Postal Address :
LIBST
Croix du Sud, 4-5
Bte L7.07.07
1348 Louvain-la-Neuve
Belgium
E-mail : Yves Dufrêne
Tel. +32 10 47 36 00
Secretariat +32 10 47 35 88
Location :
LIBST
Carnoy Bldg (SC12)
Floor 04, room C455
Campus Louvain-la-Neuve
For students and newcomers see this brochure in EN or FR
Microbiology at the nanoscale
Our goal is to push the limits of force nanoscopy beyond state-of-the-art to establish this nanotechnology as an innovative platform in biofilm research. By developing new tools, we wish to understand how pathogens use their surface molecules to guide cell adhesion and trigger infections, and to develop anti-adhesion strategies for treating biofilm-infections.
"Knowledge is limited. Imagination encircles the world.” ― A. Einstein
LATEST NEWS
May 19, 2023
Tuberculosis: sweet nanodomains on the pathogen surface help it escape our immune system
By combining the tools of nanotechnology and microbiology, the teams of Yves Dufrêne (FNRS, UCLouvain) and Jérôme Nigou (CNRS) have unraveled the sophisticated mechanism by which mycobacterial pathogens causing tuberculosis evade the immune system of the human host. In the future, these findings may help designing new anti- tuberculosis strategies.
The bacterial pathogen Mycobacterium tuberculosis, the causative agent of human tuberculosis kills a million people each year. New molecular knowledge on the infection process is urgently needed in order to develop better anti-mycobacterial therapies. To protect us from the pathogen, our immune cells are decorated with a family of proteins called pattern recognition receptors, of which the well-known DC-SIGN protein binds specific sugars (glycoligands) on the mycobacterial cell surface. Remarkably, mycobacteria have evolved ways to use this interaction to their own benefit, enabling them to escape the body’s immune system. While we know the structures of the exotic molecules involved and how they react at the population level in the test tube, we know little about how they bind in real life on the surfaces of immune cells. Using state-of-the-art atomic force microscopy, the researchers were able to map the distributions of glycoligands and DC-SIGN receptors with unprecedented single-molecule resolution. These molecular recognition imaging experiments demonstrated for the first time that glycoligands are concentrated into dense nanoscale domains on the mycobacterial surface. In addition, adhesion of bacteria to host cells was shown to induce the formation of large DC-SIGN clusters on immune cells. This study, published in Science Advances, highlights the key role of nanoclustering of both pathogen ligands and DC-SIGN host receptors, which is only possible to analyse through super-resolution, nanoscopy techniques. This fascinating mechanism might be widespread in pathogen-host interactions and may help designing new antituberculous strategies using immunomodulation.
September 1, 2022
In a study based from Scopus of the top researchers among all scientific disciplines, Stanford University ranks us #8,451 from a pool of 10 M scientists (i.e. ~0.08 %). The database provides standardized information on citations, h-index, co-authorship adjusted hm-index, citations to papers in different authorship positions and a composite indicator (c-score).
May 9, 2022
Adhesion of Staphylococcus aureus to human skin is exceptionally strong
Staphylococcus aureus is a bacterial pathogen that colonizes the skin and the nose of humans, and which can cause various diseases, such as eczema (atopic dermatitis). This microbe has become resistant to multiple antibiotics, meaning there is an urgent need to fully understand the molecular mechanisms leading to host colonization and infection, and to find alternative antibacterial therapies. In collaboration with the Trinity College Dublin, a UCLouvain team has discovered that S. aureus uses a special surface protein, FnBPB, to specifically bind to the human skin surface protein loricrin. Using nanotechniques, they found that the bond formed between FnBPB and loricrin is exceptionally strong, much stronger than the vast majority of other biomolecular bonds. Remarkably, the bond strength increases dramatically when subjected to physical stress, as occurring when we wash ourselves or during skin epidermidis turnover, pointing to an unusual "catch bond" adhesion and colonization mechanism. Under mechanical tension, biological complexes typically slip apart easily ("slip bonds"), whereas "catch bonds" counterintuitively become stronger. The FnBPB-loricrin interaction, reported in Nature Communications, provides S. aureus with a means to firmly attach to the epidermidis under physiological shear stress, increasing its ability to colonize the human skin and cause infection. This mechanism represents a promising target for anti-adhesion therapy, i.e. the design of inhibitors capable to efficiently prevent staphylococcal-skin interactions. The study was funded by an ERC advanced grant aiming at using nanotechnology to understand and overcome the adhesion of S. aureus to biomaterials and host tissues ( https://futurumcareers.com/using-nanotechnology-to-overcome-the-adhesion-of-the-bacterial-pathogen-staphylococcus-aureus).
