), and N-(p-azidophenethyl)-N-methyl-p-aminophenethylamine (III), were synthesized and characterized. These probes, containing a photolabile azido-group and an amino-group on opposite sides of the molecule, were designed for photoaffinty labeling of the cytochrome P450 (CYP) 2B active site cavity differing in distance from the heme iron. Spectroscopic studies proved that probes I and II coordinated with the heme iron via their amino-group in the enzyme active center, whereas probe III did not. This result in conjunction with data from kinetic studies suggests probes I and II are appropriate for photoaffinity labeling of the CYP 2B active center. Thus, probe II was used to identify amino acid residues within a distance of the probe length (about 16.5 A) from the heme. Analysis of a Lys-C digest of the probe II-labeled CYP 2B4 revealed a single labeled hexapeptide corresponding to position 192-197 of the CYP 2B4 sequence. Using postsource decay/matrix-assisted laser desorption ionization-time of flight, Arg197 was identified as a probe II target. The location of the labeled site in three-dimensional structures of bacterial CYPs and in CYP 2B homology models is discussed.

Affinity Labels↗
PubMed1995

Molecular cloning, characterization, and mapping of a full-length cDNA encoding human UDP-galactose 4'-epimerase.

Galactose metabolism in all organisms is catalyzed by three enzymatic steps: the galactokinase, galactose-1-phosphate uridyltransferase, and UDP galactose 4'-epimerase reactions. We report here the molecular cloning, characterization, and mapping of a full-length cDNA encoding human UDP-galactose 4'-epimerase (GALE). Our cDNA is 1488 bp long and matches the mRNA size of 1.5 kg detected in fibroblasts and lymphoblasts. The human GALE cDNA encodes a predicted protein of 348 amino acids with a molecular mass of 38,266. The human GALE enzyme is 87% identical to the rat protein, 53% identical to the homologous GAL10 protein from the yeast Kluyveromyces lactis, and 51% identical to the galE protein from the prokaryote Escherichia coli. This extraordinary degree of sequence identity has allowed us to build a homology model of the human protein based on the bacterial crystal structure. This predicted human structure is very similar to the E. coli galE enzyme, suggesting that both enzymes use similar mechanisms. The human gene encoding GALE maps, as expected, to a single locus on chromosome 1 and appears to be compact. The human GALE gene is structurally intact in 19 patients with epimerase-deficiency galactosemia, an inborn error of metabolism secondary to GALE deficiency. Therefore, we propose that this disorder is due to small mutations within the gene.

Amino Acid Sequence↗
PubMed2000

A single five-step desaturase is involved in the carotenoid biosynthesis pathway to beta-carotene and torulene in Neurospora crassa.

Phytoene desaturase Al-1 from Neurospora crassa was expressed in Escherichia coli and an active enzyme was isolated which catalyzed the stepwise introduction of up to five double bonds into the substrate phytoene. The major reaction products were 3, 4-didehydrolycopene and lycopene. Several of the desaturation intermediates, zeta-carotene, neurosporene, and lycopene, were also accepted as a substrate by Al-1. In contrast to the structurally related bacterial enzymes, the cofactor involved in the dehydrogenation reaction was NAD for Al-1. In situ competition with a neurosporene- and lycopene-converting hydratase and cyclase indicated that these enzymes can divert intermediates of the desaturation sequence. Based on the in vitro and in vivo results, the organization of the phytoene desaturase from N. crassa was proposed as an assembly of identical protein units which are responsible for the multistep reaction. However, the spatial arrangement should be loose enough to allow an exchange of individual intermediates in both directions in and out of this complex. Since gamma-carotene is not accepted as a substrate by Al-1, the formation of torulene must proceed exclusively by the cyclization of 3,4-didehydrolycopene.

Carotenoids↗
PubMed1996

The 1.6 angstroms resolution crystal structure of nuclear transport factor 2 (NTF2).

Nuclear transport factor 2 (NTF2) facilitates protein transport into the nucleus and interacts with both the small Ras-like GTPase Ran and nucleoporin p62. We have determined the structure of bacterially expressed rat NTF2 at 1.6 angstroms resolution using X-ray crystallography. The NTF2 polypeptide chain forms an alpha + beta barrel that opens at one end to form a distinctive hydrophobic cavity and its fold is homologous to that of scytalone dehydratase. The NTF2 hydrophobic cavity is a candidate for a potential binding site for other proteins involved in nuclear import such as Ran and nucleoporin p62. In addition, the hydrophobic cavity contains a putative catalytic Asp-His pair, which raises the possibility of an unanticipated enzymatic activity of the molecule that may have implications for the molecular mechanism of nuclear protein import.

