Biology Reference
In-Depth Information
Particularly in the field of natural product biosynthesis, combinatorial assembly strategies
can be useful not only for the optimization of a given pathway, but also for the
diversification of a given scaffold for the exploration of
derivatives. For
example, Shao and coworkers employed the DNA assembler method to rapidly modify
a PKS gene involved in the biosynthesis of the polyketide natural product aureothin,
generating a new derivative.
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Expanding this concept further, one can also envision
combinatorial assembly as a tool to diversify the tailoring enzymes frequently found
in natural product pathways, such as oxidoreductases, methyltransferases, and
glycosyltransferases. By exploiting the promiscuity of such enzymes, libraries of compounds
can conceivably be generated that feature diverse modifications of a conserved core
structure.
nonnatural
'
'
As an alternative to engineering via combinatorial assembly, many methods have been
devised to optimize a set of biosynthetic pathways through tuning at the transcriptional,
translational, and post-translational levels. Some examples of these techniques include the
engineering of promoters, ribosome binding sites, and intergenic regions, as well as the
scaffolding of biosynthetic proteins to direct metabolic flux. While many of these strategies
have been applied primarily to short pathways in proof-of-concept experiments, their
potential for significant contribution to the optimization of complex secondary metabolite
pathways is evident. For more details on these and other pathway optimization approaches,
refer to Chapter 3.
APPLICATIONS
As mentioned above, synthetic biology offers exciting techniques and fascinating strategies
for drug discovery and development. Advances in computational tools enable rapid
identification, characterization, and modification of novel genes and pathways, while
powerful experimental tools accelerate the assembly and optimization of large DNA
constructs. With the help of these tools, applications of synthetic biology have largely
focused on the perfection of the investigative nature of biology with the constructive nature
of engineering. In other words cells are becoming recast as true programmable and
customizable entities.
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Here we will discuss the applications of synthetic biology in both
discovery and production of drugs.
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Discovery of Novel Compounds
METAGENOMICS APPROACH TOWARDS THE DISCOVERY OF
NATURAL PRODUCTS FROM SOIL
Soil microorganisms are a rich source of natural products. However, culture-independent
analyses of environmental samples indicate that traditional laboratory cultivation
approaches have most likely missed the majority of bacterial natural products that exist in
the environment, as only a tiny fraction of soil microbes are cultivable in the
laboratory.
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To address this limitation, the concept of metagenomics was proposed in
1998 to analyze genes and pathways in samples obtained directly from the environment.
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Such a strategy explores the secondary metabolites produced by the large collections of
bacteria that are known to be present in the environment, but remain recalcitrant to
culturing.
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The isolation and subsequent examination of DNA extracted directly from naturally
occurring microbial populations (environmental DNA, eDNA) is the foundation of
metagenomics.
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The basic strategy is to isolate metagenomic DNA directly from soil, clone
the large pieces of DNA into a readily cultivable organism such as
E. coli
, and screen the
clones for biological activity (
Fig. 10.1
).
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Metagenomics is particularly appealing for novel
drug discovery from soil bacteria, as the secondary metabolite biosynthetic pathways
