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Molecular Genetics

How to Counter Resistance at the Root

The exchange of genetic material between bacteria is partly what enables them to develop new resistance to antibiotics. Researchers at the Pasteur Institute and CNRS reveal the importance of the 3D structure of the DNA sequences involved.



© D. Gopaul/Institut Pasteur

Model of the integrase tetramere (green and purple) around two DNA double helices (orange).



Bacterial resistance to antibiotics is not a novelty. Untamed strains started appearing in the 1940s, when antibiotics started being used massively. Phenomena such as incorrect diagnosis, incorrect prescription and indiscriminate self-medication have worsened the unavoidable problem of increasing resistance.

So far, the strategy to fight drug resistance has been to create new families of antibiotics. The latest to date, Vancomycin, is considered “the antibiotic of last resort,” though cases of resistance have already been reported in the United States. “Bacteria develop their weapons eventually, so we know in advance that it's a lost battle,” says Paris-based researcher Deshmukh Gopaul.1 “This is why we have to change our approach and try to understand how resistance develops way upstream.”

In environments where microorganisms mingle closely–for instance in our own intestine–genetic information can be exchanged between very different strains of bacteria. This is how a bacterium sensitive to a certain antibiotic can acquire resistance.

It is by understanding the mechanism of this genetic acquisition that the teams of Gopaul and Didier Mazel2 hope to discover new ways of controlling antibiotic resistance. More precisely, they are studying how mobile units of extra-chromosomal DNA called “integrons” are transferred, recognized, and exchanged between bacteria. Integrons can carry several genes simultaneously–genes often implicated in adaptation, resistance, and virulence.

In their recent study published in Nature,3 the researchers used crystallographic measures to explore a hypothesis put forward in earlier studies which focused solely on genetic analysis. The theory stipulates that it is by acquiring a certain tri-dimensional structure that different sequences of an integron's DNA (called attC sites) are recognized by the host's integration tool–the integrase enzyme. This integrase, which recognizes, integrates, but also excises DNA, is fundamental for the exchange of genetic material.

“The basic startling question was to figure out how this one single enzyme, which belongs to a family that usually recognizes very specific sequences of DNA, can be responsible for the exchange of such a wide variety of genetic information,” Gopaul explains. “We were able to confirm that it is by recognizing a structure, rather than a certain sequence, that the enzyme acts.”

What the researchers observed is that the integrase (a protein made up of four identical subunits) actually recognizes extra-helical bases–ones that do not pair up with the other strand–inside the attC. While two of the enzyme's molecules are involved in the recognition of these bases, the other two cleave at a specific site on the DNA backbone. This division of labor thus leads to the excision of the single stranded gene, which can then be “captured” by another integron.

The next step towards containing resistance development will be to find molecules that might be able to inhibit the enzyme's action, and therefore block the exchange process at its root.


Clémentine Wallace


Notes :

1. Biologie structurale et agents infectieux (CNRS / Institut Pasteur joint lab).
2. Génétique des génomes (CNRS / Institut Pasteur joint lab).
3. D. MacDonald et al., “Structural basis for broad DNA-specificity in integron recombination,” Nature. 440 (7088): 1157-62. 2006.

Contacts :

> Deshmukh Gopaul
> Didier Mazel


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