Proteomic Investigation Uncovers Potential Targets and Target Sites of Pneumococcal Serine-Threonine Kinase StkP and Phosphatase PhpP

Like eukaryotes, different bacterial species express one or more Ser/Thr kinases and phosphatases that operate in various signaling networks by catalyzing phosphorylation and dephosphorylation of proteins that can immediately regulate biochemical pathways by altering protein function. The human pathogen Streptococcus pneumoniae encodes a single Ser/Thr kinase-phosphatase couple known as StkP-PhpP, which has shown to be crucial in the regulation of cell wall synthesis and cell division. In this study, we applied proteomics to further understand the physiological role of pneumococcal PhpP and StkP with an emphasis on phosphorylation events on Ser and Thr residues. Therefore, the proteome of the non-encapsulated D39 strain (WT), a kinase (ΔstkP), and phosphatase mutant (ΔphpP) were compared in a mass spectrometry based label-free quantification experiment. Results show that a loss of function of PhpP causes an increased abundance of proteins in the phosphate uptake system Pst. Quantitative proteomic data demonstrated an effect of StkP and PhpP on the two-component systems ComDE, LiaRS, CiaRH, and VicRK. To obtain further information on the function, targets and target sites of PhpP and StkP we combined the advantages of phosphopeptide enrichment using titanium dioxide and spectral library based data evaluation for sensitive detection of changes in the phosphoproteome of the wild type and the mutant strains. According to the role of StkP in cell division we identified several proteins involved in cell wall synthesis and cell division that are apparently phosphorylated by StkP. Unlike StkP, the physiological function of the co-expressed PhpP is poorly understood. For the first time we were able to provide a list of previously unknown putative targets of PhpP. Under these new putative targets of PhpP are, among others, five proteins with direct involvement in cell division (DivIVA, GpsB) and peptidoglycan biosynthesis (MltG, MreC, MacP)

Bordetella pertussis outer membrane vesicles as virulence factor vehicles that influence bacterial interaction with macrophages

Gram-negative pathogenic bacteria constitutively shed outer membrane vesicles(OMVs) which play a significant role in the host-pathogen interaction, eventually determiningthe outcome of the infection. We previously found that Bordetella pertussis, the etiologicalagent of whooping cough, survives the innate interaction with human macrophages remainingalive inside these immune cells. Adenylate cyclase (CyaA), one of the main toxins of thispathogen, was found involved in the modulation of the macrophage defense response,eventually promoting bacterial survival within the cells. We here investigated whether B.pertussis OMVs, loaded with most of the bacterial toxins and CyaA among them, modulatethe macrophage response to the bacterial infection. We observed that the pre-incubation ofmacrophages with OMVs led to a decreased macrophage defense response to the encounterwith the bacteria, in a CyaA dependent way. Our results suggest that CyaA delivered by B.pertussis OMVs dampens macrophages protective function by decreasing phagocytosis andthe bactericidal capability of these host cells. By increasing the chances of bacterial survivalto the innate encounter with the macrophages, B. pertussis OMVs might play a relevant rolein the course of infection, promoting bacterial persistence within the host and eventually,shaping the whole infection process.Fil: Blancá, Bruno Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Alvarez Hayes, Jimena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Surmann, Kristin. University Medicine Greifswald; AlemaniaFil: Valdez, Hugo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Hentschker, Christian. University Medicine Greifswald; AlemaniaFil: Lamberti, Yanina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Völker, Uwe. University Medicine Greifswald; AlemaniaFil: Rodriguez, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentin

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hinzke, T., Kleiner, M., Meister, M., Schlueter, R., Hentschker, C., Pane-Farre, J., Hildebrandt, P., Felbeck, H., Sievert, S. M., Bonn, F., Voelker, U., Becher, D., Schweder, T., & Markert, S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Elife, 10, (2021): e58371, https://doi.org/10.7554/eLife.58371.The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.This work was supported by the German Research Foundation DFG (grant MA 6346/2–1 to SM), fellowships of the Institute of Marine Biotechnology Greifswald (TH, MM), a German Academic Exchange Service (DAAD) grant (TH), the NC State Chancellor’s Faculty Excellence Program Cluster on Microbiomes and Complex Microbial Communities (MK), the USDA National Institute of Food and Agriculture, Hatch project 1014212 (MK), the U.S. National Science Foundation (grants OCE-1131095 and OCE-1559198 to SMS), and The WHOI Investment in Science Fund (to SMS). We furthermore acknowledge support for article processing charges from the DFG (Grant 393148499) and the Open Access Publication Fund of the University of Greifswald

Qualitative und quantitative Untersuchungen zu posttranslationalen Modifikationen bakterieller Proteome

