Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.     

Transfection of RNA from Organ Samples of Infected Animals Represents a Highly Sensitive Method for Virus Detection and Recovery of Classical Swine Fever Virus

Translation and replication of positive stranded RNA viruses are directly initiated in the cellular cytoplasm after uncoating of the viral genome. Accordingly, infectious virus can be generated by transfection of RNA genomes into susceptible cells. In the present study, efficiency of conventional virus isolation after inoculation of cells with infectious sample material was compared to virus recovery after transfection of total RNA derived from organ samples of pigs infected with Classical swine fever virus (CSFV). Compared to the conventional method of virus isolation applied in three different porcine cell lines used in routine diagnosis of CSF, RNA transfection showed a similar efficiency for virus rescue. For two samples, recovery of infectious virus was only possible by RNA transfection, but not by the classical approach of virus isolation. Therefore, RNA transfection represents a valuable alternative to conventional virus isolation in particular when virus isolation is not possible, sample material is not suitable for virus isolation or when infectious material is not available. To estimate the potential risk of RNA prepared from sample material for infection of pigs, five domestic pigs were oronasally inoculated with RNA that was tested positive for virus rescue after RNA transfection. This exposure did not result in viral infection or clinical disease of the animals. In consequence, shipment of CSFV RNA can be regarded as a safe alternative to transportation of infectious virus and thereby facilitates the exchange of virus isolates among authorized laboratories with appropriate containment facilities.     

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii' KT0803

Members of the phylum Bacteroidetes are abundant in many marine ecosystems and are known to have a pivotal role in the mineralization of complex organic substrates such as polysaccharides and proteins. We studied the decomposition of the algal glycans laminarin and alginate by ‘Gramella forsetii'' KT0803, a bacteroidetal isolate from North Sea surface waters. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed two large polysaccharide utilization loci (PULs) that were specifically induced, one by alginate and the other by laminarin. These regulons comprised genes of surface-exposed proteins such as oligomer transporters, substrate-binding proteins, carbohydrate-active enzymes and hypothetical proteins. Besides, several glycan-specific TonB-dependent receptors and SusD-like substrate-binding proteins were expressed also in the absence of polysaccharide substrates, suggesting an anticipatory sensing function. Genes for the utilization of the beta-1,3-glucan laminarin were found to be co-regulated with genes for glucose and alpha-1,4-glucan utilization, which was not the case for the non-glucan alginate. Strong syntenies of the PULs of ‘G. forsetii'' with similar loci in other Bacteroidetes indicate that the specific response mechanisms of ‘G. forsetii'' to changes in polysaccharide availability likely apply to other Bacteroidetes. Our results can thus contribute to an improved understanding of the ecological niches of marine Bacteroidetes and their roles in the polysaccharide decomposition part of carbon cycling in marine ecosystems.     

Global Relative Quantification with Liquid Chromatography–Matrix-assisted Laser Desorption Ionization Time-of-flight (LC-MALDI-TOF)—Cross–validation with LTQ-Orbitrap Proves Reliability and Reveals Complementary Ionization Preferences

