Comparative analysis and insights into the evolution of gene clusters for glycopeptide antibiotic biosynthesis

The bal, cep, dbv, sta and tcp gene clusters specify the biosynthesis of the glycopeptide antibiotics balhimycin, chloroeremomycin, A40926, A47934 and teicoplanin, respectively. These structurally related compounds share a similar mechanism of action in their inhibition of bacterial cell wall formation. Comparative sequence analysis was performed on the five gene clusters. Extensive conserved synteny was observed between the bal and cep clusters, which direct the synthesis of very similar compounds but originate from two different species of the genus Amycolatopsis. All other cluster pairs show a limited degree of conserved synteny, involving biosynthetically functional gene cassettes: these include those involved in the synthesis of the carbon backbone of two non-proteinogenic amino acids; in the linkage of amino acids 1–3 and 4–7 in the heptapeptide; and in the formation of the aromatic cross-links. Furthermore, these segments of conserved synteny are often preceded by conserved intergenic regions. Phylogenetic analysis of protein families shows several instances in which relatedness in the chemical structure of the glycopeptides is not reflected in the extent of the relationship of the corresponding polypeptides. Coherent branchings are observed for all polypeptides encoded by the syntenous gene cassettes. These results suggest that the acquisition of distinct, functional genetic elements has played a significant role in the evolution of glycopeptide gene clusters, giving them a mosaic structure. In addition, the synthesis of the structurally similar compounds A40926 and teicoplanin appears as the result of convergent evolution.     

Fragile X mental retardation protein (FMRP) binds specifically to the brain cytoplasmic RNAs BC1/BC200 via a novel RNA-binding motif

Fragile X mental retardation protein (FMRP), the protein responsible for the fragile X syndrome, is an RNA-binding protein involved in localization and translation of neuronal mRNAs. One of the RNAs known to interact with FMRP is the dendritic non-translatable brain cytoplasmic RNA 1 BC1 RNA that works as an adaptor molecule linking FMRP and some of its regulated mRNAs. Here, we showed that the N terminus of FMRP binds strongly and specifically to BC1 and to its potential human analog BC200. This region does not contain a motif known to specifically recognize RNA and thus constitutes a new RNA-binding motif. We further demonstrated that FMRP recognition involves the 5' stem loop of BC1 and that this is the region that exhibits complementarity to FMRP target mRNAs, raising the possibility that FMRP plays a direct role in BC1/mRNA annealing.     

Neuroglobin and cytoglobin in search of their role in the vertebrate globin family

Neuroglobin and cytoglobin are two recent additions to the family of heme-containing respiratory proteins of man and other vertebrates. Here, we review the present state of knowledge of the structures, ligand binding kinetics, evolution and expression patterns of these two proteins. These data provide a first glimpse into the possible physiological roles of these globins in the animal's metabolism. Both, neuroglobin and cytoglobin are structurally similar to myoglobin, although they contain distinct cavities that may be instrumental in ligand binding. Kinetic and structural studies show that neuroglobin and cytoglobin belong to the class of hexa-coordinated globins with a biphasic ligand-binding kinetics. Nevertheless, their oxygen affinities resemble that of myoglobin. While neuroglobin is evolutionarily related to the invertebrate nerve-globins, cytoglobin shares a more recent common ancestry with myoglobin. Neuroglobin expression is confined mainly to brain and a few other tissues, with the highest expression observed in the retina. Present evidence points to an important role of neuroglobin in neuronal oxygen homeostasis and hypoxia protection, though other functions are still conceivable. Cytoglobin is predominantly expressed in fibroblasts and related cell types, but also in distinct nerve cell populations. Much less is known about its function, although in fibroblasts it might be involved in collagen synthesis.     

An oxygen imaging system for medical applications: preliminary results.

The examination of functional processes in tissue is gaining importance in medical research. As a result the imaging and monitoring of biochemical parameters in vivo is the goal of many imaging methods. One key parameter in photodynamic therapy (PDT) is the molecular oxygen concentration. Two-dimensional monitoring of oxygen is demanded for PDT but has not yet been achieved. The use of optical methods provides a possible means of measuring molecular oxygen. The basis of this method is the measurement of the luminescence lifetime of a dye that is quenched by molecular oxygen. The molecular oxygen concentration can be monitored two-dimensionally by pixel-wise determination of the luminescence lifetime with a CCD-camera. A new O(2)-imaging system based on this principle is presented in this article. The dye Ru(bpy)(3)(2+) is quenched by molecular oxygen and was used in the first experiments with the system.     

