The obligate predatory Bdellovibrio bacteriovorus possesses a neutral lipid A containing alpha-D-Mannoses that replace phosphate residues: similarities and differences between the lipid As and the lipopolysaccharides of the wild type strain B. bacteriovorus HD100 and its host-independent derivative HI100

Structural characterization of bacterial lipopolysaccharides with mass spectrometry and on- and off-line separation techniques

The focus of this review is the application of mass spectrometry to the structural characterization of bacterial lipopolysaccharides (LPSs), also referred to as "endotoxins," because they elicit the strong immune response in infected organisms. Recently, a wide variety of MS-based applications have been implemented to the structure elucidation of LPS. Methodological improvements, as well as on- and off-line separation procedures, proved the versatility of mass spectrometry to study complex LPS mixtures. Special attention is given in the review to the tandem mass spectrometric methods and protocols for the analyses of lipid A, the endotoxic principle of LPS. We compare and evaluate the different ionization techniques (MALDI, ESI) in view of their use in intact R- and S-type LPS and lipid A studies. Methods for sample preparation of LPS prior to mass spectrometric analysis are also described. The direct identification of intrinsic heterogeneities of most intact LPS and lipid A preparations is a particular challenge, for which separation techniques (e.g., TLC, slab-PAGE, CE, GC, HPLC) combined with mass spectrometry are often necessary. A brief summary of these combined methodologies to profile LPS molecular species is provided.

Isolation and classification of Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are obligate predators of Gram-negative bacteria. BALOs are isolated as plaques growing at the expense of their prey and are cultivated as two-member cultures. The growth cycle is composed of an extracellular attack phase and an intraperiplasmic elongation and replication phase. However, there are methods for obtaining host-independent (HI) mutants that grow without prey on rich media. BALOs are commonly found in the environment but generally constitute small populations; therefore, their isolation may require enrichment steps. Contamination by other bacteria during isolation necessitates efficient separation between the smaller BALO cells from the majority of larger bacteria. BALOs can also be directly detected and quantified in environmental samples using specific PCR. Synchronous cultures of both wild-type and HI derivatives can be obtained to study the different growth phases. These can be further separated by centrifugation. Classification is based on 16S rDNA analysis. Protocols relevant to these aspects of BALO detection, isolation, growth, classification, and quantitation are presented in this unit.

Chemical analysis of cellular and extracellular carbohydrates of a biofilm-forming strain Pseudomonas aeruginosa PA14

Background

Pseudomonas aeruginosa is a Gram-negative bacterium and an opportunistic pathogen, which causes persisting life-threatening infections in cystic fibrosis (CF) patients. Biofilm mode of growth facilitates its survival in a variety of environments. Most P. aeruginosa isolates, including the non-mucoid laboratory strain PA14, are able to form a thick pellicle, which results in a surface-associated biofilm at the air-liquid (A–L) interface in standing liquid cultures. Exopolysaccharides (EPS) are considered as key components in the formation of this biofilm pellicle. In the non-mucoid P. aeruginosa strain PA14, the “scaffolding” polysaccharides of the biofilm matrix, and the molecules responsible for the structural integrity of rigid A–L biofilm have not been identified. Moreover, the role of LPS in this process is unclear, and the chemical structure of the LPS O-antigen of PA14 has not yet been elucidated.

Principal Findings

In the present work we carried out a systematic analysis of cellular and extracellular (EC) carbohydrates of P. aeruginosa PA14. We also elucidated the chemical structure of the LPS O-antigen by chemical methods and 2-D NMR spectroscopy. Our results showed that it is composed of linear trisaccharide repeating units, identical to those described for P. aeruginosa Lanýi type O:2a,c (Lanýi-Bergman O-serogroup 10a, 10c; IATS serotype 19) and having the following structure: -4)-α-L-GalNAcA-(1–3)-α-D-QuiNAc-(1–3)- α-L-Rha-(1-. Furthermore, an EC O-antigen polysaccharide (EC O-PS) and the glycerol-phosphorylated cyclic β-(1,3)-glucans were identified in the culture supernatant of PA14, grown statically in minimal medium. Finally, the extracellular matrix of the thick biofilm formed at the A-L interface contained, in addition to eDNA, important quantities (at least ∼20% of dry weight) of LPS-like material.