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC–electrospray ionization workflows.Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis.Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.One-dimensional gel-based liquid chromatography mass spectrometry (GeLC-MS)¹ is a well-established technique in life science. In combination with in vivo labeling approaches such as stable isotope labeling by amino acids in cell culture (SILAC) (1) or ¹⁵N labeling (2), it allows the relative quantification of large numbers of proteins in a complex sample. Mass spectrometry (MS) measurements in such workflows are predominantly performed with electrospray ionization (ESI)-based mass spectrometers. Online coupling of a liquid chromatography (LC) system with fast MS spectra acquisition and high-mass-accuracy ESI instruments in conjunction with fractionation on both protein and peptide levels allows the analysis of very complex samples in a relatively short period of time (3). The identification and quantification of data can be done in an automatic or semi-automatic manner with a variety of well-established software packages (4).In proteomic research, matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF) is mainly used for the analysis of non-complex protein samples that do not require fractionation on the peptide level by means of liquid chromatography. In particular, the analysis of single protein spots resulting from the two-dimensional PAGE separation of complex samples is primarily carried out with this MS technique, as it allows the fast and reliable analysis of a high number of low-complex samples (5).In most LC-MALDI workflows, the LC system and the MALDI instrument are coupled offline with a fractionation step in between. Online measurement of the LC eluate is not appropriate for most MALDI systems, as the mass analyzer is a closed vacuum chamber and sample insertion is based on a lock chamber, which precludes the direct injection of an LC run. Also, the measurement speed of most MALDI instruments is too low to analyze samples of mid and high complexity online, when large numbers of peptides elute in a short time frame. The comparatively low throughput in terms of single spectrum acquisition and the restricted online coupling for most instruments are generally circumvented by the offline coupling of an LC system and a MALDI-TOF-TOF instrument through a fractionation system (6). The decoupling from the chromatographic process makes MS measurements independent of the instrument''s scan cycle time. The only restriction is the sample consumption in the ionization process. Besides counteracting excessively long cycle times of the mass spectrometer, the offline coupling also enables multiple measurements of the same LC run and therefore allows the selective analysis of single precursor ions after a first analysis of the data (7).LC-MALDI for qualitative analysis generally ranks behind the widespread LC-ESI approaches. This is mainly because the additional fractionation step leads to longer analysis times. The discrepancy in usage is even bigger for relative quantification workflows. LC-MALDI is rarely employed for the analysis of in vivo labeled samples, especially in large-scale experiments. Even though it has been shown that shot-to-shot intensity variation, which is a general drawback for quantitative MALDI analysis, can be overcome with a suitable experimental setup (8), the lack of established software tools for the analysis of these data is evident and hampers the application of LC-MALDI in large-scale experiments.Here, we describe for the first time a global analysis of in vivo ¹⁵N labeled samples with a GeLC-MS/MS workflow carried out with a MALDI-TOF-TOF instrument. In this workflow, proteins were prefractionated on a one-dimensional SDS gel and tryptically digested, and the resulting peptide mixtures were separated by means of reversed-phase LC. The LC eluate was then fractionated, which allowed offline coupling with a MALDI-TOF-TOF instrument. Data were analyzed with the Mascot Distiller software package. The same samples were also measured with an LTQ-Orbitrap as described in a paper by Hessling et al.² This second data set from the very same samples allowed cross-validation with a well-established workflow.We proved that LC-MALDI is an appropriate option for the quantitative analysis of in vivo labeled samples on a proteome-wide scale. We identified nearly 850 proteins and quantified more than 550 proteins within a reasonable analysis time. The resulting protein ratios correlate well with existing LTQ-Orbitrap data and should encourage groups equipped with a MALDI-TOF-TOF instrument to perform large-scale quantitative proteomic experiments.The measurement of the same samples with two mass analyzers, one using ESI and the other using MALDI, also allowed the investigation of possible biases of one or the other mass analyzer toward peptides with certain physicochemical characteristics. These ionization preferences principally open opportunities with both technical and biological potential for deeper analysis of proteomes and increased sequence coverage in general, but they also could allow the exploration specifically of detectable peptides and/or proteins that could not be found with a particular ionization technique. Existing comparative studies in this field are few so far. All of them are limited by technical or methodological constraints of their time. Investigations were mainly hampered by restricted technical opportunities in the past, leading to exemplary use of samples of low complexity (9, 10), the application of divergent sample preparations such as different LC systems for peptide fractionation (9), and a scale in terms of identification numbers (10, 11) that is too small to enable general conclusions. The large amount of data and the avoidance of any technical variations in the present study allowed the most comprehensive comparison of ESI- and MALDI-generated data to date and revealed physicochemical biases in the detection of peptides, which confirms the generally complementary nature of the two ionization techniques.     

Preclinical transmission of prions by blood transfusion is influenced by donor genotype and route of infection

Variant Creutzfeldt-Jakob disease (vCJD) is a human prion disease resulting from zoonotic transmission of bovine spongiform encephalopathy (BSE). Documented cases of vCJD transmission by blood transfusion necessitate on-going risk reduction measures to protect blood supplies, such as leucodepletion (removal of white blood cells, WBCs). This study set out to determine the risks of prion transmission by transfusion of labile blood components (red blood cells, platelets, plasma) commonly used in human medicine, and the effectiveness of leucodepletion in preventing infection, using BSE-infected sheep as a model. All components were capable of transmitting prion disease when donors were in the preclinical phase of infection, with the highest rates of infection in recipients of whole blood and buffy coat, and the lowest in recipients of plasma. Leucodepletion of components (<10⁶ WBCs/unit) resulted in significantly lower transmission rates, but did not completely prevent transmission by any component. Donor PRNP genotype at codon 141, which is associated with variation in incubation period, also had a significant effect on transfusion transmission rates. A sensitive protein misfolding cyclic amplification (PMCA) assay, applied to longitudinal series of blood samples, identified infected sheep from 4 months post infection. However, in donor sheep (orally infected), the onset of detection of PrP^Sc in blood was much more variable, and generally later, compared to recipients (intravenous infection). This shows that the route and method of infection may profoundly affect the period during which an individual is infectious, and the test sensitivity required for reliable preclinical diagnosis, both of which have important implications for disease control. Our results emphasize that blood transfusion can be a highly efficient route of transmission for prion diseases. Given current uncertainties over the prevalence of asymptomatic vCJD carriers, this argues for the maintenance and improvement of current measures to reduce the risk of transmission by blood products.     

