Biology subjects

Lammers, M.

Publications and source records attributed to Lammers, M..

7 recordsLinked to original sources

bioRxiv2026

Accurate and scalable demultiplexing of single-cell RNA sequencing using BEACON

Barcode-based multiplexing strategies can significantly increase sample throughput and decrease costs, while mitigating batch effects of single-cell RNA sequencing experiments. However, these approaches can be limited by inaccurate or inefficient demultiplexing, resulting in cell loss and reduced statistical power. Here, we present BEACON, a novel sample demultiplexing method that efficiently learns the background count distribution from data and removes it from individual cells, thereby improving classification accuracy. BEACON outperforms other state-of-the-art methods on multiple human data sets. We apply it to cancer cell line time course experiments in vitro, enabling the identification of genes associated with aggressive tumors in vivo. Finally, we adapt BEACON to multimodal protein-transcriptome profiling, enhancing protein signal recovery to identify a CD161-positive effector memory CD4 T-cell population with a Th17-like phenotype, which we prospectively validate. BEACON can therefore be applied to other droplet-based single-cell sequencing methodologies.

bioinformatics↗

bioRxiv2025

E3 ubiquitin ligase SKP2 limits autophagy during S. aureus infection

Ubiquitination is a posttranslational modification that affects protein function, stability, and localization and is thereby balancing protein homeostasis. During infection, ubiquitination is crucial in regulating host cell signaling pathways in pathogen recognition, clearance and mounting an efficient immune response. S. aureus is an opportunistic pathogen that is able to invade and multiply within both phagocytic and non-phagocytic mammalian cells depending on virulence factor expression of the respective S. aureus strain. Selective autophagy serves as a host defense mechanism to combat intracellular bacterial persistence by targeting and degrading intracellular pathogens. However, S. aureus can subvert autophagosomal degradation and exploit these organelles for intracellular replication. We examined the role of the E3 ligase S-phase kinase-associated protein 2 (SKP2), a component of the SKP1-Cullin1-F-box (SCF) - complex, during S. aureus infection in alveolar epithelial and in macrophage-like cells. Upon S. aureus infection, we demonstrate increased SKP2 abundance through acetylation-induced stabilization and translocation into the cytoplasm. Cytoplasmic SKP2 modulated autophagy induction. By downregulation of SKP2, the level of the autophagy marker LC3-II was elevated which was accompanied by increased survival of intracellular S. aureus. Conversely, SKP2 overexpression in host cells reduced LC3-II levels followed by reduced intracellular bacteria. These findings underscore that SKP2 is an important regulator of autophagy, preventing excessive autophagy from being exploited by S. aureus. In conclusion, our findings reveal novel molecular mechanisms involved in the interaction between host cells and S. aureus providing potential approaches for targeted therapeutic intervention. ImportanceStaphylococcus aureus is a major pathogen responsible for a wide range of human and animal infections and toxin-mediated syndromes. For many years, S. aureus was mainly recognized as an extracellular pathogen. However, it has been shown that S. aureus can survive in epithelial cells and phagocytes. Intracellular persistence complicates the treatment by protecting the bacteria from antibiotics and immune detection. Elimination of pathogens from intracellular compartments relies on cellular mechanisms such as recognition and ubiquitination by host E3 ligases followed by selective autophagy. S. aureus has developed strategies to manipulate this process by evading degradation by interfering with autophagosome formation or even exploiting the formation of autophagosomes as replication niches. The present study reveals an intricate cellular response pathway that is involved in the intracellular recognition and elimination of the pathogen. This knowledge opens new avenues towards targeted treatment.

microbiology↗

bioRxiv2021

Diversification by CofC and control by CofD govern biosynthesis and evolution of coenzyme F420 and its derivative 3PG-F420

Coenzyme F420 is a microbial redox cofactor that is increasingly used for biocatalytic applications. Recently, diversified biosynthetic routes to F420 and the discovery of a derivative, 3PG-F420, were reported. 3PG-F420 is formed via activation of 3-phospho-D-glycerate (3-PG) by CofC, but the structural basis of substrate binding, its evolution, as well as the role of CofD in substrate selection remained elusive. Here, we present a crystal structure of the 3-PG-activating CofC from Mycetohabitans sp. B3 and define amino acids governing substrate specificity. Site-directed mutagenesis enabled bidirectional switching of specificity and thereby revealed the short evolutionary trajectory to 3PG-F420 formation. Furthermore, CofC stabilized its product, thus confirming the structure of the unstable molecule, revealing its binding mode and suggesting a substrate channeling mechanism to CofD. The latter enzyme was shown to significantly contribute to the selection of related intermediates to control the specificity of the combined biosynthetic CofC/D step. Taken together, this work closes important knowledge gaps and opens up perspectives for the discovery, enhanced biotechnological production, and engineering of coenzyme F420 derivatives in the future. ImportanceThe microbial cofactor F420 is crucial for processes like methanogenesis, antibiotics biosynthesis, drug resistance, and biocatalysis. Recently, a novel derivative of F420 (3PG-F420) was discovered, enabling the production and use of F420 in heterologous hosts. By analyzing the crystal structure of a CofC homolog whose substrate choice leads to formation of 3PG-F420, we defined amino acid residues governing the special substrate selectivity. A diagnostic residue enabled reprogramming of the substrate specificity, thus mimicking the evolution of the novel cofactor derivative and successfully guiding the identification of further 3-PG-activating enzymes. Furthermore, a labile reaction product of CofC was revealed that has not been directly detected so far and CofD was shown to provide as another layer of specificity of the combined CofC/D reaction, thus controlling the initial substrate choice of CofC. The latter finding resolves a current debate in the literature about the starting point of F420 biosynthesis in various organisms.