Conclusions

We characterized the chemical structure of the LPS O-antigen and showed that the O-antigen polysaccharide is an abundant extracellular carbohydrate of PA14. We present evidence that LPS-like material is found as a component of a biofilm matrix of P. aeruginosa.

Structural investigation of bacterial lipopolysaccharides by mass spectrometry and tandem mass spectrometry

Mass spectrometric studies are now playing a leading role in the elucidation of lipopolysaccharide (LPS) structures through the characterization of antigenic polysaccharides, core oligosaccharides and lipid A components including LPS genetic modifications. The conventional MS and MS/MS analyses together with CID fragmentation provide additional structural information complementary to the previous analytical experiments, and thus contribute to an integrated strategy for the simultaneous characterization and correct sequencing of the carbohydrate moiety.

The structure of a novel neutral lipid A from the lipopolysaccharide of Bradyrhizobium elkanii containing three mannose units in the backbone

The chemical structure of the lipid A of the lipopolysaccharide (LPS) from Bradyrhizobium elkanii USDA 76 (a member of the group of slow-growing rhizobia) has been established. It differed considerably from lipids A of other Gram-negative bacteria, in that it completely lacks negatively charged groups (phosphate or uronic acid residues); the glucosamine (GlcpN) disaccharide backbone is replaced by one consisting of 2,3-dideoxy-2,3-diamino-D-glucopyranose (GlcpN3N) and it contains two long-chain fatty acids, which is unusual among rhizobia. The GlcpN3N disaccharide was further substituted by three D-mannopyranose (D-Manp) residues, together forming a pentasaccharide. To establish the structural details of this molecule, 1D and 2D NMR spectroscopy, chemical composition analyses and high-resolution mass spectrometry methods (electrospray ionisation Fourier-transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) and tandem mass spectrometry (MS/MS)) were applied. By using 1D and 2D NMR spectroscopy experiments, it was confirmed that one D-Manp was linked to C-1 of the reducing GlcpN3N and an alpha-(1-->6)-linked D-Manp disaccharide was located at C-4' of the non-reducing GlcpN3N (alpha-linkage). Fatty acid analysis identified 12:0(3-OH) and 14:0(3-OH), which were amide-linked to GlcpN3N. Other lipid A constituents were long (omega-1)-hydroxylated fatty acids with 26-33 carbon atoms, as well as their oxo forms (28:0(27-oxo) and 30:0(29-oxo)). The 28:0(27-OH) was the most abundant acyl residue. As confirmed by high-resolution mass spectrometry techniques, these long-chain fatty acids created two acyloxyacyl residues with the 3-hydroxy fatty acids. Thus, lipid A from B. elkanii comprised six acyl residues. It was also shown that one of the acyloxyacyl residues could be further acylated by 3-hydroxybutyric acid (linked to the (omega-1)-hydroxy group).

Comprehensive structure characterization of lipid A extracted from Yersinia pestis for determination of its phosphorylation configuration

We report on comprehensive structure characterization of lipid A extracted from Yersinia pestis (Yp) for determination of its phosphorylation configuration that was achieved by combining the methods of molecular biology with high-resolution tandem mass spectrometry. The phosphorylation pattern of diphosphorylated lipid A extracted from Yp has recently been found to be a heterogeneous mixture of C-1 and C-4' bisphosphate, C-1 pyrophosphate, and C-4' pyrophosphate (Proc. Natl. Acad. Sci. 2008, 105, 12742). To reduce the inherent phosphate heterogeneity of diphosphorylated lipid A extracted from Yp, we incorporated specific C-1 and C-4' position phosphatases into wild type KIM6+ Yp grown at 37 degrees C. Comprehensive high-resolution tandem mass spectrometric analyses of lipid A extracted from Yp modified with either the C-1 or C-4' phosphatase allowed for unambiguous structure assignment of monophosphorylated and diphosphorylated lipid A and distinction of isomeric bisphosphate and pyrophosphate forms. The prevalent aminoarabinose modification was determined to be exclusively attached to the lipid A disaccharide via a phospho-diester linkage at either or both the C-1 and C-4' positions.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2003-2004

