Research

The main objective of the laboratory is to obtain an extremely detailed understanding of model microorganisms that would allow, in combination with the development of new genome engineering methods, subsequent programming of cells to perform various tasks. The potential benefits of this approach are many, from the advancement of fundamental knowledge to possible applications in medicine, environmental remediation and clean energy production, among others. Many experts believe that synthetic biology can answer various critical challenges humanity is currently facing and profoundly transform the twenty-first century.

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Source: www.news.mit.edu (Liang and Yan Liang Tong)

We are also interested in genomics, in order to better understand certain diseases. The methods we developed allow us to sequence nearly complete genomes from a single cell, without any laboratory growth step being required. This approach is called to transform our understanding of many diseases such as cancer or infections caused by microorganisms or viruses difficult to cultivate under laboratory conditions.

1. Reduction of Mesoplasma florum genome to develop a cell chassis for synthetic biology

Mesoplasma florum is a microorganism belonging to the Mollicutes class (bacteria having mesoplasma_florumno cell wall). The genome of the L1 strain was completely sequenced, and is relatively small (794 223 base pairs compared to 4.6 Mb for Escherichia coli K-12 MG1655). M. florum also has many features that make it attractive as a base for a cell reduced chassis: the doubling time is fast (~41 minutes at 34°C), which provides a culture with more than a billion cells per milliliter in less than a night, it is a non-pathogenic bacterium, and it uses an alternative genetic code, which ensures that in the event of lateral transfer of genes of the bacterium to another, the proteins cannot be expressed correctly if the recipient bacterium does not use the same genetic code.

Several approaches are being used in our laboratory to reduce the genome of M. florum. First, the combination of the data from a comparative genomic analysis and a transposon mutagenesis experiment allows the identification of conserved and essential genes of this bacterium. Concomitantly, the complete genome of the bacterium was cloned in yeast, and a genome transplantation protocol was developed. This method allows utilization of the many genome engineering tools available in yeast to modify and reduce the genome of M. florum.
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Source: onlinelibrary.wiley.com

A deeper understanding of M. florum will also be obtained by performing an experimental annotation of its genome, more precise and more comprehensive than the usual predicted models. This annotation will be generated by integrating several layers of information collected using high-throughput technologies such as DNA-seq, RNA-seq, ChIP-exo, mass spectrometry, etc. These comprehensive datasets will be generated under standardized growth conditions to increase the reproducibility of the method.

When enough data is collected, reducing and modifying the genome of M. florum could be done with several approaches, including the use of transposons and CRISPR-Cas9 system, for example. A well-characterized and reduced bacterium will considerably facilitate and accelerate synthetic biology efforts, while making them more affordable and predictable. Furthermore, this modified bacterium will allow us to develop a debugging platform for biological programming.

2. Use of Escherichia coli as a model in synthetic biology

Alongside our work on M. florum, we also study the widely used bacterium Escherichia coli in order to reduce its genome and use it as a cell frame for synthetic biology. Despite having a larger genome that M. florum, E. coli has undeniable advantages, including various genetic tools and well-characterized parts for engineering its genome. A comparison of the two different systems will also be possible.

escherichia-coli-14936189To improve the tools available in E. coli, the laboratory is also trying to develop inducible gene expression systems heavily regulated by the combination of different regulatory motifs. Obtaining such systems make possible an extremely effective control of gene expression in artificial gene circuits.

Still in E. coli, we try to add the genes necessary for the production of (2R, 3R) butanediol and optimize the metabolic pathways involved in this process, in order to bring a potentially economically viable level of production. This metabolic engineering project aims to use whey generated by the Quebec dairy industry as a nutrient source to produce butanediol, a chemical compound used among others in the synthesis of various plastics.

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Source: inhabitat.com

3. Microfluidics and single cell sequencingmicrofluidique

We use microfluidics for isolating microorganisms in agarose droplets and individually sequence them. This new ultra-high throughput genomic method allows sequencing of a plurality of cells in parallel, and the exploration of genomic diversity in different experimental settings or under various pathological conditions.

 

4. Design and construction of a comprehensive open-source robotic platform for automating biology laboratory operations

The “Biobot” project, in collaboration with engineering students, aims to develop a robotic platform that would allow people working in laboratories to free themselves from repetitive and easy to run activities, therefore having more time to analyze the results and contribute to knowledge advancement. This platform will help standardization and automation of various molecular biology protocols implying the manipulation of a large amount of samples, such as DNA-seq and RNA-seq libraries preparation. Biobot was presented to the iGEM competition in Boston in 2015, where the team won a gold medal.

5. Conjugation systems study

In collaboration with the laboratory of Prof. Vincent Burrus, we try to better understand the mechanisms of antibiotic resistance dissemination, one of the most impending threats to human health and well-being. We also work on the plasmid pVCR94 (of the IncA/C incompatibility group), which propagated multi-drug resistance in Vibrio cholerae O1 El Tor during the 1994 cholera epidemic in Rwanda. More specifically, we want to understand the impact of pVCR94 on overall gene expression of V. cholerae and dissect the role of its individual genes to the global gene regulatory network of this bacterium. These results may help us better understand the horizontal gene transfer process, as well as ways to hinder or improve it depending on specific needs or contexts.

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Source: leavingbio.net

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Programmation Web Philippe Boissonneault