Discovery of a long-acting glucagon-like peptide-1 analog with enhanced aggregation propensity.

In the course of our search for new GLP-1 analogs, we screened a number of [Ser8]-GLP-1 analogs using the C-terminal helix 3 of the albumin binding domain 3 of protein G from bacterial Streptococcal G strain 148 (G148-ABD3) as appendage. Our efforts led to the discovery of [Ser8]-GLP-1 (7-35)-GVKALIDEILAA-NH2, peptide 6, as a long-acting GLP-1 analog with enhanced self-associated aggregation. Peptide 6 showed enhanced stability in rat and human plasma and an extended half-life of 5.4 h with good bioavailability in rats and subsequently prolonged therapeutic effects in diabetic mice. Analytical ultracentrifugation and TLC suggest that 6 remains oligomeric in the circulation, which accounts for its extended in vivo half-life. The present work shows the possible enhancement of medium-sized oligopeptides aggregation propensity and highlights the potential advantages of peptide aggregates for long-acting peptide drugs.

Surface roughness mediated adhesion forces between borosilicate glass and gram-positive bacteria.

It is well-known that a number of surface characteristics affect the extent of adhesion between two adjacent materials. One of such parameters is the surface roughness as surface asperities at the nanoscale level govern the overall adhesive forces. For example, the extent of bacterial adhesion is determined by the surface topography; also, once a bacteria colonizes a surface, proliferation of that species will take place and a biofilm may form, increasing the resistance of bacterial cells to removal. In this study, borosilicate glass was employed with varying surface roughness and coated with bovine serum albumin (BSA) in order to replicate the protein layer that covers orthopedic devices on implantation. As roughness is a scale-dependent process, relevant scan areas were analyzed using atomic force microscope (AFM) to determine Ra; furthermore, appropriate bacterial species were attached to the tip to measure the adhesion forces between cells and substrates. The bacterial species chosen (Staphylococci and Streptococci) are common pathogens associated with a number of implant related infections that are detrimental to the biomedical devices and patients. Correlation between adhesion forces and surface roughness (Ra) was generally better when the surface roughness was measured through scanned areas with size (2 × 2 µm) comparable to bacteria cells. Furthermore, the BSA coating altered the surface roughness without correlation with the initial values of such parameter; therefore, better correlations were found between adhesion forces and BSA-coated surfaces when actual surface roughness was used instead of the initial (nominal) values. It was also found that BSA induced a more hydrophilic and electron donor characteristic to the surfaces; in agreement with increasing adhesion forces of hydrophilic bacteria (as determined through microbial adhesion to solvents test) on BSA-coated substrates.

Rgg proteins associated with internalized small hydrophobic peptides: a new quorum-sensing mechanism in streptococci.

We identified a genetic context encoding a transcriptional regulator of the Rgg family and a small hydrophobic peptide (SHP) in nearly all streptococci and suggested that it may be involved in a new quorum-sensing mechanism, with SHP playing the role of a pheromone. Here, we provide further support for this hypothesis by constructing a phylogenetic tree of the Rgg and Rgg-like proteins from Gram-positive bacteria and by studying the shp/rgg1358 locus of Streptococcus thermophilus LMD-9. We identified the shp1358 gene as a target of Rgg1358, and used it to confirm the existence of the steps of a quorum-sensing mechanism including secretion, maturation and reimportation of the pheromone into the cell. We used surface plasmon resonance to demonstrate interaction between the pheromone and the regulatory protein and performed electrophoretic mobility shift assays to assess binding of the transcriptional regulator to the promoter regions of its target genes. The active form of the pheromone was identified by mass spectrometry. Our findings demonstrate that the shp/rgg1358 locus encodes two components of a novel quorum-sensing mechanism involving a transcriptional regulator of the Rgg family and a SHP pheromone that is detected and reimported into the cell by the Ami oligopeptide transporter.

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.

BACKGROUND: Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. RESULTS: By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. CONCLUSION: Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold) is available at http://faculty.cs.tamu.edu/shsze/ssfold.

Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae.

Gene expression regulation often involves the recognition of particular DNA or RNA sequences, called motifs. Detection and characterization of such motifs together with biological expertise allow to build gene expression regulatory maps that facilitate the comprehension of complex cellular processes. In this frame, we developed a software integrating relevant information for the detection and characterization of conserved motifs in genomic sequences. A relational database was built up to host data related to genomic information and transcriptional experiments. A user-friendly interface was designed to allow a convenient representation of these data and to run the detection motif program. A set of complementary utilities was also developed to improve the determination of motif consensus sequences and the detection of additional potential regulator targets in the genome.

Phenotypic description and antimicrobial susceptibilities of Aerococcus sanguinicola isolates from human clinical samples.

