Biology subjects

Hammerschmidt, S.

Publications and source records attributed to Hammerschmidt, S..

14 recordsLinked to original sources

bioRxiv2026

HERC4 limits oxidative stress-induced DNA damage during bacterial and viral-bacterial infection

Respiratory (co-)infections caused by influenza viruses and Streptococcus pneumoniae represent significant threats to global health. In our analysis of host cell ubiquitination, we identified reactive oxygen species (ROS) produced by S. pneumoniae as critical effectors in reducing the amount of intracellular polyubiquitinated proteins. Together with reduced ubiquitination we observed a downregulation of the E3 ligase HERC4 upon infection with S. pneumoniae in human alveolar epithelial and macrophage-like cells as well as in samples obtained from S. pneumoniae infected humans and mice. This was further aggravated in the viral-bacterial coinfection with influenza A. CRISPR-Cas9 deletion of HERC4 prior bacterial infection resulted in increased ROS-induced DNA damage, enhanced host cell apoptosis and reduced Histone 2B ubiquitination. In contrast, HERC4 overexpression diminished DNA damage indicating a role of HERC4 in DNA-damage-repair upon infection. By establishing a link between HERC4 expression and ROS-induced DNA damage and repair, we identified a potential marker for predicting the outcome of viral and bacterial (co-)infections. Targeting HERC4 expression defines a novel strategy to protect host cells from S. pneumoniae (co-)infection attenuating infection exacerbation.

microbiology↗

bioRxiv2026

Lipid-mediated regulation of pneumolysin balances vascular injury and bacterial containment during pneumococcal infection

Severe infection with Streptococcus (S.) pneumoniae is a leading cause of acute lung injury, multiorgan failure, and death despite appropriate antibiotic therapy. A major contributor to tissue damage is pneumolysin (PLY), a cholesterol-dependent pore-forming toxin that is released in large amounts during bacterial lysis. Because antibiotic treatment enhances PLY release, understanding the mechanisms that control PLY-induced host injury is critical for the development of strategies that limit tissue damage without impairing antibacterial defense. Using isolated perfused lungs and in situ two-photon imaging, we show that S. pneumoniae induces platelet and leukocyte recruitment, pulmonary edema, perfusion failure, and intravascular bacterial trapping within pulmonary arterioles. These responses required PLY and were associated with endothelial Ca{superscript 2} influx and plasma membrane permeabilization. The oxysterol 25-hydroxycholesterol (25-HC) prevented PLY-dependent Ca{superscript 2} entry, vascular leakage, and perfusion failure by reducing accessible membrane cholesterol through activation of acyl-CoA:cholesterol acyltransferase (ACAT). Unexpectedly, pneumococcal infection suppressed expression of cholesterol-25-hydroxylase (CH25H), the enzyme responsible for 25-HC synthesis, although induction of this pathway would be predicted to protect against toxin-mediated injury. We show that this downregulation results from inhibition of platelet-activating factor (PAF) receptor (PAFR) signaling by pneumococcal phosphocholine-containing cell wall components. Remarkably, both PAF itself and the anti-phosphocholine antibody TEPC directly inhibited PLY pore formation independently of PAFR, while preserving intravascular coagulation and bacterial trapping. Thus, although 25-HC protects against toxin-mediated vascular injury, its suppression may allow coagulation-dependent bacterial containment, with PAF acting as a compensatory antagonist of PLY. These findings identify a lipid-based host defense system in which 25-HC and PAF differentially regulate PLY activity to balance tissue protection with bacterial clearance and suggest new therapeutic approaches to limit the harmful effects of antibiotic-induced PLY release during pneumococcal infection.

immunology↗

bioRxiv2025

Unraveling proteomic chaos by independent component analysis - ClpX proficiency promotes the iron and oxygen limitation responses of Staphylococcus aureus and affects the intracellular bacterial behavior