September 23, 2021
New methods review: AFM force spectroscopy of single cells
Physical forces and mechanical properties have critical roles in cellular function, physiology and disease. Over the past decade, atomic force microscopy (AFM) techniques have enabled substantial advances in our understanding of the tight relationship between force, mechanics and function in living cells and contributed to the growth of mechanobiology. In the new journal Nat Rev Methods, the nBio group publishes together with two other teams a comprehensive overview of the use of AFM-based force spectroscopy (AFM-FS) to study the strength and dynamics of cell adhesion from the cellular to the single-molecule level, spatially map cell surface receptors and quantify how cells dynamically regulate their mechanical and adhesive properties. We first introduce the importance of force and mechanics in cell biology and the general principles of AFM-FS methods. We describe procedures for sample and AFM probe preparations, the various AFM-FS modalities currently available and their respective advantages and limitations. We also provide details and recommendations for best usage practices, and discuss data analysis, statistics and reproducibility. We then exemplify the potential of AFM-FS in cellular and molecular biology with a series of recent successful applications focusing on viruses, bacteria, yeasts and mammalian cells. Finally, we speculate on the grand challenges in the area for the next decade.
September 1, 2021
A protein complex involved in pathogen adhesion ruptures at 3 nanonewtons !
Staphylococci bind to the blood protein von Willebrand Factor (vWF), thereby causing endovascular infections. Whether and how this interaction occurs with the medically important pathogen Staphylococcus epidermidis is unknown. Using single-molecule experiments, we demonstrate that the S. epidermidis protein Aap binds vWF via an ultrastrong force of about 3 nN, the strongest noncovalent biological bond ever reported, and we show that this interaction is activated by tensile loading, suggesting a catch-bond behavior. Our results published in Nano Lett. point to a mechanism where force-induced unfolding of the B repeats activates the A domain of Aap, shifting it from a weak- to a strong-binding state, which then engages into an ultrastrong interaction with vWF A1. This shear-dependent function of Aap offers promise for innovative antistaphylococcal therapies.
May 13, 2021
AFM force-clamp spectroscopy captures the nanomechanics of the Tad pilus retraction
Bacterial pili are flexible and dynamic nanofilaments that fulfil a wealth of cellular functions. In a study published in Nanoscale Horizons, we investigated the nanomechanics and dynamics of Tad pilus retraction, using a platform combining a fluorescence-based piliated cell discrimination assay with atomic force microscopy (AFM) force-clamp spectroscopy. We discover that applying a constant tensile load to single pili connected to hydrophobic substrates leads to two types of transient variations in force and height, originating from pilus retraction and from hydrophobic binding. These findings support a model whereby pilus retraction and hydrophobic interactions work in concert to promote bacterial cell landing on surfaces. Our experiments emphasize the power of force-clamp AFM to understand the nanophysics and dynamics of motorized bacterial pili. In nanomedicine, our methodology may provide a means to screen for small molecules that can hinder pilus retraction in bacterial pathogens, thereby helping to prevent or treat infections.
January 4, 2021
Unravelling the molecular secrets of yeast sexuality
In a paper published in Communications Biology, we and the Lipke team (USA) - use single-cell fluidic force microscopy to investigate the molecular binding mechanisms of sexual agglutinins in budding yeast Saccharomyces cerevisiae. We report that mechanical tension enhances the strength of agglutinin interactions, supporting a new model in which physical stress induces conformational changes in the binding sites of agglutinins.