Biosynthesis of chondroitin sulfate side chains and hyaluronate time-course studies with cartilage slices of calf ribs under different conditions

The time course of double labeling with ³⁵SO₄²⁻ and [³H]glucosamine was followed in a semi-in vitro system of cartilage slices from calf ribs whose chondroitin sulfate peptide pool consistsof (A) <1% of very short undersulfated side chains of <10 disaccharide units length, (B) 3–5% of short undersulfated longer side chains (16 to 25 disaccharide units), (C) 3–5% of short, slightly oversulfated side chains (16–23 dissacharide units, very probably containing some dermatan sulfate), (D) the bulk material (74–82% of total uronate) of longest, slightly undersulfated or equally sulfated side chains (22–42 disaccharide units).After 10 min incubation rapid chain elongation with [³H]glucosamine and prelabeling with ³⁵SO₄²⁻ of endogenous acceptors are apparent. Chains of type A exhibit highest specific radioactivities. During 30–60 min incubation it is mainly chains of type B that show highest specific radioactivities, after 90 min chains of type C. On the after hand, chains of type D always incorporated the highest total amount of both precursors. Preincubation of slices for 40 min at 37°C strongly enhances labeling rates of all types whilst preincubation for 40 min in an ice-bath enhances mainly ³⁵SO₄²⁻ labeling of types A and B.After 10 min preincubation followed by ³⁵SO₄²⁻ labeling for 60 min a decrease of radioactivity of type A and a distinct increase with type B are observed during the post incubation period. After pulse chase experiment type B exhibit highest specific radioactivities. The data make it evident that under-sulfated short chondroitin sulfate side chains from very rapidly in a well organised manner and grow, by elongation and proceeding sulfation processes, to longer higher sulfated chains.The labeling of the hyaluronate pool is about half of that of the chondroitin sulfate pool after a lag phase of 10 min. The latter increases linearly after 35–45 min incubation time. However, after preincubation and chase experiments the hyaluronate pool is more highly labeled. The data indicate different precursor pools of both biosynthesis mechanisms, probably located in different cell compartments and/or different cartilage cells.     

Binding of Cholecystokinin-8 (CCK-8) Peptide Derivatives to CCKA and CCKB Receptors

Abstract: The structural requirements for the selective binding of cholecystokinin-8 (CCK-8)-related peptides to peripheral (CCK_A) receptors are not sufficiently understood. In this study, the interaction of a series of newly shortened analogues of CCK-8 with both receptor subtypes was analyzed by displacement studies using [³H]-CCK-8 and ¹²⁵l-Bolton-Hunter (BH)-CCK-8 as radioligands. The pentapeptide derivative of CCK-8, succinyl-Tyr (SO₃H)-Met-Gly-Trp-Met-phenethylamide, was found to bind selectively with high affinity to the CCK_A receptor. The replacement of Met²⁸ and/or Met³¹ by norleucine and of L-Trp³⁰ by its D-analogue had no significant effect on the binding properties of the peptide. Further C-terminal shortening resulted in a drastic loss of affinity and selectivity of the CCK receptor binding.     

Neutralizing interferon β antibodies in melanoma patients treated with recombinant and natural interferon β

The incidence and clinical significance of therapy-induced neutralizing interferon (IFNß) antibodies was studied in a group of 21 melanoma patients treated with natural IFNß and 7 patients treated with recombinant IFNß. They were treated subcutaneously with 3×10⁶ IU three times per week in an adjuvant open trial for 24 weeks after surgical removal of all detectable metastases. Of the 21 patients treated with natural IFNß, 95% developed significant levels of neutralizing antibodies after 24 weeks. In comparison, 28% of the 7 patients treated with recombinant IFNß developed neutralizing IFNß antibodies. Cross-reactivity of the antibodies could be demonstrated. Persistence of antibody titers was seen in 80% of the patients 24 weeks after cessation of treatment with natural IFNß. No correlation between the maximum antibody titers and the antibody persistence after cessation of therapy could be established. We detected a clear correlation between the formation of neutralizing antibodies and the decrease in 2-microglobulin and 2,5-oligoadenylate synthease and therefore the drop in biological activity. In this adjuvant trial there was no difference in relapse rate and time until relapse between antibody-positive and antibody-negative patients. No difference in clinical outcome could be established between the patients treated with natural IFNß and recombinant IFNß.     

