Biology subjects

Hoffmann, R.

Publications and source records attributed to Hoffmann, R..

10 recordsLinked to original sources

bioRxiv2025

Novel action of proline-rich antimicrobial peptides Api88, Api137, Onc72 and Onc112 against Pseudomonas aeruginosa and Escherichia coli in ion-rich environments.

The rise in antibiotic resistance has meant that there is a need for new strategies and one avenue is the use of proline-rich antimicrobial peptides (PrAMPs). Here we investigate how different metal ion environments (Na+, Mg2+, Ca2+) affect antimicrobial activity of PrAMPs derived from apidaecin 1b (Api88, Api137) and Oncopeltus antibacterial peptide 4 (Onc72, Onc112) against Pseudomonas aeruginosa and Escherichia coli. Initial antimicrobial testing in an ion-rich media (ion levels similar to mammalian body fluids) found that the PrAMPs were effective against E. coli but not P. aeruginosa. Both Api88 and Api137 were bactericidal, while Onc72 and Onc112 were bacteriostatic against E. coli. In a lower ion-media the activity of the PrAMPs significantly improved against both bacteria and Onc72 and Onc112 altered the mode of action to bactericidal. In low Na+, Ca2+ and Mg2+ ion conditions all of the peptides were able to penetrate the outer membrane of P. aeruginosa, however at higher ion concentrations none of the peptides were able to penetrate the outer membrane. PrAMPs were found to cause E. coli cells to swell and have a hyperpolarised membrane indicating a new mechanism of action for PrAMPs. Our data indicates that bacteria reduce susceptibility to AMPs by stabilising their LPS layer with metal ions and that the PrAMPs have secondary modes of action affecting the functionality of the bacterial membrane. Combining an ion chelator with PrAMPs may be a novel solution to combat weak antimicrobial activity in ion-rich environments such as host tissues.

microbiology↗

bioRxiv2025

Microstructural and geochemical evidence offers a solution to the cephalopod cameral deposits riddle

Orthoceratoid cephalopods are common in the Palaeozoic rock record but became extinct in the Late Triassic. Many orthoceratoids contain cameral deposits, which are enigmatic calcareous structures within their chambered shell that presumably balanced their straight conchs in a horizontal position. Since the mid-19th century, palaeontologists have attempted to understand the cameral deposit formation process. The various hypotheses include growth from cameral fluids, precipitation by a cameral mantle or even their dismissal as post-mortem structures. All of these previous interpretations have in common that they are complicated with contradictory evidence. Here, we present evidence from well-preserved Trematoceras elegans specimens from the Late Triassic St. Cassian Formation (Dolomites, northern Italy). We studied the specimens by using optical and electron beam microanalysis techniques and argue that the cameral deposits consist of primary aragonite and calcite fabrics. A fibrous microstructure, which is bilaterally symmetrically arranged with irregularities, is documented. Thin organic sheets originally delimited radial growth sectors. Based on these observations, we propose a new growth model that explicitly involves the cameral sheets. These sheets acted as an extension of the pellicle and held a thin film of supersaturated liquid in the otherwise emptied chambers by the cameral sheets via the capillary effect. Ions were supplied through the siphuncle, such as in living Nautilus, and enabled the precipitation of aragonite and calcite fabrics. This model goes beyond previous interpretations, resolves contradictory observations and has functional implications, suggesting that cameral sheets and deposits were an adaptation to increased growth rates.

paleontology↗

bioRxiv2023

Structural basis of GAIN domain autoproteolysis and cleavage-resistance in the adhesion G-protein coupled receptors

The GAIN domain is a hallmark of adhesion G-protein coupled receptors (aGPCRs) as this extracellular domain contains an integral agonistic sequence (Stachel) for activation via binding to the 7-transmembrane helical (7TM) domain of the receptor. Many aGPCRs are autoproteolytically cleaved at the GPCR proteolysis site (GPS) site within the GAIN domain formed HXS/T sequence motif. However, other aGPCR can be activated without GPS cleavage. We determined the crystal structure of the human ADGRB2/BAI2 hormone receptor (HormR) and GPCR autoproteolysis-inducing (GAIN) domains and found that this aGPCR is resistant to autoproteolysis despite the presence of a canonical HLS sequence motif at the GPS. We used structural comparisons and molecular dynamics (MD) simulations to identify structural determinants that are important for autocleavage beyond the canonical HXS/T motif. These studies characterized a conserved glycine residue and an edge-{pi} interaction of the histidine base of the GPS sequence with a phenylalanine residue that is highly conserved in cleavage-competent aGPCRs. The MD simulations showed that this interaction is important to position the imidazole group of the histidine for deprotonation of the serine or threonine nucleophile. Removal of this interaction reduced autoprote-olytic activity in the ADGRL1 receptor and restored cleavage competence of the ADGRB3 receptor in a R866H/L821F double mutant. Conservation analysis indicates that wild-type ADGRB2 and ADGRB3 are auto-cleavage-incompetent receptors.

