Synthetic organelle in E. coli

Funded PhD position: Phase separated RNA-based synthetic organelle in E. coli

This PhD project is selected and funded by the EU COFUND "4IMPACT".

Fellowship - Deadline April 5th

The fellowship includes:

  • Duration of 42 months (unlike usual fellowships that last only 36 month)
  • Funding approximately 20% higher than the usual salary.
  • Stay (secondment) of at least two months in the lab of Prof. Barbara Di Ventura, University of Freiburg (see exquisite profile below)
  • 2 500 € support for this mobility

Eligibility: MSc degree or equivalent, <1 year spent in France in past 3 years

Candidature: Please contact ariel.lindner@cri-paris.org asap if interested to candidate, sharing your CV and a stating why you are interested in this project. Deadline for application April 5th.

We believe in community diversity as a driving force of excellence. Therefore, we strongly encourage members of underrepresented groups to apply.

Background

In cells, biochemical processes often require spatial regulation and specific microenvironments to work efficiently. The efficiency of metabolic pathways is limited by short-life time of intermediates, their toxicity and diffusion in as much as by competing pathways1. Evolution has selected a solution to these challenges in a divide-and-conquer manner: intracellular compartmentalisation (e.g., eukaryotic organelles). This inspired research to rationally design synthetic counterparts for distributing the cost of metabolic pathways’ heterologous expression, compartmentalize competing cross-inhibiting pathways, and to engineer expanded metabolic capabilities to help counter real-world sustainable development challenges in energy (e.g., fuel bioproduction), health (e.g., novel antibiotics) and environmental remediation (e.g., water detoxification). Yet, current approaches fall short of robust, modular solutions for generic use in complex metabolic pathway engineering.

The rather general lack of organelles in bacteria was only partially met with various synthetic efforts, relying on: (I) lipid, protein, RNA (our work)) or DNA-based scaffolding of multiple components; (II) bacterial protein-shelled microcompartments (e.g., carboxysomes); (iii) liquid-liquid phase separated (LLPS) droplets in natural systems, made by fusing intrinsically disordered proteins with proteins of interest. We recently discovered, as part of our iGEM team work, phase separation in E. coli using CAG triple-ribonucleotide (rCAG) repeats, in absence of human protein factors. We transformed this initial observation into a modular Transcriptionally Engineered Addressable RNA Solvent droplets (TEARS, see scheme) that can recruit, via RNA-aptamer binding adaptor protein multiple proteins, enabling switch-like shunting of deoxyviolacein metabolic flux, sequestering lycopene metabolic enzymes, and clustering of α-complementation of β-galactosidase mutants for growth rescue. This work, publicly available on Bioarxiv11, is in final revision for Cell journal.

Key References (our work in bold)
  1. Alam, M.T. et al Ralser, M. Commun. 2017, 8, 1–13, doi:10.1038/ncomms16018.
  2. Martin, W. Trans. R. Soc. Lond. B Biol. Sci. 2010, 365, 847–855, doi:10.1098/rstb.2009.0252..
  3. Myhrvold, C.; Polka, J.K.; Silver, P.A. ACS Synth. Biol. 2016, 5, 1396–1403, doi:1021/acssynbio.6b00141.
  4. Dueber, J.E. et al Nat. Biotechnol. 2009, 27, 753–759, doi:1038/nbt.1557.
  5. Delebecque, C.J et al . Science 2011, 333, 470–474, doi:1126/science.1206938.
  6. Conrado, R.J. et al. Nucleic Acids Res. 2012, 40, 1879–1889, doi:1093/nar/gkr888.
  7. Parsons, J.B et al. J. Biol. Chem. 2008, 283, 14366–14375, doi:1074/jbc.M709214200.
  8. Dzuricky, M et al. Nat. Chem. 2020, 12, 814–825, doi:1038/s41557-020-0511-7.
  9. Jain, A.; Vale, R.D. Nature 2017, 546, 243–247, doi:1038/nature22386.
  10. Team:Paris Bettencourt - 2017 http://2017.igem.org/Team:Paris_Bettencourt
  11. Guo, H.;, …, Lindner, A.B. 2020 Biorxiv, doi: 10.1101/2020.07.02.182527v2 (Cell, in revision)
  12. Weber et al., Nat Chem Biol, 2019; 15(11):1085-1092)
  13. Degen A, ..., Di Ventura B. 2019 Sci Rep., 9(1):5119. doi: 10.1038/s41598-019-41492-8.

Collaborator: Prof. Barbara Di Ventura, University of Freiburg - description

I lead the Molecular and Cellular Engineering lab, located at the Institute of Biology II at the University of Freiburg. The lab consists of two very spacious rooms, a cell culture room, a microscopy room (equipped with two Zeiss microscopes: a wide-field and a confocal), and a cold room. My lab is equipped with several high-end devices, such as the Typhoon gel scanner (with 5 lasers), two Lionhearts microscopes for long-term imaging, a single-cell western blot device, the NGS Biorad protein purification machine as well as many PCR machines to make the heavy cloning we perform possible.

I am the coordinator of the BIOSS “Re-building and biotechnology”, thus my lab is also extremely well-connected to the BIOSS and can use the devices of the Signaling Factory as well. Finally, on campus, we have access to various FACS machines and other state-of-the-art microscopes. Freiburg university is renowned for being a hub for synthetic biology within Germany, with a particular focus on optogenetics, which is a very strong component of the new cluster of excellence CIBSS. My lab is active for years in the field of synthetic biology in general and optogenetics in particular.

I have just obtained an ERC Consolidator grant to establish a novel cancer therapy with synthetic biology tools. Thus, the student will be coming into a very lively environment. Regarding the specific topic of the project, we have been working on the engineering of non-ribosomal peptide synthetases since 2013, thus we have acquired through the years a strong expertise in this field. The student will be integrated in all lab activities; therefore, he/she will be regularly presenting his/her results at the group meetings and will participate in our journal club. The student will moreover have the opportunity to attend other interesting seminars on campus. My group holds a monthly joint group meeting with the Weber and Köhn groups, thus the student will also be exposed to a larger group of scientists.