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Projects / Programmes source: ARIS

Strukturni vpogled v mehanizem tvorbe površine bakterije Clostridium difficile

Research activity

Code Science Field Subfield
1.05.00  Natural sciences and mathematics  Biochemistry and molecular biology   

Code Science Field
B000  Biomedical sciences   

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
Clostridium difficile, surface (S-) layer, secondary polysaccharides, PSII biosynthesis pathway, , enzyme, crystal structure, drug target validation
Evaluation (rules)
source: COBISS
Researchers (12)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  52379  PhD Samo Guzelj  Pharmacy  Researcher  2019 - 2023  22 
2.  31952  PhD Nataša Lindič  Biochemistry and molecular biology  Researcher  2019 - 2023  32 
3.  39146  PhD Jure Loboda  Biochemistry and molecular biology  Researcher  2021 - 2023  50 
4.  29497  PhD Nikola Minovski  Pharmacy  Researcher  2019 - 2023  114 
5.  23419  PhD Janez Mravljak  Pharmacy  Researcher  2019 - 2023  201 
6.  09775  PhD Marjana Novič  Chemistry  Researcher  2019 - 2023  616 
7.  28861  PhD Stane Pajk  Pharmacy  Researcher  2019 - 2023  188 
8.  25493  PhD Andrej Perdih  Pharmacy  Researcher  2019 - 2023  262 
9.  29544  PhD Ajda Taler Verčič  Biochemistry and molecular biology  Researcher  2019 - 2020  78 
10.  04988  PhD Dušan Turk  Biochemistry and molecular biology  Head  2019 - 2023  621 
11.  26515  PhD Aleksandra Usenik  Biochemistry and molecular biology  Researcher  2019 - 2023  54 
12.  28608  PhD Barbara Zupančič  Computer intensive methods and applications  Researcher  2019 - 2020  174 
Organisations (4)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,475 
2.  0106  Jožef Stefan Institute  Ljubljana  5051606000  89,976 
3.  0787  University of Ljubljana, Faculty of Pharmacy  Ljubljana  1626973  17,522 
4.  2990  Center of excellence for integrated approaches in chemistry and biology of proteins, Ljubljana  Ljubljana  3663388  725 
Abstract
The cell wall of Gram-positive bacteria is composed of proteins and peptidoglycan with the protruding secondary polysaccharides, which differ in the chemical composition and structure among various species. The cell wall secondary polysaccharides are covalently attached to the peptidoglycan and can account for more than a half of the total cell wall mass. They form a dense network of negative charges and impact cation homeostasis, membrane permeability, antibiotic susceptibility and survival in the host. In many species they also act as the anchors to which the outermost paracrystalline protein surface layer, called the S-layer, is non-covalently attached. We have already begun to elucidate the S-layer structure of Clostridium difficile. However, the mechanisms responsible for the organization of the S-layer structure and its attachment to the peptidoglycan remain poorly understood.   C. difficile is a dangerous nosocomial pathogen. When the normal gut microbiota of a patient is compromised, C. difficile spores germinate and the infection, even when treated, can reoccur and lead to life-threatening complications. The wide-spread use of broad-spectrum antibiotics in treatment of C. difficile infections has already resulted in a number of (multiple) antibiotic resistant strains. Considering that the contact with the host takes place at the surface of the bacterium and that the S-layer of C. difficile is an essential virulence factor, it is worthwhile to study the associated processes.   Gene manipulation studies of enzymes involved in biosynthesis of C. difficile secondary polysaccharides showed that their impairment leads to bacterial growth defects, diffused cell wall, defective anchoring, altered shedding and deposition of secondary polysaccharides, as well as defects in morphology and assembly of the S-layer, changes in biofilm formation and finally, changes in virulence. This prompts us to study the mechanisms of C. difficile S-layer assembly and in particular address the enzymes involved in the biosynthesis of secondary polysaccharides. Moreover, characterization of the respective enzymes might expand our understanding in the biogenesis of other bacterial cell wall polymers.   With this proposal we plan to gain novel insight into the mechanisms underlying the biosynthesis of secondary polymers and their role in the S-layer assembly. We will study three groups of enzymes involved in biosynthesis of secondary polymers (enzymes involved in mannose conversion, glycosyltransferases, and enzymes attaching the secondary polysaccharides to the peptidoglycan). We will use complementary approaches of molecular biology, crystal structure analysis, enzyme activity measurements, structure-based virtual screening of ligands and classical inhibitor synthesis, biochemical and mass spectroscopy analysis, microscopic (optical, electronic and CryoEM) observations of bacteria or their fragments originating from wild type bacteria and those impaired by gene manipulations and inhibitors.   We believe that research systematically addressing the whole group of the respective enzymes has the potential to deliver fundamental discoveries about their roles in the biosynthesis of secondary polymers and S-layer assembly. Hence, a successful outcome of this project will lay foundations for novel drug discovery programs that have the potential to improve human healthcare in life-threatening situations of C. difficile infections in a species-specific manner and thereby reduce risks of widely spreading antibiotic resistance.
