Research

Heme enzymes are responsible for a wide variety of reactions and functions in living organisms. Heme biosynthesis in prokaryotes follows either the coproporphyrin-dependent or the siroheme-dependent metabolic pathway. In both cases, coproheme is the substrate for the final step of biosynthesis. In *Desulfovibrio desulfuricans*, it was found that the storage protein bacterioferritin stores large amounts of coproheme. These and other data in the literature suggest that coproheme could be another naturally occurring cofactor. We will investigate this lead to expand our understanding of biochemical metabolic pathways. The hypothesis is that coproheme is a naturally occurring cofactor in prokaryotic organisms. Coproheme has been shown to act as a redox-active substrate for an enzyme (coproheme decarboxylase). In this project, we will go beyond this reaction and test whether some organisms have evolved to prefer coproheme over heme b. Selected, well-studied heme enzymes reconstituted with coproheme are being studied biochemically and biophysically. This allows us to conduct a comparative assessment of the catalytic potential of coproheme enzymes. In addition, other heme enzymes from organisms that utilize the siroheme or coproporphyrin-dependent metabolic pathway are being studied in their coproheme-bound state. Furthermore, we will use computer-aided methods to search for previously unidentified coproheme-binding proteins. If this hypothesis is confirmed, we will have to rewrite the biochemistry textbooks. This basic research project will help us understand the structure-function relationships of these enzyme classes and provide important insights into the necessary conditions for efficient catalysis. Coproheme-bound enzymes are potentially of interest for biotechnological applications in industry and medicine.

Bacteria exhibit diverse biochemical capabilities, including secondary metabolite production critical for survival. Among these metabolites, mutanofactins (Mufs)—cyclic lipopeptides—have garnered attention for their role in bacterial biofilm formation, particularly in Streptococcus mutans (Smu), a primary contributor to dental caries. Synthesized via the muf gene cluster, Mufs enhance biofilm robustness, as confirmed in high biofilm-forming Smu strains. This study explores Mufs' roles in biofilm dynamics across Smu, Streptococcus mitis, and Streptococcus agalactiae. Interestingly, S. mitis, with a zinc-responsive motif in its muf promoter, shows enhanced biofilm formation in zinc-rich conditions, while S. agalactiae exhibits minimal biofilm formation despite possessing the muf cluster, underscoring the influence of additional genetic or environmental factors. Preliminary data show growth-phase-dependent muf expression: Smu upregulates Muf production in early log phase, whereas S. mitis peaks in the stationary phase. We hypothesize that Muf biosynthesis is tightly regulated by growth-phase-specific pathways varying among species. This research investigates the genetic diversity of the muf cluster and its effects on biofilm formation in single- and multi-species contexts. Environmental factors like zinc, which enhances S. mitis biofilms, will also be studied. Additionally, we will assess the antimicrobial activity of MFs and their role in interspecies communication within biofilms. Genetic manipulations, including muf promoter fusions and deletion mutants, will elucidate transcriptional regulation. We aim to explore the molecular mechanisms behind MF production, its impact on bacterial adhesion, and interspecies interactions. This work has implications for understanding microbial ecology and developing innovative strategies to combat biofilm-associated infections, including dental caries.

GlyCoNet-CRC investigates how host glycosylation patterns shape the carcinogenic microbiome within the colorectal cancer (CRC) tumor microenvironment, with a particular focus on Fusobacterium nucleatum and its recently identified polymicrobial consortia. The project addresses the following key research questions: (1) Which microbial consortia colonize CRC tumors? (2) How do microbial networks differ across tumors with different host “glycogene”expression and glycan profiles? (3) Which microbial adhesins mediate glycan-dependent colonization, invasion and persistence within the tumor microenvironment? (4) How do tumor-associated glycan profiles influence responses to conventional chemoradiotherapy in microsatellite-stable (MSS) CRC and to immunotherapy in microsatellite-instable (MSI) CRC. (5) Can co-culture models of clinically relevant bacterial consortia, established in transwell systems with commercially available cell lines and patient-derived primary cells or organoids, recapitulate clinical observations and serve as mechanistic platforms to study host–microbe interactions? (6) Can glyco-microbial biomarkers be identified for predicting therapeutic response and clinical outcome? (7) Do sex- and gender-specific factors influence microbiome composition, glycan profiles, or the functional effects of specific microbial consortia? The innovative core of the project lies in leveraging a large clinical biobank and integrating glycomics, microbiome profiling, and transcriptomic analyses to elucidate how tumor-specific glycan alterations drive microbial community assembly, adaptation, and pathogenicity – and/or vice versa. By combining patient-derived specimens, engineered cellular and organoid models, and multi-omics approaches, GlyCoNet-CRC establishes a novel precision medicine framework for CRC research. The project is expected to advance the development of predictive diagnostic tools, glycan-targeted therapeutic strategies, in vitro models for studying host–microbiome interactions, and microbiome-based risk stratification approaches, thereby redefining current concepts of CRC pathogenesis and treatment. Anchored by an interdisciplinary consortium of microbiologists, glycobiologists, surgeons, oncologists, and computational scientists, GlyCoNet-CRC will generate comprehensive open-access multi-omics datasets, glycoengineered model systems, and reproducible bioinformatic pipelines. These resources will be disseminated through repositories such as GEO, ENA, and GitHub, as well as through material transfer agreements (MTAs), thereby enabling future translational studies and supporting the development of glycan-modulating preventive, diagnostic, and therapeutic strategies in CRC.