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Synthetic bacterial lipopeptide analogs: structural requirements for adjuvanticity.

Modern vaccines aim at conferring immune protection, independently of the nature of the etiological agent causing the disease. These new therapeutics are based on highly purified antigenic moieties that offer potential advantages over traditional vaccines, including a high degree of safety and the capacity of eliciting highly specific immune responses. In spite of these advantages however, subunit vaccines tend to be poorly immunogenic in vivo, and require the coadministration of adjuvants that indirectly enhance cellular immunity. Thus, recombinant vaccines development is dependent on the design of new molecules, non-immunogenic per se, but endowed with immune modulatory properties. Synthetic analogs of bacterial lipoproteins were described more than a decade ago, but their capacity to act as adjuvants has been only recently dissected. These low molecular weight non-immunogenic molecules can be reproducibly synthetized, are safe, and of easy handling and administration. Furthermore, new experimental data from our laboratory reveal their powerful adjuvant effect on human HLA-I/II restricted T cell responses and identify the molecular and cellular requirements for optimal adjuvanticity.

Adjuvants, Immunologic↗

Structure of a bacterial photosynthetic membrane. Isolation, polypeptide composition, and selective proteolysis.

A procedure for the isolation of highly purified bacterial photosynthetic membranes from Rhodopseudomonas viridis is described. The purity of the final membrane fraction has been confirmed by electron microscopy. Seven major polypeptide bands are associated with the photosynthetic membranes, and all seven are resistant to solubilization in Triton X-100 detergent. Two pigmented bands with apparent molecular weights of 44K and 41K are thought to be cytochromes. The three polypeptides with apparent molecular weights of 38K, 32K, and 28K have been reported in reaction center preparations of other laboratories. Two low-molecular-weight (16K and 11K) bands bind bacteriochlorophyll b and may represent light-harvesting bacteriochlorophyll-protein complexes. The structures that were isolated seem to represent complete photosynthetic membranes, consisting of reaction center, electron transport, and light-harvesting components, all arranged in the regular lattice characteristic of viridis. Selective proteolysis of these membranes indicates that all membrane components are accessible to digestion by trypsin and pronase, except for the light-harvesting complexes.

Bacterial Proteins↗

Mutational analysis of the glycine-binding site of the NMDA receptor: structural similarity with bacterial amino acid-binding proteins.

Activation of the NMDA subtype of ionotropic glutamate receptors requires binding of both L-glutamate and the coagonist glycine. Site-directed mutagenesis of the NMDAR1 (NR1) subunit revealed that aromatic residues at positions 390, 392, and 466 are crucial determinants of glycine binding. Glutamate efficacy was little affected by mutations at these positions; however, inhibition of channel gating by the glycine antagonist 7-chlorokynurenic acid was drastically reduced. In addition, glutamine (Q387), valine (V666), and serine (S669) substitutions were found to reduce glycine efficacy. Since the mutated residues correspond to positions forming the binding site of homologous bacterial amino acid-binding proteins, a common amino acid-binding fold appears to be conserved from prokaryotic periplasmic proteins to glutamate receptors in the mammalian brain.

Amino Acid Sequence↗

Monitoring of bacterial growth and structural analysis as probed by FT-IR spectroscopy.

Fourier-transform infrared spectroscopy was used to explore structural changes in bacteria under different incubation conditions. In particular, differences between Bradyrhizobium japonicum (BRJ) grown in liquid and on solid media were investigated, as well as the rearrangement of BRJ after transfer from one medium to the other. The FT-IR absorption bands located between 1200 and 900 cm-1 region, vary in spectral shape and intensity when BRJ were suspended in solution medium or plated on solid medium. In agreement with the electronic micrograph data, these spectroscopic changes are due to the changes involving the bacterial wall (peptidoglycan) when BRJ are plated in agar medium. By means of this FT-IR ultrastructural study of Bradyrhizobium japonicum bacteria, it has been possible to follow and to evaluate the rate of the molecular change in bacteria without any destructive interference. This indicates that FT-IR spectroscopy can prove to be a valuable technique in the monitoring of metabolic events in bacterial cells relevant to agriculture as well as environmental and health sciences.