This review is the third update of the original review, published in 1999, on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings the topic to the end of 2004. Both fundamental studies and applications are covered. The main topics include methodological developments, matrices, fragmentation of carbohydrates and applications to large polymeric carbohydrates from plants, glycans from glycoproteins and those from various glycolipids. Other topics include the use of MALDI MS to study enzymes related to carbohydrate biosynthesis and degradation, its use in industrial processes, particularly biopharmaceuticals and its use to monitor products of chemical synthesis where glycodendrimers and carbohydrate-protein complexes are highlighted.

A Francisella mutant in lipid A carbohydrate modification elicits protective immunity

Francisella tularensis (Ft) is a highly infectious Gram-negative bacterium and the causative agent of the human disease tularemia. Ft is designated a class A select agent by the Centers for Disease Control and Prevention. Human clinical isolates of Ft produce lipid A of similar structure to Ft subspecies novicida (Fn), a pathogen of mice. We identified three enzymes required for Fn lipid A carbohydrate modifications, specifically the presence of mannose (flmF1), galactosamine (flmF2), or both carbohydrates (flmK). Mutants lacking either galactosamine (flmF2) or galactosamine/mannose (flmK) addition to their lipid A were attenuated in mice by both pulmonary and subcutaneous routes of infection. In addition, aerosolization of the mutants (flmF2 and flmK) provided protection against challenge with wild-type (WT) Fn, whereas subcutaneous administration of only the flmK mutant provided protection from challenge with WT Fn. Furthermore, infection of an alveolar macrophage cell line by the flmK mutant induced higher levels of tumor necrosis factor-α (TNF-α) and macrophage inhibitory protein-2 (MIP-2) when compared to infection with WT Fn. Bone marrow–derived macrophages (BMMø) from Toll-like receptor 4 (TLR4) and TLR2/4 knockout mice infected with the flmK mutant also produced significantly higher amounts of interleukin-6 (IL-6) and MIP-2 than BMMø infected with WT Fn. However, production of IL-6 and MIP-2 was undetectable in BMMø from MyD88^−/− mice infected with either strain. MyD88^−/− mice were also susceptible to flmK mutant infection. We hypothesize that the ability of the flmK mutant to activate pro-inflammatory cytokine/chemokine production and innate immune responses mediated by the MyD88 signaling pathway may be responsible for its attenuation, leading to the induction of protective immunity by this mutant.

Bacterial pathogens modify outer membrane components, such as lipid A or endotoxin, the lipid anchor of lipopolysaccharide, to enhance the ability to colonize, spread to different tissues, and/or avoid the host's immune defenses. Lipopolysaccharide also plays an essential role in maintaining membrane integrity and is a key factor in host innate immune recognition of Gram-negative bacterial infections. Francisella tularensis is the causative agent of the human disease tularemia and is classified as a category A select agent. Francisella novicida (Fn) is the murine counterpart of F. tularensis. The structure of Francisella spp. lipid A is unique in that it is modified by various carbohydrates that play a role in virulence and altered endotoxicity. In our study, we identified and defined the role of three genes involved in the carbohydrate modification of the base Fn lipid A structure. We showed that the lack of specific modification(s) of the Fn lipid A molecule lead to bacterial attenuation and activation of a protective immune response against a lethal wild-type infection. Therefore, alteration of Francisella lipid A structure may represent a pathogenesis strategy common to the Francisella species, and specific lipid A mutant strains may be candidates for inclusion in future vaccine studies.

