Biology subjects

Frick, J.

Publications and source records attributed to Frick, J..

5 recordsLinked to original sources

bioRxiv2026

CagA delivery by the Helicobacter pylori Cag-Type IV Secretion System confers fitness benefits and costs during stomach infection

Helicobacter pylori strains encoding the cag-pathogenicity island (cag-PAI) and the effector toxin cagA are associated with worse disease outcomes. The cag-PAI encodes the Cag type IV secretion system (Cag-T4SS) which injects CagA and other bacterial products into gastric epithelial cells. Prior work revealed that host adaptive immunity promotes recombination in the cag-PAI gene cagY to attenuate Cag-T4SS activity during chronic infection, suggesting a fitness cost to assembling an active Cag-T4SS. To explore potential selective benefits and costs for the Cag-T4SS and CagA, we employed single strain and competitive infections at both acute and chronic timepoints in wildtype mice and transgenic mice that either attenuate innate immune responses or promote gastric pathology independent of H. pylori infection to examine the relative fitness of mutant H. pylori strains. Our results suggest that an active Cag-T4SS and CagA confer a fitness benefit during initial colonization through Cag-T4SS activity-dependent epithelial cell interactions that activate cancer-related signaling pathways. However, increasing gastric inflammation confers a fitness cost to CagA translocation, promoting Cag-T4SS shutoff. Targeted and whole genome sequencing revealed multiple mechanisms of Cag-T4SS attenuation, with recombination-mediated changes in cagY prevalent at early timepoints and mutations in a variety of Cag-T4SS structural genes accumulating as disease progresses. The need for Cag-T4SS activity and CagA translocation during initial gland colonization likely underlies the mutational pattern observed. Collectively this work reveals new insights into selective constraints on the H. pylori Cag-T4SS as well as resultant genetic adaptation processes that lead to retention of the cag-PAI and virulence.

microbiology↗

bioRxiv2026

Helicobacter pylori allelic variation in cell surface genes influences human exoproteome binding and stomach tissue adherence

Helicobacter pylori, the primary etiological agent of gastric cancer, requires chronic infection to promote severe disease. Throughout colonization, the bacteria accumulate genetic variation, which can reshape the interaction between host and pathogen. In this study, we probed adherence as one important characteristic of this relationship. We leveraged a panel of H. pylori strains, representing both inter- and intra-host diversity, and BASEHIT, a comprehensive barcoded yeast display library of the human exoproteome, to evaluate the human exoprotein binding characteristics of H. pylori. We identified a set of lineage-correlated binding phenotypes and a set of polymorphic cell surface-associated loci that we predict to govern heterogeneous binding. We also identified a general increase in gastric tissue adherence during mouse passage and structural modifications in the O-antigen component lipopolysaccharide. Subsequent sequence analyses identified C-terminal repeat length reduction in either futB or glycosyltransferase family 25 galactose transferases as sufficient to alter lipopolysaccharide. Shorter repeat variants were favored during both acute and chronic colonization and conferred a colonization advantage in coinfection. Our data indicate that shorter enzymes, and the resulting shorter O-antigen repeats, are favored during infection. We hypothesize that repeat length polymorphisms modulate enzyme efficiency and disrupt the balance of competing reactions required for O-antigen synthesis. ImportanceIn this study, we used a high throughput assay to evaluate the adherence of genetically diverse Helicobacter pylori isolates to human proteins they may encounter in the stomach. We showed that more closely related H. pylori strains bind human proteins similarly. We linked changes in bacterial binding to genetic differences affecting cell surface components. In particular, H. pylori strains passaged through mice exhibited increased adherence to stomach tissue, which we associated with structural variation in the enzymes responsible for synthesizing the O-antigen portion of lipopolysaccharide. We also showed that shorter enzyme variants produce distinct O-antigen structures that enhance colonization of the mouse stomach.

microbiology↗

bioRxiv2024

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

microbiology↗

bioRxiv2022

Helicobacter pylori chronic infection selects for effective colonizers of metaplastic glands

