Saturday, July 11, 2015

synthetic genomics and genome engineering rewriting the blueprint of life


genomebiology |  Biology is now undergoing a rapid transition from the age of deciphering DNA sequence information of the genomes of biological species to the age of synthetic genomes. Scientists hope to gain a thorough mastery of and deeper insights into biological systems by rewriting the genome, the blueprint of life. This transition demands a whole new level of biological understanding, which we currently lack. This knowledge, however, could be obtained through synthetic genomics and genome engineering, albeit on a trial and error basis, by redesigning and building naturally occurring bacterial and eukaryotic genomes whose sequences are known. 

Synthetic genomics arguably began with the report from Khorana’s laboratory in 1970 of the total synthesis of the first gene, encoding an artificial yeast alanine tRNA, from deoxyribonucleotides. Since then, rapid advances in DNA synthesis techniques, especially over the past decade, have made it possible to engineer biochemical pathways, assemble bacterial genomes and even to construct a synthetic organism [1]–[11]. Genome editing approaches for genome-wide scale alteration that are not based on total synthesis of the genome are also being pursued and have proved powerful; for example, in the production of a reduced-size genome version of Escherichia coli[4] and engineering of bacterial genomes to include many different changes simultaneously [8]. 

Progress has also been made in synthetic genomics for eukaryotes. Our group has embarked on the design and total synthesis of a novel eukaryotic genome structure - using the well-known model eukaryote Saccharomyces cerevisiae as the basis for a designer genome, known as ‘Sc2.0’. The availability of a fully synthetic genome will allow direct testing of evolutionary questions that are not otherwise approachable. Sc2.0 could also play an important practical role, since yeasts are the pre-eminent organisms for industrial fermentations, with a wide variety of practical uses, including production of therapeutic proteins, vaccines and small molecules through classical and well-developed industrial fermentation technologies. 

This article reviews the current status of synthetic genomics, starting with a historical perspective that highlights the key milestones in the field (Fig. 1) and then continuing with a particular emphasis on the total synthesis of the first functional designer eukaryotic (yeast) chromosome, synIII, and the Sc2.0 Project. Genome engineering using nuclease-based genome editing tools such as zinc finger nucleases, transcription activator-like effector nucleases and RNA-guided CRISPR-Cas9 is not within the scope of this minireview (Box 1). Recent advances in gene synthesis and assembly methods that have accelerated the genome synthesis efforts are discussed elsewhere [12].