Biology subjects

Isbilir, B.

Publications and source records attributed to Isbilir, B..

4 recordsLinked to original sources

bioRxiv2025

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Electron cryomicroscopy (cryo-EM) allows high-resolution spatial visualization of biological specimens, however, it is challenging to chemically identify densities observed in cryo-EM. To overcome this, we combined cryo-EM with chemical imaging using focused ion beam secondary ion mass spectrometry (FIB-SIMS) for integrated spatio-chemical analysis of untagged specimens. We show that our correlative workflow permits sub-cellular localisation of molecules inside bacterial cells and is compatible with cryogenic light microscopy and FIB-milled lamellae of multicellular specimens. To highlight biological insights enabled by the workflow, we studied the uptake of Bisphenol-AF, a widespread chemical pollutant, by environmental bacteria, revealing the storage of these chemicals within cytosolic phase-separated aggregates in pollutant-exposed cells, where they cannot be removed by the bacterial efflux machinery despite its robust upregulation. These mechanistic insights were directly facilitated by the versatile cryo-EM-FIB-SIMS technique, showing that it is an effective avenue to map elemental and molecular signatures in near-native biological samples, which can be extended in the future for multiple applications in cell biology and imaging.

molecular biology↗

bioRxiv2024

Mapping the ultrastructural topology of the corynebacterial cell surface

Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids. Despite the occurrence of this distinctive cell envelope in several bacterial pathogens, including Corynebacterium diphtheriae, Mycobacterium tuberculosis, and Mycobacterium leprae, its ultrastructural and molecular details remain elusive. To address this, we investigated the cell envelope of C. glutamicum using electron cryotomography and cryomicroscopy of focused ion beam-milled cells. Our high-resolution images allowed us to accurately map the different components of the cell envelope into the tomographic density. Our data reveal that C. glutamicum has a variable cell envelope, with the outermost layer comprising the surface (S-)layer, which decorates the mycomembrane in a patchy manner. We further isolated and resolved the structure of the S-layer at 3.1 [A] resolution using single particle electron cryomicroscopy. Our structure shows that the S-layer of C. glutamicum is composed of a hexagonal array of the PS2 protein, which interacts directly with the mycomembrane via a coiled coil-containing anchoring segment. Bioinformatic analyses revealed that the PS2 S-layer is sparsely yet exclusively present within the Corynebacterium genus and absent in other genera of the Mycobacteriaceae family, suggesting distinct evolutionary pathways in the development of their cell envelopes. Our structural and cellular data collectively provide a high-resolution topography of the unusual C. glutamicum cell surface, features of which are shared by many pathogenic and microbiome-associated bacteria, as well as by several industrially significant bacterial species. This study, therefore, provides a strong experimental framework for understanding cell envelopes that contain mycolic acids.

microbiology↗

bioRxiv2024

Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life

Surface layers (S-layers) are two-dimensional (2D) crystalline lattices that frequently coat prokaryotic cells, playing a crucial role in protection, maintaining cellular integrity, and mediating environmental interactions. However, the molecular landscape of these abundant proteins has remained underexplored due to a lack of structural data. By employing AlphaFold2multimer together with planar symmetry constraints in a workflow validated by electron cryomicroscopy structure determination, we have elucidated the lattice structures of over 150 S-layers from diverse archaea and bacteria. Our findings unveil a multifaceted evolutionary landscape for S-layer proteins, highlighting key differences in the evolution of bacterial and archaeal S-layers. Our study allows us to discover underlying patterns in S-layer structure, organisa-tion, and cell anchoring mechanisms across the prokaryotic tree of life, deepening our understanding of the intricately complex microbial cell surfaces, which appear to have evolved proteinaceous S-layers independently on multiple occasions. This work will open avenues for rational manipulation of prokaryotic cellular interactions in multicellular microbiomes, as well as for innovative 2D biomaterial design.

molecular biology↗

bioRxiv2021

Remodeling of oxygen-transporting tracheoles drives intestinal regeneration and tumorigenesis

The Drosophila tracheal system, as the functional equivalent of mammalian blood vessels, responds to hypoxia and transports oxygen throughout the body. Although the signaling pathways involved in tracheal development and the hypoxic response are well-studied, how adult tracheae interact with their target tissues is largely unknown. Here we show that the tracheae that serve the adult intestine are dynamic and respond to enteric infection, oxidative agents, and the development of gut tumors with increased terminal branching. Increased tracheation is necessary for efficient damage-induced intestinal stem cell (ISC)-mediated midgut regeneration and sufficient to drive ISC proliferation in the absence of damage. Gut damage or tumors induce Hif-1/Sima, which, in turn, stimulates tracheole branching via the FGF(Brachless/Bnl)/FGFR(Breathless/Btl) signaling cascade. Bnl/Btl signaling is required both in the intestinal epithelium and the tracheal system for efficient damage-induced tracheal remodeling and ISC proliferation. We show that chemical or Pseudomonas-generated ROS directly affect the trachea and are necessary for branching and intestinal regeneration. Similarly, tracheole branching and the resulting increase in oxygen supply are essential for tumor growth in the midgut. Thus, we have identified a novel mechanism of visceral tracheal-intestinal tissue communication, whereby oxidative damage and tumors induce neo-tracheogenesis in adult Drosophila. This process is reminiscent of cancer-induced neo-angiogenesis in mammals.

cell biology↗