Detection and quantitative analysis of two independent binding modes of a small ligand responsible for DC-SIGN clustering

Multiple binding modes at the same binding site can explain the higher binding affinity of a pseudotrimannotrioside compared to a pseudomannobioside.

The use of glass beads cultivation system to study the global effect of the ppk gene inactivation in Streptomyces lividans

The glass beads cultivation system developed in our laboratory for physiological studies of filamentous microorganisms supports differentiation and allows complete recovery of bacterial colonies and their natural products from cultivation plates. Here, we used this system to study the global effect of ppk gene disruption in Streptomyces lividans. The ppk encoding the enzyme polyphosphate kinase (P) catalyses the reversible polymerisation of gamma phosphate of ATP to polyphosphates. The resulting are phosphate and energy stock polymers. Because P activity impacts the overall energetic state of the cell, it is also connected to secondary metabolite (e.g. antibiotic) biosynthesis. We analysed the global effects of the disruption of this gene including its influence on the production of pigmented antibiotics, on morphological differentiation, on the levels of ATP and on the whole cytoplasmic protein expression pattern of S. lividans. We observed that the S. lividans ppk mutant produced antibiotics earlier and in greater amount than the wild-type (wt) strain. On the other hand, we did not observe any obvious effect on colony morphological development. In agreement with the function of Ppk, we detected much lower levels of ATP in ppk- mutant than in the wt strain. Proteomic analysis revealed that the genes that were influenced by ppk inactivation included enzymes involved in carbon or nitrogen metabolism, phosphate transport and components of the cell translational machinery. We showed that the synthesis of translation elongation factor Tu is during sporulation much higher in ppk- mutant than in wild-type strain.

Comparative study of the life cycle dependent post-translation modifications of protein synthesis elongation factor Tu present in the membrane proteome of streptomycetes and mycobacteria

We present the results of analysis of membrane phosphoproteomes from individual morphological stages of Streptomyces coelicolor that reflect developmentally dependent heterogeneity and phosphorylation of intrinsic and externally added purified Strepomyces aureofaciens EF-Tu. Fast growing nonpathogenic Mycobacterium smegmatis was used as a non-differentiating actinomycetes comparative model. Streptomycetes membrane fraction was found to contain protein kinase(s) catalyzing phosphorylation of both its own and an externally added EF-Tu, whereas Mycobacterium membrane fraction contains protein kinase phosphorylating only its own EF-Tu.

Mutations in the keratin 9 gene in Pakistani families with epidermolytic palmoplantar keratoderma

BACKGROUND

Keratins are heteropolymeric proteins that form the intermediate filament cytoskeleton in epithelial cells. The common basic structure of all keratins is organized in a central α-helical rod domain flanked by nonhelical, variable head and tail regions. Most mutations in keratins are found in the central α-helical rod domain. Keratin 9 (K9) is expressed only in the suprabasal layers of palmoplantar epidermis. Mutations in the keratin 9 gene (KRT9) have been shown to cause epidermolytic palmoplantar keratoderma (EPPK; OMIM 144200), an autosomal dominant genodermatosis characterized clinically by diffuse hyperkeratosis limited to the palms and soles, and histologically by epidermolysis in suprabasal layers of the epidermis.

AIM

To elucidate the genetic basis of EPPK in five Pakistani families.

METHODS

Using microsatellite markers localized to the areas around the type I keratin gene cluster on chromosome 17q21, genotyping of these families was performed, followed by sequencing of the KRT9 gene.

RESULTS

The analysis resulted in the identification of two novel (p.M157K and p.Y454H) and two recurrent (p.M157T and p.R163Q) mutations in the KRT9 of all five families. All mutations occurred within the highly conserved helix initiation or termination motif of K9.

CONCLUSIONS

The affected members of all five families possess mutations in the KRT9 gene that severely affect heterodimer formation with the type II keratin partner. The results of our study further underscore the crucial role of K9 protein in the palmoplantar epidermis.

