How is computational biology revolutionizing biotechnology?

"These Xanthomonas bacteria cause high yield losses in a large number of different crops worldwide," says plant geneticist Dr. Jens Boch. "To infect, the bacteria bring a cocktail of bacterial proteins, so-called effectors, into the infected plant cells." Some of these effectors are able to reprogram the plant cells for the benefit of the bacterium by specifically activating plant genes.

The functionality of the TALEs (transcription activator-like effectors) was confirmed in 2009 by the research groups headed by Dr. Jens Boch and Prof. Dr. Ulla Bonas enlightened in a milestone publication in Science. In order to switch on plant genes, TALEs have to bind to the host cell's DNA. This binding takes place through a section in the TALE, which consists of regularly repeating amino acids, so-called repeats.

The selection of the bound DNA sequences in turn only depends on two amino acids within each repeat. The discovery of this binding mechanism revolutionized biotechnology in the years that followed. The predictability of DNA binding now made it possible to target proteins with the desired functionality to specific areas of the DNA in order to produce the desired effects there.

Researcher around Dr. Jens Boch have now discovered that there can be deviations from this regularity of the bond. "Some of the repeats in naturally occurring TALEs have a significantly larger or smaller number of amino acids than usual," explains Jens Boch, who had suspected for some time that these anomalous repeats have a significant influence on TALEs: "TALEs bind in one quite regular way to the DNA double helix. If a repeat is out of line, it should have serious consequences for the entire function. "

Another clue arose from the consideration of computer-aided predictions of possible target sequences of TALEs. Last year, with the participation of the research groups around Dr. Jens Boch, Prof. Dr. Ulla Bonas (Institute for Biology) and Dr. Jan Grau and Prof. Dr.-Ing. Stefan Posch (Institute for Computer Science) developed a computer program for predicting TALE targets and published it in the journal PLOS Computational Biology.

“Most of our predictions for TALEs with known target genes were very good and the correct targets were almost always in the first place. However, there were clear exceptions that we could not explain at first. Then we realized that this was the case with TALEs with abnormal repeats, ”said Dr. Jan Grau, main developer of the prediction program.

Motivated by this discovery, the researchers led by Dr. Jens Boch with the experimental part of the work: the investigation of the binding of anomalous repeats to the DNA using molecular biological methods. In the experiments, the doctoral students Annekatrin Richter and Jana Streubel, the first authors of the publication, as well as the Bachelor student Christina Blücher and the doctoral student Maik Reschke from the working group were able to show that anomalous repeats have two binding modes.

For one thing, they can bind to DNA in the same way as normal repeats. On the other hand, there is also the possibility that an anomalous repeat breaks out of the regular arrangement and all subsequent repeats move one position forward on the DNA. In this way, two different target sequences can be identified. Dr. Jens Boch says: "That this exception to the regular TALE structure leads to a new function is really amazing and shows how changeable and inventive nature is."

This discovery has a major impact on the breeding and selection of resistant plant varieties that can no longer be attacked by Xanthomonas bacteria. A natural mechanism of resistance is the mutation of the TALE binding sequence. Such mutations can, however, be compensated for by the abnormal repeats and resistance can thus be prevented. This discovery is also relevant for the diverse applications of TAL effectors in biotechnology, as it allows different copies of a gene in the genome to be recognized at the same time.

Article Nature-Communications: "A TAL effector repeat architecture for frameshift binding" More about Jens Boch's work in the online magazine