biochemistry↗

bioRxiv2022

Inhibition of translation termination by Drosocin, an antimicrobial peptide from fruit flies

A 19-amino acid long proline-rich antimicrobial peptide (PrAMP) Drosocin (Dro) is encoded in the fruit fly genome. Native Dro is glycosylated at a specific threonine residue, but the non-glycosylated peptide retains antibacterial activity. Dro shows sequence similarity to several other PrAMPs that bind in the ribosomal nascent peptide exit tunnel and inhibit protein synthesis by varying mechanisms. However, the target and mechanism of action of Dro remain unknown. Here we show that the primary mode of Dro action is inhibition of termination of protein synthesis. Our in vitro and in vivo experiments demonstrate that Dro stalls ribosomes at stop codons, likely sequestering class 1 release factors associated with the terminating ribosome. As the result, Dro strongly promotes readthrough of stop codons at subinhibitory concentrations. The elucidated mode of Dro action allows assigning it as the second member of the type II PrAMPs, of which only one representative, the antimicrobial peptide apidaecin (Api) produced by honeybees, was previously known. However, despite its functional similarity with Api, Dro interacts with the target in a markedly distinct way. The analysis of a comprehensive single-amino acid substitution library of endogenously expressed Dro variants shows that binding to the ribosome involves interactions of multiple amino acid residues distributed through the entire length of the PrAMP. Our data further show that the ribosome-targeting activity of non-glycosylated Dro can be significantly enhanced by single amino acid substitutions illuminating directions for improving its antibacterial properties.

molecular biology↗

bioRxiv2022

Bayesian inference reveals a complex evolutionary history of belemnites

Belemnites are an extinct group of Mesozoic coleoid cephalopods, common in Jurassic and Cretaceous marine sedimentary rocks. Despite their significance, their total group phylogeny has rarely been considered in recent decades. In contrast, most researchers restricted the assignment of families to one of the two usually recognized subgroups, the Belemnitina and the Belemnopseina. As for many fossil cephalopods, researchers have been reluctant to employ modern phylogenetic methods to illuminate belemnites evolutionary history. To overcome the "dead end" of belemnite systematics, we performed the first tip-dated Bayesian analysis of belemnite phylogeny. In our analysis, the Aulacoceratida are found as the monophyletic sister group to belemnites. The Sinobelemnitidae are resolved as paraphyletic and fall outside the Belemnitina and Belemnopseina, which make up the remaining belemnites. Belemnitina is restricted to Jurassic species with generally no or apical furrows. Holcobelidae are the earliest branching Belemnopseina. Cylindroteuthids sensu lato (including Oxyteuthidae) are nested within Belemnopseina, contrary to the common hypothesis placing them within the Belemnitina. Duvaliidae and Dicoelitidae are recovered as members of the Belemnopseina, but their precise relationship has to be evaluated based on more taxa and additional characters. We introduce the well-supported unranked clade Pseudoalveolata, which includes Dimitobelidae, Belemnitellidae, and members of the paraphyletic "Belemnopseidae". The phylogeny presented here, based on reproducible and quantitative methods, contrasts with the usually applied authoritative "stratophenetic" approach to belemnite systematics, based on the overemphasis of single characters. This result is considered the basis for future studies on belemnite phylogeny, allowing for a rigorous testing of evolutionary hypotheses. PLAIN LANGUAGE SUMMARYBelemnites were common extinct cephalopods that were closely related to todays squid and cuttlefish. The most common fossil remains of belemnites are bullet-shaped calcitic "cones" (rostrum) that cover their internal shells. Belemnites evolutionary history is not well known. Our study revealed an evolutionary tree of belemnites based on the statistical analysis of morphological features of the rostrum and calibrated to the known geological ages of the studied belemnite species. This approach was for the first time applied to belemnites and changed several aspects that were believed about their evolution.

paleontology↗

bioRxiv2022

A tumour-promoting senescent secretome triggered by platinum chemotherapy exploits a targetable TGFβR1/Akt-mTOR axis in lung cancer

Platinum-based chemotherapy is commonly used for non-small cell lung cancer (NSCLC) treatment, yet clinical outcomes remain poor. Cellular senescence and its associated secretory phenotype (SASP) can have multiple tumour-promoting activities, although these are largely unexplored in lung cancer. Here we show that cisplatin-derived SASP enhances the malignant phenotype of lung cancer cells. Using xenograft, orthotopic and KrasG12V-driven murine NSCLC models, we demonstrate that cisplatin-induced senescent cells strongly promote tumour progression. Mechanistically, we find that a TGF-{beta}-enriched SASP drives pro-proliferative effects through TGF{beta}R1 and Akt/mTOR pathway activation. We validate the translational relevance of chemotherapy-induced SASP using clinical NSCLC samples from patients who received neoadjuvant platinum-based chemotherapy. Importantly, TGF{beta}R1 inhibition with galunisertib or senolytic treatment significantly reduces tumour promotion driven by cisplatin-induced senescence. Finally, we demonstrate, using distinct murine NSCLC models, that addition of TGFBR1 inhibitors to platinum-based chemotherapy reduces tumour burden and improves survival, providing pre-clinical proof-of-concept for future trial designs.