Protein synthesis elongation factor Tu present in spores of Streptomyces coelicolor can be phosphorylated in vitro by the spore protein kinase

In vitro phosphorylation of EF-Tu was shown in cell-free extract from dormant spores of Streptomyces coelicolor by a protein kinase present in spores. EF-Tu phosphorylation was observed on both intrinsic S. coelicolor factor and externally added purified EF-Tu from S. aureofaciens, on two isoforms. Putative serine and threonine residues as potential phosphorylation targets were determined in primary sequence and demonstrated on 3D structure model of EF-Tu.

Construction and testing of a bacterial luciferase reporter gene system for in vivo measurement of nonsense suppression in Streptomyces

A reporter gene system, based on luciferase genes from Vibrio harvei, was constructed for measurement of translation nonsense suppression in Streptomyces. Using the site-directed mutagenesis the TCA codon in position 13 of the luxB gene was replaced by all of the three stop codons individually. By cloning of luxA and luxB genes under the control of strong constitutive Streptomyces promoter ermE* in plasmid pUWL201 we created Wluxl with the wild-type sequence and pWlux2, pWlux3 and pWlux4 plasmids containing TGA-, TAG- and TAA-stop codons, respectively. Streptomyces lividans TK 24 was transformed with the plasmids and the reporter system was tested by growth of the strain in the presence of streptomycin as a translation accuracy modulator. Streptomycin increased nonsense suppression on UAA nearly 10-fold and more than 20-fold on UAG. On the other hand, UGA, the most frequent stop signal in Streptomyces, the effect was negligible.

Post-translational modification(s) and cell distribution of Streptomyces aureofaciens translation elongation factor Tu overproduced in Escherichia coli

We cloned EF-Tu from Streptomyces aureofaciens on a pET plasmid and overproduced it using the T7 RNA polymerase system in Escherichia coli. Streptomyces EF-Tu represented more than 40% of the total cell protein and was stored mostly in inclusion bodies formed apically at both ends of E. coli cells. Analysis of the inclusion bodies by transmission and scanning electron microscopy did not reveal any internal or surface ultrastructures. We developed the method for purification of S. aureofaciens EF-Tu from isolated inclusion bodies based on the ability of the protein to aggregate spontaneously. EF-Tu present in inclusion bodies was not active in GDP binding. Purified protein showed a similar charge heterogeneity as EF-Tu isolated from the mycelium of S. aureofaciens and all of the isoforms reacted with EF-Tu antibodies. All isoforms also reacted with monoclonal antibodies against O-phosphoserine and O-phosphothreonine.

Infections with the ascomycete fungus Metschnikowia typographi sp.nov. in the bark beetles Ips typographus and Ips amitinus (Coleoptera, Scolytidae)

The ascomycete fungus Metschnikowia typographi sp.nov. is described. It infects the spruce bark beetles Ips typographus L. and Ips amitinus Eichl. Masses of vegetative cells and navicular asci (I. typographus 13-17 x 2 microns; I. amitinus 17-22 x 2 microns) were found in cells of the midgut epithelium and in the body cavity of infected beetles. Each ascus contains two needle-shaped ascospores flattened in the central part, 0.5-1.5 x 0.3 x 13-15 microns and pointed at both ends. The parasitic species of Metschnikowia, M. bicuspidata, M. artemiae, M. unicuspidata, M. wickerhami and M. typographi are discussed as a special group of the genus characterized by morphological characters.

Natural and acquired macrolide resistance in mycobacteria

The genus Mycobacterium contains two of the most important human pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, the etiologic agents of tuberculosis and leprosy, respectively. Other mycobacteria are mostly saprophytic organisms, living in soil and water, but some of them can cause opportunistic infections. The increasing incidence of tuberculosis as well as infections with non-tuberculous mycobacteria (NTM) in AIDS patients has renewed interest in molecular mechanisms of drug resistance in these pathogens. Mycobacteria show a high degree of intrinsic resistance to most common antibiotics. For instance, species from the M. tuberculosis complex (MTC) are intrinsically resistant to macrolides. Nevertheless, some semi-synthetic macrolides as the erythromycin derivatives clarithromycin, azithromycin and most recently the ketolides, are active against NTM, particularly Mycobacterium avium, and some of them are widely used for infection treatment. However, shortly after the introduction of these new drugs, resistant strains appeared due to mutations in the macrolide target, the ribosome. The mycobacterial cell wall with its specific composition and structure is considered to be a major factor in promoting the natural resistance of mycobacteria to various antibiotics. However, to explain the difference in macrolide sensitivity between the MTC and NTM, the synergistic contribution of a specific resistance mechanism might be required, in addition to possible differences in cell wall permeability. This mini-review summarizes the current knowledge on the natural and acquired macrolide resistance in mycobacteria, gives an overview of potential mechanisms implicated in the intrinsic resistance and brings recent data concerning a macrolide resistance determinant in the MTC.

