Biology subjects

Dabrowska, K.

Publications and source records attributed to Dabrowska, K..

6 recordsLinked to original sources

bioRxiv2024

Triadic Dynamics of Gastric Bacterial Microbiome, Phageome, and Host Genotype, with Implications for Disease Associations

The microbiota plays a key role for human health, and microbiome composition has been linked to specific health disorders many times. Different fractions of the microbiome enter dynamic interactions, particularly bacteria and bacteriophages (phages) - viruses preying on bacteria. Since the microbiome exists inside the human body, the body strongly affects the microbes, although not in a uniform way, but shaped by the extreme diversity of human genetic variants. These triadic dynamics of the bacterial microbiome, phageome, and human host genotype remain poorly understood; hence our goal in this study was to comprehend them as a holistic and interdependent system. Gastric biopsies were the source of the stomach microbiome (bacteria and phages). Genotyping of patients was conducted on blood samples. They were analyzed by next generation sequencing followed by multiway statistical comparisons of identified bacterial and phage taxa, human genetic variants, and medical data from the patients, including gastric disorder diagnostics. Commonly expected associations between presence of bacteriophages and their specific hosts were not found to be a universal principle. With comparable SNP correlations, the strongest associations between Staphylococcus and some staphylococcal phages or Enterobacteria and some enterobacteria phages were discovered. However, many more phage groups were not found to be clearly associated with their bacterial hosts, though often associated with SNPs, particularly those linked to immunological functions and body responses to bacteria and viruses. Thus, in addition to the expected effect on phage communities by shaping the communities of their bacterial hosts, the human body seems to affect phages directly, selecting for phages that survive its specific selective pressure, which can be defined by detection of particular genetic variants.

molecular biology↗

bioRxiv2024

Phageome transfer from gut to circulation and its regulation by human immunity

Bacteriophages dominate the human gut virome, yet their presence in the bloodstream remains orders of magnitude lower, suggesting that systemic dissemination is tightly regulated. How gut phages cross the intestinal barrier and which factors govern their persistence in circulation remain poorly understood, largely because prior studies characterized gut and blood viromes independently rather than in matched samples from the same individuals. Here we investigated phage translocation by shotgun metagenomics of matched colon mucosal biopsies and sera from 37 individuals with phage specific IgG profiling using a pan-phage proteome-derived phage display epitope library, complemented by an oral T4 model in mice. We found that phage abundance decreased by approximately 98% from intestinal mucosa to serum. The mucosal virome was dominated by Microviridae, which also accounted for most of the translocated phages. In the mouse model, phage titers dropped stepwise by [~]106 fold from gut content to blood, with the sharpest reduction occurring at the mucosal-lymphatic interface. Among translocated viral operational taxonomic units 93.1% lacked taxonomic assignment, yet network analysis revealed reproducible co-enrichement with annotated families including Herelleviridae and Straboviridae, which showed significantly higher gut abundance among translocated observations (FDR <0.01). IgG reactivity against a specific phage in 90% of investigated individuals was associated with the absence of that phage in the patients virome; at the collective population analysis, IgG reactivity showed a weak negative association with serum phage abundance. These observations suggest antibody-mediated clearance that limits systemic persistence. Together, these findings suggest that rare epithelial passage, lymphatic trafficking, and IgG-mediated neutralization act as sequential filters that limit which gut phages reach and persist in the circulation, with implications for phage therapy delivery and for the dissemination of accessory genetic elements beyond the intestine.

microbiology↗

bioRxiv2024

Super-resolution going viral: T4 virus particles as perfect nature-designed 3D-Bio-NanoRulers

In the burgeoning field of super-resolution fluorescence microscopy, significant efforts are being dedicated to expanding its applications into the three-dimensional domain. Various methodologies have been developed that enable isotropic resolution at the nanometer scale, facilitating the visualization of three-dimensional subcellular structures with unprecedented clarity. Central to this progress is the need for reliable 3D structures that are biologically compatible for validating resolution capabilities. Choosing the optimal standard poses a considerable challenge, necessitating, among other attributes, precisely defined geometry and the capability for specific labeling at sub-diffraction-limit distances. In this context, we introduce the use of the non-human-infecting virus, bacteriophage T4, as an effective and straightforward bio-ruler for three-dimensional super-resolution imaging. Employing DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) along with the technique of astigmatic imaging, we uncover the icosahedral capsid of the bacteriophage T4, measuring 120 nm in length and 86 nm in width, and its hollow viral tail. This level of detail in light microscopy represents a significant advancement. We further outline a simple protocol for the production and preparation of samples. Moreover, we explore the extensive potential of bacteriophage T4 as a multi-faceted 3D bio-ruler, proposing its application as a novel benchmark for three-dimensional super-resolution imaging in biological studies.