Agar↗

[Antigenic bacterial polysaccharides. 14. Structure of the O-specific polysaccharide chain of a lipopolysaccharide from Pseudomonas aeruginosa (Lányi)].

The lipopolysaccharide from Pseudomonas aeruginosa O12 (Lányi classification) gave on mild acid hydrolysis an O-specific polysaccharide built of D-ribose and N-acetyl-D-galactosamine. The disaccharide structure----4)-alpha-GalNAcp-(1----2)-beta-Ribf-(1----for the repeating unit of the polysaccharide was established by nondestructive way involving full interpretation of its 1H- and 13C-NMR-spectra, using homonuclear and selective heteronuclear 13C[1H] double resonances.

Antigens, Bacterial↗

Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling.

The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when bacteria switch their swimming mode between running and tumbling. Supercoiling is produced by two different packing interactions of flagellin called L and R. In switching from L to R, the intersubunit distance ( approximately 52 A) along the protofilament decreases by 0.8 A. Changes in the number of L and R protofilaments govern supercoiling of the filament. Here we report the 2.0 A resolution crystal structure of a Salmonella flagellin fragment of relative molecular mass 41,300. The crystal contains pairs of antiparallel straight protofilaments with the R-type repeat. By simulated extension of the protofilament model, we have identified possible switch regions responsible for the bi-stable mechanical switch that generates the 0.8 A difference in repeat distance.

Crystallography, X-Ray↗

Role of bacterial cell surface structures in Escherichia coli biofilm formation.

Various cell surface molecules and structures have been implicated in biofilm formation in Escherichia coli. This review presents an overview of the occurrence, production and interaction of these components, their influence at one or more developmental stages of biofilm formation, and their potential role as virulence factors in pathogenic E. coli strains.

Biofilms↗

New types of liposidomycins produced by Streptomyces that inhibit bacterial peptidoglycan synthesis. Structure elucidation of fatty acid components by tandem mass spectrometry.

The structures of the fatty acid components of various new liposidomycins were determined using tandem mass spectrometry; the negative FAB/MS/MS/MS technique for liposidomycins with a 3-methylglutaric acid moiety and the negative FAB/MS/MS technique for liposidomycins without a 3-methylglutaric acid moiey. This structural information was obtained by analysis of peaks due to charge-remote fragmentations for 3-hydroxycarboxylate anions or carboxylate anions which were generated from liposidomycin molecules in a mass spectrometer. The MS/MS/MS technique that can exclude the matrix-derived and/or interfering ions showed higher sensitivity than the MS/MS technique.

Aminoglycosides↗

Morpho-structural variations of bacterial spores after treatment in steam vacuum assisted autoclave.

This study intended to verify, through microbiological techniques and TEM investigations, the killing of bacterial spores after treatment in steam autoclave, and to propose strictly morphological considerations about the target of this sterilisation process. Autoclave is the most common device for sterilising instruments in order to prevent cross infections in dental offices. The autoclave efficiency has been improved in the last years and part of this improvement is related to both a better and more correct use of the autoclave system and to the technological innovations introduced in the last generation of devices. However, associations as ADA or CDC suggest to regularly verify the process of 'autoclaving' through biological indicators (BI). The most commonly used BI are made of spores strips or suspensions of Bacillus Subtilis (pb 168) and Bacillus Stearothermophilus (ATCC 10149). They visually prove, changing colours on enzymatic base, the death of micro-organism and if the physical parameters, necessary for sterilisation, have been achieved. These two strains of endospore-forming bacteria were processed and prepared following two different techniques: Karnovsky fixed and epon embedded--phosphotungstic acid fixed for direct observation. The kind and the extent of analysed modifications are extremely various: from deep lacerations, which changed the spore structure, to little clefts which let the cytoplasm go out.

Bacillus subtilis↗

Nucleoprotein structures at positively regulated bacterial promoters: homology with replication origins and some hypotheses on the quaternary structure of the activator proteins in these complexes.

The quaternary structure of regulatory proteins undoubtedly plays an important role in the initiation of transcription and DNA replication. To date, the best-characterized regulatory proteins are oligomers in which promoters are bound together by isologous interactions. From the examples presented in this article, it appears that the formation of certain nucleoprotein complexes implicated in transcription initiation might involve heterologous rather than isologous interactions, allowing differentiation between two classes of transcription activators. Nucleoprotein structures present at the oriC replication origin and at malB promoters show striking homologies.

