How plants repair themselves
A research group at the Helmholtz Centre Berlin has found the crucial genetic switch
Plants are living things. They grow, breathe, and turn carbon dioxide into oxygen using photosynthesis. How this happens exactly hasn’t yet been researched down to the last detail. However, Gert Weber, biochemist and structural biologist at Helmholtz-Zentrum Berlin (HZB), is hot on the scent of the crucial processes in the plant genome. Together with Japanese researchers at the University of Kyoto, his “Macromolecular Crystallography” team was able to decode the three-dimensional structure of a crucial protein.
“Plants don’t have one but three genomes (which are the sum of their genetic information),” says Weber. The nucleus, which contains the blueprints for all proteins, comprises about 30,000 genes. The surrounding cell plasma contains two more smaller genomes. With about 50-200 genes each, their activities reside in the mitochondria, the cellular power plants, and in the chloroplasts, which are responsible for photosynthesis and give the plants their colour. These processes are steered by the DNA. Their genetic information is copied to the so-called messenger RNA (mRNA) which then creates the protein.
Around 450 million years ago, land plants developed a special mechanism called RNA editing, which they use to correct the messenger RNA without the genome in the nucleus having to change its blueprints. “By doing this, plants can control certain processes like photosynthesis in the chloroplasts or cell respiration in the mitochondria,” says Weber.
The important foundations for investigating RNA editing in plans were laid thirty years ago by a team led by plant physiologist Axel Brennicke, who was a professor at Free University Berlin (FU Berlin) and, from 1994, at the University of Ulm. "He discovered the whole system at the same time as two other working groups," says Weber. Mizuki Takenaka, who joined Brennicke's team as a post-doc from Japan in 2001 and is now a researcher at the University of Kyoto, also made significant contributions to this. “I have been working with him since 2010, we are friends, and he is the lead author of our study,” says Weber, who studied biology in Göttingen and got his PhD at the Max Planck Institute for Biophysical Chemistry, also based in Göttingen.
As a post-doc at FU Berlin, he started focusing on structural biology as part of the Professor Markus Wahl working group, especially on the RNA editing project. It was difficult to produce these proteins, says the 44-year-old. In 2016, he received a one-year substitute professorship at the University of Greifswald, where co-author Tatjana Barthel, now a PhD student at HZB, also became involved in the project.
Weber then continued the work at HZB. The Macromolecular Crystallography team, headed by Manfred Weiss, helped him to successfully complete the project and to have it published. Data from the MX beamlines of Bessy II revealed the structure of the so-called DYW domains, the catalytic centre of RNA editing in plants, for the first time. A domain is the smallest stably folded structure within a protein.
Studies had shown that certain proteins containing a DYW domain played a central role in RNA editing. These proteins are activated only when they have reached the mitochondria and chloroplasts from the nucleus. For the longest time, they could not be produced in a laboratory. Much like the exact structures of DYW domains, it was largely unknown how activation works.
The German-Japanese team led by Mizuki Takenaka and Gert Weber has now succeeded in solving the problem. A zinc atom at the centre of the DYW domain has a catalytic effect. Close to this, they found a structural element that is, in effect, a switch, capable of switching the catalytic function of the zinc atom on and off. These results also offer prospects for biotechnological or medical applications. They could be used to recode certain genes without changing the DNA – an advantage compared to the genetic scissors that are currently being used.
However, the structural biologist still enjoys picking up the scissors now and again. In his spare time, he likes to work in his home garden. “I am typically responsible for heavy-duty tasks like building raised beds or transporting soil,” he says, laughingly.
Dr. Paul Janositz for Adlershof Journal