Synthesis and Characterisation of a Multiphosphorylated Phosphophoryn Repeat Motif; H-[Asp-(Ser(<Emphasis Type="Italic">P</Emphasis>))<Subscript>2</Subscript>]<Subscript>3</Subscript>-Asp-OH

Protein phosphorylation is a critical mechanism in the regulation of cellular biochemical pathways and phosphopeptides can play an important role in determining function. However, the use of phosphopeptides especially multiphosphorylated peptides is hampered by their low abundance, difficulty in isolation from biological samples and in their chemical synthesis. Here we describe methodologies for the Fmoc synthesis, purification and mass spectral analysis of the multiphosphorylated sequence H-[Asp-(Ser(P))₂]₃-Asp-OH from phosphophoryn a protein involved in dentine mineralization. Critical steps in the synthesis of phosphophoryn using Fmoc-Ser(PO₃Bzl,H)-OH as the building block were double acylation steps for each residue, alternating HBTU and HATU as the acylating agents and synthesis on a chlorotrityl resin which was essential for complete removal of the benzyl-side chain protecting groups. The synthetic phosphophoryn was only effectively purified by anion exchange and size exclusion chromatography as both alkaline and acid buffers failed to aid in purification by reversed phase HPLC. MALDI-TOF analysis of phosphophoryn was achieved with good sensitivity (20 fmol/ml) and resolution using the DNA matrix 3-hydroxypicolinic acid, whereas typical protein/peptide matrices failed to provide mass spectra. The synthetic phosphophoryn peptide was found to bind calcium, binding 6 mol of calcium per mole of peptide. In conclusion the methodology described here can be easily adopted for the synthesis and analysis of a wide variety of multiphosphorylated peptides.     

Production of single chain Fab (scFab) fragments in Bacillus megaterium

Background

The demand on antigen binding reagents in research, diagnostics and therapy raises questions for novel antibody formats as well as appropriate production systems. Recently, the novel single chain Fab (scFab) antibody format combining properties of single chain Fv (scFv) and Fab fragments was produced in the Gram-negative bacterium Escherichia coli. In this study we evaluated the Gram-positive bacterium Bacillus megaterium for the recombinant production of scFab and scFvs in comparison to E. coli.

Results

The lysozyme specific D1.3 scFab was produced in B. megaterium and E. coli. The total yield of the scFab after purification obtained from the periplasmic fraction and culture supernatant of E. coli was slightly higher than that obtained from culture supernatant of B. megaterium. However, the yield of functional scFab determined by analyzing the antigen binding activity was equally in both production systems. Furthermore, a scFv fragment with specificity for the human C reactive protein was produced in B. megaterium. The total yield of the anti-CRP scFv produced in B. megaterium was slightly lower compared to E. coli, whereas the specific activity of the purified scFvs produced in B. megaterium was higher compared to E. coli.

Conclusion

B. megaterium allows the secretory production of antibody fragments including the novel scFab antibody format. The yield and quality of functional antibody fragment is comparable to the periplasmic production in E. coli.     

Improving image analysis in 2DGE-based redox proteomics by labeling protein carbonyl with fluorescent hydroxylamine

Recent advances in redox proteomics have provided significant insight into the role of oxidative modifications in cellular signalling and metabolism. At present, these techniques rely heavily on Western blots to visualize the oxidative modification and corresponding two dimensional (2D) gels for detection of total protein levels, resulting in the duplication of efforts. A major limitation associated with this methodology includes problematic matching up of gels and blots due to the differences in processing and/or image acquisition. In this study, we present a new method which allows detection of protein oxidation and total protein on the same gel to improve matching in image analysis. Furthermore, the digested protein spots are compatible with standard MALDI mass spectrometry protein identification. The methodology highlighted here may be useful in facilitating the development of biomarkers, assessing potential therapeutic targets and elucidating new mechanisms of redox signalling in redox-related conditions.     

