Alexandre Dubé, MSc

Research professional / Lab manager
e-mail:
alexandre.dube.4 [at] ulaval.ca

Biography

I started a bachelor’s degree in Biochemistry in 2006 at Université Laval. During the first year of my degree, I realized that it was important to start early in research. I searched for an internship and found one in Dr Yves Bourbonnais’ laboratory. The goal of my internship was to study the effect of mutations on the antimicrobial activity of a peptide. In the following semesters, Dr Bourbonnais introduced me to the beautiful world of Saccharomyces cerevisiae when he switched me to the project of a PhD student in his lab: Isabelle Gagnon-Arsenault. I learned to use this model organism when studying the activation and maturation of an endopeptidase (Yps1) involved in the response to stress and cell wall regulation.

Having enjoyed my time in research, I decided to start a master’s degree in Biochemistry in 2009 also in Dr Bourbonnais’ laboratory. During these two years, I studied the function of the N-entrance loop of Yps1p that showed me the importance of post-translational modifications in the regulation of cellular processes. At the same time, I also tried to identify genes implicated in the membrane anchoring of a specific class of protein: the glycosylphosphatidylinositol-anchored (GPI) protein. This part of my project gave me an overview of high-throughput research, since I looked at GPI protein secretion in more than 5000 yeast mutants. I had the opportunity to show my results in Vancouver at an international yeast meeting. My master’s degree also gave me the opportunity to meet Christian, since he was on my committee.

In 2011, I finished my master’s degree and decided to start working. It is at that point that Christian hired me as a research assistant. In his lab, I have learned about evolution and speciation and I have deepened my knowledge of protein functionality. After 4 years, I went back to Dr Bourbonnais’ laboratory for 1 year during which I deepened my knowledge on the regulation of the metabolism of yeast and on lipids’ central role in biological systems. I am back in Christian’s laboratory and I now work to develop new techniques with the genome edition system CRISPR/Cas.

 

Research interests

I am particularly interested in understanding how a mutation in protein sequence can affect its stability and function. I use methods such as protein fragment complementation assays (PCA), CRISPR/Cas and experimental evolution to better understand these effects. Lately, I have been interested in understanding the effect that the environment can have on membrane composition and how a cell responds to an imbalance in lipid composition.

Publications

Biot-Pelletier D, Bettinazzi S, Gagnon-Arsenault I, Dubé AKD, Bédard C, Nguyen THM, Fiumera HL, Breton S, and Landry CR. Evolutionary trajectories are contingent on mitonuclear interactions. Molecular Biology and Evolution, Volume 40, Issue 4, msad061 (2023) 
Cisneros AF*, Gagnon-Arsenault I*, Dubé AKD, Després PC, Kumar P, Lafontaine K, Pelettier JN, and Landry CR. Epistasis between promoter activity and coding-mutations shapes gene evolvability. Science Advances, 9.5: eadd9109 (2023) 
Després PC, Cisneros AF, Alexander EMM, Sonigara R, Gagné-Thivierge C, Dubé AK, and Landry CR. Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use. Nature Ecol Evol (2022) 

Després PC, Dubé AK, Yachie N, and Landry CR. High-throughput gene mutagenesis screening using base edititng. Yeast Functional Genomics pp 331-348 (2022) 

Dubé AK, Dandage R, Dibyachintan S, Dionne U, Després PC, and Landry CR. Deep mutational scanning of PPIs between partners expressed from their endogenous loci. Yeast Functional Genomics pp 237-259 (2022) 

Dionne U, Bourgault E*, Dubé AK*, Bradley D*, Chartier FJM*, Dandage R, Dibyachintan S, Després PC, Gish GD, Hang Pham NT, Létourneau M, Lambert JP, Doucet N, Bisson N, and Landry CR. Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. Nature Communications 12, 1597 (2021)

Ascencio D, Diss G, Gagnon-Arsenault I, Dubé AK, DeLuna A, & Landry CR, Expression attenuation as a mechanism of robustness against gene duplication. PNAS 118 (6) (2021)

