Scientists from the J. Craig Venter Institute (JCVI) and Synthetic Genomics Inc. (SGI) this week announced in Science their engineering of a fully synthetic bacterium to have the smallest genome of any self-replicating organism – just 473 genes (totalling 531,000 bases) – which they have dubbed JCVI-syn3.0.
“This paper signifies a major step toward our ability to design and build synthetic organisms from the bottom up with predictable outcomes. The tools and knowledge gained from this work will be essential to producing next generation production platforms for a wide range of disciplines,” said Dr. Gibson, Vice President, DNA Technologies, SGI and a senior member of the team.
In what is a tour-de-force of synthetic biology, Hutchison et al used the first synthetic cell, Mycoplasma mycoides JCVI-syn1.0 (which they had created in 2010), and multiple “design, build, test” cycles to gradually discard the non-essential genes, and reduce the genome to a minimal set.
To do this, the researchers divided the genome of JCVI-syn1.0, which contains 901 genes, into eight parts, and deleted each part in turn to see whether the resulting genome was viable. This informed which genes would go into the next build and, combined with transposon mutagenesis to systematically disrupt function of individual genes, enabled a picture of which genes were and weren’t required to be formed.
But unlike JCVI-syn1.0, where an existing bacterial genome was copied and transplanted into another cell, the genome of these minimal cells is like nothing in nature. Senior author J. Craig Venter, CEO and Founder of JCVI, says that the cell constitutes a brand new, artificial species.
While JCVI-syn3.0 is only just smaller than the Mycoplasma genitalium’s 600,000 base genome, it’s doubling time is significantly faster (3 hours versus weeks), making it much more workable as an experimental organism.
The project was not without challenges – an initial design failed to produce a viable cell, and it was only with improvements in the transposon mutagenesis method did the team identify a class of quasi-essential genes that are not absolutely critical for viability but are needed for robust growth.
Finally, the researchers reordered the remaining genes, aligning ones that work in common pathways to “tidy up” the genome, to make future research using this organism more straightforward – which will be critical for breakthroughs in fields such as cell-based production.
”This important milestone lays the foundation to rationally design and engineer bio-based production systems. For example, we see a very large opportunity to revolutionize the discovery and manufacture of life-saving medicines produced biologically, an ever increasing portion of today’s most innovative medicines” said Oliver Fetzer, SGI CEO.
A major outcome of this minimal cell program are new tools and semi-automated processes for whole genome synthesis, many of which are commercially accessible through kits, instruments and services provided by SGI.
Nevertheless, even with all these discoveries it is perhaps what remains undiscovered that is most intriguing to scientists in this field – of the 473 genes required, the function of 149 remain unknown.
Yes – despite its small size, about 17% of JCVI-syn3.0’s genome remains a black box, hinting at the presence of novel functions essential for life – and promising new insights into basic biology.