Synthetic Biology Building on Nature's Inspiration: Interdisciplinary Research Team Summaries (2010) / Chapter Skim
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IDR Team Summary 6: How can genomics be leveraged to develop coherent approaches for rapidly exploring the biochemical diversity in and engineering of non-model organisms?
IDR Team Summary 6: How can genomics be leveraged to develop coherent approaches for rapidly exploring the biochemical diversity in and engineering of non-model organisms?
Pages 53-60
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From page 53... ...
For compelling technical reasons, most molecular dissection of biological systems has focused on a bedrock group of five model organisms which include fruit flies, bakers yeast, roundworms, E coli, and mice; the vast majority of breakthroughs in modern biology has come from work on these systems.
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From page 54... ...
Key Questions • How do we identify environmental sources for metagenomics analyses that are most likely to contain organisms capable of novel biosynthetic strategies that will be of immediate value to synthetic biology efforts? • How do we identify novel synthetic and signal transduction pathways from genomic information alone even when we are not able to culture a given organism?
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From page 55... ...
• When it is possible to identify valuable biosynthetic pathways, how can the machinery responsible for this new chemistry be systematically identified, transplanted and modified to enhance synthetic biology efforts? • Are there general principles of polyculture life that can be revealed by metagenomics which will aid efforts to create robust, optimized polycultures for synthetic biology efforts?
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From page 56... ...
Metagenomics, the analysis of genetic material gathered from environmental samples rather than from individual species, has given researchers the opportunity to look beyond the petri dish, beyond culturable cells, to the immense diversity of life in the world around them. For compelling technological reasons, most molecular dissections of biological systems have focused on a bedrock group of five model organisms: fruit flies, baker's yeast, roundworms, Escherichia coli (E.
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From page 57... ...
Complicating things further, repetitive DNA sequences in a genomic sample can combine with the short read lengths generated by these rapid techniques to produce overlapping sequences that aren't actually found in nature. But developing better DNA sequencing is hardly a new idea; the search for new techniques is ongoing, and the task itself wouldn't exist without the breakthroughs that have already been made.
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From page 58... ...
One technique would be bulk geographic sampling, taking metagenomic samples across a planetary grid or taking representative samples from different ecological regions, but the team deemed such a comprehensive method impractical at best; apart from being logistically intensive, it would simply be adding to the scores of unexplored genetic data that we already have, unless these data passed through the bottleneck of wet biochemistry. The question was also raised of how useful such a program would ultimately be.
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From page 59... ...
The functions of these organisms that allow them to survive could be exploited in other organisms to allow them to survive in similar environments, and even to clean up those environments. In any case, the discussions of the IDR team touched upon many aspects of metagenomics, resulting in interesting suggestions for colleagues in synthetic biology to consider, from better database management and technology to the development of rational, inexpensive methods of targeted environmental sampling to exploit the diversity of the natural world.
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