Hamilton Smith

Synthetic Genomics: Working with Whole Bacterial Genomes


Abstract

Using a computer analogy, one can think of a cell’s cytoplasm as the hardware and the genome as the operating system. In the case of simple organisms such as bacteria, it is likely that scientists in a few years will be able to design and write new operating systems, and construct new strains of bacteria that can do useful things.
It is now possible in some special cases to take a bacterial genome sequence from a computer database, assemble that sequence from synthetic oligonucleotides, and clone it in yeast as a centromeric plasmid. The genome can then be engineered using yeast genetic tools, or it can be engineered during the prior chemical synthesis step. The engineered synthetic genome can be installed into a recipient cell cytoplasm, a process that we have called “transplantation”. Under appropriate selection for the new genome, the original components of the recipient cytoplasm are replaced in early divisions and the cell takes on a phenotype determined by the synthetic genome. The new cell now operates under the control of the designed synthetic genome. In the future, we expect that scientists will be able to construct cells that are controlled by synthetic genomes that are designed to make a variety of useful products.
As an example of the above, we obtained the sequence of the bacterium, Mycoplasma mycoides subspecies capri and chemically synthesized it in a series of steps. We started with 1100, 1kb cassettes made from oligonucleotides, assembled them 10-at-a-time in yeast to make 110, 10 kb pieces. These were taken 10-at-a-time and assembled to make eleven 100 kb pieces. These were then assembled in yeast, using the yeast’s natural recombination system. The full-sized genome was transplanted from yeast into M. capricolum, a related species, which has a cytoplasm suitable for expressing the synthetic M. mycoides genome. The resulting “synthetic” cell contains a number of designed features, but phenotypically is very similar to a wild type M. mycoides cell.
Our next step is to remove in a step-wise fashion the non-essential genes of the synthetic M. mycoides genome to produce a minimal cell. By study of such a minimal cell, we hope to gain a better understanding of the essentials of cellular life.
Recommended reading:
Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA 3rd, Smith HO, Venter JC, Glass JI. Creating Bacterial Strains from Genomes that have been Cloned and Engineered in Yeast. Science. 2009 Sep 25;325(5948):1693-6.
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010 Jul 2;329(5987):52-6.


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