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Research Summary:

Microbial genome engineering protocols

Current gene synthesis and assembly methods, combined with high-throughput multiplex genome modification protocols, open up new possibilities in microbial genome construction. However, in order to manipulate whole genomes at will, further technical improvements are needed. In the past, we have developed a set of simple tools and protocols for homologous recombination-based, precise manipulation of bacterial genomes. Currently we are adapting these methods to high-throughput protocols both for random deletion-generation and for more specific, multiplex genome modifications.

Minimizing the genomes of E. coli strains

As E. coli evolved in the intestinal tracts of animals, it has many genes that are not relevant to practical applications and some that may be detrimental. The objective is to eliminate as many of these unnecessary/unknown genes as possible to develop core-genome strains of E. coli K-12 MG1655 with robust metabolic performance. By streamlining the genome, simpler and more stable cells could be developed. We have described the deletion of up to 70 genomic segments of MG1655, resulting in a >20% reduction of the genome (Kolisnychenko et al., 2002; Pósfai et al., 2006, Karcagi et al. 2016). Currently we are pursuing additional genome reduction and optimization involving K-12 and other strains

Genome architecture and evolution

Genomes are more than their gene content. When designing artificial microbial genomes, architectural principles, such as the domain structure, the copy number, orientation, and position of genomic elements, have to be taken into account. Our genome modification protocols and reduced-genome strains provide excellent tools and platforms to construct genome variations designed to uncover these principles.