Predatory mechanisms of Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are predatory, Gram-negative delta-proteobacteria with a complex developmental lifecycle. In the free-living attack phase they are highly motile and seek out prey bacteria that they invade. The ensuing intracellular growth and replication is characterized by the development of a long filament that septates into individual cells that differentiate further into the flagellated attack-phase bacterium. The prey bacterium is lysed and motile predators are released. BALOs have recently been considered to have potential as living antibiotics. The idea of using predatory bacteria as therapeutic agents to combat pathogenic Gram-negative bacteria is intriguing, as they can prey upon human pathogenic bacteria including Salmonella, Pseudomonas and Escherichia coli. However, our current knowledge of the amazing biology of these prokaryotes that cause the systematic destruction of Gram-negative bacteria is still rather limited. More has to be learned about their predatory lifestyle before their application as therapeutic agents will become feasible.

The structure and function of Francisella lipopolysaccharide

A key factor in the biology of Francisella spp. is lipopolysaccharide (LPS). Francisella LPS has many unique structural properties and poorly activates proinflammatory responses due to its lack of interaction with toll-like receptor 4 (TLR4). The LPS of this organism can be modified by various carbohydrates including glucose, mannose and galactosamine, which affect various aspects of virulence. Spontaneously occurring colony variants of F. tularensis have altered LPS. This altered LPS may account for the novel phenotypes of these variants that include effects on susceptibility to killing by normal human serum, intracellular survival and animal virulence. Mutants devoid of O-antigen (directed mutants in O-antigen biosynthetic genes) show reduced intracellular survival and mouse virulence. Thus, this surface component is important in F. tularensis pathogenesis, and the inability of the LPS to alarm the immune system coupled with its frequent modification/alteration likely aid the success of this pathogen during human infection.

MS/MS approach for characterization of the fatty acid distribution on mycobacterial phosphatidyl-myo-inositol mannosides

Phosphatidyl-myo-inositol mannosides (PIM) are not only important structural components of the mycobacterial envelope but also are major non-peptidic antigens of the host innate and acquired immune responses. Indeed, they are ligands of TLR-2 and they activate CD1-restricted T lymphocytes. In addition, PIM constitute the basic structure of the lipidic anchor of two lipoglycans, lipomannans and lipoarabinomannans, which are important immunomodulators in the course of tuberculosis. The fatty acyl substituents present on PIM molecules play a crucial role for both their physical properties and biological activities. PIM contain four acylation sites, two on the glycerol, one on a mannose, and one on the myo-inositol units. We propose here an analytical procedure, based on mass spectrometry, to determine the structure of the fatty acids present on each of these different acylation sites. We show that the nature of the fatty acids located on both positions of glycerol can be deduced from IRMPD analysis of negative precursor ions from native PIM species, while the fatty acids located on myo-inositol and mannose units can be identified by MALDI-TOF CID MS of protonated and cationized molecular ions. Thus, the combination of MS/MS data obtained from positive and negative pseudomolecular ions generated by ESI or MALDI appears as a powerful approach for the structural characterization of the PIM acyl form structure.

Bdellovibrio: growth and development during the predatory cycle

Predatory Bdellovibrio enter the periplasm of other Gram-negative bacteria, growing within and consuming them. Unravelling molecular details of this intimate association between bacterial predator and prey is challenging yet fascinating, and might lead to novel antibacterials in the future. Pioneering physiological and biochemical studies described the predatory life of Bdellovibrio in the 1960s and 1970s, later followed by recombinant DNA work in the 1990s, which led to a revival in Bdellovibrio molecular research. This revival continues in the 21st century with the advent of a genome sequence. Now worldwide research is underway on the comparative genomics and transcriptomics of predatory bacteria, and will illuminate the evolutionary adaptations to become predatory, and will hopefully ultimately illuminate how the predatory processes of Bdellovibrio can be employed against pathogenic bacteria and for humankind.