Posttranslationale Proteinmodifikationen beeinflussen Proteinaktivitäten und Signalwege innerhalb einer Zelle und haben somit vielfältige Auswirkungen auf den Stoffwechsel von Bakterien. Um die genauen Mechanismen besser verstehen zu können, wurde in dieser Arbeit das Phosphoproteom von Streptococcus pneumoniae D39 untersucht. Der Schwerpunkt lag dabei in der Entwicklung besserer Auswertestrategien und der damit einhergehenden verbesserten Identifizierung von Phosphoproteinen. Um dies zu bewerkstelligen, wurden die Proteinextrakte durch gelfreie und gelbasierte Methoden aufgetrennt. Die Auswertung der Experimente erfolgte zunächst durch klassische Proteinidentifizierung mit Hilfe von Proteindatenbanken. Zusätzlich wurden Spektrenbibliotheken von S. pneumoniae D39 aufgebaut und diese für eine bessere Proteinidentifizierung sowie Phosphoproteinidentifizierung genutzt. Anschließend wurden zur Quantifizierung des Phosphoproteoms dieses Pathogens verschiedene Quantifizierungsmethoden getestet und modifiziert. Hierbei wurde zum einen das Phosphoproteom einer Kinasedeletionsmutante von S. pneumoniae D39 über die Spotintensitäten von 2D Gelen mit dem Wildtyp verglichen. Zusätzlich wurden die Auswirkungen dieser Kinase auf das globale S. pneumoniae D39 Proteom mittels SILAC sowie der neu erstellten Spektrenbibliothek aufgezeigt. Eine weitere etablierte Quantifizierungsmethode für Phosphoproteine in der Arbeit war die Kombination von metabolischer Markierung und 2D Gelen. Die Veränderung des Phosphoproteoms wurde an dem industriell bedeutsamen Bakterium Bacillus pumilus anhand von oxidativem Stress aufgezeigt.Investigations of posttranslational protein modifications such as phosphorylations in bacteria have gotten more and more relevant in the last years. Protein phosphorylations participate in important regulatory processes in several organisms. Knowledge about the adaption triggered by proteins and protein modifications can serve to find strategies to facilitate prevention and therapy of severe illnesses such as pneumonia for example, which can be caused by the pathogen Streptococcus pneumoniae. To obtain more knowledge on the impact of protein phosphorylations, the phosphoproteome of S. pneumoniae D39 was comprehensively investigated in the framework of this dissertation. Hereby, the focus lay on improving phosphoprotein identification using spectral libraries. Furthermore, the proteome and phosphoproteome of the pathogen was quantified with several methods. Hereby, the impact of the serine threonine kinase StkP was elucidated by comparing spot intensities on two-dimensional gels between the wildtype and a stkP deletion mutant. Additionally, the influence of this kinase on the pathogen‘s proteome was monitored using SILAC labelling and the generated spectral libraries. Moreover, also the economically used organism Bacillus pumilus was under investigation during this thesis. This organism was employed to successfully test the combination of 2D gels and metabolic labelling to quantitatively determine the outcome of oxidative stress on protein phosphorylations

Major Determinants of Airway Epithelial Cell Sensitivity to S. aureus Alpha-Toxin: Disposal of Toxin Heptamers by Extracellular Vesicle Formation and Lysosomal Degradation

Alpha-toxin is a major virulence factor of Staphylococcus aureus. Monomer binding to host cell membranes results in the formation of heptameric transmembrane pores. Among human model airway epithelial cell lines, A549 cells were most sensitive toward the toxin followed by 16HBE14o- and S9 cells. In this study we investigated the processes of internalization of pore-containing plasma membrane areas as well as potential pathways for heptamer degradation (lysosomal, proteasomal) or disposal (formation of exosomes/micro-vesicles). The abundance of toxin heptamers upon applying an alpha-toxin pulse to the cells declined both in extracts of whole cells and of cellular membranes of S9 cells, but not in those of 16HBE14o- or A549 cells. Comparisons of heptamer degradation rates under inhibition of lysosomal or proteasomal degradation revealed that an important route of heptamer degradation, at least in S9 cells, seems to be the lysosomal pathway, while proteasomal degradation appears to be irrelevant. Exosomes prepared from culture supernatants of toxin-exposed S9 cells contained alpha-toxin as well as low amounts of exosome and micro-vesicle markers. These results indicate that lysosomal degradation of internalized toxin heptamers may be the most important determinant of toxin-resistance of some types of airway epithelial cells

Improving Proteome Coverage for Small Sample Amounts: An Advanced Method for Proteomics Approaches with Low Bacterial Cell Numbers

Abstract Proteome analyses are often hampered by the low amount of available starting material like a low bacterial cell number obtained from in vivo settings. Here, the single pot solid‐phase enhanced sample preparation (SP3) protocol is adapted and combined with effective cell disruption using detergents for the proteome analysis of bacteria available in limited numbers only. Using this optimized protocol, identification of peptides and proteins for different Gram‐positive and Gram‐negative species can be dramatically increased and, reliable quantification can also be ensured. This adapted method is compared to already established strain‐specific sample processing protocols for Staphylococcus aureus, Streptococcus suis, and Legionella pneumophila. The highest species‐specific increase in identifications is observed using the adapted method with L. pneumophila samples by increasing protein and peptide identifications up to 300% and 620%, respectively. This increase is accompanied by an improvement in reproducibility of protein quantification and data completeness between replicates. Thus, this protocol is of interest for performing comprehensive proteomics analyses of low bacterial cell numbers from different settings ranging from infection assays to environmental samples

