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Impact of systems biology on metabolic engineering
Other Talks in the Series: Systems Biology
Systems biology graphical notation (SBGN)
- Prof. Huaiyu Mi
- University of Southern California, USA
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- Dr. Samik Ghosh
- The Systems Biology Institute, Japan
So my name is Jens Nielsen, and I'm going to talk about impact of systems biology on metabolic engineering. OK, so I have a background as a chemical engineer and have always been interested in biological systems, so I started to quite early to look into modeling of microorganisms. And that has then led to further also using these models for engineering these microorganisms for different kind of applications. So currently, my group is working very much on engineering yeast for production of different chemicals and biofuels. But in this context, we're using a lot of systems biology tools for analysis of yeast metabolism.
So we go to the first slide, which shows basically the so-called biorefinery concept. According to this concept, the objective is to take biomass, pre-treat that, degrade it to get sugars that can then be used by microbial fermentation to produce fuels and chemicals, as illustrated to the right. And one typically applied cell factory is yeast, and I'll come back and talk a little bit more about that. But in connection with that, the enabling technology is what we call metabolic engineering. That means that we are engineering these factories such that their metabolism can efficiently convert these sugars to these different fuels and chemicals. There are already quite a lot of processes running like this, of course, the most famous being production of bioethanol. But in the future, we are likely to see that some of these process facilities can be upgraded to produce new biofuels and biochemicals that have higher value and may be better use.
Next slide shows the typical process of metabolic engineering. So it typically starts with modeling and design. Typically, one goes in looks into metabolism and finds how are we going to change the metabolism in order to produce this new chemical compound. Then we move on to string construction. The resulting strains are characterized by fermentation. Phenotypic characterization, where we kind of narrow in and see what was the impact of these genetic modifications we introduced. Often, we combine that with a very detailed phenotypic characterization using omics analysis. This can be, for example, looking into transcription profiling, proton profiling, or metabolomics, and so on. Often when we have these data here, we need to integrate them in the context of models, and this can lead to refinement of the model and then the model can be used to further the identification of new design strategies. So this is what we normally refer to as the metabolic engineering cell factory. And what is very clear is that we have the things marked to the left here, is very much the core of what we normally call systems biology, namely, high throughput analysis and also modeling and integrated analysis of these kind of data. So traditionally, modeling has played an active role in metabolic engineering, but there are still relatively few examples where modeling has really led to the design of this. And one of the reasons of this as we go to the next slide