First Successful Genome Transplant In Bacteria

eldavojohn writes "Researchers reported the first genome transplant from one bacterium to another, thereby transforming the species from M. mycoides to M. capricolum. The research, published in Science, shows that it is possible to achieve a success rate of 1 in 150,000 genome transplants in bacteria. While this may not seem like very good odds, it's actually a major step towards synthetic life, opening up the possibility of tailoring bacteria to our needs. The article mentions medical uses and fuel production as possible applications."

A step forward, but questions remain

[rritterson]

While this work is a good step forward toward the ability to insert completely synthetic genomes into living cells, there are some questions left unanswered by the paper that demand answers before the technique can be widely adopted. First, the authors only speculate freely on how the mycoides genome made it into the capricolum cells. It's believed that perhaps two capricolum cells fuse around a mycoides genome, but no evidence to support this claim is given in the paper. Second, the authors do only a single PCR of a single gene to look for the presence of capricolum DNA in the supposed 'new' mycoides cells. This is not nearly enough testing, in my opinion, especially compared to the extensive testing they did on the cells in order to prove the mycoides DNA was present, in it's original genomic form, without insertions.

Until we know how the DNA got there and where the original DNA went, the technique will remain a laboratory curiosity and not something, for example, that can be used in any sort of medical fashion. Still, the paper is fascinating and raises some interesting philosophical questions about what constitutes the information belonging to a species.

Re:Strong containment

[TheMeuge]

What are you talking about?

The proteins made by this bacteria are still identical to the parent strain. The cell wall and membrane composition of the recipient cells also don't change. Furthermore, the makeup of all the daughter bacteria will be identical to the parent strain as well. There is nothing new about the daughter cells... and certainly nothing "synthetic" in the way you seem to understand the term.

However, in reference to the article, I wonder... given the ease of transforming bacteria with plasmids... or using recombination-based transduction with phages, what the benefit of whole-genome transfer is, other than to shorten the time required to transfer large blocks of genes.

Brought to you ny the

[geekoid]

"Ignorance breeds fear" Dept.

Re:Strong containment

[jshriverWVU]

Agree, at least in respect to what the article did. But down the road if they start doing research on creating custom DNA strands (in essense synthetic life) because it wouldn't be mapped to an identical natural strand. It can potentially be bad. This can also be very good. If they can create a custom made bacteria that attacks cancer cells, or whatever possible health benefits can be made is good. Just making the point they need to make sure they keep the research contained, especially if they start making non-naturally occurring DNA sequences.

Re:Strong containment

[ichigo 2.0]

Well no, of course not. But understanding the genome will help us develop countermeasures to evolving threats. Auditing the genes to discover flaws and exploits, if you will.

Re:A step forward, but questions remain

[stevied]

It's believed that perhaps two capricolum cells fuse around a mycoides genome, but no evidence to support this claim is given in the paper.

I haven't read the paper (not interested enough to pay £££ for it), but there was this in TFA: "They suspect that cell fusion may play an important role in mediating the transplant due to the optimal concentrations of fusion solution." I don't know whether they tried running the experiment multiple times with different concentrations (including zero) of this agent, but if so, a correlation between the concentration and the number of bacteria that survive the antibiotic would be circumstantial evidence in favour the suggested mechanism ..

Re:Strong containment

[tloh]

There are several concepts that often get muddled in discussions of genetic engineering. A couple things that need to be clarified about your comment:

    In the context of this current example. A genome transplant simply puts an existing set of genes into a microbe that didn't have it before. It isn't synthetic, it is still natural in the sense that it isn't created by man completely from scratch. So existing antibiotic would still be effective if it can target the genome donor.

    Escaping containment is probably not as big a problem as most people think. The reality of the matter is that the principles of evolution works to our favor here. When we do this kind of genetic manipulation, we create something that "works" to our satisfaction. However the methods we use are always very messy and inelegant. A success rate of 1 in 150,000 is mentioned. In order to make the process work for us, we often have to put in extra genes that help us keep track of the bacteria but does nothing to help the microbe live and survive. Our handi-work can never stand toe to toe with nature's evolutionarily derived babies. *Those* guys have had millions(billions) of years to perfect and optimize the process of surviving (and more importantly competing) in the natural environment. Laboratory subjects like the ones mentioned in the article are grown as mono-cultures where you have bacterial medium, the microbe of interest and nothing else. They live like pampered socialites. You put them in the wild and they would completely out-competed by their natural counterparts who have better survival traits like more robust metabolic pathways to better utilize available nutrients or faster response to environmental cues. Within a couple of generations, our lab subjects would most likely be either out competed to extinction or be in such a low activity state as to be insignificant.

    So it is actually the reverse that you need to worry about. Our creation doesn't damage the ecosystem, it is the ecosystem that poses a greater danger to our interests. One of my professors gave a great example that nicely illustrates the situation. Not many people realized that without human intervention, corn can not grow. The food crop that we know as corn has been selectively breed over thousands of years from an ancestral weed that resembles wild grass. Left to itself, a corn field would simply shrivel and die because the plants have no way to disperse it's seeds. (The kernels can't jump out of the husk by themselves.)

    The thing is humans create/modify plants/animals/bacteria for specific purposes of which "natural" survivability is a very low priority. We grow corn primarily so that it can produce big meaty seeds for us to eat. But for that matter it also becomes the favorite food of many other organisms. Sure, we care about how much of the food intended for our stomachs end up in the bellies of crop pests, but the main purpose of growing corn isn't to make them vulnerable to crop pests, it is to feed us and ours.

So in conclusion, any handi-work of ours from the brilliant, but still learning minds of our smartest geneticists would more likely than not, *NOT* menace the natural ecosystem.

Re:Little do they really understand.

[SpinyNorman]

The first wetware implementations of artificial life will of course be using nature's building blocks, but you have to start somewhere. What this work provides is an "test environment" for running the artifical DNA that Venter et al are designing.

I'm sure that later (maybe within our lifetime) we'll be able to design out own life forms completely from scratch, but rather ironically intelligent design really is the hard way to do it. Nature used the dumb brute force algorithm (cf Deep Blue playing chess) of running a gazillion experiments in parallel and doing so for hundreds of millions of years ... we don't yet have the capability of exploring the search space so thoroughly, but a local exploration from a known good point (i.e. artificial DNA) is a different matter.