Improving Proteome Coverage for Small Sample Amounts: An Advanced Method for Proteomics Approaches with Low Bacterial Cell Numbers

Abstract Proteome analyses are often hampered by the low amount of available starting material like a low bacterial cell number obtained from in vivo settings. Here, the single pot solid‐phase enhanced sample preparation (SP3) protocol is adapted and combined with effective cell disruption using detergents for the proteome analysis of bacteria available in limited numbers only. Using this optimized protocol, identification of peptides and proteins for different Gram‐positive and Gram‐negative species can be dramatically increased and, reliable quantification can also be ensured. This adapted method is compared to already established strain‐specific sample processing protocols for Staphylococcus aureus, Streptococcus suis, and Legionella pneumophila. The highest species‐specific increase in identifications is observed using the adapted method with L. pneumophila samples by increasing protein and peptide identifications up to 300% and 620%, respectively. This increase is accompanied by an improvement in reproducibility of protein quantification and data completeness between replicates. Thus, this protocol is of interest for performing comprehensive proteomics analyses of low bacterial cell numbers from different settings ranging from infection assays to environmental samples

WIdO-Report: Entwicklung der Krankenhausfallzahlen während des Coronavirus-Lockdowns

Die weltweite Ausbreitung von Infektionsfällen mit dem neuen Coronavirus (SARS-CoV-2) hat Deutschland bereits Ende Januar 2020 mit den ersten nachgewiesenen Fällen bei einem Autozulieferer in München erreicht. Frühzeitig wurden Maßnahmen zur Eindämmung der Coronavirus-Pandemie in Deutschland ergriffen. Der gesellschaftliche Lockdown und die Vorbereitung des Gesundheitssystems auf die befürchtete Überlastung des Kliniksektors durch schwer erkrankte Infizierte haben zu massiven Rückgängen der Fallzahlen in der stationären Versorgung geführt. Mit dem vorliegenden Beitrag informiert das Wissenschaftliche Institut der AOK (WIdO) darüber, bei welchen Erkrankungen und Behandlungen Fallzahländerungen im Zusammenhang mit der Pandemie feststellbar sind und diskutiert mögliche Ursachen für diese Entwicklungen. Der notwendig differenzierte Blick auf die Nebeneffekte der ersten Welle der Coronavirus-Pandemie gibt zugleich Hinweise für mögliche weitere, bundesweite oder regionale Lockdown-Maßnahmen während des weiteren Voranschreitens der Coronavirus-Infektionen in Deutschland

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin-Benson-Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys

Deficiency in FTSJ1 Affects Neuronal Plasticity in the Hippocampal Formation of Mice

Simple Summary Neuronal plasticity refers to the brain’s ability to adapt in response to activity-dependent changes. This process, among others, allows the brain to acquire memory or to compensate for a neurocognitive deficit. We analyzed adult FTSJ1-deficient mice in order to gain insight into the role of FTSJ1 in neuronal plasticity. These mice displayed alterations in the hippocampus (a brain structure that is involved in memory and learning, among other functions) e.g., in the form of changes in dendritic spines. Changes in dendritic spines are considered to represent a morphological hallmark of altered neuronal plasticity, and thus FTSJ1 deficiency might have a direct effect upon the capacity of the brain to adapt to plastic changes. Long-term potentiation (LTP) is an electrophysiological correlate of neuronal plasticity, and is related to learning and to processes attributed to memory. Here we show that LTP in FTSJ1-deficient mice is reduced, hinting at disturbed neuronal plasticity. These findings suggest that FTSJ1 deficiency has an impact on neuronal plasticity not only morphologically but also on the physiological level. Abstract The role of the tRNA methyltransferase FTSJ1 in the brain is largely unknown. We analyzed whether FTSJ1-deficient mice (KO) displayed altered neuronal plasticity. We explored open field behavior (10 KO mice (aged 22–25 weeks)) and 11 age-matched control littermates (WT) and examined mean layer thickness (7 KO; 6 WT) and dendritic spines (5 KO; 5 WT) in the hippocampal area CA1 and the dentate gyrus. Furthermore, long-term potentiation (LTP) within area CA1 was investigated (5 KO; 5 WT), and mass spectrometry (MS) using CA1 tissue (2 each) was performed. Compared to controls, KO mice showed a significant reduction in the mean thickness of apical CA1 layers. Dendritic spine densities were also altered in KO mice. Stable LTP could be induced in the CA1 area of KO mice and remained stable at for at least 1 h, although at a lower level as compared to WTs, while MS data indicated differential abundance of several proteins, which play a role in neuronal plasticity. FTSJ1 has an impact on neuronal plasticity in the murine hippocampal area CA1 at the morphological and physiological levels, which, in conjunction with comparable changes in other cortical areas, might accumulate in disturbed learning and memory functions