A Comparison of Mouse Parvovirus 1 Infection in BALB/c and C57BL/6 Mice: Susceptibility,Replication, Shedding,and Seroconversion

This study characterized the effects of challenge with a field isolate of mouse parvovirus 1 (MPV1e) in C57BL/6NCrl (B6) and BALB/cAnNCrl (C) mice. We found that C mice were more susceptible to MPV1e infection than were B6 mice; ID₅₀ were 50 to 100 times higher after gavage and 10-fold higher after intraperitoneal injection in B6 as compared with C mice. To evaluate the host strain effect on the pathogenesis of MPV1e, B6 and C mice were inoculated by gavage. Feces and tissues, including mesenteric lymph nodes (MLN), ileum, spleen and blood, were collected for analysis by quantitative PCR (qPCR) to assess infection and fecal shedding and by RT-qPCR to evaluate replication. Peak levels of MPV1e shedding, infection, and replication were on average 3.4, 4.3, and 6.2 times higher, respectively, in C than in B6 mice. Peaks occurred between 3 and 10 d after inoculation in C mice but between 5 and 14 d in B6 mice. Multiplexed fluorometric immunoassays detected seroconversion in 2 of 3 C mice at 7 d after inoculation and in all 3 B6 mice at 10 d. By 56 d after inoculation, viral replication was no longer detectable, and fecal shedding was very low; infection persisted in ileum, spleen, and MLN, with levels higher in C than B6 mice and highest in MLN. Therefore, the lower susceptibility of B6 mice, as compared with C mice, to MPV1e infection was associated with lower levels of infection, replication, and shedding and delayed seroconversion.Abbreviations: B6, C57BL/6; C, BALB/c; MFI, median fluorescence intensity; MFIA, multiplexed fluorometric immunoassay; MLN, mesenteric lymph node; MMV, mouse minute virus; MPV, mouse parvovirus; NS1, nonstructural protein 1; qPCR, quantitative PCR; r, recombinant; Rn, normalized reporter value; VP2, virus capsid protein 2Parvoviruses are small (20 to 28 nm), nonenveloped icosahedral single-stranded DNA viruses that infect a diverse range of vertebrate and arthropod species. Much of what is understood about the biology and pathogenesis of autonomous parvoviruses has been derived from studies of the original murine parvoviral isolates, particularly the prototypic and immunosuppressive strains of mouse minute virus (MMV).^9,13,32 Because autonomous parvoviruses have a requirement and predilection for proliferating cells to replicate, they are primarily teratogenic pathogens. In contrast, rodent parvovirus infections of older animals are usually asymptomatic, because the cells that divide in mature animals, such as enterocytes, lymphoreticular cells, and hematopoietic cells, are largely spared.^2,47,48 The most common parvovirus of laboratory mice, mouse parvovirus 1 (MPV1), was first isolated²⁹ from mouse T-lymphocyte cultures that had lost viability or the ability to proliferate when stimulated. In contrast to MMV,^10,27,40 MPV1 has not been shown to cause disease in newborn or immunodeficient mice^19,45 but nevertheless has been reported to modulate the immune response of infected mice.^30,31Adventitious infections of laboratory mice with MPV1 and other parvoviruses continue to occur regularly, despite biosecurity improvements that have successfully excluded once-common pathogens such as Sendai virus.^22,37,39 One reason for the continued occurrence of these infections is that nonenveloped parvovirus virions are environmentally stable and resistant to disinfection.^18,49 Furthermore, related to their tendency to persist in host tissues even after seroconversion and their predilection for dividing cells, parvoviruses have been among the most frequent viral contaminants of transplantable tumor lines and other rodent-derived biologic reagents.^34,35 Inoculation of parvovirus-contaminated biologic reagents into experimental animals can contribute to the incidence of parvoviral outbreaks. Currently, mouse populations typically are housed in microisolation cages and are monitored for MPV1 infections through the use of soiled bedding sentinels. An MPV1 infection of the principal animals may not be transmitted to sentinels when the prevalence of infection is low, as is often the case after contamination, or when the sentinels are comparatively resistant to infection because of their genetic background or age.^7,16,17 However, a recent study found that sentinel age did not affect the likelihood of MPV1 infection.¹⁷The C57BL/6 (B6) mouse strain is popular in biomedical research and is commonly used as the background strain for spontaneous and genetically engineered mutations. We and others have noted that B6 mice are less likely to be MPV1 seropositive than are mice of other strains and stocks, even in facilities where MPV1 is widespread.⁴⁴ There has been speculation that B6 mice might not seroconvert when infected with MPV1. However, data reported here and by others^7,15 indicate that B6 mice are less likely to seroconvert because they are comparatively resistant to MPV1 infection; when they become infected, they do seroconvert. The current study evaluated whether resistance of B6 mice to infection with MPV1, as compared with BALB/c (C) mice, varies with virus inoculation route and correlates with differences in the time course and levels of viral infection, replication, and shedding and of humoral immunity.Most studies of MPV1 in mice have been performed with the cultivable MPV1a strain.^{7,19,30,31,45} Cultivable murine parvoviruses are known to differ from wildtype strains genetically and in their cell tropisms, pathogenicity, and transmissibility in vivo. For example, MPV1d, a noncultivable field isolate, was more readily transmitted to sentinels than was MPV1a.¹¹ We therefore chose to perform the current experiments with MPV1e,^3,4 a representative field strain that we originally isolated from an adventitiously infected barrier colony⁴⁴ and that has been propagated only in mice.     