Després PC, Dubé AK, Seki M, Yachie N, Landry CR. Perturbing proteomes at single residue resolution using base editing. Nature communications 11 (1), 1-13 (2020)

Marchant A, Cisneros A, Dubé A, Gagnon-Arsenault I, Ascencio D, Jain H, Aubé S, Eberlein C, Evans-Yamamoto D, Yachie N & Landry C, The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. eLife 8: e46754 (2019)

Bleuven C, Dubé AK, Nguyen GQ, Gagnon-Arsenault I, Martin H, and Landry CR, A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology. MicrobiologyOpen 8 (7), e00773 (2019)

Durand E, Gagnon-Arsenault I, Hallin J, Hatin I, Dubé A, Nielly-Thibault L, Namy O and Landry C, Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. Genome Research 29 (6), 932-943 (2019)

Després PC, Dubé AK, Nielly-Thibault L, Yachie N, Landry CR. Double selection enhances the efficiency of target-AID and Cas9-based genome editing in yeast. G3: Genes, Genomes, Genetics 8 (10), 3163-3171 (2018)

Chrétien AE, Gagnon-Arsenault I, Dubé AK, Barbeau X, Després PC, Lamothe C, Dion-Côté AM, Lagüe P & Landry CR, Extended linkers improve the detection of protein-protein interactions (PPIs) by dihydrofolate reductase protein-fragment complementation assay (DHFR PCA) in living cells. Molecular & Cellular Proteomics 17:373-383 (2018)

Eberlein C, Nielly-Thibault L, Maaroufi H, Dubé AK, Leducq JB, Charron G & Landry CR, The rapid evolution of an onholog contributes to the ecological specialization of incipient yeast species. Molecular Biology and Evolution 34:2173-2186 (2017)

Filteau M, Hamel V, Pouliot MC, Gagnon-Arsenault I, Dubé AK & Landry CR, Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. Molecular Systems Biology 11:832 (2015)

Rochette S, Diss G, Filteau M, Leducq JB, Dubé AK & Landry CR, Genome-wide protein-protein interaction screening by protein-fragment complementation assay (PCA) in living cells. Journal of Visual Experiment e52255 (2015)

Filteau M, Diss G, Torres-Quiroz F, Dubé AK, Schraffl A, Bachmann VA, Gagnon-Arsenault I, Chrétien AÈ, Steunou AL, Dionne U, Côté J, Bisson N, Stefan E & Landry CR, Systematic identification of signal integration by protein kinase A. Proceedings of the National Academy of Sciences 112:4501-4506 (2015)

Leducq JB, Charron G, Samani P, Dubé AK, Sylvester K, James B, Almeida P, Sampaio JP, Hittinger CT, Bell G & Landry CR, Local climatic adaptation in a widespread microorganism. Proceedings of the Royal Society B: Biological Sciences 281:20132472 (2014)

Charron G, Leducq JB, Bertin C, Dubé AK & Landry CR, Exploring the northern limit of the distribution of Saccharomyces cerevisiae and Saccharomyces paradoxus in North America. FEMS Yeast Research 14:281-288 (2014)

Diss G, Dubé AK, Boutin J, Gagnon-Arsenault & Landry CR, A systematic approach for the gentic dissection of protein complexes in living cells. Cell Reports 3:2155-2167 (2013)

Freschi L, Torres-Quiroz F, Dubé AK & Landry CR, qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells. Molecular BioSystems 9:36-43 (2013)

Gagnon-Arsenault I, Marois Blanchet FC, Rochette S, Diss G, Dubé AK & Landry CR, Transcriptionnal divergence plays a role un the rewiring of protein interaction networks after gene duplication. Journal of Proteomics 81:112-125 (2013)

Leducq JB, Charron G, Diss G, Gagnon-Arsenault I, Dubé AK & Landry CR, Evidence for the robustness of protein complexes to inter-species hydridization. Plos Genetics 8:e1003161 (2012)