Identification of the EcoKI and EcoR124I Type I restriction--modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis

Effectively optimized and reproducible procedure for monitoring the composition of type I restriction-modification endonucleases EcoKI and EcoR124I by non-equilibrium pH gradient two-dimensional (2-D) gel electrophoresis is described. Three subunits of the enzyme complex, which widely differ from one another in their isoelectric points and molar mass, were identified in crude cell extracts of E. coli. For the first time all three subunits of both EcoKI and EcoR124I were detected as distinct spots on a single 2-D gel. A sensitive immunoblotting procedure was suggested suitable for routine use in determining the identity of individual subunits. Potential application of this method for detailed studies of regulation of the function and stoichiometry of the enzyme complexes is discussed.

Major proteins related to chlortetracycline biosynthesis in a Streptomyces aureofaciens production strain studied by quantitative proteomics

Changes in synthesis and abundance of proteins associated with chlortetracycline (CTC) production in Streptomyces aureofaciens were investigated by two-dimensional polyacrylamide gel electrophoresis of proteins pulse-labelled in vivo with L-[35S]methionine. Eleven individual protein spots were selected as being related to formation of the antibiotic. Expression of these prominent proteins was not observed in the non-producing mutant; moreover, they were overexpressed in cultures grown in the presence of benzyl thiocyanate, a specific stimulator of CTC biosynthesis used in industrial fermentations. The expression kinetics of the selected proteins was assessed using the technique of computer-assisted image analysis with the EQIAS software and the elongation factor Tu as an internal standard. Interestingly, the kinetic profiles were generally not identical. including those of anhydrotetracycline monooxygenase and the 13-kDa subunit of tetracycline dehydrogenase, two enzymes involved, in the terminal sequential steps of the CTC biosynthetic pathway. The presence of more forms of these enzymes with different charge characteristics was observed. The data presented demonstrated how dramatically the industrial microorganism can change its protein repertoire during the production phase; at least five proteins were nearly comparable in level to the most prominent proteins, exemplified by elongation factor Tu.

A comparison of methods for pharmacophore generation with the catalyst software and their use for 3D-QSAR: application to a set of 4-aminopyridine thrombin inhibitors

The method of structure-based pharmacophores for use in 3D-QSAR as implemented by Gillner and Greenidge is further examined. Conformational models are generated using both Catalyst and Macromodel. K(i) estimates obtained with the pharmacophore models are compared with observed values for a set of 4-aminopyridine thrombin inhibitors.

Colonoscopic polypectomy in chronic colitis: conservative management after endoscopic resection of dysplastic polyps

BACKGROUND & AIMS

Adenomatous polyps are by definition dysplastic and pathologically indistinguishable from the dysplasia-associated lesion or mass (DALM) described in 1981. Yet, adenomatous polyps in noncolitic colons are usually removed definitively endoscopically, whereas DALMs are regarded as harbingers of colon cancer, mandating colectomy.

METHODS

Since 1988, all of our patients with chronic ulcerative or Crohn's colitis and dysplastic polyps and no coexistent dysplasia in flat mucosa underwent colonoscopic polypectomy. Biopsy specimens were obtained also adjacent to polypectomy sites, from strictures, and throughout the colon at 10-cm intervals. Follow-up colonoscopies and biopsies were performed within 6 months after polypectomy and yearly thereafter.