Human cardiac-derived adherent proliferating cells reduce murine acute Coxsackievirus B3-induced myocarditis

Background

Under conventional heart failure therapy, inflammatory cardiomyopathy typically has a progressive course, indicating a need for alternative therapeutic strategies to improve long-term outcomes. We recently isolated and identified novel cardiac-derived cells from human cardiac biopsies: cardiac-derived adherent proliferating cells (CAPs). They have similarities with mesenchymal stromal cells, which are known for their anti-apoptotic and immunomodulatory properties. We explored whether CAPs application could be a novel strategy to improve acute Coxsackievirus B3 (CVB3)-induced myocarditis.

Methodology/Principal Findings

To evaluate the safety of our approach, we first analyzed the expression of the coxsackie- and adenovirus receptor (CAR) and the co-receptor CD55 on CAPs, which are both required for effective CVB3 infectivity. We could demonstrate that CAPs only minimally express both receptors, which translates to minimal CVB3 copy numbers, and without viral particle release after CVB3 infection. Co-culture of CAPs with CVB3-infected HL-1 cardiomyocytes resulted in a reduction of CVB3-induced HL-1 apoptosis and viral progeny release. In addition, CAPs reduced CD4 and CD8 T cell proliferation. All CAPs-mediated protective effects were nitric oxide- and interleukin-10-dependent and required interferon-γ. In an acute murine model of CVB3-induced myocarditis, application of CAPs led to a decrease of cardiac apoptosis, cardiac CVB3 viral load and improved left ventricular contractility parameters. This was associated with a decline in cardiac mononuclear cell activity, an increase in T regulatory cells and T cell apoptosis, and an increase in left ventricular interleukin-10 and interferon-γ mRNA expression.

Conclusions

We conclude that CAPs are a unique type of cardiac-derived cells and promising tools to improve acute CVB3-induced myocarditis.     

Comparative Proteome Analysis of Spontaneous Outer Membrane Vesicles and Purified Outer Membranes of Neisseria meningitidis

Outer membrane vesicles (OMVs) of Gram-negative bacteria receive increasing attention because of various biological functions and their use as vaccines. However, the mechanisms of OMV release and selective sorting of proteins into OMVs remain unclear. Comprehensive quantitative proteome comparisons between spontaneous OMVs (SOMVs) and the outer membrane (OM) have not been conducted so far. Here, we established a protocol for metabolic labeling of neisserial proteins with ¹⁵N. SOMV and OM proteins labeled with ¹⁵N were used as an internal standard for proteomic comparison of the SOMVs and OMs of two different strains. This labeling approach, coupled with high-sensitivity mass spectrometry, allowed us to comprehensively unravel the proteome of the SOMVs and OMs. We quantified the relative distribution of 155 proteins between SOMVs and the OM. Complement regulatory proteins, autotransporters, proteins involved in iron and zinc acquisition, and a two-partner secretion system were enriched in SOMVs. The highly abundant porins PorA and PorB and proteins connecting the OM with peptidoglycan or the inner membrane, such as RmpM, MtrE, and PilQ, were depleted in SOMVs. Furthermore, the three lytic transglycosylases MltA, MltB, and Slt were less abundant in SOMVs. In conclusion, SOMVs are likely to be released from surface areas with a low local abundance of membrane-anchoring proteins and lytic transglycosylases. The enrichment of complement regulatory proteins, autotransporters, and trace metal binding and transport proteins needs to be explored in the context of the pathogenesis of meningococcal disease.     

PD-0332991, a CDK4/6 Inhibitor,Significantly Prolongs Survival in a Genetically Engineered Mouse Model of Brainstem Glioma

Diffuse intrinsic pontine glioma (DIPG) is an incurable tumor that arises in the brainstem of children. To date there is not a single approved drug to effectively treat these tumors and thus novel therapies are desperately needed. Recent studies suggest that a significant fraction of these tumors contain alterations in cell cycle regulatory genes including amplification of the D-type cyclins and CDK4/6, and less commonly, loss of Ink4a-ARF leading to aberrant cell proliferation. In this study, we evaluated the therapeutic approach of targeting the cyclin-CDK-Retinoblastoma (Rb) pathway in a genetically engineered PDGF-B-driven brainstem glioma (BSG) mouse model. We found that PD-0332991 (PD), a CDK4/6 inhibitor, induces cell-cycle arrest in our PDGF-B; Ink4a-ARF deficient model both in vitro and in vivo. By contrast, the PDGF-B; p53 deficient model was mostly resistant to treatment with PD. We noted that a 7-day treatment course with PD significantly prolonged survival by 12% in the PDGF-B; Ink4a-ARF deficient BSG model. Furthermore, a single dose of 10 Gy radiation therapy (RT) followed by 7 days of treatment with PD increased the survival by 19% in comparison to RT alone. These findings provide the rationale for evaluating PD in children with Ink4a-ARF deficient gliomas.