Genomics for white and environmental biotechnology

We also use NGS genome analyses to characterize microorganisms for industrial biotechnology. In addition, we develop methods for the qualitative and quantitative detection of complex microbial metagenomes and transcriptomes for environmental biotechnology.

Transcriptome analyses for the analysis of active genes

We also use NGS genome analyses for experimental transcriptome analyses, for example to find out which genes of bacterial or fungal strains are active for the synthesis of desired products.

One example is the analysis of genes in the genome of Pseudozyma aphidis for the synthesis of biosurfactants. The fungus produces a unique combination of four different biosurfactant variants, each of which is suitable for different applications in cosmetics or as a detergent. Here, a cluster of five adjacent genes was identified, which contains the information for the synthesis of the biosurfactants. This knowledge provides the basis for switching off the genes for three variants in favor of a higher yield of only one variant – a prerequisite for economic use as a biosurfactant producer.   

Identification of new enzymes

Another example is an integrated approach for the identification of novel P450-enzymes with the potential for targeted conversion of fine chemicals within industrial processes. Here we have contributed to the success of the project with de-novo sequencing procedures of non-characterized bacteria and fungi followed by a functional annotation of the genomes, as well as identification of active genes via gene expression analyses.

Characterization of microorganism populations in biogas plants

Since the direct sequencing of a microorganism sample eliminates the time-consuming step of cultivation in the laboratory, even those microorganisms can be identified whose natural growth conditions can only be inadequately simulated experimentally. Biogas plants are an example of such an extremely heterogeneous microbial community with up to hundreds of different bacteria. Although biogas production is a long-established process, the microorganisms involved and their reaction paths are still largely unknown.

In various projects we focus on identifying the complex compositions and interactions of the microbial communities involved in biogas production by means of metagenome and metatranscriptome analyses using Next-Generation Sequencing (NGS). Using bioinformatics methods, we have already identified over 200 species involved in the biogas process and determined their shares in the overall biocoenosis. These insights may lead to optimized processes in biogas production through targeted manipulation of microbial composition.

Synthetic biology successfully combines aspects of engineering, chemistry, informatics and biology. Different research fields of synthetic biology have evolved over recent years. These contain, for example, the de-novo design of complete organisms, the utilization of “building bricks” that can be used to engineer tailor-made synthesis pathways for the production of platform chemicals or orthogonal biosystems that are useful tools for protein biochemistry. These orthogonal pairs can be used to generate modified, synthetic proteins.

In the Functional Genomics group, we use different orthogonal pairs to integrate synthetic amino acids, especially amino acids with photocrosslinker reactivity, site-specifically into proteins. With this approach, for example, virulence factors of the human pathogenic yeast Candida albicans are analyzed for their protein-protein interactions.

Furthermore, synthetic biology provides solutions for current challenges in pharmacy, medicine and biology.