Synthetic Biology Interdisciplinary Challenge 6
How can genomics be leveraged to develop coherent approaches for rapidly exploring the biochemical diversity in and engineering of non-model organisms?

Challenge Summary
The spectrum of biological organisms on earth provides an extraordinary repertoire of biochemical synthetic and signal processing systems that can be borrowed intact or modified to accomplish synthetic biological goals. Such efforts depend on a detailed understanding of the reactions that an organism carries out as well as the molecular players (e.g., proteins and metabolites) responsible for conducting these reactions. 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, round worms, E. coli, and mice- the vast majority of breakthroughs in modern biology has come from work on these systems. There are a few other organisms like arabodopsis (mustard weed), zebrafish, and the frog Xenopus laevis. However, it requires a huge investment of time and resources to turn a wild organism in to an experimentally tractable system, so researchers naturally try to get the most mileage out of the model organisms we already have. While understandable from a practical point of view, this focus comes at an enormous cost, as many of the most desirable reactions are not found in the common model organism. For example, none of the “big five” are able to directly harness energy from light through photosynthesis.  Yet photosynthesis is the keystone of biofuels efforts.

The emerging field of metagenomics promises to help overcome this limitation and allow us to better exploit the full biological diversity of the world we live in. Metagenomics takes advantage of the revolution in DNA sequencing technologies to define genetic material recovered directly from environmental samples. Traditional microbiology studies cultivated clonal cultures. Metagenomics, in contrast, enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment. One of the first results to come from metagenomics was the realization that species identification efforts based on organisms that can be cultured had vastly underestimated the true level of biodiversity. While this conclusion is well accepted, identifying and exploiting the mass of information obtainable from these new life forms represents a major challenge and one that we are only now beginning to address.

Automated DNA synthesis has rapidly improved in fidelity, length, speed and cost.  This enables the nucleotide information from sequencing and metagenomic efforts to be converted into a physical DNA sequence without the exchange of genetic or cellular material. So-called synthetic metagenomics refers to mining of databases for functional sequences, the “printing” of this information, and screening for function.  This methodology will revolutionize enzyme/pathway/genetic circuit discovery, sequence-function mapping, and annotation of sequences.  Novel bioinformatic methods will be needed to identify genes to be synthesized and to analyze the functional information.

A number of applications could require the forward programming of meta communities.  Understanding the natural language and metabolic interdependencies of natural communities will aid in this process.  Natural systems will yield more quorum sensing circuits that enable multiple channels by which cells can be programmed to communicate.  Understanding the metabolic origins for symbiosis will enable multiple cells to be programmed to interact in a fermenter to achieve stable populations and predicable product titers.

Key Questions

• How do we identify environmental sources for metagenomics analyses that are most likely to contain organism 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? For example, comparative genomics, analysis of the environmental conditions in which organisms are found, metabolomics on polycultures.
• Are there general strategies for increasing the spectrum of novel organisms that can be cultured?
• For those organisms that can be cultured, can we build a robust toolkit for establishing the basic infrastructure needed to carryout systematic functional analyses of that organism to identify novel biosynthetic pathways? For example, rapid strategies for creating collections of tagged and deleted strains. Integrated use of microarrays, proteomics, and metabolomics.
• 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?