Synthetic Biology Parts, Devices and Applications

256 12 Metabolic Channeling Using DNA as a Scaffold

DNA‐binding domains consequently defines the order of the enzymes of the

metabolic pathway, which are genetically fused to the DNA‐binding domains.

The overall speed and effectiveness of reaction catalysis can be improved by

the presence of a DNA scaffold

A protein scaffold has similar characteristics to the DNA scaffold but is protein

based. In contrast to the DNA scaffold, where no natural examples are known,

protein scaffolds also occur in nature

The DNA‐target site or DNA‐binding element is a nucleotide sequence that is

recognized by the DNA‐binding domain

DNA program stands for the defined order of DNA‐target sites on the DNA

scaffold. Spacers in the DNA sequence separate the DNA‐target sites on the

DNA program, which determines the spatial orientation of the enzymes

bound to the DNA relative to each other

Substrate channeling is the transfer of a product of one enzyme directly to the

next enzyme with minimal release into the bulk solution. The result of

substrate channeling is an improved overall reaction efficiency compared to

the situations where the enzymes are randomly distributed within the

cytoplasm

The synthetic DNA‐binding protein is a designed protein that binds a prede­

fined DNA sequence. Individual modules of zinc fingers or TAL proteins are

used for the construction of synthetic DNA‐binding domains. Each module of

the zinc finger has a defined specificity for the nucleotide triplet on the DNA

molecule. Similarly, each module of the TAL protein can bind a single prede­

fined nucleotide

Spatial organization is a defined arrangement of components in space. Within

the context of metabolic engineering, this means that biosynthetic enzymes

are fixed in a defined arrangement imposed by the scaffold

The fusion protein or chimeric protein is a protein created through the

joining of two or more genes that code for individual proteins or protein

domains. In our case, this refers to the fusion of an enzyme and a DNA‐

binding domain

References

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engineering of intergenic regions in operons tunes expression of multiple genes.

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(accessed 23 March 2014).

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pubmed/17239639 (accessed 6 March 2013).

3 Bloom, J.D., Meyer, M.M., Meinhold, P., Otey, C.R., MacMillan, D., and Arnold,

F.H. (2005) Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol.,

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