Synthetic RNA biology

Prof. Dr. Beatrix Suess

We explore regulatory RNAs in all of their diverse forms and shapes. Our research interests include natural RNAs found in bacteria and other model organisms as well as the design of aptamers and synthetic riboswitches. Our goal is to fully understand these regulatory elements in their structure, function and range of applications.

RNA performs many diverse and essential roles that considerably transcend the mere transmission of genetic information. The last decade saw the identification of a plethora of regulatory RNAs participating in crucial steps of gene expression. The molecular basis originates from the conformational flexibility and functional versatility of this macromolecule: like proteins, RNA can adopt complex three-dimensional structures for the precise presentation of chemical moieties that is essential for its function as a biological catalyst, regulator or structural scaffold.

Our key interest is to study the ways in which RNA exerts regulation. We search for unknown regulatory RNAs across different domains of life, create artificial ones and modify them for an in-depth understanding of their function and capabilities. Our goal is to comprehensively understand regulatory RNAs in all of their forms and use their potential in synthetic biology, medicine and biotechnology.

Aptamers, synthetic riboswitches and biosensors

A main focus of our research is the development of engineered riboswitches that can be applied as genetic regulatory devices for synthetic biology. These regulatory elements result from direct RNA-ligand interactions and are perfect model systems to study the molecular basis underlying this novel type of regulation. Riboswitches consist solely of RNA. They are characterised by binding of a small molecule effector (ligand?) to the so-called aptamer domain, which results in a conformational change of the downstream expression platform that determines output. The modular organisation of riboswitches and the possibility that small molecule-binding aptamers can be selected in vitro against almost any molecule of choice have recently led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology.

While many RNA aptamers binding to a multitude of small molecules have been identified, only very few are capable of acting as riboswitches. We therefore established a pipeline that integrates the in vitro selection process, next generation sequencing and in vivo screening for rapid identification of those aptamers that have the potential to be engineered into riboswitches. Thus, we implemented RNA Capture-SELEX in our riboswitch developmental pipeline to integrate the required selection for high-affinity binding with the equally necessary RNA conformational switching. In a combination of genetic, biochemical and structural studies we address the question how regulation of riboswitching aptamers works at the molecular level. Finally, we explore applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression and to develop new strategies e.g. for controlling RNA stability or alternative splicing by synthetic riboswitches in bacteria, archaea and eukaryotes.

In addition, we also employ synthetic riboswitches to build logical gates and complex genetic circuits. For these purposes, we like to use bioinformatic support such as machine or deep learning. Due to their excellent binding properties, aptamers are also well suited as biosensors, for example to detect contamination with pollutants, antibiotics or drug residues in food or drinking water. Here we develop easy-to-use, fast and safe biosensors.

Finding regulatory RNAs in Streptomyces

Streptomycetes are highly relevant soil bacteria in biotechnology best known for their complex life cycle and ability to produce a wide range of secondary metabolites. Using RNAseq, we identified and characterized several small non coding RNAs (sRNAs) in the model organism Streptomyces coelicolor. Our specific focus lies on sRNAs that potentially affect the production of secondary metabolites, such as antibiotics and other pharmacologically active compounds.