biophysics↗

bioRxiv2023

Identification of cross-reacting IgG hotspots to prevent immune evasion of SARS-CoV-2 variants

The major factor that shapes the global perspective for increase or diminution of successive pandemic waves of COVID-19 is the immunological protection. The SARS-CoV-2 virus constantly develops new variants, and capability of immune evasion is among the major factors that promote variant spreading in the human population. After two years of the pandemic and virus evolution, it is almost impossible to explain effects of all possible combinations different viral strains, a few types of vaccinations or new variants infecting an individual patient. Instead of variant-to-variant comparisons, identification of key protein regions linked to immune evasion could be efficient. Here we report an approach for experimental identification of SARS-CoV-2 protein regions that (i) have characteristics of cross-reacting IgG hot-spots, and (ii) are highly immunogenic. Cross-reacting IgG hot spots are regions of protein frequently recognized in many variants by cross-reacting antibodies. Immunogenic regions efficiently induce specific IgG production in SARS-CoV-2 infected patients. We determined four regions that demonstrate both significant immunogenicity and the activity of a cross-reacting IgG hot-spot in protein S, and two such regions in protein N. Their distribution within the proteins suggests that they may be useful in vaccine design and in serological diagnostics of COVID-19.

immunology↗

bioRxiv2022

Escaping antibody responses to bacteriolytic enzymes Pal and Cpl-1 by epitope scanning and engineering

Bacteriolytic enzymes are promising antibacterial agents, but they can cause a typical immune response in vivo. In this study, we used a targeted modification of two antibacterial endolysins, Pal and Cpl-1. We identified the key immunogenic amino-acids, and designed and tested new, bacteriolytic variants with altered immunogenicity. One new variant of Pal (257-259 MKS [->] TFG) demonstrated decreased immunogenicity while a similar mutant (257-259 MKS [->] TFK) demonstrated increased immunogenicity. A third variant (280-282 DKP [->] GGA) demonstrated significantly increased antibacterial activity and it was not cross-neutralized by antibodies induced by the wild-type enzyme. We propose this variant as a new engineered endolysin with increased antibacterial activity that is capable of escaping cross-neutralization by antibodies induced by wild-type Pal. We show that efficient antibacterial enzymes that avoid cross-neutralization by IgG can be developed by epitope scanning, in silico modelling, and substitutions of identified key amino acids with a high rate of success. Importantly, this universal approach can be applied to many proteins beyond endolysins and has the potential for design of numerous biological drugs.

bioengineering↗

bioRxiv2021

Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity

The E3 ubiquitin ligases CHIP/CHN-1 and UFD-2 team up to accelerate ubiquitin chain formation. However, it remained largely unclear how the high processivity of this E3 set is achieved. Here we studied the molecular mechanism and function of the CHN-1/UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. The HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding and promotes the auto-inhibited CHN-1 state by acting on the conserved position of the U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitinate S-Adenosylhomocysteinase (AHCY-1), an enzyme crucial for lipid metabolism. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation. HIGHLIGHTSO_LIE3 ligase UFD-2 stimulates ubiquitylation activity of CHIP/CHN-1 C_LIO_LIUFD-2 binding promotes dimerization of CHIP/CHN-1 U-box domains and utilization of E2 enzymes C_LIO_LIHSP70/HSP-1 by latching the U-box and TPR domains stabilizes the autoinhibitory state of CHIP/CHN-1, limiting interactions with E2s and UFD-2 C_LIO_LIAssembly with UFD-2 enables CHIP/CHN-1 to regulate lipid metabolism by ubiquitylation of S-Adenosylhomocysteinase C_LI

molecular biology↗