This report describes the clinical sources and phenotypic characterization of 16 isolates of Aerococcus sanguinicola. Sixteen conventional tests were used to describe and differentiate the 16 isolates of A. sanguinicola from 30 strains of Aerococcus viridans, 27 strains of Aerococcus urinae, and a single strain each of Aerococcus christensenii and Aerococcus urinaehominis. The phenotypic characterizations of the type strains for each species and 14 A. sanguinicola isolates were also compared in the two reference laboratories. A. sanguinicola are catalase-negative, vancomycin-susceptible, gram-positive cocci arranged in clusters and tetrads, as are all Aerococcus species except A. christensenii (which is arranged in short chains). All 16 isolates of A. sanguinicola were leucine aminopeptidase and pyrrolidonylarylamidase positive, which is unique to this species among the aerococci. All A. sanguinicola isolates grew in broth containing 6.5% NaCl, hydrolyzed hippurate, and were variable in the bile-esculin test. None of the isolates deaminated arginine or were Voges-Proskauer positive. The type strain of A. sanguinicola was isolated from a blood culture of a patient living in Denmark. Seven additional isolates were from patients living in Canada, all with urinary tract infections (six were female). Eight isolates were from patients living in five different states in the United States; five were from patients with urinary tract infections, and three were from blood cultures of one patient each with pneumonia, suspected endocarditis, and unknown clinical conditions. The antimicrobial susceptibility patterns were unremarkable; all isolates tested were susceptible to penicillin, amoxicillin, cefotaxime, cefuroxime, erythromycin, chloramphenicol, vancomycin, quinupristin-dalfopristin (Synercid), rifampin, linezolid, and tetracycline. Six of the 15 cultures were resistant to ciprofloxacin and levofloxacin, but all 15 strains were susceptible to sparfloxacin. High-level resistance was detected for meropenem (2 strains) and trimethoprim-sulfamethonazole (1 strain). Intermediate resistance was detected for trimethoprim-sulfamethoxazole (10 strains) and clindamycin (3 strains).

Microencapsulation of Aerococcus viridans with catalase and its application for the synthesis of dihydroxyacetone phosphate.

Dihydroxyacetone phosphate is essential for the synthesis of polyhydroxylated compounds used as components or precursors of active pharmaceutical substances, such as antibiotics or glycosidase inhibitors. Dihydroxyacetone phosphate was produced by enzymatic oxidation of L-alpha-glycerophosphate in the presence of glycerophosphate oxidase or Aerococcus viridans coimmobilized with a hydrogen peroxide-decomposing enzyme. The microencapsulation of A. viridans with catalase in sodium alginate showed a conversion of 98.5%; the conversion percentage remained constant in all five runs. Liquid chromatography of the product revealed that the product peak corresponded to that of the dihydroxyacetone phosphate internal standard. This indicated a high degree of product purity.

Construction of multivalent sialyl Le(x) from the type Ia group B Streptococcus capsular polysaccharide.

The type Ia group B Streptococcus (GBSIa) capsular polysaccharide was specifically degraded by partial Smith oxidation of 2,3-diol of the Glc in the backbone to fragments representing asialo core repeating units. Sialylation of these oligomers furnished GBSIa multiple repeating units. One, two and three repeating units of GBSIa were obtained pure, and the higher oligomers were obtained as mixtures. After enzymatic fucosylation oligosaccharides carrying bivalent, trivalent and other multivalent sialyl Le(x) epitopes presented as appendages on an oligolactoside scaffold were obtained.

On the interpretation of quantitative structure-function activity relationship data for lactate oxidase.

The native flavin, FMN, has been removed from the l-lactate oxidase of Aerococcus viridans, and the apoprotein reconstituted with 12 FMN derivatives with various substituents at the flavin 6- and 8-positions. Impressive linear relationships are exhibited between the sum of the Hammett final sigma(para) and final sigma(ortho) parameters and the redox potentials of the free flavins, and between the redox potentials of the free and enzyme-bound flavins. Rapid reaction kinetics studies of the reconstituted enzymes with the substrates l-lactate and l-mandelate show an increase in the reduction rate constant with increasing redox potential, except that, with lactate, a limiting rate constant of approximately 700 s(-1) is obtained with flavins of high potential. Similar breakpoints are found in plots of the rate constants for flavin N5-sulfite adduct formation and for the reaction of the reduced enzymes with molecular oxygen. These results are interpreted in terms of a two-step equilibrium preceding the chemical reaction step, in which the second equilibrium step provides an upper limit to the rate with which the particular substrate or ligand is positioned with the flavin in the correct fashion for the observed chemical reaction to occur. The relationship of rate constants for flavin reduction and N5-sulfite adduct formation with flavin redox potential below the observed breakpoint indicate development of significant negative charge in the transition states of the reactions. In the case of reduction by substrate, the results are consistent either with a hydride transfer mechanism or with the so called "carbanion" mechanism, in which the substrate alpha-proton is abstracted by an enzyme base protected from exchange with solvent. These conclusions are supported by substrate alpha-deuterium isotope effects and by solvent viscosity effects on sulfite binding.

Endocarditis due to Aerococcus urinae: diagnostic tests, fatty acid composition and killing kinetics.