microbiology↗

bioRxiv2020

An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella

Deubiquitinating enzymes (DUBs) are important regulators of the posttranslational protein ubiquitination system. Mammalian genomes encode about hundred different DUBs, which can be grouped into seven different classes. Members of other DUB classes are found in pathogenic bacteria, which use them to target the host defense. By combining bioinformatical and experimental approaches, we address the question if the known DUB families have a common evolutionary ancestry and share conserved features that set them apart from other proteases. By systematically comparing family-specific Hidden-Markov-Models, we uncovered distant relationships between established DUBs and other cysteine protease families. Most DUB families share a conserved aromatic residue linked to the active site, which restricts the cleavage of substrates with sidechains at the S2 position, corresponding to Gly-75 in ubiquitin. By applying these criteria to Legionella pneumophila ORFs, we identified lpg1621 and lpg1148 as deubiquitinases, characterized their cleavage specificities, and confirmed the importance of the aromatic gatekeeper motif for substrate selection.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗

bioRxiv2020

Lipids as currency in ecological interactions: Competition and facilitation between two lipid scavenging parasitoids

Interspecific interactions in nature often revolve around the acquisition of nutrients. Depending on the organisms metabolic requirements, competition for specific essential nutrients may occur, which selects for increased abilities to monopolize, consume and store these nutrients. Lipid scavengers are organisms that rely on exogenous lipid acquisition as they lack the ability to synthesize fatty acids de novo or in sufficient quantity. Most parasitoid insects are lipid scavengers: they obtain all required lipids by feeding on their hosts as larvae. Here we study the nutritional ecology of competitive interactions between native Nasonia vitripennis and introduced Tachinaephagus zealandicus. While the former was already known to lack lipogenesis, we show that T. zealandicus also relies on host lipids. The interactions between the two species were studied using competition experiments, in which oviposition of T. zealandicus on a host was followed by multiparasitism by N. vitripennis. The outcome of competition was determined by the duration of the time lag between oviposition events. N. vitripennis was superior when arriving 3 days after oviposition by T. zealandicus. In contrast, 9 days after oviposition of T. zealandicus we observed complete reversal, and no N. vitripennis offspring were able to develop. Only when N. vitripennis laid eggs 15 days after T. zealandicus oviposition, both species could emerge from the same host. However, N. vitripennis realizes only 10% of its potential fitness at this time point because prior parasitization by the gregarious T. zealandicus compartmentalizes the host resources, limiting the spread of N. vitripennis venom. This study shows that successful reproduction of N. vitripennis at 15 days was achieved by hyperparasitizing, a capability that provides a fitness benefit to N. vitripennis, as it extends the time window that hosts are available for parasitization. Choice tests with hosts at different time intervals after T. zealandicus oviposition revealed a partial mismatch in N. vitripennis females between competition avoidance and offspring performance, which may be linked to the limited co-evolutionary time between native and introduced species. We discuss our results in the context of nutritional ecology and, specifically, the role of lipids in ecological interactions.

ecology↗

bioRxiv2019

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

BackgroundParasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biocontrol, and infecting aphids requires overcoming both aphid defenses and their defensive endosymbionts. ResultsWe present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp), highly syntenic, and the most AT-rich reported thus far for any arthropod (GC content: 25.8% and 23.8%). This nucleotide bias is accompanied by skewed codon usage, and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and age-specific energy demands. We identify expansions of F-box/Leucine-rich-repeat proteins, suggesting that diversification in this gene family may be associated with their broad host range or with countering defenses from aphids endosymbionts. The absence of some immune genes (Toll and Imd pathways) resembles similar losses in their aphid hosts, highlighting the potential impact of symbiosis on both aphids and their parasitoids. ConclusionsThese findings are of fundamental interest for insect evolution and beyond. This will provide a strong foundation for further functional studies including coevolution with respect to their hosts, the basis of successful infection, and biocontrol. Both genomes are available at https://bipaa.genouest.org.

genomics↗

bioRxiv2018

Gene regulatory mechanisms underlying the evolutionary loss of a polygenic trait

Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these involve loss-of-function mutations in one or more trait-specific genes. Parasitoid insects are fatty acid auxotrophs: they lost the ability to convert dietary sugars into fatty acids, a trait that is ubiquitous among non-parasitoid animals and is enabled by a highly conserved set of genes. Earlier research suggests that lack of lipogenesis is caused by changes in gene regulation, rather than gene decay. We compared transcriptome-wide responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within four hours after feeding, but there was little overlap at the gene level between the responses of the two species. Even at the pathway-level, there were sharp differences between the expression profiles of the two species, especially in carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (MCD) and HMG-CoA synthase differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network analysis indicates most genes involved in these pathways to be highly connected, which suggest they have pleiotropic effects and could explain the absence of gene degradation. Our results indicate that modification of expression levels of only a few non-connected genes, such as MCD, is sufficient to enable complete loss of lipogenesis in N. vitripennis.

evolutionary biology↗