With today’s increasing demand for resources and a clear trend toward fossil-fuel free, sustainable energy, the world is looking for alternatives. An emerging modern technique that could change the way we produce resources is to use synthetic biology or hacked biology to create microbes that can work in biotechnology. This approach enables in situ alteration of the bacterial cellular machinery to generate metabolites and direct the ‘bugs’ to produce clean and cost effective molecules from renewable starting materials for various industrial or medical applications. A model organism that is currently used in initial research stages is Escherichia coli (of various strains), but the technique could be potentially extended beyond microorganisms and even beyond complex living cells.
By inserting and fine-tuning genetic information within Escherichia coli, it is possible to assemble complex enzymatic pathways for rapid and diverse chemical production. Inducible bacterial promotors, such as Isopropyl β-D-1-thiogalactopyranoside (IPTG) promoters, are commonly used to activate gene transcription, switching on engineered biosynthetic pathways.
To gain insights of the changes that occur when model organisms are altered, a holistic high-throughput omics approach (e.g. transcriptomics, proteomics, metabolomics) is often used. Untargeted metabolomics using gas chromatography (GC) coupled with high resolution accurate mass (HRAM) can track the metabolic shifts caused by promotor induction in the bacteria. In the application note, Understanding Synthetic Biology Using the Q Exactive GC Orbitrap GC-MS/MS System and High-Resolution…, a Thermo Scientific Q Exactive GC Orbitrap GC-MS/MS system was used to study such metabolic changes. This technology offers the advantages of high sensitivity, large dynamic range (to cover a wide range of metabolite concentrations), high resolution, and excellent mass accuracy that is commonly needed to detect and identify individual metabolites. Metabolites identification was simplified by using dedicated HRAM metabolomics library retention time index information, significantly increasing the confidence in compound identification, one of the most critical steps in metabolomics. These preliminary results show that that increased levels of IPTG promoted a depletion of sugars and decreased the levels of several amino acids. Sugar metabolism is needed to provide the energy for protein biosynthesis, while the reduction in amino acids highlights the demand for raw material.
Coupling synthetic biology with metabolomics is the focus of many research laboratories and although there is a lot of work ahead, examples such as this indicates that the road toward a cleaner, safer and more sustainable world is becoming smoother.