Resource allocation in bacteria

Johannes Geiselmann, Natale Scaramozzino, Yves Markowicz

For a bacterium to adapt efficiently to a changing environment, it must allocate the available resources (food) as optimally as possible. In the illustration opposite, a carbon source (S) is transformed into precursors (P, essentially amino acids) that will be used to make two types of macromolecules: the replication and gene expression machinery (GEM) and the metabolic and structural protein components (MM). Growth is maximal when the allocation of resources to the different components of the cell is optimal. We build mathematical models of this resource allocation (in daily collaboration with the Microcosm team) and test experimentally the predictions of the models (e.g. the Maximic project).
The experiments measure the behavior of wild type bacteria, but we also build very specific strains (synthetic biology), with genomic modifications for measurement (labeling with different fluorescent proteins) or behavior modification (deletion or modification of gene expression control). Thus, we have, for example, constructed a strain in which the expression of RNA polymerase is under external control. In the same strain we have introduced genes coding for the production of a product of biotechnological interest (X). We are exploring strategies to maximize the production of X.
To conduct these experiments, we have built a multiplexed mini-bioreactor system allowing to control growth parameters and to measure in real time absorbance and fluorescence spectra of the population or in single cells by cytometry. Gene expression can be controlled by optogenetics.
We not only study the optimization of growth or production of a particular strain of bacteria, but also develop cooperative systems between different species. Projects are carried out on consortia of bacteria of the same type (E. coli) or between very different species, for example in the CtrlAB. project, always in close interaction with the Microcosm team of INRIA.

Regulation of curli production and biofilm formation

Stéphan Lacour 

We are investigating the genetic determinants of curli expression and secretion.  Curli are fine aggregated fimbriae present on the cell surface of enterobacteria and responsible for substrate colonization, the first step in biofilm formation. We are completing the regulatory network controlling the transcription and translation of csg operons. In particular, we are studying the expression of the regulator CsgD, which is essential for the expression of curli structural genes (csgBA), but also for cellulose production and the repression of class 2 and 3 flagellar genes. Most importantly, we want to identify the RNA-RNA interaction that controls CsgD translation and explain temperature-dependent curli expression.


Corinne Dorel, Université de Lyon & Akira Ishihama, Hosei University, Tokyo, Japan