Recent results

Bacteria can grow in the presence of antibiotics

Antibiotics are molecules that are used to treat bacterial infections. They work by interfering with essential processes for the cell's growth and induce cell death. The antibiotics that we use in the clinic are often derived from natural products, isolated by studying the interactions between different microbial species. It has been proposed that bacteria and other microbes produce molecules not only to kill their competitors but also to comunicate with them. How do microbes comunicate ? What are they telling each other?

Microbes (such as yeast, bacteria, viruses, archea, paramecium, amoebas, algae...) live in complex communities that may be associated with a host such as a plant or an animal. As they grow and use the nutrients that they find in their environment they produce molecules that can be useful or even essential for other microbes' growth. However, some of these microbial communities are also in competition with each other for nutrients and other resources and therefore they have an interest in limiting their neighbor's growth, without necessarily killing them.

Bacteria have thus evolved mechanisms to continue growing in the presence of low concentrations of antibiotics, concentrations that are not high enough to kill them but still perturb specific cellular processes. It is important to understand how this adaptation takes place because antibiotic concentrations can vary in space and time within a patient's body and bacteria that have adapted to growth to sublethal concentrations of antibiotics can then have a better chance to survive as the antibiotic concentration is increased.

Gene expression regulation and DNA replication

One of our recent results come from the study of the regulation of gene expression by the DnaA protein.

The DnaA protein is responsible for the initiation of DNA replication at the origin (oriC). However it also has another job: regulating the expression of a set of genes coding for proteins important for the DNA replication process. One of these proteins is an enzyme called ribonucleotide reductase, or RNR for short, that makes the building blocks of DNA.

We purified DnaA from the other bacterial proteins and we mixed it with the DNA fragment that contains the regulatory sequence of the gene (promoter). We observed that when DnaA was at low concentrations it would bind to a small region, its specific site as determined by the DNA sequence (black boxes on the right). As the DnaA concentration increased a larger region of the DNA was bound. These are the lower affinity sites.

The DnaA protein can form multimeric structures (see the cartoon in the picture on the right) that allow it to cover large regions of the DNA and thus stop the RNA polymerase enzyme from recognizing the start site of transcription (red arrows). We have shown that in the cell sometimes there is not enough proteins to form these higher order structures. When just a few DnaA molecules bind to the higher affinity sites they can have the opposite effect on transcription, and actually help RNAP find the right spot to bind (green arrows).

We have also shown that the formation of the DnaA multimers depends on temperature, which can explain why the DnaA gene is more expressed as the temperature is decreased (dashed red line).

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