October 27, 2020
Bacterial pathogens with a strong grip
During pathogenesis, bacterial pathogens adhere to host surfaces through specific receptor-ligand bonds that experience strong hydrodynamic forces. It is commonly accepted that such adhesion complexes slip apart more easily under increasing external shear ("slip bonds"). However, it has become clear that mechanical stimulation can also promote cell adhesion through "catch bonds" complexes that, counterintuitively, strengthen under force, similarly to a Chinese finger trap. Until recently microbial catch-bond mechanisms had only been identified and thoroughly characterized at the molecular level for the Escherichia coli FimH adhesion protein. The longer-lived bonds formed by FimH and mannose residues on endothelial cells eventually favor pathogen adhesion, during urinary tract infections. A recent LIBST study published in Nature Communications provides the first direct and quantitative demonstration of a catch-bond in a Gram-positive pathogen, by means of atomic force microscopy. The authors discover that the interaction between staphylococcal surface protein SpsD and fibrinogen, a crucial component of the extracellular matrix, is extremely strong and exhibits a catch binding behavior up to a critical force orders of magnitude higher than previously investigated purified complexes. This provides the pathogen with a mechanism to tightly control its adhesive function during colonization and infection, staphylococci being highly involved in vascular and skin diseases. This work, funded by ERC, improves our understanding of the molecular details behind stress-dependent bacterial adhesion and could pave the way for the development of antiadhesive therapies able to inhibit such phenomena. See also "When bacteria hang on tight".
June 4, 2020
Fast chemical force microscopy reveals hydrophobic nanodomains on mycobacteria
In a new study published in Nanoscale Horizons, we show that fast quantitative imaging (QI) AFM combined with hydrophobic tips is a powerful tool to quantitatively map hydrophobic properties of bacterial pathogens, at high spatiotemporal resolution (∼10 min for 128 × 128 pixels images). We focus on Mycobacterium abscessus, a multidrug-resistant bacterial pathogen causing severe lung infections in cystic fibrosis patients. We discover that the transition from a smooth to a rough colony morphology, caused by the loss of cell envelope associated glycopeptidolipids (GPLs), leads to a dramatic change in surface hydrophobicity, smooth bacteria displaying unusual nanodomains with varying degrees of hydrophobicity. These results show that GPLs modulate the nanoscale distribution of hydrophobicity of M. abscessus, which is critical for regulating bacterial adhesion and aggregation, as well as virulence and pathogenicity. This study demonstrates the power of QI-AFM as a nanoimaging tool for probing the hydrophobic properties of cell surfaces in relation to function, at high speed and spatial resolution.
April 14, 2020
Mechanobiology: what makes bacterial pathogens so stiff?
Bacteria are surrounded by mechanically rigid cell envelopes, which play important roles in controlling cellular processes like growth, division, adhesion as well as resistance to drugs and environmental stresses. In the prototypical pathogen Escherichia coli, it has long been believed that peptidoglycan was the only biopolymer that conveys mechanical strength to the cell envelope. However, in a study published in Nature Communications, the teams of Yves Dufrêne and Jean-François Collet (WELBIO investigator) at the UCLouvain have identified the key roles of the lipoprotein Lpp in defining the E. coli cell envelope mechanics, using state-of-the-art nanoimaging techniques combined with genetic manipulation. They discovered that Lpp has a dual function, by covalently connecting peptidoglycan to the outermost cellular membrane and by precisely tuning the size of the periplasmic space. The researchers also found that Lpp-dependent cell mechanics has a major impact on antibiotic sensitivity, functional mutations in the protein increasing drastically the efficacy of vancomycin. This study, funded by the Excellence of Science (EOS), WELBIO and ERC fundings, demonstrates the power of coupling nanotechnology and molecular biology methods for understanding the molecular details behind bacterial stiffness, and for linking cellular mechanics to function, a grand challenge in current mechanobiology. The results show promise for the design of innovative antibacterial drugs targeting the molecular machineries that stabilize the cell envelope.
See the Nature Microbiology blog for more details.
See Daily Science
January 20, 2020
Mechanomicrobiology: how bacteria sense and respond to forces
Microorganisms have evolved to thrive in virtually any terrestrial and marine environment, exposing them to various mechanical cues mainly generated by fluid flow and pressure as well as surface contact. Cellular components enable bacteria to sense and respond to physical cues to optimize their function, ultimately improving bacterial fitness. Owing to newly developed biophysical techniques, we are now starting to appreciate the breadth of bacterial phenotypes influenced by mechanical inputs: adhesion, motility, biofilm formation and pathogenicity. In this Nature Reviews Microbiology, with the Alex Persat team, we discuss how microbiology and biophysics are converging to advance our understanding of the mechanobiology of microorganisms.
