Sc2.0
From SC2.0
The synthetic yeast genome project WIKI
Contents |
Introduction
Welcome to Sc2.0, the synthetic yeast genome WIKI.
This is a forum for engaging the yeast and synthetic biology communities in a new initiative to synthesize yeast chromosomes, and eventually, the genome, from the “bottom up”, and, to get your suggestions on how to design yeast 2.0. An important aspect of this will be to leverage the formidable collective knowledgebase of the yeast and synthetic biology communities. We are creating this as an open-source public resource; hence this WIKI.
This will be a costly project and at current prices, this project can only be done once, so we seek your help to do it right the first time and learn the maximum from this adventure. We specifically solicit advice and proposals on design principles, proposed alterations, phenotype monitoring, safety issues and relevant software/software development. At this point we are relatively committed to a “bottom-up” strategy because the proof of principle has been done and it seems straightforward. Help us make this project a community showpiece by contributing your ideas! All serious proposals will be considered; if your proposals are implemented, you may be asked to participate directly.
Goals
Main article: Goals of the Synthetic Yeast Project
A few of the main goals of Sc2.0, the synthetic yeast genome project, are outlined here.
Why Yeast?
S. cerevisiae is the organism of choice for these studies because the genomic and related resources that are available are, quite simply, better than for any other organism on the planet. There are eukaryotes with smaller genomes, to be sure, but the extent of knowledge about these species pales by comparison to S. cerevisiae. This offers the opportunity to bring to bear the extensive universe of yeast systems biology information to the design of chromosomes for the organism. Undoubtedly the synthetic yeast will differ from the native organism, and the multitude of genetic assays available for the organism can be used to understand any phenotypic differences that might be observed.
Design Principles
Main article: Design Principles
Perhaps the single most difficult and controversial aspects of the project is deciding exactly what to make. Some basic design principles, such as not making changes deemed too "risky" are outlined here. We want a live yeast at the end of the day!
Basic Methodology
Main article: Methodology
A "bottom up" iterative strategy in which 30-120 kb segments of synthetic yeast DNA are incorporated into the yeast genome by homologous recombination, a process which occurs very efficently and accurately in S. cerevisiae, is outlined here.
Proposed Alterations
Main article: Alterations to wild type yeast
We will introduce rather conservative changes to the genome sequence, initially deleting or relocating genomic features using strategies we feel, from first principles, are unlikely to reduce fitness significantly. At the same time, we will be introducing site specific recombination sequences, allowing subsequent in vitro evolution of new yeast strains based on the synthetic progenitor. This opens up a whole new dimension of not just one synthetic genome but expands this to the analysis of whole populations of synthetic genomes for future studies. The basic approach will be to flank the coding regions we deem “potentially dispensible” with site-specific recombination sites, allowing in vitro evolution to “tell us” what is in fact dispensible when, at some point in the future, we transiently express the appropriate recombinase and select for the survivors. We have also developed a microarray strategy that will allow us to easily detect which regions of the genome have been deleted in such survivors, allowing a general exploration of the limits of chromosome structure, the deduction of minimal eukaryotic genome structures and gene/feature adjacency rules in genomes to be deduced. In this section, we list the major changes already planned for in Sc2.0. Click on the subheadings to get into the details.
- PCRTags
- Telomeres
- Transposable Elements
- tRNA genes
- Introns
- Genes unnecessary for laboratory viability
- Recoding Strategies
- Incorporation of site-specific recombination sites
Related Technology
Main article: Synthetic Technology
- PCRTag microarray
- Evolution experiments
- Other site-specific recombination strategies
Phenotype Monitoring
Main article: Phenotype Monitoring
Making sure that incorporation of synthetic segments has not made profound changes to yeast growth is important. The simplest strategy is monitoring colony size, but some other ideas are outlined here.
Software Development
Main article: Software Development
The vast number of sequence changes must be made systematically and documented as the project proceed. Also, a system is required to keep track of many versions of the genome sequence as it is designed. Special software is required for the project and is described here.
Safety Issues
Main article: Safety Issues
Safety is a major concern of the Synthetic Biology community. While yeast is generally regarded as safe and consumed by billions of humans daily, we take safety concerns seriously in the project and will consider any reasonable request to incorporate safety features into Sc2.0
Frequently Asked Questions
Main article: FAQ
Teams and Advisors
Main article: Teams and Advisors
Sponsors
Main article: Sponsors
The National Science Foundation
Other Synthetic Projects
Main article: Notable Links
