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Genome vagabonds

The genome never stays the same but is constantly undergoing changes. Specific, mutation-inducing genes, known as mobile DNA elements, developed very early during evolution. These short DNA sequences are able to change their position in the genome and mobilise entire gene groups as well as switch genes on and off. Professor Bodo Rak and his team in the Department of Molecular Genetics of Bacteria at the University of Freiburg are investigating the effect of mobile DNA fragments on the evolution of Escherichia coli bacteria.

In many cases, mutations are fatal for organisms. However, sometimes they can also create new survival strategies, which could be beneficial in a constantly changing environment. It is therefore a matter of controversy whether the genome harbours mechanisms that can induce mutations. During evolution, short DNA fragments developed that propagate by inserting copies of themselves at different places in the genome. Such mobile DNA elements, also known as ‘jumping genes’ or ‘selfish genes’, move around in the genome potentially disturbing the function of other genes at the place where they insert. “But they can also have positive effects,” said Prof. Bodo Rak of the Department of Molecular Genetics of Bacteria at the Institute of Biology III at the University of Freiburg.

A switch for the metabolism

Rak and his team are investigating a mobile DNA element in Escherichia coli which affects the metabolism of organic molecules known as ß glucosides. Representatives of this substance class are produced by plants to fend off bacterial intruders. Therefore, E. coli bacteria do not take up or metabolise such toxic substances. However, occasionally a jumping DNA fragment will induce a mutation in the bacterial genome and change this ß glucoside abstinence. In consequence, the bacteria produce proteins that take up ß glucosides via the bacterial membrane and degrade them. The chemical degradation of the ß glucosides also leads to glucose, which the bacteria can then use as a source of energy. If the available ß glucosides are examples of the non-toxic representatives of this substance class, then the bacteria will survive and even proliferate better than their competitors.
Prof. Bodo Rak’s team uses specific media to quantitatively visualise the switching on of certain metabolic pathways through a mobile DNA element (red areas within the colourless bacteria colonies, right). The colonies on the left lack the mobile element and do not switch on the metabolic pathway under investigation. (Photo: Workgroup Prof. Bodo Rak)
Structure of the mobile DNA element IS150 investigated by Rak’s team (Photo: Workgroup Prof. Bodo Rak)
“The mobile DNA element under investigation is an integral part of the E. coli genome,” said Rak. “It works like a switch that activates the ß glucoside metabolism.” And since this switch does occasionally have an evolutionary advantage, it was able to establish itself in the E. coli genome and is transferred from one E. coli generation to another.

Accelerated evolution

Mobile DNA elements occur in the genomes of all organisms. Twenty mobile element families are known in bacteria and each of them has up to 100 representatives. They ‘jump’ to different locations in the genome, affect different genes and display different degrees of activity. How is their behaviour regulated? Why does a specific mobile element insert in a particular location of the DNA and not in another? “We still lack information that would enable us to answer these questions satisfactorily,” said Rak adding that, “we are hoping that our experiments will come up with detailed information soon.” However, many researchers all over the world are working with mobile elements and have already discovered another aspect of their behaviour: In bacteria, mobile elements accelerate evolution by changing the genome of individuals as well as by mediating changes between different bacterial cells.
Mobile DNA elements can also be exchanged between two bacteria. They leave the bacterial genome and insert into ring-shaped DNA structures known as plasmids. Many bacteria have such plasmids in addition to their main genome. These plasmids, including their freight, are transferred from one bacterium to another by way of a bridge that forms between the bacterial membranes. In the new bacteria, the mobile DNA elements leave their plasmid vehicle and insert into the new genome. During this process, the mobile elements might have taken along an intact gene of their original host by copying it and excising it from its original location.

A huge gene building set

This might occasionally pose problems for human beings, for example when the transferred gene mediates resistance to antibiotics. As bacteria can exchange this gene among each other, antibiotics will soon lose their effect. However, the bacteria benefit from the exchange. Similar processes therefore happen very frequently, bacteria are constantly changing their genome, taking up useful genes and discarding useless ones. “The world of bacteria is nothing more than a huge building set of genes that are continuously rearranging autonomously,” said Rak. “Many combinations are tried out, some combinations work well and others turn out to be useless.” And mobile DNA elements ensure that the ‘bacterial construction site’ is kept going.

mn – 26th May 2008
© BIOPRO Baden-Württemberg GmbH
Further information:
Prof. Dr. Bodo Rak
University of Freiburg
Institute of Biology III
Molecular Genetics of Bacteria
Schänzlestrasse 1
79104 Freiburg i. Br.
Tel.: +49-(0)761/203-2729
Fax: +49-(0)761/203-2769
E-mail: Bodo.Rak@biologie.uni-freiburg.de
Website address: https://www.biooekonomie-bw.de/en/articles/news/genome-vagabonds