In the opportunistic pathogen Staphylococcus aureus, protein homeostasis is largely mediated by the Caseinolytic protease (Clp) system. The proteases ClpXP and ClpCP are crucial for general and targeted proteolysis, which rely on the unfoldases ClpX and ClpC interacting with specific targets. However, the global effect on the proteome especially under infection-relevant stresses is not well-understood. To assess the effect of ClpX deficiency during infection-related processes, mass spectrometry-based global proteome profiles of S. aureus HG001 wild-type, an isogenic {Delta}clpX mutant, and a clpX complemented strain were recorded under control conditions as well as iron and oxygen limitation. The proteomic profiles revealed specific ClpX- and stress-dependent changes. A set of 24 robust stress-independent ClpX modulated proteins was identified and the stress-dependent influences were unraveled by independent component analysis (using the iModulon approach). These analyses revealed a role of ClpX in e.g., cell division, cell envelope homeostasis, the quinone stress response and prophage activation. Moreover, ClpX-dependent stress-specific effects were observed in the {Delta}clpX mutant, e.g. reduced induction of the heme uptake system under iron limitation and a dampened Rex-controlled oxygen limitation response. This revealed in particular that ClpX is central for heme homeostasis in S. aureus. Furthermore, in a Galleria infection model, the S. aureus {Delta}clpX mutant was attenuated compared to the wild-type HG001. This is consistent with a drastically reduced intracellular replication of the {Delta}clpX-mutant in cell culture-based infection experiments, however, high intracellular persistence of the {Delta}clpX mutant was also observed. This highlights the relevance of ClpX for bacterial fitness and virulence. ImportanceDuring infection processes, pathogens cope with host-mediated stressors. In response to those stressors, bacteria adapt their gene expression as well as their proteome profile. In the pathogen Staphylococcus aureus, protein homeostasis is mainly controlled by the Clp system. In particular, ClpX is the most conserved Clp unfoldase and is involved in overall regulation of virulence and bacterial fitness. However, the majority of ClpX targets remains elusive in S. aureus. With our proteomics approach and in depth data analysis, we provide a resource for global insight into ClpX-dependent adaptation of S. aureus physiology under infection-relevant conditions. Based on this, we uncover ClpXs role as a central player in the iron and oxygen limitation response. In addition, we demonstrate the importance of ClpX in S. aureus bacterial fitness in infection processes. However, reduced levels of ClpX lead to high intracellular persistence, which questions ClpXs suitability as a therapeutical target.

microbiology↗

bioRxiv2025

PneumoWiki: A pan-genome-based database for the pathogen Streptococcus pneumoniae

The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that exhibits more than 100 different capsular serotypes and considerable genomic variation. S. pneumoniae is also an important model organism for basic and biomedical research, with a number of strains with different characteristics being used. To address this, we have created the manually curated pan-genome database PneumoWiki (https://pneumowiki.med.uni-greifswald.de) that integrates genomic data from 43 S. pneumoniae strains with various aspects of functional annotation. All data relating to a specific gene and gene product are compiled on a Gene page. In addition to the gene and protein sequences and annotation from NCBI RefSeq, the Gene pages contain data on, for example, gene essentiality, protein function and localization, and transcriptional regulation. The information is supplemented with links to the data sources as well as to other databases and relevant literature. The basic concept of PneumoWiki is the interlinked presentation of pan-genome-based and strain-specific information. Therefore, register tabs with strain names at the top of the Gene pages allow switching between orthologous genes and the corresponding pan-genome page. The pan-genome gene pages contain a summary with functional information and the occurrence of the gene, an orthologue table for the 43 S. pneumoniae strains, a multiple-strain genome viewer as well as a protein sequence alignment. PneumoWiki was developed as a user-friendly tool and is available free of charge. The data collected in PneumoWiki are accessible via various download options to support bioinformatic applications. Overall, PneumoWiki is a resource for the pneumococcal research community that supports the analysis and interpretation of research data and, in particular, enables the integration of the knowledge available for different S. pneumoniae strains.

microbiology↗

bioRxiv2025

The global proteome of Streptococcus pneumoniae EF3030 under nutrient-defined in vitro conditions