Selective attraction and reproductive performance of a harpacticoid copepod in a response to biofilms

The relationship between monobacterial films and the preference of harpacticoid copepods for such films was investigated using still water multiple-choice assays with natural biofilm and sterile conditions as controls. Adult Schizopera sp. were most attracted by a heterogeneous natural biofilm, followed by monospecies-biofilms of Rhodovulum sp., Vibrio proteolyticus, and Flexibacter sp. The preferred bacterial films stemmed from different phylogenetic and physiological groups. The results indicated that the harpacticoid Schizopera sp. was effectively and differentially attracted by bacterial films. Since bacteria constitute a substantial portion of the organic carbon available at the sea bottom as nutritive sources for harpacticoid copepods, we subsequently examined the influence of 9 bacterial strains and a natural biofilm as a nutrient source on the growth and reproductive performance of ontogenetic stages (nauplii and copepodids) of Schizopera sp. The food value of bacterial strains was assayed in terms of life table data that provided growth parameters. All variables were affected by the type of food offered. A diet on Rhodovulum sp. resulted in optimal growth performance of nauplii and copepodids demonstrating that bacteria can be used as a sole diet to support postembryonic development. The present study is the first to link behavioral preferences to bacterial biofilms with life history parameters when cultivating harpacticoid copepods on the same bacterial strains as the only diet. This study revealed a discrepancy between the biofilm favored (natural biofilm) and the one leading to maximal reproductive performance (monobacterial film of Rhodovulum sp. MB253) as indicated by major life table data as net reproductive rate (R_o), mean generation time (T_m), and capacity for increase (r_c).     

Genome-scale metabolic representation of Amycolatopsis balhimycina

Infection caused by methicillin-resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin biosynthesis in Amycolatopsis balhimycina. The balhimycin yield obtained by A. balhimycina is, however, low and there is therefore a need to improve balhimycin production. In this study, we performed genome sequencing, assembly and annotation analysis of A. balhimycina and further used these annotated data to reconstruct a genome-scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC-genome (～ 69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR for functional annotation and then integrated annotated data with biochemical and physiological information available for this organism to reconstruct a genome-scale metabolic model of A. balhimycina. The resulting metabolic model contains 583 ORFs as protein encoding genes (7% of the predicted 8,585 ORFs), 407 EC numbers, 647 metabolites and 1,363 metabolic reactions. During the analysis of the metabolic model, linear, quadratic and evolutionary programming algorithms using flux balance analysis (FBA), minimization of metabolic adjustment (MOMA), and OptGene, respectively were applied as well as phenotypic behavior and improved balhimycin production were simulated. The A. balhimycina model shows a good agreement between in silico data and experimental data and also identifies key reactions associated with increased balhimycin production. The reconstruction of the genome-scale metabolic model of A. balhimycina serves as a basis for physiological characterization. The model allows a rational design of engineering strategies for increasing balhimycin production in A. balhimycina and glycopeptide production in general.     

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

Tandem affinity purification (TAP) is a generic two-step affinity purification protocol that enables the isolation of protein complexes under close-to-physiological conditions for subsequent analysis by mass spectrometry. Although TAP was instrumental in elucidating the yeast cellular machinery, in mammalian cells the method suffers from a low overall yield. We designed several dual-affinity tags optimized for use in mammalian cells and compared the efficiency of each tag to the conventional TAP tag. A tag based on protein G and the streptavidin-binding peptide (GS-TAP) resulted in a tenfold increase in protein-complex yield and improved the specificity of the procedure. This allows purification of protein complexes that were hitherto not amenable to TAP and use of less starting material, leading to higher success rates and enabling systematic interaction proteomics projects. Using the well-characterized Ku70-Ku80 protein complex as an example, we identified both core elements as well as new candidate effectors.