The antimicrobial activity of the appetite peptide hormone ghrelin

The present study examined the antimicrobial activity of the peptide ghrelin. Both major forms of ghrelin, acylated ghrelin (AG) and desacylated ghrelin (DAG), demonstrated the same degree of bactericidal activity against Gram-negative Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa), while bactericidal effects against Gram-positive Staphylococcus aureus (S. aureus) and Enterococcus faecalis (E. faecalis) were minimal or absent, respectively. To elucidate the bactericidal mechanism of AG and DAG against bacteria, we monitored the effect of the cationic peptides on the zeta potential of E. coli. Our results show that AG and DAG similarly quenched the negative surface charge of E. coli, suggesting that ghrelin-mediated bactericidal effects are influenced by charge-dependent binding and not by acyl modification. Like most cationic antimicrobial peptides (CAMPs), we also found that the antibacterial activity of AG was attenuated in physiological NaCl concentration (150mM). Nonetheless, these findings indicate that both AG and DAG can act as CAMPs against Gram-negative bacteria.     

Direct repeat-mediated deletion of a type IV pilin gene results in major virulence attenuation of Francisella tularensis

Francisella tularensis, the causative agent of tularaemia, is a highly infectious and virulent intracellular pathogen. There are two main human pathogenic subspecies, Francisella tularensis ssp. tularensis (type A), and Francisella tularensis ssp. holarctica (type B). So far, knowledge regarding key virulence determinants is limited but it is clear that intracellular survival and multiplication is one major virulence strategy of Francisella. In addition, genome sequencing has revealed the presence of genes encoding type IV pili (Tfp). One genomic region encoding three proteins with signatures typical for type IV pilins contained two 120 bp direct repeats. Here we establish that repeat-mediated loss of one of the putative pilin genes in a type B strain results in severe virulence attenuation in mice infected by subcutaneous route. Complementation of the mutant by introduction of the pilin gene in cis resulted in complete restoration of virulence. The level of attenuation was similar to that of the live vaccine strain and this strain was also found to lack the pilin gene as result of a similar deletion event mediated by the direct repeats. Presence of the pilin had no major effect on the ability to interact, survive and multiply inside macrophage-like cell lines. Importantly, the pilin-negative strain was impaired in its ability to spread from the initial site of infection to the spleen. Our findings indicate that this putative pilin is critical for Francisella infections that occur via peripheral routes.     

Investigating the suitability of the Calgary Biofilm Device for assessing the antimicrobial efficacy of new agents

This study investigated the suitability of the Calgary Biofilm Device (CBD), originally designed as a test surrogate for indwelling medical devices, for assessing the efficacy of antimicrobials developed for food and food contact surface disinfection applications. The conditions for the development of uniform biofilms from pure and mixed bacterial cultures of wild type Escherichia coli and Listeria innocua were optimized. We were able to recover approximately 2 x 10(6) colony forming units (CFU) from the biofilms formed on the individual pegs of the device in 24 h. Further, the parameters for the consistent release of the cells from the biofilms were optimized; test showed that the number of cells released was uniform and reproducible. The consistency and reproducibility of the biofilms formed on the pegs was evaluated using scanning electron microscopy and by plate count method. The efficacies of disinfectants on cells residing in biofilms versus planktonic cells were compared. For both species, higher concentrations of disinfectants were needed to eliminate attached cells as compared with planktonic cells. This study establishes the value of the CBD for generating consistent biofilms from either pure or mixed cultures. These biofilms can be used to assess efficacies of disinfectants against cells that have colonized the surfaces of foods and food-processing equipment. Such a system could serve as a standard surrogate for evaluating new disinfectants designed to reduce or eliminate biofilms from food-contact surfaces.     