Streptococcus pneumoniae is a pathobiont that colonises the upper respiratory tract of humans without causing symptoms but can cause a range of life-threatening diseases including pneumonia, sepsis, and meningitis. It also causes less severe, non-invasive infections such as otitis media and sinusitis. This bacterium thrives in the nasopharynx, where nutrient availability is limited, and has adapted to this environment by developing mechanisms to survive host stress and regulate protein abundance. To study the molecular biology of S. pneumoniae under in vitro and infection-related conditions, a suitable cultivation medium is essential for reproducible experiments. In this study, we optimized a chemically-defined minimal medium that mimics the in vivo nutrient-limited condition and used it for proteome analysis. This optimized medium not only shortened the lag phase but also improved the growth of S. pneumoniae clinical isolates and other streptococcal species. We applied this medium to analyse the global proteome of the pneumococcal colonising strain EF3030, focusing on the transition from the early to late log phase. Our proteomic analysis revealed distinct patterns of protein abundance in different functional categories including metabolism, amino acid synthesis, natural competence, RNA synthesis, cell wall synthesis, protein degradation, and stress responses. Notably, choline-binding protein CbpD, competence factors ComGA and ComEA as well as proteins involved in processing internalized single-stranded DNA (ssDNA) such as Dpr and DprA were higher in abundance in the late log phase. This proteomic profiling provides valuable insights into the pathophysiology of strain S. pneumoniae EF3030 under defined nutrient conditions.

microbiology↗

bioRxiv2023

The role of pneumococcal extracellular vesicles on the pathophysiology of the kidney disease Hemolytic Uremic Syndrome

Streptococcus pneumoniae-induced hemolytic uremic syndrome (Sp-HUS) is a kidney disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute kidney injury. This disease is frequently underdiagnosed and its pathophysiology is poorly understood. In this work, we compared clinical strains, isolated from infant Sp-HUS patients, to a reference pathogenic strain D39, for host cytotoxicity and further explored the role of Sp-derived extracellular vesicles (EVs) in the pathogenesis of a HUS infection. In comparison with the WT strain, pneumococcal HUS strains caused significant lysis of human erythrocytes and increased the release of hydrogen peroxide. Isolated Sp-HUS EVs were characterized by performing dynamic light-scattering microscopy and proteomic analysis. Sp-HUS strain released EVs at a constant concentration during growth, yet the size of the EVs varied and several subpopulations emerged at later time points. The cargo of the Sp-HUS EVs included several virulence factors at high abundance, i.e., the ribosomal subunit assembly factor BipA, the Pneumococcal Surface Protein A (PspA), the lytic enzyme LytC, several sugar utilization and fatty acid synthesis proteins. Sp-HUS EVs strongly downregulated the expression of the endothelial surface marker PECAM-1 and were internalized by human endothelial cells. Sp-HUS EVs elicited the release of pro-inflammatory cytokines (IL-1{beta}, IL-6) and chemokines (CCL2, CCL3, CXCL1) by human monocytes. These findings shed new light on the overall function of Sp-EVs, in the scope of infection-mediated HUS, and suggest new avenues of research for exploring the usefulness of Sp-EVs as therapeutic and diagnostic targets. ImportanceStreptococcus pneumoniae is a life-threatening human pathogen associated with severe illnesses in the upper respiratory tract. Disseminated infections also occur, as the kidney disease hemolytic uremic syndrome. Even though vaccination is available, this pathogen is responsible for a worldwide high mortality rate, especially among children from least developed countries, where vaccination strategies are poor or inexistent. It is estimated that 30% of invasive pneumococcal diseases are caused by antibiotic resistant bacteria, leading to the classification of "serious threat" by the World Health Organization. In order to prevent cases of severe illness, investigation in the direction of new vaccine candidates is of upmost importance. Pneumococcal extracellular vesicles pose as ideal candidates for a serotype-independent vaccine formulation. To this purpose, the aspects of vesicle formation, cargo allocation and function need to be understood in detail. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/526387v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1f5faeborg.highwire.dtl.DTLVardef@2c6176org.highwire.dtl.DTLVardef@1b29245org.highwire.dtl.DTLVardef@a119ea_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Competence remodels the pneumococcal cell wall providing resistance to fratricide and surface exposing key virulence factors

