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In Becker et al (2011), the authors increase the expression of several genes through different methods. For some genes (e.g., lysA, ddh), they achieve overexpression by integrating an additional copy of the gene and its flanking regions. On the other hand, for other genes (e.g., lysC, dapB, fbp, and the tkt operon) they take another approach and instead replace the native promoter with a strong constitutive promoter (Psod or Petfu).

Is there an advantage of one technique over the other? Why was one technique preferred over the other one for certain genes?

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Modifying promoters can give finer, more targeted control of expression than changing copy numbers. In the paper you referenced, for the ddh gene, it sounds like they just wanted to boost production of that protein, so making a second copy made sense. But with some of the other genes, they wanted to alter metabolite fluxes through a more complex pathway. Copying a whole operon would not achieve this, because then you would just get two pathways doing the exact same thing. But even copying the one or two genes in the operon that you want to investigate might change their relation to the other genes in the operon. Bacterial operons are generally organized such that the genes for the transcriptional regulators are located adjacent to the genes they regulate. This proximity is necessary for the proper functioning of the operon, and if you copy a gene, depending on where you put the copy, it may not function as it usually does. In these cases, it's better to mess with the promoters because you can leave the organization of the operon largely intact.

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