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Dr. Benedikt Beckmann

Lebenswissenschaftliche Fakultät · Institut für Biologie

Projekte

Kooperationen

Themen

Genregulation Infektionsbiologie Molekularbiologie Proteinstruktur RNA-Protein-Komplexe Strukturbiologie

Zusammenfassung

Dr. Beckmann erforscht, wie Bakterien wie Salmonella Typhimurium während einer Infektion speziesübergreifende RNA-Protein-Komplexe mit menschlichen Wirtszellen bilden. Sein Fokus liegt darauf, neue Mechanismen der Wirt-Pathogen-Interaktion zu verstehen, insbesondere wie bakterielle Effektorproteine mit humanen RNA-Molekülen zusammenwirken. Diese Erkenntnisse könnten langfristig zu besseren Strategien gegen bakterielle Infektionen führen — relevant für Pharmazie, Diagnostik und Infektionsbekämpfung in Klinik und Industrie.

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Stammdaten

Identität, Organisation und Kontakt aus HU-FIS.

Dr. Benedikt Beckmann

HU-FIS-Profil ↗

Fakultät: Lebenswissenschaftliche Fakultät
Institut: Institut für Biologie
ORCID: 0000-0001-7566-4408

Forschungsprojekte

Cross-species RNA-protein complexes in infection
Quelle ↗
Ziel des Projekts ist es, einen neuen Aspekt der Wirts-Mikrobeninteraktion zu untersuchen. Unser Hauptaugenmerk ist dabei das Bakterium Salmonella Typhimurium. In Vorarbeiten haben wir in Salmonella Hinweise auf speziesübergreifende RNA-Proteinkomplexe gefunden, die sich während einer Infektion von humanen Wirtszellen bilden können: 1. Wir haben mehrere Effektorproteine gefunden, bei denen wir eine RNA-bindende Funktion vorhergesagt haben. Wir werden testen, ob diese Proteine Wirts-RNA binden und die RNA-Transkripte identifizieren.2. Salmonella sekretiert extrazelluläre Vesikel, die RNA beinhalten. Wir werden untersuchen, was mit dieser RNA während einer Infektion in der Wirtszelle geschieht und mit welchen Wirtsfaktoren sie interagiert. In beiden Fällen werden wir untersuchen, ob diese speziesübergreifenden Interaktionen dabei helfen, die Wirtszelle währen der Infektion zu manipulieren und wie wichtig diese posttranskriptionellen Komplexe für eine erfolgreiche Infektion sind. Dies könnte neue Wege zur Bekämpfung von bakteriellen Infektionen eröffnen.

Publikationen

13Auswahl der wichtigsten Publikationen — Quelle: OpenAlex.

The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions
2016
Pflügers Archiv - European Journal of Physiology · DOI
Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.
TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs
2019
Nucleic Acids Research · DOI

In recent years, hundreds of novel RNA-binding proteins (RBPs) have been identified, leading to the discovery of novel RNA-binding domains. Furthermore, unstructured or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids. However, these advances in understanding RBPs are limited mainly to eukaryotic species and we only have limited tools to faithfully predict RNA-binders in bacteria. Here, we describe a support vector machine-based method, called TriPepSVM, for the prediction of RNA-binding proteins. TriPepSVM applies string kernels to directly handle protein sequences using tri-peptide frequencies. Testing the method in human and bacteria, we find that several RBP-enriched tri-peptides occur more often in structurally disordered regions of RBPs. TriPepSVM outperforms existing applications, which consider classical structural features of RNA-binding or homology, in the task of RBP prediction in both human and bacteria. Finally, we predict 66 novel RBPs in Salmonella Typhimurium and validate the bacterial proteins ClpX, DnaJ and UbiG to associate with RNA in vivo.

Fast and unbiased purification of RNA-protein complexes after UV cross-linking

2019

Methods · DOI

Post-transcriptional regulation of gene expression in cells is facilitated by formation of RNA-protein complexes (RNPs). While many methods to study eukaryotic (m)RNPs rely on purification of polyadenylated RNA, other important regulatory RNA classes or bacterial mRNA could not be investigated at the same depth. To overcome this limitation, we developed Phenol Toluol extraction (PTex), a novel and unbiased method for the purification of UV cross-linked RNPs in living cells. PTex is a fast (2-3 h) and simple protocol. The purification principle is solely based on physicochemical properties of cross-linked RNPs, enabling us to interrogate RNA-protein interactions system-wide and beyond poly(A) RNA from a variety of species and source material. Here, we are presenting an introduction of the underlying separation principles and give a detailed discussion of the individual steps as well as incorporation of PTex in high-throughput pipelines.