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Case Study: The Synthetic Yeast Genome Project – Sc2.0

Challenge: To create a functional synthetic yeast genome

Solution: Synthesis of ~10 kb chunks for the chromosome assembling

The Sc2.0 Project, led by Dr. Jef Boeke at the Johns Hopkins University (now at the New York University), is the first attempt to synthesize a eukaryotic cell genome, that of Saccharomyces cerevisiae. The goal of the Sc2.0 Project is to synthesize the entire yeast genome, which consists of 16 linear chromosomes, about 6,000 genes and a total of 12 Mb nonredundant of DNA. The synthetic yeast genome with a built-in diversity generator that will enable researchers to discover how yeast organizes genome and how genomes might be improved to create more robust organisms. This project lays the foundation for future specific purposes, such as creating new medications or biofuels.

One of the goals of Sc2.0 project is to study and test yeast chromosome structure, minimal eukaryotic genome length, and gene content. To facilitate gene rearrangement, Dr. Boeke and colleagues designed the Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) system[1]. More than 5,000 loxP sites have been introduced in the final genome, each flanking one coding sequence. An exogenous-introduced Cre expression can create innumerable unique deletions and rearrangements. With an appropriate selection system, one can easily isolate novel yeast strains that may have desired phenotypes such as better ethanol yield. Thus Sc2.0 will have potential application for industrial microbiology, and may have a big economic value in the future.

In 2011, the first designer yeast chromosome arm, synIXR, was successfully synthesized and shown to support robust yeast cell growth[2]. To construct the remainder of the synthetic genome, incorporating SCRaMbLE and other designer features, requires DNA synthesis on an unprecedented scale. To this end, GenScript has been invited by Dr. Boeke to participate in the Sc2.0, and in 2012 GenScript has volunteered to synthesize the long arm of yeast chromosome VI, which consists of a total of 170 kb of DNA. This was predesigned by JHU researchers, consisting of 17 “Chunk” fragments. Each of these fragments measures average 10 kb and the longest measures greater than 13 kb. These Chunk fragments contain multiple bi-directional LoxP sites (highly repeat sequences), many poly A sites, and one telomere. These are the most challenging DNA synthesis for any biotech companies. GenScript has done the synthesis successfully and delivered all 17 Chunk fragments to JHU within 2 months (now, the turnaround time of ~10 kb high-qualified Gene Synthesis has shorten to be within 23 days in GenScript, learn more). Later, these 17 Chunk fragments were ligated into 6 Super-Chunk fragments. Those 6 Super-Chunk fragments were introduced into the yeast one after the other, and replaced the corresponding wild-type yeast chromosome VI long arm.

Dr. Lesley Mitchell, a senior research associate of Dr. Boeke Laboratory, is in charge of chromosome VI synthesis. She spoke very highly of GenScript: “Finally, I'd like to say how pleased I am with all of the DNA GenScript has provided for this collaboration. The turnaround time on the first few fragments was outstanding and allowed me to start working on synVI immediately. Further, the quality of the DNA you've sent has been excellent. As a result, the integration of synVI is almost complete!”

By participating in the Sc2.0 Project, GenScript has demonstrated the incomparable capability in synthesizing long DNA with very high efficiency and high reliability. GenScript is proud to be the first purely commercial entity partner in the Sc2.0 International Consortium whose goal is to build a first designer synthetic eukaryotic genome with big potential economic value in the industrial application.

Further reading:

Why build a synthetic genome? Starting from scratch gives you a chance to design the genome with valuable new features you want, and get rid of evolutionary hangers-on that you don't need. Sc2.0 aims to make chromosomes:

  1. Stronger by ditching destabilizing transposons;
  2. Leaner by removing sequences that appear to be 'junk';
  3. More agile, through SCRaMbLE, a built-in inducible diversity generator that will accelerate the development of yeast strains optimized for practical uses, such as industrial fermentation of agricultural products into biofuels or producing medically important enzymes.

More information:

Reference:

Dymond, J. and J. Boeke, The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng Bugs, 2012. 3(3): p. 168-71.

peptide news book

Dymond, J.S., et al., Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011. 477(7365): p. 471-6.

 
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