Competence development in the human pathogen Streptococcus pneumoniae controls several features such as genetic transformation, biofilm formation and virulence. Competent bacteria produce so called fratricins such as CbpD, that kill non-competent siblings by cleaving peptidoglycan (PGN). CbpD is a choline-binding protein (CBP) that binds to phosphorylcholine residues found on wall- and lipoteichoic acids (WTA and LTA) that together with PGN are major constituents of the pneumococcal cell wall. Competent pneumococci are protected against fratricide by producing the immunity protein ComM. How competence and fratricide contribute to virulence is unknown. Here, using a genome-wide CRISPRi-seq screen, we show that genes involved in teichoic acid biosynthesis are essential during competence. We demonstrate that LytR is the major enzyme mediating the final step in WTA formation, and that, together with ComM, is essential for immunity against CbpD. Importantly, we show that key virulence factors PspA and PspC become more surface-exposed at midcell during competence, in a CbpD-dependent manner. Together, our work supports a model in which activation of competence is crucial for host adherence by increased surface exposure of its various CBPs.

microbiology↗

bioRxiv2022

The choline-binding proteins PspA, PspC and LytA of Streptococcus pneumoniae and their role on host cellular adhesion and damage

Streptococcus pneumoniae is a Gram-positive opportunistic pathogen that can colonize the upper respiratory tract. It is a leading cause of a wide range of infectious diseases, including community-acquired pneumonia, meningitis, otitis media and bacteraemia. Pneumococcal infections cause 1-2 million deaths per year, most of which occur in developing countries, where this bacterial species is probably the most important pathogen during early infancy. Here, we focused on choline-binding proteins (CBPs), i.e., PspC, PspA and LytA, and their integration into and interaction with the cell wall of S. pneumoniae. The three pneumococcal proteins have different surface-exposed regions but share related choline-binding anchors. These surface-exposed pneumococcal proteins are in direct contact with host cells and have diverse functions. PspC and PspA bind several host plasma proteins, whereas LytA plays a role in cell division and the lytic phase. We explored the role of the three CBPs on adhesion and pathogenicity in a human host by performing relevant imaging and functional analyses, such as electron microscopy, confocal laser scanning microscopy and functional quantitative assays targeting biofilm formation and the haemolytic capacity of S. pneumoniae. In vitro biofilm formation assays and electron microscopy experiments were used to examine the ability of knockout mutant strains lacking the lytA, pspC or pspA genes to adhere to surfaces. The mutant strains were compared with the S. pneumoniae D39 reference strain. We found that LytA plays an important role in robust synthesis of the biofilm matrix. PspA and PspC appeared crucial for the haemolytic effects of S. pneumoniae on human red blood cells. Furthermore, all knockout mutants caused less damage to endothelial cells than wild-type bacteria, highlighting the significance of CPBs for the overall pathogenicity of S. pneumoniae. Hence, in addition to their structural function within the cell wall of S. pneumoniae, each of these three surface-exposed CBPs controls or mediates multiple steps during bacterial pathogenesis.

immunology↗

bioRxiv2021

Alpha-hemolysin of Staphylococcus aureus impairs thrombus formation

Toxins are key virulence determinants of pathogens and can impair the function of host immune cells including platelets. Insights into pathogen toxin interference with platelets will be pivotal to improve treatment of patients with bacterial bloodstream infections. In this study, we deciphered the effects of Staphylococcus aureus toxins -hemolysin, LukAB, LukDE and LukSF on human platelets and compared the effects with the pore forming toxin pneumolysin of Streptococcus pneumoniae. In contrast to pneumolysin, -hemolysin initially activates platelets as indicated by CD62P and IIb{beta}3 integrin expression, but the resulting pores also induce alterations in the phenotype of platelets and induce apoptosis of platelets. The presence of small amounts of -hemolysin (0.2 {micro}g/mL) in whole blood abrogates thrombus formation indicating that in systemic infections with S. aureus the stability of formed thrombi is impaired. This might be of high clinical relevance for S. aureus induced endocarditis of the aortic valves. Stabilizing the thrombi by inhibiting -hemolysin induced impairment of platelets likely reduces the risk for septic (micro-)embolization. However, in contrast to pneumolysin, -hemolysin induced platelets damage could not be neutralized by intravenous immune globulins. In contrast to -hemolysin, S. aureus bi-component pore forming leukocidins LukAB, LukED and LukSF do not bind to platelets and had no significant effect on platelet activation and viability. Main point 1: -hemolysin forms pores in platelets, which first activate but then result in apoptosis and impairs thrombus formation and stability Main point 2: Polyvalent immunoglobulins do not neutralize the mode of action of the toxin