Bacteria↗

Sorbistin, a new aminoglycoside antibiotic complex of bacterial origin. III. Structure determination.

The structures of sorbistins A1, A2, B, C and D have been determined including stereo-chemistry. Sorbistins A1, A2 and B are composed of a 4-acyl-amino-4-deoxy-D-glucose and 1,4-diamino-1,4-dideoxy-D-sorbitol, the latter compound being hitherto undescribed in literature. Sorbistins C and D have the same aglycone of 1,4-diamino-1,4-dideoxy-D-sorbitol, which is linked with D-glucose and 4-amino-4-deoxy-D-glucose, respectively, through a glycosidic bond.

Aminoglycosides↗

Structural studies on bacterial luciferase using energy transfer and emission anisotropy.

The distance between specific sites on bacterial luciferase was estimated by energy transfer. Luciferase was fluorescently labeled by reaction of an essential sulfhydryl group with N-(1-pyrene)maleimide and N-[p-(2-benzoxazolyl)phenyl]meleimide. Both of the modified enzymes bind 8-anilino-1-naphthalenesulfonate (Ans) with affinities similar to that exhibited by the native luciferase. Using each of the two fluorescent probes as a donor and the bound Ans as an acceptor, the energy transfer efficiencies were determined by the resulting enhancement of fluorescence of the acceptor. The corresponding distance was calculated to be in the range of 21 to 37 A. Energy-transfer studies were also carried out using fluorescence lifetime measurements of bound ANS, acting as a donor with bound FMN as an acceptor. The corresponding distance was calculated to be between 30 and 58 A. Using samples of luciferase:Ans complex and luciferase modified with N-(1-pyrene)maleimide, the rotational correlation time of the enzyme-dye conjugate as awhole was found to be 47 +/- 2 ns. The observed rotational correlation time is much longer than that calculated for luciferase assuming a spherical structure, thus indicating an elongated form for the luciferase-dye conjugate.

Anilino Naphthalenesulfonates↗

Biosynthesis of bacterial glycogen. Primary structure of Escherichia coli 1,4-alpha-D-glucan:1,4-alpha-D-glucan 6-alpha-D-(1, 4-alpha-D-glucano)-transferase as deduced from the nucleotide sequence of the glg B gene.

The nucleotide sequence of the glg B gene, coding for branching enzyme (EC 2.4.1.18), was elucidated. It consists of 2181 base pairs specifying a protein of 727 amino acids. The deduced amino acid sequence was consistent with the amino acid analysis that was obtained with the pure protein as well as with the molecular weight determined from sodium dodecyl sulfate-gel electrophoresis. The deduced amino acid sequence was also consistent with the amino-terminal amino acid sequence and the amino acid sequence analysis of various peptides obtained from CNBr degradation of purified branching enzyme.

1,4-alpha-Glucan Branching Enzyme↗

Photoemission and near-edge X-ray absorption fine structure studies of the bacterial surface protein layer of Bacillus sphaericus NCTC 9602.

The electronic structure of the regular, two-dimensional bacterial surface protein layer of Bacillus sphaericus NCTC 9602 has been examined by photoemission (PE) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Both the O 1s and the N 1s core-level PE spectra show a single structure, whereas the C 1s core-level spectrum appears manifold, suggesting similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in the different functional groups of the amino acids. This result is supported by the element-specific NEXAFS spectra of the unoccupied valence electronic states, which exhibit a series of characteristic NEXAFS peaks that can be assigned to particular molecular orbitals of the amino acids by applying a phenomenological building-block model. The relative contributions of the C-O, C-N, and C-C bond originating signals into the C 1s PE spectrum are in good agreement with the number ratios of the corresponding bonds calculated from the known primary structure of the bacterial surface protein. First interpretation of the PE spectrum of the occupied valence states is achieved on the basis of electronic density-of-states calculations performed for small peptides. It was found that mainly the pi clouds of the aromatic rings contribute to both the lowest unoccupied and the highest occupied molecular orbitals.

