Mélanie Berbon

Bacillus subtilis is widely studied in the microbial secondary metabolite (SM) field due to its rich variety of important natural products and genetic tractability. We report a pigment observed in B. subtilis soil isolate MB9_B4 on certain media. We characterize the conditions where this pigment is produced and identify the corresponding biosynthetic gene cluster (BGC) using a comparative genomic approach exploiting our strain collection containing other isolates with pigment production ability. The responsible BGC carried several genes, which were annotated as parts of the tryptophan biosynthesis pathway, possibly originating from duplication and divergence of originally primary metabolism. Identification of the pigment gene cluster additionally led to the discovery of additional pigment BGC carrier B. subtilis isolates, some of which were described at the earliest in 1896 under the name Bacillus aterrimus , referring to a characteristic dark pigmentation (the Latin “aterrimus” meaning very black). In addition, we employed solid-state nuclear magnetic resonance and Fourier transform infrared spectroscopies to characterize the chemical groups of the pigment. This study describes the chemical and biological features of a new class of SM BGC, which we hope will serve to improve the current BGC discovery pipelines in Bacilli . IMPORTANCE: Identification of novel microbial secondary metabolites (SMs) and their biosynthetic gene cluster (BGC) has become increasingly difficult, especially in Bacilli , as the tools for screening and genome mining are dependent on clear function or similarity to already known BGCs. Pigments are SMs identified by their absorption of visible light, resulting in a certain color perceived by our eyes at sufficient concentrations. Thereby, pigments provide evidence of a BGC without knowing the sequence or function. Expanding the known repertoire of SM BGCs with novel BGCs will further reinforce the identification of a broader set of BGCs by mining tools such as antiSMASH.

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

Cancer, the second leading cause of death and illness in Europe, drives the urgent need for innovative therapies, with drug repurposing offering a rapid, cost-effective solution for developing life-saving treatments ¹. The RePo-SUDOE project is an Interreg EU co-funded initiative aiming to position the SUDOE region (Spain, Portugal, and France) as a European leader in drug repurposing. To support this goal, the project involves the creating of an open-access database of therapeutic targets, the identification of promising drugs or therapies with potential biological effects, and the application of both computational and experimental methods to assess their interactions with relevant targets. The YAP/TAZ-TEAD complex, regulated by the Hippo pathway, plays a pivotal role in driving tumorigenesis and cancer progression, and has been chosen as the starting point for this project due to its strong potential in advancing cancer therapies. This complex contains three well-defined interaction interfaces, which represent attractive targets for identifying compounds capable of disrupting its oncogenic activity ^2-5. To explore this potential, we conducted an extensive bibliographic review and selected three compounds previously reported to disrupt the YAP-TEAD interaction. Building on these preliminary findings, we now aim to develop standardized protocols using biophysical techniques such as Surface Plasmon Resonance (SPR) and Bio-Layer Interferometry (BLI) to study drug-target interactions and ensure accurate, reproducible, and detailed results. These protocols will be pivotal for advancing drug repurposing efforts in the SUDOE region, with potential applications across a wide range of diseases.

The development of new drugs is hindered by high failure rates, substantial costs, and prolonged timelines, highlighting the importance of drug repurposing (or drug repositioning) as a key strategy to identify new therapeutic applications for existing drugs. Despite its potential, collaboration within the SUDOE space, concerning Portugal, Spain, and France, remains limited, as evidenced by a bibliometric analysis that reveals their relatively modest contribution to global drug repurposing research in comparison to leading countries, such as China, USA, and UK. The RePo-SUDOE project aims to address this gap by bringing together diverse partners to advance drug repurposing technologies and enhance the region’s competitiveness in this field. The project includes three key objectives: (i) raising awareness and understanding of drug repurposing technologies, positioning SUDOE’s R&D centers as leaders in European research; (ii) fostering multidisciplinary collaboration and identifying opportunities for innovative drug repurposing initiatives across the SUDOE space through the establishment of a transnational network with a key focus of developing methodologies for drug repurposing for cancer treatment; (iii) creating a prototype of a three-dimensional visualization room for biological systems with virtual and augmented reality technologies to explore drug–target interactions, engaging STEAM students and researchers in immersive learning. The RePo-SUDOE project brings together diverse partners from the SUDOE space to collaborate on drug repurposing, making scientific information more accessible, and using advanced visualization technologies to strengthen the field in this geographic region.

Summary Paragraph: Multiple system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown cause, typically affecting individuals aged 50–60 and leading to death within a decade ^1–3 . It is characterized by glial cytoplasmic inclusions (GCIs) composed of fibrillar alpha-synuclein (aSyn) ^4–8 , whose formation shows parallels with prion propagation ^9,10 . While fibrils extracted from MSA brains have been structurally characterized ¹¹ , their ability to replicate in a “protein-only” manner has been questioned ¹² , and their capacity to induce GCIs in vivo remains unexplored. By contrast, the synthetic fibril strain 1B ^13,14 , assembled from recombinant human aSyn, self-replicates in vitro and induces GCIs in mice ¹⁵ - suggesting direct relevance to MSA - but awaited scrutiny at an atomic scale. Here, we report high-resolution structural analyses of 1B fibrils and of fibrils extracted from diseased mice injected with 1B that developed GCIs (1B ^P ). We show in vivo that conformational templating enables fibril strain replication, resulting in MSA-like inclusion pathology. Remarkably, the structures of 1B and 1B ^P are highly similar and mimic the fold of aSyn observed in one protofilament of fibrils isolated from MSA patients ¹¹ . Moreover, reinjection of crude mouse brain homogenates containing 1B ^P into new mice reproduces the same MSA-like pathology induced by the parent synthetic seed 1B. Our findings identify 1B as a synthetic pathogen capable of self-replication in vivo and reveal structural features of 1B/1B ^P that may underlie MSA pathology, offering insights for therapeutic strategies.

Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht.

Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross‐β amyloid fibrils HET‐s, and HELLF by employing a specific isotope‐labeling approach and magic‐angle‐spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of “breathing motions” over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic‐core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross‐β architecture.