Sustainable Products With Synthetic Biology

The Western world has developed a significant dependence on petroleum, which emits greenhouse gases upon combustion. These gases are well known as being harmful to the environment, and as a fossil fuel, the supply of petroleum itself is finite—fossil fuels will run out. We’ve been aware of these problems for years; so what are we doing about it?

Well, synthetic biology techniques can be used to design living factories, which are capable of producing chemicals previously only attainable through expensive extraction, or nonrenewable resources. Amyris (Emeryville, CA) has developed genetic engineering and screening technologies that enable the modification of the molecular pathways in which microorganisms metabolize sugars. Essentially, they are designing microorganisms, primarily yeasts, to convert plant-based sugars into renewable hydrocarbon molecules.

So how did this all come about? Amyris initially developed its core technology while looking into the sustainable and stable microbial-based production of antimalarial drugs. The industrial-scale synthetic biology platform the company developed is now being applied to provide alternatives to petroleum-based products. Focusing on a class of isoprenoids, Amyris’s brand of trans-β-farnesene is a liquid long-chain renewable hydrocarbon that can be easily adapted to serve as an alternative to fossil fuel-derived products. The hydrocarbon chain can be easily modified to provide:

  • Sulfur-free renewable diesel
  • Surfactants used in soaps and shampoos
  • Fragrance oils
  • Emollients
  • Industrial and automotive lubricants.

These tailor-made hydrocarbons are biodegradable and nontoxic, don’t yield sulfur, and have lower emissions than fossil fuels.

Taking the technology to the real world

As with any new advances, they are only truly relevant if they can be applied to the real world. Amyris has done this with over 300 public buses in Brazil now running on a blend of Amyris’s renewable diesel. This number is sure to increase in the future.

In order to enable the rapid development of these biological factories for widespread use, a robust and reliable high-throughput pipeline is a must. One such method, Rapid Yeast Strain Engineering (RYSE), is an ideal solution for generating synthetic genomes. Relying on incorporating DNA linker pairs at the ends of every DNA section, RYSE enables multiple assembly methods to be used to “stitch” them together.

Through the cloning and freezing of each DNA assembly, the company has created an extensive bank, detailing sequences of known function and activity. An idea can be entered into the proprietary software, in the form of a genotype, which is then translated into the required DNA assemblies. The software can also design oligos if the DNA is not readily stored in the bank. The exact order of DNA molecules is determined and assembled using sophisticated robots. All strains built undergo high-throughput screening, where they are assayed for a variety of target molecules.

When new DNA parts are required, time is extremely critical, with the need to obtain novel genes or DNA parts in less than one week. Up to 750-bp, double-stranded, sequence-verified genomic blocks (IDT gBlocks® Gene Fragments), designed with 30–50 bp overlaps, are combined 3–6 fragments at a time with terminal primers using PCR. These parts are then further assembled, often with other genes, resulting in DNA assemblies 2–25 kb long. These are then integrated to create a new yeast strain (biological factory), which is able to metabolize plant sugars and produce renewable hydrocarbon chains.

So for all of you who are concerned that nothing is being done about the forthcoming fossil fuel shortage, have confidence—there are options in the pipeline. As with all good things, it just takes time.

Ellen Prediger is Director, Scientific Communication, IDT, Coralville, IA, U.S.A.;