Amino Acids↗

Vanadate inhibits the ATPase activity and DNA binding capability of bacterial MutS. A structural model for the vanadate-MutS interaction at the Walker A motif.

MutS, a member of the ABC ATPases superfamily, is a mismatch DNA-binding protein constituent of the DNA post-replicative mismatch repair system (MMRS). In this work, it is shown that the ATPase activity of Pseudomonas aeruginosa and Escherichia coli MutS is inhibited by ortho- and decavanadate. Structural comparison of the region involved in the ATP binding of E.coli MutS with the corresponding region of other ABC ATPases inhibited by vanadate, including the myosin- orthovanadate-Mg complex, showed that they are highly similar. From these results it is proposed that the orthovanadate inhibition of MutS ATPase can take place by a similar mechanism to that described for other ATPases. Docking of decavanadate on the ATP-binding region of MutS showed that the energetically more favorable interaction of this compound would take place with the complex MutS- ADP-Mg, suggesting that the inhibitory effect could be produced by a steric impediment of the protein ATP/ADP exchange. Besides the effect observed on the ATPase activity, vanadate also affects the DNA-binding capability of the protein, and partially inhibits the oligomerization of MutS and the temperature-induced inactivation of the protein. From the results obtained, and considering that vanadate is an intracellular trace component, this compound could be considered as a new modulator of the MMRS.

Adenosine Diphosphate↗

Biosynthesis of bacterial glycogen: primary structure of Salmonella typhimurium ADPglucose synthetase as deduced from the nucleotide sequence of the glgC gene.

The nucleotide sequence of a 1.4-kilobase-pair fragment containing the Salmonella typhimurium LT2 glgC gene coding for ADPglucose synthetase was determined. The glgC structural gene contains 1,293 base pairs, having a coding capacity of 431 amino acids. The amino acid sequence deduced from the nucleotide sequence shows that the molecular weight of ADPglucose synthetase is 45,580. Previous results of the total amino acid composition analysis and amino acid sequencing (M. Lehmann and J. Preiss, J. Bacteriol. 143:120-127, 1980) of the first 27 amino acids from the N terminus agree with that deduced from nucleotide sequencing data. Comparison of the Escherichia coli K-12 and S. typhimurium LT2 ADPglucose synthetase shows that there is 80% homology in their nucleotide sequence and 90% homology in their deduced amino acid sequence. Moreover, the amino acid residues of the putative allosteric sites for the physiological activator fructose bisphosphate (amino acid residue 39) and inhibitor AMP (amino acid residue 114) are identical between the two enzymes. There is also extensive homology in the putative ADPglucose binding site. In both E. coli K-12 and S. typhimurium LT2, the first base of the translational start ATG of glgA overlaps with the third base TAA stop codon of the glgC gene.

Amino Acid Sequence↗

Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S-transferase supergene family.

The nucleotide sequence of a cloned 2.8-kilobase-pair BamHI-PstI fragment containing dcmA, the dichloromethane dehalogenase structural gene from Methylobacterium sp. strain DM4, was determined. An open reading frame with a coding capacity of 287 amino acids (molecular weight, 37,430) was identified as dcmA by its agreement with the N-terminal amino acid sequence, the total amino acid composition, and the subunit size of the purified enzyme. Alignment of the deduced dichloromethane dehalogenase amino acid sequence with amino acid sequences of the functionally related eucaryotic glutathione S-transferases revealed three regions containing highly conserved amino acid residues and indicated that dcmA is a member of the glutathione S-transferase supergene family. The 5' terminus of in vivo dcmA transcripts was determined by nuclease S1 mapping to be 82 base pairs upstream of the GTG initiation codon of dcmA. Despite a putative promoter sequence with high resemblance to the Escherichia coli -10 and -35 consensus sequences, located at an appropriate distance from the transcription start point, dcmA was only marginally expressed in E. coli. The strong induction of dichloromethane dehalogenase in Methylobacterium sp. by dichloromethane was abolished by deleting the 1.3-kilobase-pair upstream region of dcmA. Plasmid constructs devoid of this region directed expression of dichloromethane dehalogenase at a constitutively induced level.

Amino Acid Sequence↗