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Anke Becker: looking closely at biological systems

Not that long ago, it took six months or more to sequence a single gene. Nowadays, modern genomics means that it takes less than a week to sequence an entire microorganism. This development means that scientists are more interested than ever in looking into biological systems as a whole. Professor Dr. Anke Becker from the University of Freiburg is investigating how groups of genes and molecules interact with each other. She is particularly interested in the signalling interactions between symbiotic bacteria and their host plants. Besides being a biologist, she has also knowledge of the fields of bioinformatics and robotics, indispensable for researchers investigating biological systems.

Prof. Dr. Anke Becker © private

Anke Becker, born in 1967 in Bad Godesberg, has always been interested in biology, and was determined to study the subject. However, she was not interested in nature in the usual sense of the word. "I found that the biology we were taught at our grammar school in Neuss close to Düsseldorf was quite boring," recalls Becker who is now professor of systems biology at the University of Freiburg and head of a research group at the Centre for Biosystems Analysis in Freiburg (ZBSA). "I was more interested in molecular biology, a subject that was still quite exotic at the time." In order to assuage her curiosity for this subject, she decided to attend molecular biology lectures at the University of Düsseldorf. After doing her school leaving examination, the ZVS (Zentralstelle für die Vergabe von Studienplätzen - Central Office for the Allocation of Places in High Education) allocated her a place at the University of Bielefeld. "This proved to be an excellent move, although the city did not really appeal to me at first," said Becker.

Becker was interested in how the genes and molecules in a biological system, for example a bacterium, interact with each other in order to accomplish processes as complex as cell division or communication with other organisms. The University of Bielefeld, which is housed in one single enormous building, brought together a large number of disciplines as a result of their close vicinity to each other. "It was easy for biologists to attend chemistry, physics or informatics lectures, and vice versa. Interdisciplinary thinking happened automatically," said Becker. This interdisciplinarity would later become a decisive factor in her success in the area of systems biology. But her first big success came even earlier.

Haphazard finding

Alfalfa plants with symbiotic rhizobia (right) grow a lot faster than plants without the nitrogen-binding bacteria. © Prof. Dr. Anke Becker

During her doctoral thesis in the Department of Genetics at the University of Bielefeld between 1991 and 1994, Anke Becker investigated signalling molecules of bacteria that are known as rhizobia. These soil microbes live in symbiosis with plants such as alfalfa, peas and beans and help the plants to acquire nitrogen from the air. The diazotrophic (bacteria that fix nitrogen) bacteria establish inside the root nodules without being fended off by the plants. It therefore has to be assumed that the plants can differentiate between benevolent bacteria and other, potentially harmful bacteria. 

The plants also control the entire cell cycle of the bacteria and once symbiotic structures have been formed, determine which nitrogen-fixing enzymes are generated. The plants also ensure that rhizobial DNA replicates and cells do not.

Alfalfa cells with numerous small bacteroids (these are the symbiotic form of nitrogen-fixing, shown in black, symbiotic bacteria) © Prof. Dr. Anke Becker

Becker discovered a bacterial enzyme, a tyrosine kinase, which is able to modify the length of long-chain sugar molecules in the bacterial envelope that serve as recognition signals. This was the first of many enzymes discovered in this bacterium. "And it was pure luck," said Becker explaining that "the protein was in a tube that we were going to discard, but which somehow I ended up using as a counterweight in the centrifuge for a sample that I was more interested in."

Anke Becker completed her doctoral thesis in 1994 and remained in Bielefeld to continue post-doctoral research. At the time, there was a growing number of computer scientists who were becoming interested in biological data. The first projects were being undertaken in Bielefeld with the goal of sequencing larger regions of bacterial genomes. The scientists' work became simpler as more and more gene sequences became known.

Black rot disease is caused by Xanthomonas bacteria. Becker and her team are investigating the molecular and genetic interactions between host and pathogen. © Prof. Dr. Anke Becker

Becker also expanded her field of interest and started to look into molecules that are exchanged between pathogenic bacteria and their host plants. She very often had to write computer programmes for analysing, sorting and interpreting her experimental data. At the same time she also increasingly had the opportunity to work with computer scientists. The areas of genomic research and systems biology have been growing rapidly since 1994.

The disciplines become indistinct 

After a one-year stay at the Massachusetts Institute of Technology (MIT) in Boston, where she gained insights into sugar chemistry methods, Becker returned to Bielefeld where she habilitated in genetics in 2000. Another personal success followed. She was part of a team that deciphered the complete genome of Sinorhizobium meliloti, one of the first two Rhizobium sequences known. This knowledge enabled Becker to work on more complex issues. She was able to look at different genes and examine their interactions. Becker's then team was one of the first research groups to use automated methods, including microarray technology, which can be used to find out which genes are expressed at a particular point in time in a cell. Between 2000 and 2007, Becker was head of Transcriptomics and Robotics at the Centre for Biotechnology at the University of Bielefeld.

Individual Sinorhizobium meliloti bacteria under the electron microscope © Prof. Dr. Anke Becker

At the beginning of 2008, she moved to the University of Freiburg, a move that was made possible thanks to the FORSYS Systems Biology Initiative of the German Federal Ministry of Education and Research. The Freiburg Initiative of Systems Biology (FRISYS), located at the Interfaculty Centre for Biosystems Analysis, offers an excellent environment for cooperation between biologists, computer scientists and mathematicians. Laboratory automation is still one of Becker's special fields of interest. Together with computer specialists, Becker and her team of researchers are currently establishing an entire "production line", involving robots that incubate, pipette, centrifuge, shake and microscope samples in a high-throughput and highly precise manner. "Many people have asked us what we actually are - biologists, computer scientists or engineers," said Becker. "Modern systems biology has in fact become very interdisciplinary and the frontiers between traditional disciplines are gradually disappearing." In addition to investigating the signalling between bacteria and their plant hosts, Becker is also conducting systematic and genome-wide investigations on the role of small RNAs in the regulation of cell processes. She is also interested in protein-DNA interactions and the communication between bacteria in a bacterial colony.

One project, which Anke Becker is very excited by, focuses on the cell division of rhizobia. "The replication of the bacterial genome and the division of the cells is anything but chaotic," said Becker. "The cell needs to know at all times where the genome starts, where its centre is and which part has already been replicated, and where the dividing wall has to be inserted between parent and daughter cell." The move to Freiburg has increased Becker's workload as part of her research group and cooperation partners from previous projects are still in Bielefeld. "I have never travelled so much by train as I have done over the last few months," said Becker laughing, at the same time as making it clear that she is very much looking forward to her future work at the University of Freiburg and the ZBSA.

Further information:
Prof. Dr. Anke Becker
Institute for Biology III
University of Freiburg
Schänzlestraße 1
or:
Centre for Biosystems Analysis (ZBSA)
Habsburger Str. 49
79104 Freiburg
Tel.: +49 (0)761/203-97167 (ZBSA) / -6948 (Biology)
E-Mail: anke.becker(at)biologie.uni-freiburg.de

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