cancer biology↗

bioRxiv2022

Reduced PDE4D7 expression in prostate cancer correlates with down-regulation of genomic elements within the upstream PDE4D coding region on chromosome 5

PDE4D7 expression is diminished during progression of PCa and the phosphodiesterase has been proposed as a prognostic biomarker. RNA sequencing of PCa tissue identified sequences in the PDE4D coding region on Chr5q12 exhibiting similarities in mRNA expression profile to PDE4D7. As previously identified, PART1 had a significantly similar expression pattern to PDE4D7 across samples. However, other genes also matched expression to PDE4D7, including miRNAs and lncRNAs. These novel PDE4D7 associated genes represent putative PCa biomarkers and could have mechanistic roles in PCa progression.

cancer biology↗

bioRxiv2021

Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data

Spliced fusion-transcripts are typically identified by RNA-seq without elucidating the causal genomic breakpoints. However, non poly(A)-enriched RNA-seq contains large proportions of intronic reads spanning also genomic breakpoints. Using 1.274 RNA-seq samples, we investigated what additional information is embedded in non poly(A)-enriched RNA-seq data. Here, we present our novel, graph-based, Dr. Disco algorithm that makes use of both intronic and exonic RNA-seq reads to identify not only fusion transcripts but also genomic breakpoints in gene but also in intergenic regions. Dr. Disco identified TMPRSS2-ERG fusions with genomic breakpoints and other transcribed rearrangements from multiple RNA-sequencing cohorts. In breast cancer and glioma samples Dr. Disco identified rearrangement hotspots near CCND1 and MDM2 and could directly associate this with increased expression. A comparison with matched DNA-sequencing revealed that most genomic breakpoints are not, or minimally, transcribed while also revealing highly expressed translocations missed by DNA-seq. By using the full potential of non poly(A)-enriched RNA-seq data, Dr. Disco can reliably identify expressed genomic breakpoints and their transcriptional effects.

bioinformatics↗

bioRxiv2020

The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the microbiome-host interaction.

BackgroundColorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide analyses between healthy individuals and cancer patients suggest a role for the human intestinal microbiota. Nevertheless, which microbial molecules are involved in this communication is largely unknown, with current studies mainly focusing on short chain fatty acids and amino acid metabolites as potential mediators. However, quorum sensing peptides are not yet considered in this microbiome-host interaction: their in vivo presence nor any in vivo host-effect have been reported. ResultsFor the first time, we showed that a quorum sensing peptide metabolite, EntF* produced by intestinal microbiota (E. faecium), is present in the blood circulation of mice. Moreover, it significantly promotes colorectal cancer metastasis in vivo, with metastatic lesions found in both liver and lung tissues, using an orthotopic mice model evaluating bioluminescence as well as macroscopic and microscopic presence of metastatic tumour nodules. In vitro tests on E-cadherin expression levels thereby indicated that the first, second, sixth and tenth amino acid of EntF* were critical for the epithelial-mesenchymal transition (EMT) effect, responsible for tumour metastasis. ConclusionThis paper adds a new group of molecules, the quorum sensing peptides, as an additional causative factor explaining the microbiome-host interaction. The presence of a selected quorum sensing peptide (metabolite) in the mouse was proven for the first time and its in vivo effect on colorectal metastasis was demonstrated. We anticipate our in vivo results to be a starting point for broader microbiome-health investigations, not only limited to colorectal cancer metastasis, but also for developing novel bio-therapeutics in other disease areas, giving due attention to the QSP produced by the microbiome.

molecular biology↗

bioRxiv2020

A common molecular mechanism for cognitive deficits and craving in alcoholism

Alcohol-dependent patients commonly show impairments in executive functions that facilitate craving and can lead to relapse. The medial prefrontal cortex, a key brain region for executive control, is prone to alcohol-induced neuroadaptations. However, the molecular mechanisms leading to executive dysfunction in alcoholism are poorly understood. Here using a bi-directional neuromodulation approach we demonstrate a causal link for reduced prefrontal mGluR2 function and both impaired executive control and alcohol craving. By neuron-specific prefrontal knockdown of mGluR2 in rats, we generated a phenotype of reduced cognitive flexibility and excessive alcohol-seeking. Conversely, restoring prefrontal mGluR2 levels in alcohol-dependent rats rescued these pathological behaviors. Also targeting mGluR2 pharmacologically reduced relapse behavior. Finally, we developed a FDG-PET biomarker to identify those individuals that respond to mGluR2-based interventions. In conclusion, we identified a common molecular pathological mechanism for both executive dysfunction and alcohol craving, and provide a personalized mGluR2-mechanism-based intervention strategy for medication development of alcoholism.

neuroscience↗