RESULTS

Colonoscopy in 48 patients with chronic colitis (mean duration, 25.4 years) resected 70 polyps (60 in colitic and 10 in noncolitic mucosa). Polyps were detected on screening colonoscopies (29%) and on surveillance (71%). Pathology was tubular adenoma in all polyps from noncolitic mucosa and low-grade dysplasia (57), high-grade dysplasia (2), or carcinoma (1) in polyps from colitic mucosa. Subsequent colonoscopies (mean follow-up, 4.1 years) revealed additional polyps in 48% but no carcinomas. Surgical resection (6 patients) for recurrent polyps confirmed colonoscopic findings. No dysplasia or cancers in flat mucosa were found at surgery or on follow-up colonoscopies.

CONCLUSIONS

In patients with chronic colitis who have no dysplasia in flat mucosa, colonoscopic resection of dysplastic polyps can be performed effectively, just as in noncolitic colons.

Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities

A fast analytical formula (TDND) has been derived for the calculation of approximate atomic and molecular solvent-accessible surface areas (SASA), as well as the first and second derivatives of these quantities with respect to atomic coordinates. Extending the work of Stouten et al. (Molecular Simulation, 1993, Vol. 10, pp. 97-120), as well as our own (Journal of Computational Chemistry, 1999, Vol. 20, pp. 586-596), the method makes use of a Gaussian function to calculate the neighbor density in four tetrahedral directions in three-dimensional space, sometimes twice with different orientations. SASA and first derivatives of the 2366 heavy atoms of penicillopepsin are computed in 0.13 s on an SGI R10000/194 MHz processor. When second derivatives are computed as well, the total time is 0.23 s. This is considerably faster than timings reported previously for other algorithms. Based on a parameterization set of nineteen compounds of different size (11-4346 atoms) and class (organics, proteins, DNA, and various complexes) consisting of a total 23,197 atoms, the method exhibits relative errors in the range 0.2-12.6% for total molecular surface areas and average absolute atomic surface area deviations in the range 1.7 to 3.6 A(2).

Characterisation of two putative protein Ser/Thr kinases from actinomycete Streptomyces granaticolor both endowed with different properties

The structural genes, pkg4 and pkg3, encoding two putative protein serine/threonine kinases in Streptomyces granaticolor, have been cloned and sequenced. The genes were isolated after screening genomic sublibraries with specific probes obtained by PCR amplification of chromosomal DNA using degenerate primers which correspond to amino acid sequences highly conserved in eukaryotic protein Ser/Thr kinases. The sequences of these genes predict polypeptide chains of 761 and 780 amino acids for Pkg4 and Pkg3, respectively. The genes are separated by only 2 bp and therefore probably constitute an operon. pkg4, which is positioned upstream of pkg3, contains a UUALeu codon suggesting a developmental-dependent mode of expression. The amino-terminal half of both proteins clearly shares similarities with the family of protein Ser/Thr kinases. Both proteins studied also possess a region rich in Pro and Ala residues and a repeating motif of 11 amino acid residues, the function of which is unknown, in the carboxy-terminal domain. Expression of pkg4 in Escherichia coli gave rise to two different forms: a soluble protein autophosphorylated at threonine residues and an insoluble form phosphorylated at threonine and serine residues. In contrast, when pkg3 was expressed in E. coli, no autophosphorylation was detected either in vivo or in vitro.

Antibiotic resistance gene cassettes derived from the omega interposon for use in E. coli and Streptomyces

Three antibiotic resistance gene cassettes, derived from the omega interposon (Prentki and Krisch (1984) Gene 29, 303-313) were constructed. These cassettes carry different antibiotic resistance genes, conferring resistance to geneticin, hygromycin or viomycin, flanked by short inverted repeats containing transcription and translation termination signals and synthetic polylinkers. These cassettes were designated omega aac, omega hyg and omega vph. Resistance phenotypes conferred by these constructions are selectable in E. coli and Streptomyces. These cassettes can be used for insertional mutagenesis or for vector construction.

The Effect of Bacillus thuringiensis M-exotoxin on Trematode Cercariae

The effect of Bacillus thuringiensis israelensis eluate containing water-soluble exotoxin (M-exotoxin) was observed by its use on cercariae of seven trematode species. To the most sensitive species to the toxic effect of the mentioned toxin belonged schistosome furcocercariae (human species Schistosoma mansoni and avian parasite Trichobilharzia szidati). Under the influence of the toxin, surface syncytial structure (tegument) was separated from underlying tissues, with subsequent disintegration of internal organs connected with disruption of acetabular glands and release of their proteolytic content.

