Biology subjects

Suess, B.

Publications and source records attributed to Suess, B..

4 recordsLinked to original sources

bioRxiv2025

A unique mechanism explaining the outstanding performance of a newly discovered doxycycline riboswitch

Synthetic riboswitches offer a versatile and protein-independent solution for conditional gene regulation. They consist of a regulatory domain and an aptamer domain that binds a specific ligand, with their performance largely depending on the ability of the aptamer to control the regulatory domain. Expanding the range of synthetic riboswitches therefore requires the discovery and characterization of new regulatory aptamers. In the present study, we identified a doxycycline-binding aptamer with outstanding regulatory properties in both yeast and human cells which are based on a unique structural dynamic upon ligand binding. Single-molecule force spectroscopy revealed that doxycycline binding strongly stabilizes an intermediate aptamer conformation offering mechanistic insights into its function. The identification of the aptamer through a combination of parallel SELEX and subsequent in vivo screening in yeast, also provided valuable insights into selection dynamics and the first proof for the effectiveness of RNA Capture-SELEX in aptamer selection. Together, the presented data deepen our understanding of regulatory aptamer selection and functionality while adding a high-performing doxycycline-responsive aptamer to the synthetic biology toolbox.

molecular biology↗

bioRxiv2025

NAND Hybrid Riboswitch Design by Deep Batch Bayesian Optimization

The design of large genetic circuits requires genetic regulatory devices capable of performing complex logic operations. Hybrid riboswitches, synthetically enhanced compact RNA elements (<100 nucleotides) that form a tertiary structure with the ability to specifically bind two different target molecules, can be used to design genetic regulators that emulate Boolean logic. When inserted into the 5 UTR of an mRNA, these devices can regulate translation initiation upon specific binding of one or both ligands. The goal of this study is to design hybrid riboswitches that emulate Boolean NAND logic in yeast. We propose a novel machine learning-based design framework combining high-throughput in vivo screening and deep Bayesian optimization. Through an initial screening, we discovered a hybrid riboswitch with NAND behavior. Using batch Bayesian optimization with an ensemble neural network as surrogate, we further improve the NAND functionality of our hybrid riboswitch with respect to a performance score, thereby achieving near digital NAND behavior. With its focus on model-based and score-driven design, our proposed method can complement experiment driven approaches by allowing fine grained adaptation of functionality, including constructs sensitive to single nucleotide changes.

synthetic biology↗

bioRxiv2024

Ultrahigh-throughput discovery of modified aptamers as specific and potent enzyme inhibitors

Enzymes are instrumental to life and key actors of pathologies, making them relevant drug targets. Most enzyme inhibitors consist of small molecules. Although efficient, their development is long, costly and can come with unwanted off-targeting. Substantial gain in specificity and discovery efficiency is possible using biologicals. Best exemplified by antibodies, these drugs derived from living systems display high specificity and their development is eased by harnessing natural evolution. Aptamers are nucleic acids sharing functional similarities with antibodies while being deprived of many of their limitations. Yet, the success rate of inhibitory aptamer discovery remained hampered by the lack of an efficient discovery pipeline. In this work, we addressed this issue by introducing an ultrahigh-throughput strategy combining in vitro selection, microfluidic screening and bioinformatics. We demonstrate its efficiency by discovering a modified aptamer that specifically and strongly inhibits SPM-1, a beta-lactamase that remained recalcitrant to the development of potent inhibitors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/608213v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@b15e8forg.highwire.dtl.DTLVardef@b7259forg.highwire.dtl.DTLVardef@6f24borg.highwire.dtl.DTLVardef@d4f48_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

CD20 as a gatekeeper of the resting stage of human B cells

CD20 is a B cell specific membrane protein and a target of therapeutic antibodies such as rituximab (RTX)1. In spite of the prominent usage of anti-CD20 antibodies in the clinic little is known about the biological function of CD202. Here we show that CD20 controls the nanoscale organization of receptors on the surface of resting B lymphocytes. A CRISPR/Cas-based ablation of CD20 in Ramos B cells results in a relocalisation of the IgM B cell antigen receptor (IgM-BCR) and the co-receptor CD19. The resulting IgM-BCR/CD19 signaling synapse leads to transient B cell activation followed by plasma cell differentiation. Similarly to CD20-deficient Ramos cells, naive human B cells treated with rituximab in vitro or isolated from patients during rituximab administration display hallmarks of transient activation characterized by the formation of the IgM-BCR/CD19 signaling synapse, followed by CD19 and IgM-BCR downregulation. Moreover, increased expression of specific plasma cell genes can be observed after rituximab treatment in relapsed CLL patients. In summary we identify CD20 as a gatekeeper of the resting state on human B cells and demonstrate that a disruption of the nanoscale organization of the B cell surface via CD20 deletion or anti-CD20 treatment profoundly alters B cell fate.

immunology↗