microbiology↗

bioRxiv2021

A novel innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins

Sensing of pathogens by ubiquitination is critical for maintaining cytosolic sanctity. However, universal ubiquitination targets on bacteria, especially of proteinaceous origin, remain unidentified. Here, we unveil a novel strategy, involving recognition of degron-like motifs for identification of first protein-based ubiquitination substrates on phylogenetically distinct bacteria. Such motifs can form a new class of intra-cytosolic pathogen associated molecular patterns (PAMPs) as their incorporation enables identification of non-ubiquitin targets by host Ub-ligases. We find SCFFBW7 E3-ligase, supported by the regulatory kinase, GSK3{beta}, is crucial for effective pathogen detection and clearance. This may explain the enhanced risk of infections in Chronic Lymphocytic Leukaemia patients bearing FBXW7 mutations. We conclude that exploitation of such ubiquitous pathogen sensing strategy allows conservation of cellular resources and boost anti-microbial immunity. One Sentence SummaryUbiquitination of bacterial surface proteins fosters sensing and clearance of diverse pathogens

microbiology↗

bioRxiv2021

A semisynthetic glycoconjugate provides expanded cross-serotype protection against Streptococcus pneumoniae

Streptococcus pneumoniae infections are the leading cause of child mortality globally. Current vaccines fail to induce a protective immune response towards a conserved part of the pathogen, resulting in new serotypes causing disease. Therefore, new vaccine strategies are urgently needed. Described is a two-pronged approach combining S.pneumoniae proteins, pneumolysin and PspA, with a precisely defined synthetic oligosaccharide, whereby the carrier protein acts as a serotype-independent antigen to provide additional protection. Proof of concept in mice and swine models revealed that the conjugates inhibit colonization of the nasopharynx, decrease the bacterial load and reduce disease severity in the bacteria challenged model. Immunization of piglets provided the first evidence for the immunogenicity and protective potential of synthetic glycoconjugate vaccine in a large animal model. A combination of synthetic oligosaccharides with proteins from the target pathogen opens the path to create broadly cross-protective ("universal") pneumococcal vaccines.

immunology↗

bioRxiv2021

Atypical N-glycosylation of SARS-CoV-2 impairs the efficient binding of Spike-RBM to the human-host receptor hACE2

SARS-CoV-2 internalization by human host cells relies on the molecular binding of its spike glycoprotein (SGP) to the angiotensin-converting-enzyme-2 (hACE2) receptor. It remains unknown whether atypical N-glycosylation of SGP modulates SARS-CoV-2 tropism for infections. Here, we address this question through an extensive bioinformatics analysis of publicly available structural and genetic data. We identified two atypical sequons (sequences of N-glycosylation: NGV 481-483 and NGV 501-503), strategically located on the receptor-binding motif (RBM) of SGP and facing the hACE2 receptor. Interestingly, the cryo-electron microscopy structure of trimeric SGP in complex with potent-neutralizing antibodies from convalescent patients revealed covalently-linked N-glycans in NGV 481-483 atypical sequons. Furthermore, NGV 501-503 atypical sequon involves the asparagine-501 residue, whose highly-transmissible mutation N501Y is present in circulating variants of major concerns and affects the SGP-hACE2 binding-interface through the well-known hotspot-353. These findings suggest that atypical SGP post-translational modifications modulate the SGP-hACE2 binding-affinity affecting consequently SARS-CoV-2 transmission and pathogenesis.

molecular biology↗

bioRxiv2020

Same, Same, but Different: Molecular Analyses of Streptococcus pneumoniae Immune Evasion Proteins Identifies new Domains and Reveals Structural Differences between PspC and Hic Variants

