Engineered bacteria to power industrial applications

Towards this goal, the EU-funded ST-FLOW (Standardisation and orthogonalisation of the gene expression flow for robust engineering of NTN (new-to-nature) biological properties) project focused on all the steps – starting from the assembly of DNA sequences all the way to the production of engineered bacteria.

Researchers were particularly interested in designing and engineering bacterial strains tailored for biocatalysis and environmental biosensing. In the bottom-up approach, they merged libraries of gene expression signals with suitable reporter systems and revisited some gaps in our knowledge of gene expression flow.

The consortium developed coherent vector platforms for physical/automated assembly of DNA pieces. A DNA assembly workflow called modular overlap-directed assembly with linkers (MODAL) was developed for connecting the DNA sequences of distinct functional parts.

Considerable effort was expended on the identification of mRNA motifs that influence degradation and translation of given transcripts as well as quantification of transcription rate. To this end, researchers devised experimental protocols to estimate the rate at which RNA polymerase pass through a given promoter position, envisioning the actual process within a bacterial cell.

A novel combinatorial approach was set up for engineering protease cleavage sites within a protein of interest. This would facilitate a proteomic switch capable of changing the whole metabolic regime of the bacteria under examination. The deliverables of the study included a range of bacterial strains with novel properties such as the capacity to detect arsenic.

Collectively, the ST-FLOW study transformed a set of principles for physical composition into predictable functional properties of prokaryotic systems. The generated knowledge and tools will help overcome the size limitations of natural bacteria and endow them with novel properties.

These engineered prokaryotes are expected to address key biotechnological needs as biosensors of medically-important small molecules as well as the detection of environmental pollutants.