Direct Spatial Control of Epac1 by Cyclic AMP

Epac1 is a guanine nucleotide exchange factor (GEF) for the small G protein Rap and is directly activated by cyclic AMP (cAMP). Upon cAMP binding, Epac1 undergoes a conformational change that allows the interaction of its GEF domain with Rap, resulting in Rap activation and subsequent downstream effects, including integrin-mediated cell adhesion and cell-cell junction formation. Here, we report that cAMP also induces the translocation of Epac1 toward the plasma membrane. Combining high-resolution confocal fluorescence microscopy with total internal reflection fluorescence and fluorescent resonance energy transfer assays, we observed that Epac1 translocation is a rapid and reversible process. This dynamic redistribution of Epac1 requires both the cAMP-induced conformational change as well as the DEP domain. In line with its translocation, Epac1 activation induces Rap activation predominantly at the plasma membrane. We further show that the translocation of Epac1 enhances its ability to induce Rap-mediated cell adhesion. Thus, the regulation of Epac1-Rap signaling by cAMP includes both the release of Epac1 from autoinhibition and its recruitment to the plasma membrane.Cyclic AMP (cAMP) is an important second messenger that mediates many cellular hormone responses. It has become more and more appreciated that, along with the cAMP effector protein kinase A (PKA), Epac proteins also play pivotal roles in many cAMP-controlled processes, including insulin secretion (23, 39), cell adhesion (9, 17, 25, 49, 60), neurotransmitter release (22, 53, 63), heart function (13, 35, 54), and circadian rhythm (38). Epac1 and Epac2 are cAMP-dependent guanine nucleotide exchange factors (GEFs) for the small G proteins Rap1 and Rap2 (12, 24). They contain a regulatory region with one (Epac1) or two (Epac2) cAMP-binding domains, a Dishevelled, Egl-10, Pleckstrin (DEP) domain, and a catalytic region for GEF activity (11). The binding of cAMP is a prerequisite for catalytic activity in vitro and in vivo (11). Recently, the structures of both the inactive and active conformations of Epac2 were solved (51, 52). This revealed that in the inactive conformation, the regulatory region occludes the Rap binding site, which is relieved by a conformational change induced by cAMP binding.Like all G proteins of the Ras superfamily, Rap cycles between an inactive GDP-bound and active GTP-bound state in an equilibrium that is tightly regulated by specific GEFs and GTPase-activating proteins (GAPs). The GEF-induced dissociation of GDP results in the binding of the cellularly abundant GTP, whereas GAPs enhance the intrinsic GTPase activity of the G protein, thereby inducing the inactive GDP-bound state. Besides Epac, several other GEFs for Rap have been identified, including C3G, PDZ-GEF, and RasGRP, and these act downstream of different signaling pathways (7). Since Rap localizes to several membrane compartments, including the Golgi network, vesicular membranes, and the plasma membrane (PM) (2-4, 37, 42, 48), the spatial regulation of its activity is expected to be established by the differential distributions of its upstream GEFs, each activating distinct pools of Rap on specific intracellular locations.Similarly to Rap, Epac1 also is observed at many locations in the cell, including the cytosol, the nucleus, the nuclear envelope, endomembranes, and the PM (5, 11, 14, 21, 29, 47). These various locations may reflect the many different functions assigned to Epac1, such as the regulation of cell adhesion, cell junction formation, secretion, the regulation of DNA-dependent protein kinase by nuclear Epac1, and the regulation of the Na⁺/H⁺ exchanger NHE3 at the brush borders of kidney epithelium (19, 21, 26). Apparently, specific anchors are responsible for this spatial regulation of Epac1. Indeed, Epac1 was found to associate with phosphodiesterase 4 (PDE4) in a complex with mAKAP in cardiomyocytes (13), with MAP-LC bound to microtubules (62), and with Ezrin at the brush borders of polarized cells (M. Gloerich, J. Zhao, and J. L. Bos, unpublished data).In this study, we report the unexpected observation that, in addition to the temporal control of Epac1 activity, cAMP also induces the translocation of Epac1 toward the plasma membrane. Using confocal fluorescence microscopy, total internal reflection fluorescence (TIRF) microscopy, and fluorescence resonance energy transfer (FRET)-based assays for high spatial and temporal resolution, we observed that the translocation of Epac1 is immediate and that Epac1 approaches the PM to within ∼7 nm. In line with this, Epac1-induced Rap activation was registered predominantly on this compartment. Epac1 translocation results directly from the cAMP-induced conformational change and depends on the integrity of its DEP domain. We further show that Epac1 translocation is a prerequisite for cAMP-induced Rap activation at the PM and enhances Rap-mediated cell adhesion. Thus, cAMP exerts dual regulation on Epac1 for the activation of Rap, controlling both its GEF activity and targeting to the PM.     

