Biology subjects

Suerbaum, S.

Publications and source records attributed to Suerbaum, S..

7 recordsLinked to original sources

bioRxiv2025

Functional and intricate interaction network connecting Helicobacter pylori Cag Type 4 Secretion System surface proteins with outer membrane proteins HopQ and HopZ

The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a complex type IV secretion system (CagT4SS) which is an important virulence factor of H. pylori. Recently, structural detail on the CagT4SS has been substantially improved by cryo-EM. However, important structural and functional information, in particular on protein interactions between T4SS surface proteins, and of T4SS surface proteins with other proteins, is missing. In the present study, we followed the hypothesis that H. pylori T4SS external proteins may form a surface protein assembly, together with other, non-CagT4SS proteins, which may also be essential for T4SS function. Using interaction screens of H. pylori CagT4SS surface proteins, followed by biochemical and functional characterization, we have enhanced the knowledge on protein-protein interactions of CagT4SS extracellular proteins. This also includes newly identified interactions of CagT4SS surface proteins, for instance the VirB2 homolog CagC, the VirB5 homolog CagL and the surface protein CagN of unknown function, with outer membrane proteins HopQ and HopZ. We have further identified and quantitated direct interactions of T4SS surface proteins with outer membrane proteins HopZ and HopQ, which play a role in T4SS functions, and of both HopZ and HopQ with themselves and with host cell factors CEACAM and integrin. Furthermore, we determined an influence of pH on interactions between HopQ/HopZ and CagT4SS components. Utilizing protein tag insertions in H. pylori, we detected surface-exposed association of HopQ and HopZ with T4SS components on bacteria without or with (for HopQ) human gastric epithelial cells. Functionally antagonistic roles of HopQ and HopZ were uncovered in T4SS-dependent early pro- inflammatory human epithelial cell activation. In summary, we identified a network of interactions between H. pylori outer membrane proteins and CagT4SS surface proteins and characterized them as functionally important for transport processes. This will help to refine structural and functional details regarding surface-exposed proteins of the CagT4SS.

microbiology↗

bioRxiv2025

Decoding Helicobacter pylori Resistance: Machine Learning Enhanced Prediction of Antibiotic Susceptibility using Whole-Genome Sequencing

BackgroundHelicobacter pylori is a significant risk factor for gastric cancer, peptic ulcers, and MALT lymphoma. Rising antibiotic resistance rates complicate treatment strategies. While nucleotide sequence based assays are reliable in predicting clarithromycin and levofloxacin resistance, predicting metronidazole resistance is more challenging due to diverse metabolic pathways contributing to resistance, and high genomic variability. MethodsWe assembled a cohort of 483 H. pylori clinical isolates, combining whole-genome sequencing with phenotypic susceptibility testing. Machine learning models (SVM, XGBoost, FNN) were trained on genomic variants to predict resistance phenotypes. A sliding-window approach and SHAP-based importance scoring were used for feature selection to identify biologically relevant mutations, improving prediction accuracy, particularly for metronidazole resistance. ResultsThe best-performing FNN model improved metronidazole resistance prediction by 16% compared to conventional (non-ML, single polymorphisms) sequence-based detection methods applied to the same strain collection. Feature selection identified 32 feature sets, with 11 sets significantly improving F1-scores over the baseline. Combining 2-4 feature sets revealed 53 synergistic combinations across all models. Validation showed that 87% of these combinations significantly outperformed non-ML molecular testing, with 16 combinations achieving F1-scores above 0.65. ConclusionMachine-learning can significantly improve the performance of sequence-based susceptibility testing for metronidazole in H. pylori. Novel candidate predictive markers identified from whole-genome data offer testable hypotheses about yet unexplored mechanisms of metronidazole resistance. These findings support the potential for ML-based approaches to enable more accurate susceptibility-guided therapies.

microbiology↗

bioRxiv2024

The Helicobacter pylori orphan ATTAAT-specific methyltransferase M.Hpy99XIX plays a central role in the coordinated regulation of genes involved in iron metabolism

H. pylori genomes contain a large and variable portfolio of methyltransferases (MTases), creating a highly diverse methylome. Here, we characterize a highly conserved ATTAAT-specific MTase, M.Hpy99XIX, the only H. pylori MTase never associated with an endonuclease ("orphan" MTase). Inactivation of M.Hpy99XIX resulted in a significant change in the transcription of >100 genes, despite the fact that only a small subset of their promoter regions contained an ATTAAT target motif. Patterns of transcriptional change showed significant correlations with changes reported for H. pylori mutants in the ArsRS regulators involved in iron regulation. The MTase inactivation also caused a higher susceptibility to diverse metal ions as well as iron chelation and oxidative stress. These phenotypes could be traced back to the methylation of single motifs in the promoter regions of iron transporters frpB1 and fecA1. Altogether, methylation of individual motifs in promoters can have a large downstream effect causing major changes to metabolic pathways. These findings suggest that the methylome represents a universal and dynamic interface connecting genome diversity and transcriptional regulation. Very recently, a new ecospecies Hardy of H. pylori has been reported. M.Hpy99XIX is present in the majority of "normal" (Ubiquitous) H. pylori strains, whereas no single Hardy strain contained this gene, consistent with other reported differences between Hardy and Ubiquitous strains related to iron/metal homeostasis. ATTAAT methylation is intricately connected with the bacterial transcriptional network, highlighting the important role of bacterial epigenetic modifications in bacterial physiology and pathogenesis.

microbiology↗

bioRxiv2023

Methylome evolution through lineage-dependent selection in the gastric pathogen Helicobacter pylori

The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation showed that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection shapes both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.

microbiology↗

bioRxiv2023

Vaccination with Helicobacter pylori attachment proteins protects against gastric cancer

Most cases of gastric cancer are caused by chronic Helicobacter pylori infection, but the lack of early onco-diagnostics and a high risk for antibiotic resistance hampers early intervention through eradication of H. pylori infection by antibiotics. We reported on a protective mechanism where H. pylori gastric mucosal attachment can be reduced by natural antibodies that block the binding of its attachment protein BabA. Here we show that challenge infection with H. pylori induced response of such blocking antibodies in both human volunteers and in rhesus macaques, that mucosal vaccination with BabA protein antigen induced blocking antibodies in rhesus macaques, and that vaccination in a mouse model induced blocking antibodies that reduced gastric mucosal inflammation, preserved the gastric juice acidity, and fully protected the mice from gastric cancer caused by H. pylori.

immunology↗

bioRxiv2021

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

Helicobacter pylori lives in the human stomach and has a population structure which resembles that of its host. However, H. pylori from Europe and the Middle East trace a substantially higher fraction of ancestry from modern African populations than the humans that carry them. Here, we used a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations compared to either non-segregating or synonymous sites, implying selection to remove them. We used simulations to show that demographic bottlenecks can lead to long-term segregation of deleterious mutations, despite high rates of homologous recombination, but that population fitness can be restored by migration of small numbers of bacteria from non-bottlenecked populations, leading to mosaic patterns of ancestry like that seen for H. pylori. We conclude that H. pylori have been able to spread repeatedly from Africa by outcompeting strains that carried deleterious mutations accumulated during the original out-of-Africa bottleneck.

evolutionary biology↗

bioRxiv2018

The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori

Helicobacter pylori encodes a large number of Restriction-Modification (R-M) systems despite its small genome.R-M systems have been described as \"primitive immune systems\" in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H.pylori strain harbours a unique set of R-M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H.pylori genome sequences analyzed. Transcriptome analysis of two H.pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300.10 genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects.Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.

microbiology↗