PspC and Hic proteins of Streptococcus pneumoniae are some of the most variable microbial immune evasion proteins identified to date. Due to structural similarities and conserved binding profiles it was assumed over a long time that these pneumococcal surface proteins represent a protein family, comprising eleven subgroups. Recently, however, by evaluating more proteins larger diversity of individual proteins became apparent. In contrast to previous assumptions a pattern evaluation of six PspC and five Hic variants, each representing one of the previously defined subgroups, revealed distinct structural and likely functionally regions of the proteins, and identified nine new domains and new domain alternates. Several domains are unique to PspC and Hic variants, while other domains are shared with other S. pneumoniae and bacterial virulent determinants. This understanding improved pattern evaluation on the level of full-length proteins, allowed a sequence comparison on the domain level and furthermore identified domains with a modular composition. This novel concept allows a better characterization of variability, and modular domain composition of individual proteins, enables a structural and functional characterization at the domain level and furthermore shows substantial structural differences between PspC and Hic proteins. Such knowledge will also be useful for molecular strain typing, characterizing PspC and Hic proteins from new clinical S. pneumoniae strains, including those derived from patients who present with pneumococcal hemolytic uremic syndrome. Furthermore this analysis explains the role of multifaceted intact PspC and Hic proteins in pathogen host interactions. and can provide a basis for rational vaccine design. Author SummaryThe human pathobiont Streptococcus pneumoniae expresses highly polymorphic PspC or Hic proteins, which bind a repertoire of host immune regulators and combine antigenic variation with conserved immune evasion features. Understanding domain composition of each protein encoded by more than 60 000 pspC or hic genes deposited in the data banks defines their diversity, a role in immune escape and can furthermore delineate structure function approach for single protein domains. PspC and Hic proteins show variable domain composition and sequence diversity, which explain differences in binding of human regulators and likely in immune escape. The results of our analyses provide insights in the domain composition of these diverse immune evasion proteins, identifies new domains, defines domains which are unique to PspC or Hic variants, and identifies domains which are shared with other bacterial immune evasion proteins. These data have implication on cell wall attachment, surface distribution and in immune escape.

microbiology↗

bioRxiv2018

Pneumococcal metabolic adaptation and colonization is regulated by the two-component regulatory system 08

Streptococcus pneumoniae two-component regulatory systems (TCS) enable adaptation and ensure its maintenance in host environments. This study deciphers the impact of the TCS08 on pneumococcal gene expression and its role in metabolic and pathophysiological processes. Transcriptome analysis and real-time PCR demonstrated a regulatory effect of the TCS08 on genes involved mainly in environmental information processing, intermediary metabolism, and colonization by S. pneumoniae D39 and TIGR4. Striking examples are genes of the fatty acid biosynthesis, arginine-deiminase system, and psa operon encoding the manganese ABC transport system. In silico analysis confirmed that TCS08 is homologous to Staphylococcus aureus SaeRS and a SaeR-like binding motif is displayed in the promotor region of pavB, the upstream gene of the tcs08 operon encoding a surface-exposed adhesin. Indeed, PavB is regulated by the TCS08 as confirmed by immunoblotting and surface abundance assays. Similarly, Pilus-1 of TIGR4 is regulated by TCS08. Finally, in vivo infections using the acute pneumonia and sepsis models showed a strain dependent effect. Loss of function of HK08 or TCS08 attenuated D39 virulence in lung infections. The RR08 deficiency attenuated TIGR4 in pneumonia, while there was no effect on sepsis. In contrast, lack of HK08 procured a highly virulent TIGR4 phenotype in both pneumonia and sepsis infections. Taken together, these data indicate the importance of TCS08 in pneumococcal fitness to adapt to the milieu of the respiratory tract during colonization.\n\nIMPORTANCEStreptococcus pneumoniae interplays with its environment by using 13 two-component regulatory systems and one orphan response regulator. These systems are involved in the sensing of environmental signals thereby modulating pneumococcal pathophysiology. This study aimed to understand the functional role of genes subject to control by the TCS08. The identified genes play a role in transport of compounds such as sugars or amino acids. In addition, the intermediary metabolism and colonization factors are modulated by TCS08. Thus, TCS08 regulates genes involved in maintaining pneumococcal physiology, transport capacity and adhesive factors to enable optimal colonization, which represents a prerequisite for invasive pneumococcal disease.

microbiology↗