Job opportunities

A PhD position is available at the DynAMic laboratory of Vandoeuvre-lès-Nancy.

To apply send the following pieces by 30 April 2018 to Pr Nathalie Leblond-Bourget and Dr Nicolas Soler:

– CV and covering letter
Academic records of your M1 and M2 (or equivalent) with ranking in your promotion. An average of 12/20 is required for your M2 year or equivalent (or 1st semester if current year).
– Letter(s) of recommendation
Full description of your M2 (or long-term) internship subject

E-mails: nathalie.leblond@univ-lorraine.fr, nicolas.soler@univ-lorraine.fr

Summary of the PhD topic:

State of Art: In bacteria, acquisition of new genes mainly occurs via horizontal gene transfer, which result from exchanges between bacterial cells. These transfers are responsible for the emergence of pathogenic bacteria and  antibiotic multi-resistant bacteria that are of great concern for public health. Conjugation is one of the major mechanisms of horizontal transfer within bacteria. During the conjugative event, ADN is transmitted from one donor to one recipient cell though a conjugative mating pore. Researchers of the DynAMic lab are interested in genetic mobile elements which can be transferred by conjugation and which are integrated within bacterial genomes. There are two types of such elements: the integrative and conjugative elements (ICEs) and the integrative mobilizable elements (IMEs)1. ICEs encode all the genes necessary to their transmission and therefore transfer autonomously. IMEs, encode only part of the transfer functions and must hijack the machinery of conjugation of autonomous elements to spread from one bacterium to another1, 2. In addition to genes involved in their transfer, all ICEs and IMEs also encode genes that may be important for the host adaptation to environment, such as virulence genes and resistance to different antibiotics. It is therefore important to understand how these elements disseminate between bacteria in order to develop innovative solutions to combat the spread of antibiotic resistance. ICEs and IMEs are particularly widespread in the genomes of oral and intestinal microbiota, in particular within genomes of Streptococcus strains3, 4, a bacterial genus studied in the laboratory.

Objectives: Currently, very little data are available on the mechanism of ICE transfer in Gram+ bacteria and the transfer mechanistics of IMEs is still poorly studied. The goal of the PhD work will be to answer these questions. To do this, the candidate will characterize genes and proteins of the ICESt3 conjugation module characterized in Streptococcus thermophilus, the model studied in the lab and for which transfer was demonstrated. The PhD student will generate deletion mutants for each gene of the ICESt3 conjugation module. The ability of these mutants will be tested to conjugate in order to determine which of these genes are essential for conjugation. Among genes of the conjugation module, one encodes a relaxase and another a coupling protein, 2 proteins involved in the early stages of conjugation. Through biochemical and biophysical approaches, the PhD student will study interactions of these proteins with each other and with DNA to determine how transfer of ICESt3 is initiated. In parallel, and in partnership with the CRM2 laboratory, these proteins will be crystallized in order to solve their three-dimensional structure.  The catalytic residues or the residues involved in interactions with other proteins and with DNA will be identified by a targeted mutagenesis approach will be performed on key residues and the functionality of these mutants will be tested in conjugation experiments. The PhD student will also characterize the interactions between ICE relaxase and coupling protein with those of IMEs in order to understand the initial stages of the mobilization process. Characterization of the ICESt3 conjugation pore proteins will be done. These proteins will be purified from membranes and their interactions with each other will be analyzed. In collaboration with partners specialized in structural biology and molecular modeling, the 3D structure of, all or part of, the conjugative pore will be determined.

Requested skills: The applicant should have experience in molecular microbiology and/or in protein biochemistry. An average of at least 12/20 in the first semester of M2 is required.

References:

1 Bellanger X et al, 2014.  doi: 10.1111/1574-6976.12058. Review.

2 Guédon G et al., 2017. doi: 10.3390/genes8110337. Review

3 Ambroset C et al., 2016. doi: 10.3389/fmicb.2015.01483.

4 Coluzzi C et al., 2017. doi: 10.3389/fmicb.2017.00443.

 


A permanent position for an INRA research scientist is available at the DynAMic laboratory of Vandœuvre-lès-Nancy. The research topic is on biochemistry of the conjugation machinery of Gram+ bacteria.

Applications are open until 2018 mars 5, at 17h on http://jobs.inra.fr/offers/emploi_perm

Contact : Pr Nathalie Leblond-Bourget, head of the ICE-TeA team.

E-mail : nathalie.leblond@univ-lorraine.fr. Phone : (+33) 3 72 74 51 46

The DynAMic laboratory is a research unit headed by INRA and Lorraine University. The laboratory is interested in the evolution of bacterial genomes, in gene transfers and their impact on bacterial adaptation. The successful candidate will join one of the two teams of the unit: the ICE-TeA team (ICE-Transfer and Adaptation), composed of 1 professor, 5 assistant professors, 1 INRA senior researcher, 3 technicians, and non-permanent staff (1 post-doc, 1 PhD and 1 technician at the moment).

ICEs (Integrative and Conjugative Elements) are mobile genetic elements integrated in bacterial genomes, that can excise from the chromosome and transfer by conjugation. They often carry genes conferring an adaptive potential for the host cell, as antibiotic resistance or virulence genes. ICEs are autonomous for their transfer, encoding a conjugation pore belonging to type IV secretion systems (T4SS).

The candidate will join a research axis of the team aiming at the understanding of the molecular and structural mechanisms allowing the recruitment of the DNA to be transferred and the assembly of the conjugation pore of firmicutes (Gram+), belonging to the genus Streptococcus.

The candidate will possess a robust experience in protein biochemistry. He-she will characterize the conjugation machinery of ICEs, deciphering structure-function relationships of the multiprotein complex that defines the conjugation pore. He-she will develop strategies to control gene transfers, in collaboration with specialists in structural biology and molecular modelling. As the conjugation is a transmembrane complex, an expertise in membrane protein purification would be a plus, as basis in 3D structure determination.

The DynAMic unit is located within the scientific technopole Henri Poincaré, a prosperous environment allowing multidisciplinary interactions. Several platforms are available, including the ones of the scientific federation EFABA (INRA- Lorraine University) and the biophysics platform of the Biopôle (CNRS-Lorraine University). The DynAMic unit has also developed a scientific network of local collaborators including cristallographs, chemists and computer scientists, aiming at the understanding of gene transfers performed by ICEs, and at the inhibition of these transfers. We also collaborate internationally with Elisabeth Grohmann’s laboratory (working on Gram+ conjugative plasmids), and with Gabriel Waksman’s laboratory (expert of cryoEM).