Global Distribution and Evolution of a Toxinogenic Burkholderia-Rhizopus Symbiosis

Toxinogenic endobacteria were isolated from a collection of Rhizopus spp. representing highly diverse geographic origins and ecological niches. All endosymbionts belonged to the Burkholderia rhizoxinica complex according to matrix-assisted laser desorption ionization-time of flight biotyping and multilocus sequence typing, suggesting a common ancestor. Comparison of host and symbiont phylogenies provides insights into possible cospeciation and horizontal-transmission events.Bacterial symbionts and their metabolic potential play essential roles for many organisms. They may benefit from improved fitness, survival, and even acquired virulence (7, 12, 22). In the course of our studies of the biosynthesis of rhizoxin, the causative agent of rice seedling blight (10), we found that the phytotoxin is produced not by the fungus Rhizopus microsporus but by symbiotic bacteria (Burkholderia rhizoxinica) that reside within the fungus cytosol (13, 15, 23). Furthermore, cloning and sequencing of the rhizoxin biosynthesis gene cluster revealed the molecular basis of bacterial toxin production (14). In sum, this represents an unparalleled example for a symbiosis in which a fungus harbors bacteria for the production of a virulence factor. In analogy, we found that the first reported “mycotoxins” from lower fungi, the highly toxic cyclopeptides rhizonin A and B (25, 28), are also produced by symbiotic bacteria (Burkholderia endofungorum) and not by the fungus (16). While both rhizoxins and rhizonins have been believed to promote zygomycoses (21), there is no indication for toxin-producing endosymbiotic bacteria in clinical isolates (18).In nature, toxin production plays a pivotal role in the development of the fungus-bacterium association. Studies of the evolution of host resistance indicate that the association resulted from a pathogenicity mutualism shift in insensitive zygomycetes (24). The fungus lost its ability to sporulate independently and became totally dependent on endobacteria for reproduction through spores, thus warranting the persistence of the symbiosis and its efficient distribution through vegetative spores (17).To gain a broader view of the occurrence, biosynthetic potential, and relationship of toxinogenic endofungal bacteria, we investigated a collection of Rhizopus spp. consisting of 20 isolates classified as R. microsporus (of which 13 belong to R. microsporus var. microsporus, four to R. microsporus var. chinensis, two to R. microsporus var. oligosporus, and one to R. microsporus var. rhizopodiformis), one isolate classified as Rhizopus sp., and one Rhizopus oryzae strain. We initially monitored the presence of bacterial symbionts by PCR using universal primers (16S rRNA genes) and rhizoxin production in all available Rhizopus strains. Liquid cultivation of fungi in production medium with and without antibiotic followed by organic solvent extraction yielded crude extracts that were analyzed by high-performance liquid chromatography (HPLC) and mass spectrometry (MS). In total, eight fungal strains were identified or confirmed as rhizoxin positive and thus expected to harbor endosymbionts. In all cases, this assumption was verified by PCR and confocal scanning microscopy. By means of an optimized protocol, we finally succeeded in the isolation and cultivation of all eight bacterial symbiont strains in pure cultures (isolates B1 to B8) (Table ​(Table11).

TABLE 1.

Fungal strains and their bacterial endosymbionts