Date : 22/03/2012

Laboratory
INRA MICALIS Institute team: CPE "Commensalims and Pathogeny of Enterococci" (France)
KTH Royal Institute of Technology team: Computational Biology Numerical Analysis and Computing Science (Sweden)
UMR1319, INRA
Domaine de Vilvert - Bat. 222
78352 Jouy-en-Josas
Website and Website
Main discipline : Synthetic Biology
Lab director : Stéphane Aymerich

PhD Supervisor
Francis Repoila
phone: +33 1 34 65 20 69

Subjects
1.: Bacterial gene expression control
2.: Synthetic biology/Modeling
3.: RNA metabolism

Tools and Methodologies
1.: Bacterial genetics and physiology
2.: .RNA sequencing & biochemistry
3.: Mathematical modeling & statistics

Summary of lab's interests
We are interested in the genes and genetic programs that enable the bacterium Enterococcus faecalis to colonize and live as commensal in human gastrointestinal track (GIT) during our entire life, and under certain circumstances to become a deadly opportunistic pathogen. Epidemiological studies have shown that this dual life style relies on the capacity of the bacterium to adapt to harsh environments. One major focus in the lab is the comprehensive understanding of these adaptation processes by i) deciphering regulatory mechanisms controlling them, and ii) delineating transcriptional and posttranscriptional regulons involved during these physiological changes. It is noteworthy that in contrast to eukaryotes, inferring transcriptional and posttranscriptional regulons in bacteria solely from deep RNA sequencing data (RNAseq) is, up to date, not possible without the aid of genetic data. The ambition of this project is to associate the power of statistical physics for the modeling and the analysis of systems biology to perform gene regulation studies at molecular level, even with genetically uncharacterized bacteria.

Summary of project
To undertake our comprehensive analysis, we have developed a novel RNA tagging method (Fouquier d'Hérouel et al., 2011) enabling us to distinguish each transcript in the cell as the result of RNA synthesis (i.e. primary transcripts from transcription) or RNA processing (cleavage or degradation). By RNAseq this method gives access to the primary and the processed transcriptome of E. faecalis, which for the first time in bacteria should enable to infer regulatory networks and regulons via transcriptomic studies solely. The proposal relies on i) experimental work to generate RNAseq data, and ii) computing for data analysis and modeling. It is expected that the person in charge will contribute to both aspects. To do so and fully benefit from the multifaceted competences gathered in this collaborative project, the PhD researcher will spend half time in the lab of each supervisor: at Micalis Institut in Jouy-en-Josas (advisor: F. Repoila in charge of microbiological aspects and RNA chemistry) and at the Royal institute of technology (KTH) in Stockholm (advisor: E. Aurell in charge of mathematical and computing developments). The project is made up of three parts: 1) Gauging the sensitivity of the RNAseq method by measuring variations of targeted transcript populations via known transcriptional and posttranscriptional regulators that trigger specific positive and negative effects. 2) Transcriptional and posttranscriptional regulons will be infered from variation amounts measured for each form of RNA in samples collected at various time after an environmental cue is applied to cells. Through these kinetic experiments, variations of each primary RNA will reflect transcriptional changes of the corresponding gene and each processed transcripts will unveil its posttranscriptional controls. Adaptation to bile salts and to an oxidative stress will be studied as these two environmental cues the bacterium has to cope within the host. 3) DNA and RNA analysis of promoter regions and RNA processing sites. Predictions will benefit from transcription regulators and RNase E. faecalis mutants available in the lab.

Interdisciplinarity of the project
This proposal relies on the cross-feeding of two fields of expertise: i) Biology: generating data for the project requires mastering RNA biochemistry, microbial genetics and physiology (expertise provided by INRA's lab); ii) Physics: processing and computing of the raw data from RNAseq require strong expertise in mathematics and physics, especially in statistics and systems biology (expertise provided by KTH's lab). This multidisciplinary project will require a good understanding of RNA biophysics and chemistry, and the development of mathematical models, hence a solid background in both domains in indispensable. Aurell 's group is part of the European Scientific Coordination Network (GDRE) "Evolution, Regulation, Signalling" directed by Prof M Vergassola (Institut Pasteur, URA 2171) which will organize yearly workshops/conferences over the time-frame of this project, and where the PhD student will attend. As part of the training the PhD researcher will be strongly encouraged to apply for fellowships to cover mobility expenses. In addition, this proposal has been submitted to a "Contrat Jeune Scientifique" funding from INRA. If granted, the young researcher will be funded to attend international meetings in order to strengthen his/her professional network and will receive 2 years postdoctoral fellowship.

Do you have an available funding for this project ?
As INRA laboratory, a "Contrat Jeune Scientifique" application has been submitted. Expenses for experiments will be taken from an ANR grant submitted. Application to EMBO and FEMS will be submitted to cover mobility expenses. Aurell's group has support from other sources for the computational and data storage tasks in the project.