Significance for science
The proposed project is a competitive initiative in a challenging area of biomedical science related to a well-known health problem of (nosocomial) bacterial infections and increasing antibiotic resistance aiming to have a worldwide impact. C. difficile is a Gram positive bacterium and can be a normal inhabitant of the human/mammal intestinal tract. However, disruption of the normal gut microbiota usually following antibiotic therapy leads to C. difficile (super)infection and potentially severe necrotizing disease of the large intestine.   The outermost surface of C. difficile is composed of a protein structure called the S-layer, an essential virulence factor that is non-covalently attached to the cell wall through secondary polysaccharides. The lack of insight in the mechanisms underlying S-layer formation suggests to explore the enzymes involved in biosynthesis of secondary polysaccharides and to pin point the role of secondary polysaccharides in the S-layer assembly process. The proposed project will be the first to provide structural and biochemical insight into the proteins involved in the biosynthesis of secondary polysaccharides of C. difficile and will lay the foundation for the future studies investigating the S-layer composition and structure by providing materials, such as proteins and small molecule compounds, structural insight, and new methodologies, such as structure determination of 2D protein assemblies by electron microscopy and (point) mutations in C. difficile genome by recently characterized endogenous CRISPR-Cas system. The gained knowledge and methodologies will be applicable to other Gram positive bacteria with homologous secondary polysaccharide biosynthetic pathways and microbes enclosed in S-layers.    We believe that the results of the project will illuminate possible ways of preventing infections with C. difficile and provide foundations for novel drug discovery programs.   We expect that published research in top ranking journals will increase visibility of Slovenian science.
Significance for the country
The proposed project is a competitive initiative in a challenging area of biomedical science related to a well-known health problem of (nosocomial) bacterial infections and increasing antibiotic resistance aiming to have a worldwide impact. C. difficile is a Gram positive bacterium and can be a normal inhabitant of the human/mammal intestinal tract. However, disruption of the normal gut microbiota usually following antibiotic therapy leads to C. difficile (super)infection and potentially severe necrotizing disease of the large intestine.   The outermost surface of C. difficile is composed of a protein structure called the S-layer, an essential virulence factor that is non-covalently attached to the cell wall through secondary polysaccharides. The lack of insight in the mechanisms underlying S-layer formation suggests to explore the enzymes involved in biosynthesis of secondary polysaccharides and to pin point the role of secondary polysaccharides in the S-layer assembly process. The proposed project will be the first to provide structural and biochemical insight into the proteins involved in the biosynthesis of secondary polysaccharides of C. difficile and will lay the foundation for the future studies investigating the S-layer composition and structure by providing materials, such as proteins and small molecule compounds, structural insight, and new methodologies, such as structure determination of 2D protein assemblies by electron microscopy and (point) mutations in C. difficile genome by recently characterized endogenous CRISPR-Cas system. The gained knowledge and methodologies will be applicable to other Gram positive bacteria with homologous secondary polysaccharide biosynthetic pathways and microbes enclosed in S-layers.    We believe that the results of the project will illuminate possible ways of preventing infections with C. difficile and provide foundations for novel drug discovery programs.   We expect that published research in top ranking journals will increase visibility of Slovenian science.
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