Science - September 6, 2012

Evolution can switch fast in bacteria

The evolution of bacteria appears to be a faster and more complex process than hitherto believed. This conclusion was reached by a talented MSc student in the course of her final research project.

The researchers analysed all the genomes of bacteria published to date.
It is something out of the ordinary for a science student to get their final thesis published, especially in an excellent journal.  Mariana Matus-Garcia from Mexico managed this feat with her research in the department of Systems and Synthetic Biology. 'She was a very good student who really put her own stamp on the project', says her supervisor, assistant professor Mark van Passel proudly. 'She has been accepted all over the place now, Cambridge, Heidelberg, but in the end she chose the top university MIT.'

Matus-Garcia's research focused on the 'on-off switch' in bacterial genes, known as the promotor. This little bit of coding for a gene determines whether it is switched 'on' or 'off'. Genes that you need for survival, for example, need to stay constantly switched on. Others are only needed if the bacterium is swimming in an acid environment or in the dark, for instance. The researchers now show that these 'on-off switches' regularly leap from gene to gene in the course of the evolution of bacteria.
 When a gene gets a new promoter it can also develop a new function. What is more, disused or 'stolen' genes can start working. If this rearrangement leads to the emergence of useful new varieties of the bacterium, evolution can select. The conclusion that this kind of leap occurs so often makes clear that there is even more variation in bacteria for evolution to choose from.
During the experiment, Van Passel analysed 1362 bacterial genomes with a computerized system. He looked for promoters that strongly resembled each other. When two unrelated genes have one of these promoters, it has probably just been duplicated. Then you need to keep an eye on whether this change cannot be explained in some other way. 'In the end we found totally identical promoters in 60 to 70 percent of cases', says Van Passel. 'In some species of bacteria there are as many as 90 to 100 throughout the whole genome.'
 That promoters make leaps across genes was known on an anecdotal level, Van Passel explains. 'A colleague once sent by post bacteria that were negative for a certain characteristic. But the gene they had immobilized turned out to keep on reactivating itself. When the people on the receiving end cultivated the bacteria, it was switched on again.' Van Passel's results now show that the process is actually quite common. Even on short evolutionary timescales and in all kinds of different species of bacteria.
 Exactly how the promoters make these leaps is largely unclear as yet. Van Passel has a few possible explanations: 'The promoters have a characteristic repeat code on their sides. This can mean that they hitch a ride on the activity of other mobile DNA.' It is also possible for duplication to take place by chance. Van Passel: 'In view of the fact that we found 4000 of them, it is not necessarily the case that they all work according to this mechanism.'
 The research, on which Bioinformatics researcher Harm Nijveen collaborated too, came out in Nucleic Acids Research at the end of August.