The rational design of industrial production strains is carried out by applying emerging genome research technologies. High throughput sequencing, transcriptomics, proteomics and metabolomics in combination with bioinformatics play a crucial role.
Previous and Current Research
A. Pühler retired from the Chair of Genetics at the Faculty of Biology, Bielefeld University, in 2008. With a Senior Research Professorship at the Center for Biotechnology (CeBiTec), however, he continued his research at Bielefeld University. In particular, he started the Research Group "Genome Research of Industrial Microorganisms" involved in various research projects funded by the EU, the BMBF, the BMEL and industrial companies. At the moment, A. Pühler is the coordinator of the BMBF joint-project de.NBI – German Network for Bioinformatics Infrastructure and the Head of Node of ELIXIR-Germany.
Until his retirement, A. Pühler was engaged in the establishment of a nation-wide research network for the genome analysis of bacteria playing a role in agriculture, environment and industrial biotechnology (GENOMIK and GENOMIK Plus). The network, funded by the BMBF, was composed of partners from universities, research institutes and industrial companies with Bielefeld University as a center where the emerging technologies of genome sequencing and microarray analyses were available.
At the CeBiTec, A. Pühler continued to analyze genome sequences of microorganisms, plants and animals. Of biotechnological importance was a larger project with the goal to establish the genome sequence of the Chinese hamster and derived CHO cell lines. This sequencing project was conducted in collaboration with the University of Natural Resources and Life Sciences, Vienna (BOKU Wien) and the pharmaceutical company Novartis, Basel.
The research group of A. Pühler is currently involved in two industrial projects dealing with the bacterial production of acarbose and xanthan. Acarbose is a medical compound synthesized by Actinoplanes sp. and produced by Bayer AG, Wuppertal. The substance is used for the treatment of Diabetes mellitus type 2. Xanthan, produced by Jungbunzlauer AG, Wulzeshofen, Austria, is an exopolysaccharide synthesized by Xanthomonas campestris pv. campestris. It is used as a thickening agent for various purposes. Both research projects, well equipped with postdocs and Ph.D. students, use omics technologies to unravel the transcriptional regulation and to improved product formation in production strains. Both industrial projects are carried out in double supervision, in case of Actinoplanes research together with J. Kalinowski and in case of Xanthomonas research together with K. Niehaus.
Since several years, A. Pühler and A. Schlüter, member of the research group, are busy with the analysis of microbial communities residing in industrial-scale biogas production plants and agricultural soils by metagenomics, metatranscriptomics and metaproteomics techniques). Corresponding projects were and are funded by the European Commission (in the frame of the Horizon 2020 initiative), BMBF, BMEL and in cooperation with the DOE Joint Genome Institute (JGI), Walnut Creek, California, USA.
Future Projects and Aims
The industrial projects for the production of acarbose and xanthan will be continued. The aim of these two projects is to enhance the production of both biosubstances by employing omics technologies.
Also the metagenome analysis of the microbial communities of biogas production plants is ongoing. The interpretation of metagenome- and metatranscriptome data depend on the application and advancement of diverse bioinformatics tools. Therefore, this type of work is performed in close cooperation with A. Sczyrba from the Computational Metagenomics group of the CeBiTec.