Protein profiles of Streptomyces aureofaciens producing tetracyclines: reappraisal of the effect of benzyl thiocyanate

Cell protein profiles of submerged cultures of Streptomyces aureofaciens cultivated in the absence or presence of 12 microM benzyl thiocyanate (BT) were analyzed by one-dimensional SDS polyacrylamide gel electrophoresis. Substantial increase in the intensity of the 13, 35, 37, 60, and 100 kDa protein bands was observed in cultures treated with BT. Similar increase in the 35, 37, and 60 kDa bands was found in a mutant blocked in the last chlortetracycline biosynthesis step. Effect of BT on the solid medium-grown cultures was also observed, with a more intensive substrate mycelium pigmentation and alteration in the spore size and shape as the most characteristic features. Earlier studies of BT effect involving those on the stimulation of chlortetracycline biosynthesis are summarized and a possible signal-transducing mechanism is discussed from the point of view of adaptation of S. aureofaciens to the uncoupling of oxidative phosphorylation.

The use of protein synthesis elongation factor EF-Tu as internal calibration standard in two-dimensional electrophoretic studies of differentiation in Streptomyces

Protein synthesis elongation factor EF-Tu is presented as an internal calibration standard for quantitative analysis of two-dimensional (2-D) protein electrophoresis gels. EF-Tu was selected on the basis of concentration measurements in cell-free extracts from Streptomyces aureofaciens, grown under conditions leading to production of tetracyclines, and separated on one-dimensional (1-D) and 2-D electrophoresis gels. The results demonstrated that the amount of EF-Tu synthesized in S. aureofaciens under conditions of slow growth during production of tetracyclines is constant in proportion to all other de novo synthesized proteins regardless of their total number. This makes EF-Tu an ideal internal protein standard for quantitation of protein spots on 2-D electrophoresis gels. For such quantitative analysis we developed a computer-aided image analysis system which provides preparation of a gel image for further analysis including calibration, background subtraction and cleaning for streaking in both directions. The system can locate any resolvable spot in the gel and measure the integrated density of the spot, even in the case of irregular spot shape in crowded and overlapping spot regions.

In vitro measurement of translation accuracy of ribosomes isolated from streptomycin-resistant mutant of Streptomyces granaticolor

Accuracy of activity of ribosome isolated from UV-light-induced streptomycin-resistant R-21 mutant of Streptomyces granaticolor was measured in an E. coli-derived system translating poly(U) with a high rate and accuracy. Ribosomes from the R-21 mutant strain were shown to be resistant to streptomycin and about two-fold more accurate than those from the wild type. The mutant strain was found to be resistant to 1000 mg/L streptomycin (Stm) during vegetative growth while it sporulated on agar plates containing only up to 200 mg/L of Stm. The growth rate of the R-21 mutant in complex liquid medium was indistinguishable from that of the wild-type strain.

Bacillary epithelioid angiomatosis involving the liver, spleen, and skin in an AIDS patient with concurrent Kaposi's sarcoma

The simultaneous findings of bacillary epithelioid angiomatosis and Kaposi's sarcoma of the skin with visceral hepatosplenic bacillary epithelioid angiomatosis is reported in a patient with acquired immune deficiency syndrome. Liver biopsy showed periportal peliotic spindle cell foci that initially were misinterpreted as Kaposi's sarcoma. After antibiotic therapy induced rapid clinical improvement, repeated liver biopsy showed resolution of the previously noted lesions. Although the violaceous skin lesions all appeared similar clinically, some resolved completely and some progressed. One of the latter was biopsied and had the histologic features of Kaposi's sarcoma. The differential diagnosis is discussed.

Distinguishing benign and malignant melanocytic lesions with the AgNOR method

A silver staining technique has recently been devised to aid in the differentiation between benign and malignant melanocytic lesions. This study showed a statistically significant difference between the staining of silver-nucleolar organizer regions (AgNORs) in melanocytic nevi and that of AgNORs in malignant melanomas.

