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Riboswitch controled network dynamics

Research unit

UPR 9002 - Architecture et réactivité de l'ARN (IBMC)
15, rue Rene Descartes 67084 - Strasbourg Cedex

Group

Name: Biophysique et Biologie Structurale

Group leader: DUMAS Philippe - d.dumas@ibmc-cnrs.unistra.fr

Group leader's phone: 03 88 41 70 02

Website: Visit website

Group organization:
- Chercheurs: 4
- ITA: 2
- Doctorants: 2
- Post-Docs: 0
- Autres: 1

Publications of the team linked to the topic (3 last years):
1) KinITC: a new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry.
Burnouf D, Ennifar E, Guedich S, Puffer B, Hoffmann G, Bec G, Disdier
F, Baltzinger M, Dumas P. (2012)
J Am Chem Soc., 134(1):559-65.


2) Regulation mechanisms and temperature dependence of TPP riboswitches
Guedich S, Puffer B, Hoffmann G, Jossinet F, Baltzinger M, Thore S, Ennifar E, Dumas P and Burnouf D.
soumis à Nucleic Acids Research.
3)

About PhD

PhD Director: BURNOUF Dominique - d.burnouf@ibmc-cnrs.unistra.fr

Phone: 03 88 41 70 02

Junior advisor: non

Co-tutely: non

Co-Director: non

About PhD topic :

Title: Riboswitch controled network dynamics

Project: RNA is a key player in regulatory processes in all organisms, notably in the control of gene expression. Riboswitches are dynamic and modular non coding RNA, found essentially in bacteria and archae (one single class of thiamine pyrophosphate binding (TPP) riboswitch has been observed in eukaryotes yet) and control gene expression at the transcriptionnal or translationnal level. Riboswitches are also model systems to study both RNA folding and plasticity, and regulatory network organisation.
We have recently characterized the full kinetics of ligand binding and folding of two E. coli riboswitches that control two operons of the TPP biosynthesis pathway. To do that, we have developped a new analytical method that uses ITC data to derive all thermodynamics and kinetics parametersof each step of the kinetic model (Burnouf et al, 2012, JACS, 134,559. We show that the kinetics and thermodynamic parameters of homologous riboswitches are different.
The project aims at deciphering how several homologous regulatory elements with different characteristics could work together in the frame of a regulatory network, to produce an integrated response that ensure the control and stability of TPP cellular concentration. This project, connected to RNA dynamic and regulation tuning, opens to synthetic biology and bioltechnology.
The strategy aims first at characterizing the natural regulatory network of the TPP biosynthetic pathway in E.coli, by quantifying in various conditions of culture and induction, the different mRNA, proteins, substrates and products of a minimal network gathering eleven genes organized in three riboswitches controlled operons. Experimental approaches will use QRT-PCR, dPCR, RNAseq, RNA-chips and EC-MS² . These quantitative data will be integrated in a dynamic numerical simulation of the network, through a continuing dialog between biological data and in silico modeling in order to best describe the natural regulatory network. Then the natural network will be engineered to modify the riboswitches( deletion, swapping, ...)and the functioning of the variant network will be analyzed according to the same procedure. By altering the natural network, we will identify the main nodes of the system and evaluate the contribution of each regulatory component according to its dynamics properties and location within the network.

Wished skills: Interest for the proposed subject, enthusiasm curiosity and motivation, basic knowledge in molecular biology , microbiology,
biophysics.Programming skills are appreciated.

Expertises which will be acquired during the training: Molecular biology of DNA and RNA, biophysics (cristallogenesis,
cristallography, ITC,SPR,fast kinetics) structural and dynamic modeling, programming and numerical simulation