Figure 1: The Sleeping Beauty transposase – DNA complex showing intimate interaction of the protein (blue) with specific transposon end (grey) and target (black) DNA that governs and regulates a series of chemical steps during transposition.
The Barabas group uses structural and molecular biology approaches to investigate how DNA rearrangements are carried out and regulated, and uses this knowledge to develop their applications in research and medicine.
Previous and current research
Our research focuses on transposons, a class of mobile genetic elements that can autonomously move from one location to another in the genome. They drive genetic diversity, adaptation and evolution and constitute a large fraction of most genomes. However, the physiological roles of transposons are just starting to be unravelled. They largely contribute to antibiotic resistance transfer in bacteria, creating a pressing public health concern. Recent discoveries also show that they have key functions in gene regulation, development, immunity, and neurogenesis in animals. Finally, these ‘jumping’ DNA elements offer innovative tools for genetics and human gene therapy.
To better understand transposition and facilitate applications, we investigate the molecular mechanisms of their movement and regulation using a diverse methodological toolbox inclusding structural and molecular biology, biochemistry, biophysics, bioinformatics, microbiology, and cell biology approaches. We strive to understand the structure of functional transposition complexes, the chemistry they use to cut and paste DNA, their target-site selection, their abundance in genomes (Smyshlyaev et al. 2013; Bock et al. 2014), and their regulation in the cell. Major focus is on eukaryotic transposons that provide genetic tools, antibiotic resistance-carrying elements, and transposon regulation by small RNAs.
This transposon is a prime tool in vertebrate genetics and human gene/cell therapy. We study its structure and mechanisms, investigate how it interacts with other components of human host cells, and develop advanced variants for genetic engineering. We have recently determined the crystal structure of the catalytic part of the Sleeping Beauty transposase, which allowed us to design novel hyperactive variants for therapeutic applications (Voigt et al., 2016, Press Release: Designing gene therapy).
Target site-specific transposons
One of the main obstacles in gene therapy is integration of the therapeutic gene at unwanted locations. Our work revealed that the IS608 transposon uses part of its own sequence to guide integration to a specific site via base pairing (Barabas et al., 2008). We are now testing if this target recognition mode can be extended to select unique genomic sites.
Antibiotic resistance carrying elements
The spread of antibiotic resistance is one of today’s biggest medical challenges. Conjugative transposons (CTns) actively transfer resistance genes across bacterial cells and species, consituting a great risk for resistance dissemination. We study the mechanisms of CTn movement at atomic detail and in bacterial communities with the ultimte goal of desiging intervention startegies to limit their spreading.
To avoid deleterious outcomes, higher eukaryotes keep their transposons under tight control. One major control mechanism is provided by small RNAs and our group investigates these processes in prokaryotes (Schulz et al., 2014) and eukaryotes. Our recent work on the piRNA pathway has revealed the structure and function of a novel factor called Zucchini (Voigt et al., 2012).
Future projects and goals
- Develop novel genetic engineering tools for synthetic biology.
- Study the mechanism and regulation of a class of ‘beneficial’ transposons that are involved in the development of ciliated protists.