Chronic gastric infection with Helicobacter pylori can lead to progressive tissue changes that culminate in cancer, but how H. pylori adapts to the changing tissue environment during disease development is not fully understood. In a transgenic mouse gastric metaplasia model, we found that strains from unrelated individuals differed in their ability to infect the stomach, to colonize metaplastic glands, and to induce proliferation and alter the expression of metaplasia-associated proteins. H. pylori isolates from different stages of disease from a single individual had differential ability to colonize healthy and metaplastic gastric glands. Exposure to the metaplastic environment selected for high gastric colonization by one of these strains. Complete genome sequencing revealed a unique alteration in the frequency of a variant allele of the putative adhesin sabB, arising from a recombination event with the related sialic acid binding adhesin (SabA) gene. Mutation of sabB strongly reduced adherence to both normal and metaplastic gastric tissue in multiple strain backgrounds and highly attenuated stomach colonization. Thus, the changing gastric environment during disease development promotes bacterial adhesin gene variation associated with enhanced gastric colonization. ImportanceChronic infection with Helicobacter pylori is the primary risk factor for developing stomach cancer. As disease progresses H. pylori must adapt to a changing host tissue environment that includes induction of new cell fates in the cells that line the stomach. We tested representative H. pylori isolates collected from the same patient during early and later stages of disease in a mouse model where we can rapidly induce disease-associated tissue changes. Only the later-stage H. pylori strains could robustly colonize the diseased stomach environment. We also found that the ability to colonize the diseased stomach was associated with genetic variation in a putative cell surface adhesin gene called sabB. Additional experiments revealed that SabB promotes binding to stomach tissue and is critical for stomach colonization by the late-stage strains. Thus, H. pylori diversifies its genome during disease progression and these genomic changes highlight critical factors for bacterial persistence.

microbiology↗

bioRxiv2021

Pivotal Roles for Ribonucleases in Streptococcus pneumoniae Pathogenesis

RNases perform indispensable functions in regulating gene expression in many bacterial pathogens by processing and/or degrading RNAs. Despite the pivotal role of RNases in regulating bacterial virulence factors, the functions of RNases have not yet been studied in the major human respiratory pathogen Streptococcus pneumoniae (pneumococcus). Here, we sought to determine the impact of two conserved RNases, the endoribonuclease RNase Y and exoribonuclease polynucleotide phosphorylase (PNPase), on the physiology and virulence of S. pneumoniae serotype 2 strain D39. We report that RNase Y and PNPase are essential for pneumococcal pathogenesis as both deletion mutants showed strong attenuation of virulence in murine models of invasive pneumonia. Genome-wide transcriptomic analysis revealed that nearly 200 mRNA transcripts were significantly up-regulated, whereas the abundance of several pneumococcal sRNAs, including the Ccn (CiaR Controlled Noncoding RNA) sRNAs, were altered in the {Delta}rny mutant relative to the wild-type strain. Additionally, lack of RNase Y resulted in pleiotropic phenotypes that included defects in pneumococcal cell morphology and growth in vitro. In contrast, {Delta}pnp mutants showed no growth defect in vitro, but differentially expressed a total of 40 transcripts including the tryptophan biosynthesis operon genes and numerous 5-cis-acting regulatory RNAs, a majority of which were previously shown to impact pneumococcal disease progression in mice using the serotype 4 strain TIGR4. Altogether our data suggest that RNase Y exerts a global impact on pneumococcal physiology, while PNPase-mediates virulence phenotypes, likely through sRNA regulation. IMPORTANCEStreptococcus pneumoniae is a notorious human pathogen that adapts to conditions in distinct host tissues and responds to host cell interactions by adjusting gene expression. Ribonucleases (RNases) are key players that modulate gene expression by mediating the turnover of regulatory and protein-coding transcripts. Here, we characterized two highly conserved RNases, RNase Y and PNPase, and evaluated their impact on the S. pneumoniae transcriptome for the first time. We show that PNPase influences the levels of a narrow set of mRNAs, but a large number of regulatory RNAs primarily implicated in virulence control, whereas RNase Y has a more sweeping effect on gene expression, altering levels of transcripts involved in diverse cellular processes including cell division, metabolism, stress response, and virulence. This study further reveals that RNase Y regulates expression of genes governing competence by mediating the turnover of CiaR-controlled-noncoding (Ccn) sRNAs.

microbiology↗