Figure 1: Five crystal structures of the IS608 transpososome together with associated biochemical data elucidate the entire pathway of single-stranded DNA transposition and show how it selects its integration site.
Figure 2: Crystal structure of the primary piRNA biogenesis factor Zucchini reveals its endonuclease function.
The Barabas group uses structural and molecular biology approaches to investigate how DNA rearrangements are carried out and regulated, with the ultimate goal of facilitating their applications in research and therapy.
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 and evolution and constitute about half of the human genome. However, the physiological roles of transposons are just starting to be unravelled. Recent studies show that they have key functions in gene regulation, development, immunity, and neurogenesis (Beck et al., 2011). Moreover, these ‘jumping’ DNA elements offer attractive tools for genetics and human gene therapy.
To better understand transposition and facilitate its applications we investigate the molecular mechanisms of their movement and regulation using structural biology, 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, and their regulation in the cell.
This transposon is a prime tool in vertebrate genetics. We study its structure and mechanisms, investigate how it interacts with other components of human host cells, and develop advanced variants for genetic engineering.
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), and could provide a solution. 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 public health concerns. Conjugative transposons provide a powerful mechanism to transfer resistance between bacteria: we survey their abundance in bacterial genomes and communities and study the mechanisms of two elements from Helicobacter and Enterococcus.
To avoid deleterious outcomes, cells must keep their transposons under control. One major control mechanism is provided by small RNAs and our group investigates these processes in prokaryotes and eukaryotes. Our recent work on the piRNA pathway has revealed the structure and function of a novel factor called Zucchini.
Future projects and goals
- Develop novel genetic engineering tools and explore their applications in transgenesis and synthetic biology.
- Study the mechanism and regulation of a class of ‘beneficial’ transposons that are involved in the development of ciliated protists.