Characterization of outer membrane protein fractions ofBdellovibrionales

Bdellovibrio-and-like organisms (BALOs) are predatory bacteria that prey upon Gram-negative bacteria and are taxonomically subsumed in the order Bdellovibrionales. Despite their unique lifestyle, these bacteria show remarkable genotypic diversities. The outer membrane of the predators is likely to play an important role during the recognition and invasion stage, as well as in the intraperiplasmic growth phase. In this study, the outer membrane protein fractions of type strains of Bdellovibrio, Bacteriovorax and Peredibacter were investigated, revealing the presence of outer membrane proteins (Omps) similar to the major Omps of Bdellovibrio bacteriovorus. The primary structures of these Omps of Bdellovibrio sp. W, Bacteriovorax stolpii and Peredibacter starrii were elucidated by a combined mass spectrometric-reverse genetic approach. The similarity between the analyzed Omps of the investigated BALOs ranges from 32% to 89% showing conserved amino acid regions in their primary structure.

Fate of predator and prey proteins during growth of Bdellovibrio bacteriovorus on Escherichia coli and Pseudomonas syringae prey

A two-dimensional electrophoretic analysis of protein distribution followed by identification of selected proteins by mass spectrometry was performed on fresh bdellovibrio cultures containing attack phase cells of the predatory bacterium Bdellovibrio bacteriovorus strain 109J-1 and the remains of an Escherichia coli or a Pseudomonas syringae pv. tomato prey. Cleavage of the peptidoglycan-associated outer membrane proteins (OMPs) OmpA in E. coli and OprF in P. syringae occurred in both prey. The tryptic peptides obtained from the cleavage products of OmpA and OprF were all located within the 19-kDa pronase-resistant N-terminal parts of the corresponding proteins. The predator cell fraction was separated from the prey ghosts in fresh bdellovibrio cultures by centrifugation on a Percoll-sucrose cushion. Proteins from each fraction were separated by two-dimensional electrophoresis and identified by mass spectrometric analysis. As no prey OMP could be detected in the predator cell fraction, it was concluded that prey OMPs are not transferred to the predator, as had been suggested previously. However, a protein from the predator was found bound to ghost cell envelopes. This protein may correspond to a protein earlier suggested to be associated with the prey outer or cytoplasmic membranes. Along with recently described polypeptides from B. bacteriovorus strains 100 and 114, it forms a new family of putative outer membrane proteins.

Application of sustained off-resonance irradiation infrared multiphoton dissociation tandem mass spectrometry to the analysis of biomolecules

A modified pulse sequence for infrared multiphoton dissociation (IRMPD) experiments on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer in conjunction with sidekick trapping is presented. For IRMPD tandem mass spectrometry experiments gated trapping is normally applied. It ensures that the ions remain on-axis and, thus, cross the laser beam which is aligned on-axis in commercially available instruments. Sidekick trapping is used to capture more ions in the ICR cell in order to increase the signal intensity. However, it may lead to off-axis ion motion, which reduces or even excludes interaction with the laser beam. In this contribution sustained off-resonance irradiation (SORI) was applied to overcome this disadvantage of sidekick trapping. SORI is normally used in conjunction with collision-induced dissociation (CID) experiments to increase the kinetic energy of the ions. Here, SORI is used to influence the cyclotron motion during the laser irradiation time, which leads to temporary intersection of the ion trajectory with the laser beam. With this easy-to-handle experimental setup, IRMPD of ions captured with sidekick trapping leads again to the generation of fragment ions as is demonstrated with several biologically relevant samples like peptides, lipids and glycolipids.

