I want to design an artificial metabolic pathway in bacteria or just using responsible enzymes to produce certain products such as H2 or other biofuels. Where can I start with? Do you have some thoughts about this?
could work by stopping methanogens to exist in the pathway so H2 could be produced instead getting methane.
On of our students made this on E.Coli by inserting genes and blocking some pathways.I'll check if I can find the thesis.
Thank you very much, Dr. Zhang. I read some of those amazing papers before. As you pointed out that the "Thauer limit" is the inherent barrier for bacteria to produce H2 commercially acceptable. So that is why a lot of enzyme-based synthetic pathways have been designed and many of them do significantly improve the yield and efficiency.
For photosynthetic bacteria such as cyanobacteria, I am thinking the Thauer limit might be a less problem because the bacteria can get the external energy source, sunlight. But the problem for cyanobacteria is the low yield and low efficiency to produce H2. Maybe we can design a synthetic pathway from that photosynthetic system to improve the yield and efficiency.
You have a very genuine query. Well, to start with you select the substrates that you want to investigate and then use the database of metabolic pathways like KEGG and see how you can proceed. It is a very good database where you can virtually plot the pathway as you will be told about different steps with the types of enzymes involved. Try it, Success is guaranteed.
For commodity fuel production, the key is to reduce COST.
Re-combining multiple enzymes from one/different organisms to make a pathway/system work is the first step but not enough. It is very critical that the designer pathways should have NAD(P)H balance and ATP free or balance, since coenzymes and ATP are expensive. Another important thing to consider is how to completely use the substrate (eg., sugars) for desire chemicals as it will also increase the cost. At this point, the solution is to recycle the byproduct waste so that organic substrate can be reused and completely convert into CO2, for example. The feature of the pathway is to have a cyclic pathway design. This is why many of the natural biochemical pathways are cyclic such as TCA cycle, Calvin cycle,fatty acid biosynthesis and pentose phosphate pathway.
Zhang's papers are excellent examples for the pathway design strategy. For example, they designed a biopathway to completely oxidize one glucose into 6 CO2 and all the reducing power from glucose is extracted to make 12 H2, through a chimeric pentose phosphate pathway. Based on that design, many kinds of sugars can fit into a similar pathway to produce H2 or electricity.
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