[Epidemiologic data of rupture of the fibular ligament of the upper ankle joint]

Epidemical studies of fibular ligament lesions of the ankle joint lateral ligamentous lesions at the ankle joint are one of the most accidental injuries. It is necessary to bestow great care on prevention and therapy to avoid after effects. We report about 150 cases of acute injuries of the fibular ligament lesions of the ankle joint in 1987 treated by surgery and followed up to explore the cause of injury, its dimensions, the groups of patients and time of accident. Corresponding to literature sports activities were mostly the reason of accidents followed by casional accidents and industrial accidents. Mainly young people suffered from this injury preferring men. The part of reruptures was 14%. In 61.3% both Lig. fibulotal. ant. and Lig. fibulocalc. were ruptured followed by isolated rupture of the Lig. fibulotal.ant. in 32.7% of the cases.

Characterization of an asporogenous mutant of Streptomyces aureofaciens with increased resistance to several aminoglycoside antibiotics

An asporogenous spontaneous mutant of Streptomyces aureofaciens named ASR1 was selected on streptomycin gradient plates. The mutant is very stable and differs in ultrastructure and morphology, it is prototrophic but it lost the ability to grow well on soybean extract medium and produces one-tenth tetracyclines of the parent. The ASR1 mutant has a 3-4-fold increased resistance to streptomycin and is cross-resistant to other aminoglycosides. Comparison of the protein profiles from both strains on SDS gels revealed a very low expression of a 29.5 kDa protein in the ASR1 mutant which is overexpressed in both vegetative cells and spores of the parental strain.

How many EF-Tu molecules participate in aminoacyl-tRNA binding and peptide bond formation in Escherichia coli translation?

We have observed that two EF-Tu.GTP cycles are required to make one peptide bond during steady-state translation in an accurate and fast poly(U) translation system prepared from Escherichia coli. We have also found that there are two complexes of EF-Tu.GTP bound to one molecule of aminoacyl-tRNA under our experimental conditions. We suggest, on the basis of these data, that aminoacyl-tRNA enters the ribosomal A-site in a pentameric complex together with two EF-Tu and two GTP molecules. When the tRNA is delivered to the ribosome two GTP molecules are hydrolyzed. It is possible that the functional role of such an EF-Tu dimer is related to the function of the two L7/L12 dimers in the large ribosomal subunit.

Content, distribution and stability of protein-synthesis elongation factor Tu in subcellular fractions of vegetative cells and spores of Streptomyces aureofaciens

The protein synthesis elongation factor Tu (EF-Tu) was identified in dormant spores of Streptomyces aureofaciens and its content and distribution in vegetative cells and dormant spores were determined. Cell-free homogenates from spores were found to contain a EF-Tu cleaving membrane bound protease. The protease cleaved aggregated EF-Tu much less efficiently than non-aggregated factor in cell homogenates. The relative content of EF-Tu and ribosomes in dormant spores was very similar to that found in exponentially growing vegetative cells.

Molecular properties of elongation factor Tu from Streptomyces aureofaciens and Escherichia coli

Some molecular properties of the elongation factor Tu of protein synthesis purified in an aggregated state from gram-positive Streptomyces aureofaciens were studied and compared with those of Tu from gram-negative Escherichia coli. Electrofocussing under reducing conditions showed that the molecule of EF-Tu from S. aureofaciens has an isoelectric point shifted more to the acidic side compared with EF-Tu from E. coli. A comparison of amino acid composition revealed minor differences in the content of several amino acids in the two factors and showed that EF-Tu from S. aureofaciens contains four half-cystines per molecule. Under denaturing conditions only two mercapto groups reacted with 5,5'-dithiobis(2-nitrobenzoic acid). Limited tryptic digestion of aggregated EF-Tu from S. aureofaciens yields six fragments: the four main fragments are of a similar size as those of the E. coli factor. All fragments detected after trypsin digestion of S. aureofaciens EF-Tu were immunologically cross-reactive with antibodies against E. coli EF-Tu. However, even after 2 h of the reaction there still remains a small part of streptomycete factor uncleaved, which documents high resistance of aggregated EF-Tu towards trypsin.