Amino Acid Sequence↗
PubMed1994

Comparison between rodent carcinogenicity test results of 44 chemicals and a number of predictive systems.

A comparison is made between a number of predictive systems including bacterial mutagenicity, structure alert and chronic toxicity (Tennant et al., 1990), COMPACT, Hazardexpert, and DEREK, with the outcome of the two species rodent carcinogenicity bioassay for 44 chemicals conducted under the NTP protocol. It is shown that, following minor updating of the rodent data in the light of pathology reports, there is a generally good agreement between various predictions and the actual carcinogenicity results. In particular, a combination of two methods of prediction produces an over 80% concordance with the rodent bioassay. Possible reasons for various discrepancies are discussed in light of xenobiotic metabolism and activation mechanisms of chemical carcinogenesis.

Animals↗
PubMed1995

Structure, function and immunochemistry of bacterial exopolysaccharides.

There has been much written on bacterial exopolysaccharides (EPS) and their role in virulence. Less has been published regarding EPS in free living species. This review focuses on that subject, emphasizing their functions in the environment and the use of antibody probes to study them.

Bacterial Capsules↗
PubMed2005

Inferring the pattern of spontaneous mutation from the pattern of substitution in unitary pseudogenes of Mycobacterium leprae and a comparison of mutation patterns among distantly related organisms.

The pattern of spontaneous mutation can be inferred from the pattern of substitution in pseudogenes, which are known to be under very weak or no selective constraint. We modified an existing method (Gojobori T, et al., J Mol Evol 18:360, 1982) to infer the pattern of mutation in bacteria by using 569 pseudogenes from Mycobacterium leprae. In Gojobori et al.'s method, the pattern is inferred by using comparisons involving a pseudogene, a conspecific functional paralog, and an outgroup functional ortholog. Because pseudogenes in M. leprae are unitary, we replaced the missing paralogs by functional orthologs from M. tuberculosis. Functional orthologs from Streptomyces coelicolor served as outgroups. We compiled a database consisting of 69,378 inferred mutations. Transitional mutations were found to constitute more than 56% of all mutations. The transitional bias was mainly due to C-->T and G-->A, which were also the most frequent mutations on the leading strand and the only ones that were significantly more frequent than the random expectation. The least frequent mutations on the leading strand were A-->T and T-->A, each with a relative frequency of less than 3%. The mutation pattern was found to differ between the leading and the lagging strands. This asymmetry is thought to be the cause for the typical chirochoric structure of bacterial genomes. The physical distance of the pseudogene from the origin of replication (ori) was found to have almost no effect on the pattern of mutation. A surprising similarity was found between the mutation pattern in M. leprae and previously inferred patterns for such distant taxa as human and Drosophila. The mutation pattern on the leading strand of M. leprae was also found to share some common features with the pattern inferred for the heavy strand of the human mitochondrial genome. These findings indicate that taxon-specific factors may only play secondary roles in determining patterns of mutation.

Animals↗
PubMed2005

Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity.

The diversity of the culturable microbial communities was examined in two sponge species-Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga-Flavobacterium-Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.

Animals↗
PubMed2002

Triacylglycerols in prokaryotic microorganisms.

Triacylglycerols (TAG) are fatty acid triesters of glycerol; there are diverse types of TAG with different properties depending on their fatty acid composition. The occurrence of TAG as reserve compounds is widespread among eukaryotic organisms such as yeast, fungi, plants and animals, whereas occurrence of TAG in bacteria has only rarely been described. However, accumulation of TAG seems to be widespread among bacteria belonging to the actinomycetes group, such as species of Mycobacterium, Streptomyces, Rhodococcus and Nocardia. Fatty acids in acylglycerols in cells of Rhodococcus opacus PD630 accounted for up to 87% of the cellular dry weight. TAG biosynthesis, justifying an oleaginous status, seems to be restricted mainly to this group of bacteria, but occurs to a minor extent also in a few other bacteria. The compositions and structures of bacterial TAG vary considerably depending on the microorganism and on the carbon source, and unusual acyl moieties, such as phenyldecanoic acid and 4,8,12 trimethyl tridecanoic acid, are also included. The principal function of bacterial TAG seems to be as a reserve compound. Other functions that have been discussed include regulation of cellular membrane fluidity by keeping unusual fatty acids away from membrane phospholipids, or acting as a sink for reducing equivalents. In recent years, basic aspects of the physiology and biochemistry of bacterial TAG accumulation, and the molecular biology of the lipid inclusion bodies have been reported. TAG are used for nutritional, therapeutic and pharmaceutical purposes and serve as a source of oleochemicals.

Bacteria↗