Two cases of Aerococcus urinae endocarditis are reported. The organism is not included in any database of commercial identification systems at this time. Formation of tetrades and positive reactions for leucine arylamidase and beta-glucuronidase pointed strongly to A. urinae. The cellular fatty acid pattern was similar to that of Aerococcus viridans, with predominantly C16:0, C18:1 omega 9c and C18:0; the presence of C18:1 omega 7t differentiated our isolates from A. viridans and can support the diagnosis of A. urinae. Furthermore, susceptibility to penicillin but resistance to cotrimoxazole represents a pattern opposite to that of A. viridans. Minimal inhibition concentrations of gentamicin and netilmicin were < or = 64 mg/l but those of tobramycin were > or = 256 mg/l. Penicillin combined with either gentamicin or netilmicin showed distinct synergy in killing kinetics. These combinations seem to be the appropriate regimen to treat A. urinae endocarditis.

[A biological model study of the effect of Aerococcus viridans on pathogenic bacteria]. / Vyvchennia na biolohichnykh modeliakh vplyvu Aerococcus viridans na patohenni bakteriï.

Morphological researches studies showed that the treatment of infected skin wounds with Aerobact quickly eliminated inflammation, promoted regeneration of damaged tissues, that actively stimulated formation of granulations. A decrease of S. aureus virulence which completely or partially loose lethal and necrotic activity is one of the reasons of the observed phenomenon. On the model of S. typhimurium infection the expressed protective action of bacteria of Aerococcus genus was shown; this gives us a good prospect in the expansion of the indications for application of probiotic Aerobact.

Conservation of the major cold shock protein in lactic acid bacteria.

Primers designed from consensus regions of the major cold shock gene of different bacterial species were used in PCR amplification of Lactic Acid Bacteria (LAB). An appropriately-sized PCR product was obtained from Lactococcus lactis subsp. lactis LL43-1 and MG1363; Lactococcus lactis subsp. cremoris LC10-1, LC11-1, and LC12-1; Streptococcus thermophilus ST1-1; Enterococcus faecalis EF1-1; Lactobacillus acidophilus LA1-1; Lactobacillus helveticus LH1-1; Pediococcus pentosaceus PP1-1; and Bifidobacterium animalis BA1-1. The PCR products were cloned and sequenced. The deduced amino acid sequences displayed high sequence similarity with the major cold shock proteins of Escherichia coli and Bacillus subtilis and the human Y-box factor. The amino acid residues of the cold shock domain implicated in nucleic acid binding in several unrelated species were also highly conserved in the LAB strains. It is possible, therefore, that this protein in LAB may also act as a transcriptional enhancer to other cold shock genes and/or act as an RNA chaperone unwinding tightly folded RNA molecules.

Modification of peptidoglycan precursors is a common feature of the low-level vancomycin-resistant VANB-type Enterococcus D366 and of the naturally glycopeptide-resistant species Lactobacillus casei, Pediococcus pentosaceus, Leuconostoc mesenteroides, and Enterococcus gallinarum.

The biochemical basis for the acquired or natural resistance of various gram-positive organisms to glycopeptides was studied by high-pressure liquid chromatographic analysis of their peptidoglycan UDP-MurNAc-peptide precursors. In all cases, resistance was correlated with partial or complete replacement of the C-terminal D-Ala-D-Ala-containing UDP-MurNAc-pentapeptide by a new precursor with a modified C terminus. Nuclear magnetic resonance analysis by sequential assignment showed that the new precursor encountered in Enterococcus faecium D366, a strain belonging to the VANB class, which expresses low-level resistance to vancomycin, was UDP-MurNAc-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-lactate, identical to that previously found in the VANA class, which expresses high-level resistance to vancomycin. High-pressure liquid chromatographic analyses, composition determinations, and digestion by R39 D,D-carboxypeptidase demonstrated the exclusive presence of the new precursor in Lactobacillus casei and Pediococcus pentosaceus, which are naturally highly resistant to glycopeptides. The low-level natural resistance of Enterococcus gallinarum to vancomycin was found to be associated with the synthesis of a new precursor identified as a UDP-MurNAc-pentapeptide containing a C-terminal D-serine. The distinction between low and high levels of resistance to glycopeptides appeared also to depend on the presence or absence of a substantial residual pool of a D-Ala-D-Ala-containing UDP-MurNAc-pentapeptide.

Use of low molecular mass RNA profiles to identify lactic acid bacteria and related organisms associated with foods.

Fourteen strains of lactic acid bacteria and species of Brochothrix, Carnobacterium, Enterococcus, Erysipelothrix, Kurthia and Listeria were examined using low molecular mass RNA (5S rRNA and tRNA) profiles. These profiles were developed on denaturing polyacrylamide gels. Gel strengths between 9 and 14% were tested to improve resolution of distinct bands for densitometrical analysis. Profiles generated on 12% gels proved to be the best for scanning. Scans of class 2 tRNAs by densitometry showed a characteristic profile for each genus. In the case of Lactobacillus each species studied gave a unique profile. The technique of low molecular mass RNA profiling may provide a useful means for identifying different bacteria from ecosystems such as meats.