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Artificial Life

Story location: Home / science /
07/Nov/2011

Last year the Craig Venter Institute announced that they had created an artificial bacterium. I thought I should follow up last months discussion of the Origin of Life with an overview of the claims, even though it is now considered 'old news' now.

Traditionally, genetically modified organisms (GMOs) are created by taking the DNA from an existing organism and identifying the gene responsible for a particular behaviour. In the most widely publicised cases, this has involved taking crop plants and adding genes from other species to add resistance to pesticides or to make the plant create an insect-repelling chemical.

DNA

DNA is a double-stranded molecule which means is consists of two polymers held alongside each other by Hydrogen Bonds, which are bonds between Hydrogen atoms and either Oxygen or Nitrogen atoms and are weaker than those which hold molecules together. The individual units of DNA are the four 'Bases': Adenine, Cytosine, Guanine and Thymine. The two strands of DNA line up with the bases paired off in a specific manner: a Cytosine always bonds with a Guanine and a Thymine always bonds with an Adenine.

A typical bacteria (for example e.coli) DNA contains around 4-5 million of these base pairs (bp) and contains around 4,000 genes. The function of most of these genes is known (or at least suspected), and like parts in a typical machine, some of these genes are essential for survival (such as ones which control essential cell functions) while others appear to be less important and may only be required under unusual circumstances (such as genes which allow bacteria to adapt to different food sources or which change behaviour when toxins are detected). Still more genes appear to serve no useful purpose or may be duplicates of existing genes.

A Less Than Minimal Genome

The goal of the artificial genome project was to create a minimal genome which contained only the essential genes. The e.coli genome is quite large but there are bacteria with much smaller genomes, such as Mycoplasma genitalium. This actually has the smallest genome of any non-symbiotic bacteria at only half a million base pairs and around 520 genes. This was the original target of the experiment and the researchers wanted to determine which of its genes were essential for growth under laboratory conditions. They made mutations where some of the genes had been disrupted but ignored genes where the function was already known to be essential. The bacteria has 480 genes which produce proteins and all but 100 of these appeared to be essential. The functions of some of the essential genes are still unknown.

Unfortunately, m.genitalium grows very slowly so the lessons learned from that were applied to other mycoplasma bacteria. The DNA they finally used was from m.mycoides which has a genome roughly twice the size.

Assembling the Genome

The new artificial genome would contain all of the essential genes without any of those considered to be unnecessary (or at least, not critical for survival in the well defined laboratory conditions). The sequence was split into shorter fragments of around 1000bp and each of these fragments was manufactured from individual bases. These shorter lengths were combined together in a series of steps to ultimately produce the full length DNA. This results in DNA which should contain sufficient genes for a viable cell, but which was made artificially instead of being assembled from fragments obtained from existing cells.

This new DNA also contained some 'watermark' regions to help identify the bacteria as containing the artificial DNA.

The Next Step

The only artificial part of the cell was the DNA, and that was build based on an existing genome, so the cell cannot really be described as truly artificial. It is still a major accomplishment to actually manufacture an entire chromosome since nothing on that scale had been achieved before.

All of the cellular machinery was already in place. Plain DNA on its own is useless and needs to be within a cell before it can perform any functions.

[This is the reason why viruses cannot function outside a cell and need to infect a host in order to replicate - a virus is typically composed of a strand of DNA (or the related RNA) enclosed within a protein shell. The shell is designed to both protect the contents and to help trick its way into a cell. Once inside, the cells DNA replicating machinery is co-opted to manufacture additional copies of the virus]

To make a truly artificial cell, there need to be structures in place to manufacture proteins from the templates present in the DNA (using processes called Transcription and Translation). If the cell is to be able to reproduce then there needs to be a method of duplicating the DNA and partitioning the new DNA and any important proteins and cellular machinery into two halves of the cell before it splits. All of this is complicated and not fully understood.

A truly artificial genome would also need to be written 'from scratch' instead of being assembled from pre-existing components. This is also beyond current abilities since we don't understand the functions of all the essential genes.

In summary, we are still a long way from being able to manufacture life from first principles. At the moment, nearly all of the stages currently require borrowing parts of existing cells. Back in the 18th century, it was generally believed that 'Organic' chemicals based around carbon chains could only be produced by living organisms, hence the name. At the moment we are still at that stage regarding living cells. The hurdles to artificial life are much greater than those to manufacturing chemicals but eventually they will be solved one at a time. It may take decades or even hundreds of years, but it is likely to be cracked eventually.

References

Essential genes of a minimal bacterium, Glass et.al, PNAS, 10 January 2006, vol. 103, no. 2, pp425-430

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome, Gibson et.al, Science, vol. 329, 2 July 2010