Structural characterization of complex bacterial glycolipids by Fourier transform mass spectrometry

Bacterial glycolipids are complex amphiphilic molecules which are on the one hand of utmost importance for the organization and function of bacterial membranes, and which on the other hand play a major role in the activation of cells of the innate and adaptive immune system of the host. Already small alterations of their chemical structure may influence the biological activity tremendously. Due to their intrinsic biological heterogeneity [number and type of fatty acids, saccharide structures, and substitution with e.g. phosphate (P), 2-aminoethyl- (pyro)phosphate groups (P-Etn) or 4-amino-4-deoxyarabinose (Ara4N)], separation of the different components are a prerequisite for unequivocal chemical and NMR structural analyses. In this contribution the structural information which can be obtained from heterogeneous samples of glycolipids by Fourier transform (FT) ion cyclotron resonance mass spectrometric methods is described. By means of recently analysed complex biological samples the possibilities of high resolution electrospray ionization FT-MS are demonstrated. Capillary skimmer dissociation, as well as tandem mass spectrometry MS/MS analysis utilizing collision-induced dissociation and infrared multiphoton dissociation, are compared and their advantages to provide structural information of diagnostic importance are discussed.

Elucidation of the molecular structure of lipid A isolated from both a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharides using electrospray ionization quadrupole time-of-flight tandem mass spectrometry

The chemical structure of lipid A, isolated by mild acid hydrolysis from a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharide, was investigated using electrospray ionization quadrupole time-of-flight (QqToF) hybrid tandem mass spectrometry and showed a great degree of microheterogeneity. The chemical structure of the main constituent of this heterogeneous mixture was identified as a beta-D-(1 --> 6) linked D-glucosamine disaccharide substituted by two phosphate groups, one being bound to the non-reducing end at position O-4' and the other to the position O-1 of the reducing end of the D-glucosamine disaccharide. The location of the fatty acids linked to the disaccharide backbone was established by identifying diagnostic ions in the conventional QqToF-MS scan. Low-energy collision tandem mass spectrometry analysis of the selected precursor diagnostic ions confirmed, unambiguously, their proposed molecular structures. We have established that myristyloxylauric (C14:0(3-O(12:0))) acid residues were both N-2' and O-3' linked to the non-reducing end of the D-GlcN residue, and that two 3-hydroxymyristic (C14:0(3-OH)) acid chains acylated the remaining positions of the reducing end. The MS and MS/MS data obtained allowed us to determine the complex molecular structure of lipid A. The QqToF-MS/MS instrument has shown excellent superiority over a conventional quadrupole-hexapole-quadrupole tandem instrument which failed to fragment the selected precursor ion.

Bdellovibrio bacteriovorus strains produce a novel major outer membrane protein during predacious growth in the periplasm of prey bacteria

Bdellovibrio bacteriovorus is a predatory bacterium that is capable of invading a number of gram-negative bacteria. The life cycle of this predator can be divided into a nonreproductive phase outside the prey bacteria and a multiplication phase in their periplasm. It was suggested that during the reproduction phase, B. bacteriovorus reutilizes unmodified components of the prey's cell wall. We therefore examined the outer membranes of B. bacteriovorus strains HD100 (DSM 50701) and HD114 (DSM 50705) by using Escherichia coli, Yersinia enterocolitica, and Pseudomonas putida as prey organisms. The combined sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometric analyses revealed novel and innate major outer membrane proteins (OMPs) of B. bacteriovorus strains. An incorporation of prey-derived proteins into the cell wall of B. bacteriovorus was not observed. The corresponding genes of the B. bacteriovorus strains were elucidated by a reverse-genetics approach, and a leader peptide was deduced from the gene sequence and confirmed by Edman degradation. The host-independent mutant strain B. bacteriovorus HI100 (DSM 12732) growing in the absence of prey organisms possesses an OMP similar to the major OMPs of the host-dependent strains. The similarity of the primary structure of the OMPs produced by the three Bdellovibrio strains is between 67 and 89%. The leader peptides of all OMPs have a length of 20 amino acids and are highly conserved. The molecular sizes of the mature proteins range from 34.9 to 37.6 kDa. Secondary-structure predictions indicate preferential alpha-helices and little beta-barrel structures.

A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective

Predatory bacteria remain molecularly enigmatic, despite their presence in many microbial communities. Here we report the complete genome of Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that invades and consumes other Gram-negative bacteria. Its surprisingly large genome shows no evidence of recent gene transfer from its prey. A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules.