Discover the publications from the Landry Lab 

Preprints and submitted papers

The substrate quality of CK2 target sites has a determinant role on their function and evolution

Bradley D, Garand C, Belda H, Gagnon-Arsenault I, Treeck M, Elowe S, and Landry CR


Most biological processes are regulated by peptide-recognition modules (PRMs) that bind to short linear motifs (SLiMs). Such interactions are rapidly reversible and often occur at low affinity. The protein kinase domain represents one such binding module, and known substrates may have full or only partial matches to the kinase recognition motif, a property known as ‘substrate quality’. However, it is not yet clear whether differences in substrate quality represent neutral variation along the phosphosite sequence or if these differences have functional consequences that are subject to selection. We explore this question in detail for the acidophilic kinase CK2. CK2 is well-characterised, clinically important, and a fundamental enzyme for many aspects of cell biology. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions whereas minimal substrates are phosphorylated at lower stoichiometries, are more dynamic during the cell cycle, and have regulatory functions. Optimal CK2 sites also tend to be older and more conserved than minimal sites, and evolutionary simulations indicate that the substrate quality of CK2 phosphosites is often tuned by selection. For intermediate target sites, increases or decreases to substrate quality may be deleterious, which we demonstrate experimentally for a CK2 substrate at the kinetochore. The results together suggest that minimal and optimal phosphosites are strongly differentiated in terms of their functional and evolutionary properties.

Read more on bioRxiv

Cross-feeding affects the target of resistance evolution to an antifungal drug

Durand R, Jalbert-Ross J, Fijarczyk A, Dubé AK, and Landry CR


Pathogenic fungi are a cause of growing concern. Developing an efficient and safe antifungal is challenging because of the similar biological properties of fungal and host cells. Consequently, there is an urgent need to better understand the mechanisms underlying antifungal resistance to prolong the efficacy of current molecules. A major step in this direction would be to be able to predict or even prevent the acquisition of resistance. We leverage the power of experimental evolution to quantify the diversity of paths to resistance to the antifungal 5-fluorocytosine (5-FC), commercially known as flucytosine. We generated hundreds of independent 5-FC resistant mutants derived from two genetic backgrounds from wild isolates of Saccharomyces cerevisiae. Through automated pin-spotting, whole-genome and amplicon sequencing, we identified the most likely causes of resistance for most strains. Approximately a third of all resistant mutants evolved resistance through the pleiotropic drug response, a potentially novel mechanism in response to 5-FC, marked by cross-resistance to fluconazole. For the majority of the remaining two thirds, resistance was acquired through loss-of-function mutations in FUR1, which encodes an important enzyme in the metabolism of 5-FC. We describe conditions in which mutations affecting this particular step of the metabolic pathway are favored over known resistance mutations affecting a step upstream, such as the well-known target cytosine deaminase encoded by FCY1. This observation suggests that ecological interactions may dictate the identity of resistance hotspots.

Read more on bioRxiv

Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins

Lemieux P, Bradley D, Dubé AK, Dionne U, and Landry CR


Protein-protein interactions (PPIs) drive many cellular processes. Some PPIs are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of two paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and by characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the pre-duplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the closest ancestor of the two domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that intramolecular interaction between a SH3 and its host protein evolves through time, making domains not functionally equivalent even when they have the same binding specificity.

Read more on bioRxiv

Lifestyles shape genome size and gene content in fungal pathogens

Fijarczyk A, Hessenauer P, Hamelin RC, and Landry CR


Fungi have a wide range of lifestyles and hosts. We still know little about the impact of lifestyles on their genome architecture. Here, we combined and annotated 562 fungal genomes from the class Sordariomycetes and examined the coevolution between 12 genomic and two lifestyle traits: pathogenicity and insect association. We found that pathogens tend to evolve a larger number of protein-coding genes, tRNA genes, and have larger non-repetitive genome sizes than non-pathogenic species. In contrast, species with a pathogenic or symbiotic relationship with insects have smaller genome sizes and genes with longer exons; they also have fewer genes if they are vectored by insects, compared to species not associated with insects. Our study demonstrates that pathogen genome size and complexity are the result of an interplay between drift, imposed by symbiosis and small effective population size, which leads to genome contraction, and the adaptive role of gene amplification, which leads to genome expansion.

Read more on bioRxiv

Mapping Gene-Microbe Interactions: Insights from Functional Genomics Co-culture Experiments between Saccharomyces cerevisiae and Pseudomonas spp

Nguyen Q G, Jain M, Landry CR and M Filteau


Microbial interactions contribute to shape ecosystems and their functions. The interplay between microorganisms also shapes the evolutionary trajectory of each species, by imposing metabolic and physiological selective pressures. The mechanisms underlying these interactions are thus of interest to improve our understanding of microbial evolution at the genetic level. Here we applied a functional genomics approach in the model yeast Saccharomyces cerevisiae to identify the fitness determinants of naïve biotic interactions. We used a barcoded prototroph yeast deletion collection to perform pooled fitness competitions in co-culture with seven Pseudomonas spp natural isolates. We found that co-culture had a positive impact on fitness profiles, as in general the deleterious effects of loss of function in our nutrient-poor media were mitigated. In total, 643 genes showed a fitness difference in co-culture, most of which can be explained by a media diversification procured by bacterial metabolism. However, a large fraction (36%) of gene-microbe interactions could not be recaptured in cell-free supernatant experiments, showcasing that feedback mechanisms or physical contacts modulate these interactions. Also, the gene list of some co-cultures was enriched with homologs in other eukaryote species, suggesting a variable degree of specificity underlying the mechanisms of biotic interactions and that these interactions could also exist in other organisms. Our results illustrate how microbial interactions can contribute to shape the interplay between genomes and species interactions, and that S. cerevisiae is a powerful model to study the impact of biotic interactions.

Read more on bioRxiv

Published work in 2023 & 2022

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

Hénault M, Marsit S, Charron G, and Landry CR


Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.

Read more on eLife

Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs

Aubé S, Nielly-Thibault L, and Landry CR


How changes in the different steps of protein synthesis—transcription, translation and degradation—contribute to differences of protein abundance among genes is not fully understood. There is however accumulating evidence that transcriptional divergence might have a prominent role. Here, we show that yeast paralogous genes are more divergent in transcription than in translation. We explore two causal mechanisms for this predominance of transcriptional divergence: an evolutionary trade-off between the precision and economy of gene expression and a larger mutational target size for transcription. Performing simulations within a minimal model of post-duplication evolution, we find that both mechanisms are consistent with the observed divergence patterns. We also investigate how additional properties of the effects of mutations on gene expression, such as their asymmetry and correlation across levels of regulation, can shape the evolution of paralogs. Our results highlight the importance of fully characterizing the distributions of mutational effects on transcription and translation. They also show how general trade-offs in cellular processes and mutation bias can have far-reaching evolutionary impacts.

Read more in PLoS Genetics

A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics

Kienzle L, Bettinazzi S, Choquette T, Brunet M, Hosseini Khorami H,  Jacques JF, Moreau M, Roucou X, Landry CR, Angers A, and Breton S


Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases. 

Read more on BMC Biology

Breaking spore dormancy in budding yeast transforms the cytoplasm and the solubility of the proteome

Plante S, Moon KM, Lemieux P, Foster LJ, and Landry CR


The biophysical properties of the cytoplasm are major determinants of key cellular processes and adaptation. Many yeasts produce dormant spores that can withstand extreme conditions. We show that spores of Saccharomyces cerevisiae exhibit extraordinary biophysical properties, including a highly viscous and acidic cytosol. These conditions alter the solubility of more than 100 proteins such as metabolic enzymes that become more soluble as spores transit to active cell proliferation upon nutrient repletion. A key regulator of this transition is the heat shock protein, Hsp42, which shows transient solubilization and phosphorylation, and is essential for the transformation of the cytoplasm during germination. Germinating spores therefore return to growth through the dissolution of protein assemblies, orchestrated in part by Hsp42 activity. The modulation of spores’ molecular properties are likely key adaptive features of their exceptional survival capacities.

Read more on PLoS Biology

Evolutionary trajectories are contingent on mitonuclear interactions

Biot-Pelletier D, Bettinazzi S, Gagnon-Arsenault I, Dubé AK, Bédard C, Nguyen THM, Fiumera HL, Breton S, and Landry CR


Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths towards higher fitness. To test this prediction, we submitted 1344 populations derived from seven mitonuclear genotypes of Saccharomyces cerevisiae to more than 300 generations of experimental evolution in conditions that either select for a mitochondrial function, or that do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.

Read more in Molecular Biology and Evolution

Epistasis between promoter activity and coding mutations shapes gene evolvability

Cisneros AF*, Gagnon-Arsenault I*, Dubé AKD, Després PC, Kumar P, Lafontaine K, Pelettier JN, and Landry CR


The evolution of protein-coding genes proceeds as mutations act on two main dimensions: regulation of transcription level and the coding sequence. The extent and impact of the connection between these two dimensions are largely unknown because they have generally been studied independently. By measuring the fitness effects of all possible mutations on a protein complex at various levels of promoter activity, we show that promoter activity at the optimal level for the wild-type protein masks the effects of both deleterious and beneficial coding mutations. Mutations that are deleterious at low activity but masked at optimal activity are slightly destabilizing for individual subunits and binding interfaces. Coding mutations that increase protein abundance are beneficial at low expression but could potentially incur a cost at high promoter activity. We thereby demonstrate that promoter activity in interaction with protein properties can dictate which coding mutations are beneficial, neutral, or deleterious.

Read more in Science Advances

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Peris D, Ubbelholde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leduq JB, Charron G, Landry CR, Libkind D,  Goncalves C, Goncalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, and Hittinger CT.


Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

Read more in Nature Communications

Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance

Hénault M, Marsit S, Charron G, and Landry CR


Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. While uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae. Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which lead to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype-specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism and the emergence of reproductive isolation

Read more in Genome Research

Correlation between protein abundance and sequence conservation: what do recent experiments say?

Bédard C*, Cisneros AF*, Jordan D, and Landry CR  


Cells evolve in a space of parameter values set by physical and chemical forces. These constraints create associations among cellular properties. A particularly strong association is the negative correlation between the rate of evolution of proteins and their abundance in the cell. Highly expressed proteins evolve slower than lowly expressed ones. Multiple hypotheses have been put forward to explain this relationship, including, for instance, the requirement for higher mRNA stability, misfolding avoidance, and misinteraction avoidance for highly expressed proteins. Here, we review some of these hypotheses, their predictions, and how they are supported to finally discuss recent experiments that have been performed to test these predictions..

Read more in Current Opinion in Genetics and Development

Asymmetrical dose-responses shape the evolutionary trade-off between antifungal resistance and nutrient use

Després PC, Cisneros AF, Alexander EMM, Sonigara R, Gagné-Thivierge C, Dubé AK, and Landry CR  


Antimicrobial resistance is an emerging threat for public health. The success of resistance mutations depends on the trade-off between the benefits and costs they incur. This trade-off is largely unknown and uncharacterized for antifungals. Here, we systematically measure the effect of all amino acid substitutions in the yeast cytosine deaminase Fcy1, the target of the antifungal 5-fluorocytosine (5-FC, flucytosine). We identify over 900 missense mutations granting resistance to 5-FC, a large fraction of which appear to act through destabilization of the protein. The relationship between 5-FC resistance and growth sustained by cytosine deamination is characterized by a sharp trade-off, such that small gains in resistance universally lead to large losses in canonical enzyme function. We show that this steep relationship can be explained by differences in the dose–response functions of 5-FC and cytosine. Finally, we observe the same trade-off shape for the orthologue of FCY1 in Cryptoccocus neoformans, a human pathogen. Our results provide a powerful resource and platform for interpreting drug target variants in fungal pathogens as well as unprecedented insights into resistance–function trade-offs.

Read more in Nature Ecology & Evolution

Ten simple rules for improving communication among scientists

Bautista C, Alfuraiji N,  Drangowka-Way A, Gangwani K, de Flamingh A, and Bourne PE


Communication is a fundamental part of scientific development and methodology. With the advancement of the internet and social networks, communication has become rapid and sometimes overwhelming, especially in science. It is important to provide scientists with useful, effective, and dynamic tools to establish and build a fluid communication framework that allows for scientific advancement. Therefore, in this article, we present advice and recommendations that can help promote and improve science communication while respecting an adequate balance in the degree of commitment toward collaborative work. We have developed 10 rules shown in increasing order of commitment that are grouped into 3 key categories: (1) speak (based on active participation); (2) join (based on joining scientific groups); and (3) assess (based on the analysis and retrospective consideration of the weaknesses and strengths). We include examples and resources that provide actionable strategies for involvement and engagement with science communication, from basic steps to more advanced, introspective, and long-term commitments. Overall, we aim to help spread science from within and encourage and engage scientists to become involved in science communication effectively and dynamically.

Read more in PLoS Computational Biology

The evolution of post-translational modifications

Bradley D


Post-translational modifications (PTMs) are chemical modifications that can regulate the activity and function of proteins. From an evolutionary perspective, they also represent a fast mechanism for the generation of phenotypic diversity and divergence. Advances in mass spectrometry have now enabled the identification of over 600 distinct PTM classes collectively spanning an order of 106 unique sites. However, the chemical detection of PTMs has lagged far behind their functional characterisation, and relatively little is still known about the selective constraints that govern PTM evolution. In particular, the true fraction of PTM sites that are functional — and thus subject to selection — remains an open question. Here, I review advances made in the past two years towards understanding the evolution of PTMs and their associated enzymes.

Read more in Current Opinion in Genetics and Development

High-throughput gene mutagenesis screening using base editing

Després PC, Dubé AK, Yachie N, and Landry CR


Base editing is a CRISPR-Cas9 genome engineering tool that allows programmable mutagenesis without the creation of double-stranded breaks. Here, we describe the design and execution of large-scale base editing screens using the Target-AID base editor in yeast. Using this approach, thousands of sites can be mutated simultaneously. The effects of these mutations on fitness can be measured using a pooled growth competition assay followed by DNA sequencing of gRNAs as barcodes.

Read more in Yeast Functional Genomics

Deep mutational scanning of PPIs between partners expressed from their endogenous loci in vivo

Dubé AK, Dandage R, Dibyachintan S, Dionne U, Després PC, and Landry CR


Deep mutational scanning (DMS) generates mutants of a protein of interest in a comprehensive manner. CRISPR-Cas9 technology enables large-scale genome editing with high efficiency. Using both DMS and CRISPR-Cas9 therefore allows us to investigate the effects of thousands of mutations inserted directly in the genome. Combined with protein-fragment complementation assay (PCA), which enables the quantitative measurement of protein-protein interactions (PPIs) in vivo, these methods allow for the systematic assessment of the effects of mutations on PPIs in living cells. Here, we describe a method leveraging DMS, CRISPR-Cas9, and PCA to study the effect of point mutations on PPIs mediated by protein domains in yeast.

Read more in Yeast Functional Genomics

SRC homology 3 domains: multifaceted binding modules

Dionne U, Percival LJ, Chartier FJM,  Landry CR, and Bisson N. 


The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.

Read more in Trends in Biochemical Sciences

Yeast from temperate forests

Mozzachiodi SBai FYBaldrian PBell GBoundy-Mills KBuzzini P. Čadež NCubillos FADashko SDimitrov RFisher KJGibson BGouliamova DGreig DHeistinger LHittinger CTJecmenica MKoufopanou VLandry CR, …,  Liti G, Boynton, P. 


Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts’ niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here, we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts’ contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.

Read more in Yeast

Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery

Evans-Yamamoto D, Rouleau FD, Nanda P, Makanae K, Liu Y, Després PC, Matsuo H, Seki M, Dubé AK, Ascencio D, Yachie N, and Landry CR


Barcode fusion genetics (BFG) utilizes deep sequencing to improve the throughput of protein–protein interaction (PPI) screening in pools. BFG has been implemented in Yeast two-hybrid (Y2H) screens (BFG-Y2H). While Y2H requires test protein pairs to localize in the nucleus for reporter reconstruction, dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA) allows proteins to localize in broader subcellular contexts and proves to be largely orthogonal to Y2H. Here, we implemented BFG to DHFR-PCA (BFG-PCA). This plasmid-based system can leverage ORF collections across model organisms to perform comparative analysis, unlike the original DHFR-PCA that requires yeast genomic integration. The scalability and quality of BFG-PCA were demonstrated by screening human and yeast interactions for >11 000 bait-prey pairs. BFG-PCA showed high-sensitivity and high-specificity for capturing known interactions for both species. BFG-Y2H and BFG-PCA capture distinct sets of PPIs, which can partially be explained based on the domain orientation of the reporter tags. BFG-PCA is a high-throughput protein interaction technology to interrogate binary PPIs that exploits clone collections from any species of interest, expanding the scope of PPI assays.

Read more in Nucleic Acids Research



Fijarczyk A, Hénault M, Marsit S, Charron G, Landry CR. Heterogeneous mutation rates and spectra in yeast hybrids. Genome Biology and Evolution 13 (12), evab282

Dandage R, Landry CR. Identifying features of genome evolution to exploit cancer vulnerabilities. Cell Systems 12 (12), 1127-1130

Berger CS, Laroche J, Maaroufi H, Martin H, Moon KM, Landry CR, Foster LF, Aubin-Horth N. The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions. Parasites & vectors 14 (1), 1-20

Drouin M, Hénault M, Hallin J, Landry CR. Testing the genomic shock hypothesis using transposable element expression in yeast hybrids. Frontiers in Fungal Biology 2, 729264

Suzuki G, Saito Y, Seki M, Evans-Yamamoto D, Negishi M, Kakoi K, Kawai H, Landry CR, Yachie N, Mitsuyama T. Machine learning approach for discrimination of genotypes based on bright-field cellular images. npj Systems Biology and Applications 7 (1), 31  

Marsit S, Hénault M, Charron G, Fijarczyk A, Landry CR. The neutral rate of whole-genome duplication varies among yeast species and their hybrids. Nature Communications 12 (1), 3126

Berger CM, Landry CR.  Yeast proteins do not practice social distancing as species hybridize. Current Genetics 67 (5), 755-759

Hénault M. The challenge of predicting transposable activity in hybrids. Current Genetics 67 (4), 567-572

Dionne U, Bourgault E, Dubé AK, Bradley D, Chartier FJM, Dandage R, Dibyachintan S, Després PC, Gish GD, Pham NTH, Létourneau M, Lambert JP, Doucet N, Bisson N, Landry CR. Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. Nature communications 12 (1), 1597

Ascencio D, Diss G, Gagnon-Arsenault I, Dubé AK, DeLuna A, Landry CR. Expression attenuation as a mechanism of robustness against gene duplication. Proceedings of the National Academy of Sciences 118 (6), e2014345118


Dandage R*, Berger CM*,  Gagnon-Arsenault I, Moon KM, Stacey RG, Foster LJ, & Landry CR. Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid . Molecular Biology and Evolution 38 (4), 1384-1401

Bautista C, Marsit S, & Landry CR. Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions. Evolutionary Applications 14 (3), 758-769.

Samuel Plante and Christian R Landry (2020). Closely related budding yeast species respond to different ecological signals for spore activation. Yeast 38 (1), 81-89

Gama Braga L, Cisneros A, Mathieu M, Clerc M, Garcia P, Lottin B, Garand C, Thebault P, Landry CR, & Elowe S. The BUBR1 pseudokinase domain promotes efficient kinetochore PP2A-B56 recruitment to regulate spindle checkpoint silencing and chromosome alignmentCell Reports 33 (7), 108397 (2020) 

Hénault M, Marsit S, Charron G & Landry CR. The effect of hybridization on transposable element accumulation in an undomesticated fungal species. eLife 9, e60474 (2020)

Samuel Plante and Christian R Landry. Purification of yeast spores to investigate their dynamic of activation. Current Protocols in Microbiology 59 (1), e123 (2020)

Fijarczyk A, Hénault M, Marsit S, Charron G, Fischborn T, Nicole-Labrie L, & Landry CR. The genome sequence of the Jean-Talon strain, an archeological tetraploid beer yeast from Québec. G3: Genes, Genomes, Genetics 10 (9), 3087-3097 (2020)

Horianopoulos L, Gluck-Thaler E, Benoit Gelber I , Cowen LE, Geddes-McAlister J, Landry CR, Schwartz IS, Scott JA, Sellam A, Sheppard DC, Spribille T, Subramaniam R,Walker AK, Harris SD, Shapiro RS & AC. Gerstein. The Canadian Fungal Research Network: current challenges and future opportunities  Canadian Journal of Microbiology67(1): 13-22. (2020)

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)

Hallin J, Cisneros AF, Hénault M, Fijarczyk A, Dandage R, Bautista C, & Landry CR.  Similarities in biological processes can be used to bridge ecology and molecular biology. Evolutionary Applications 13 (6), 1335-1350 (2020)

Hessenauer P*, Fijarczyk A*, Martin H, Prunier J, Charron G, Chapuis J, Bernier L, Tanguay P, Hamelin RC & Landry CR. Hybridization and introgression drive genome evolution of Dutch elm disease pathogens. Nat Ecol Evol 4 (4), 626-638 (2020)

Bleuven C, Nguyen GQ, Després PC, Filteau M, Landry CR. Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on yeast natural populationsThe ISME Journal 14 (6), 1410-1421 (2020)

Cooke, S.J., V.M. Nguyen, D. Anastakis, S.D. Scott, M.R. Turetsky, A. Amirfazli, A. Hearn, C.E. Milton, L. Loewen,  E.E. Smith,  D.R. Norris, K.L. Lavoie, A. Aiken, D. Ansari, A.N. Antle, M. Babel, J. Bailey, D.M. Bernstein, R. Birnbaum, C. Bourassa, A. Calcagno, A. Campana, B. Chen, K. Collins, C.E. Connelly, M. Denov, B. Dupont, E. George, I. Gregory-Eaves, S. High, J.M. Hill, P.L. Jackson, N. Jette, M. Jurdjevic, A. Kothari, P. Khairy, S.A. Lamoureux, K. Ladner, C.R. Landry, F. Légaré, N. Lehoux, C. Leuprecht, A.R. Lieverse,  A. Luczak, M.L. Mallory,  E. Manning, A. Mazalek, S.J. Murray, L.L. Newman, V. Oosterveld, P. Potvin,  S. Reimer-Kirkham, J. Rowsell, D. Stacey, S.L. Tighe, D.J. Vocadlo, A.E. Wilson and A. Woolford. 2020. Diverse perspectives on interdisciplinarity from Members of the College of the Royal Society of CanadaFACETS5(1): 138-165 (202)


Hallin J & CR Landry. Regulation plays a multifaceted role in the retention of gene duplicates. PLOS Biology

Dandage R. & Landry CR. Paralog dependency indirectly affects the robustness of human cells. Molecular Systems Biology 15:e8871 (2019)

Charron G, Marsit S, Henault M, Martin H & CR Landry. Spontaneous whole-genome duplication restores fertility in interspecific hybrids. Nature Communications 10: 4126 (2019)

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

Nielly-Thibault L & CR Landry, Differences between the de novo proteome and its non-functional precursor can result from neutral constraints on its birth process, not necessarily from natural selection alone. Genetics  10.1534/genetics.119.302187 (2019)

Dandage R, Després PC, Yachie N & CR Landry, beditor: A computational workflow for designing libraries of guide RNAs for CRISPR base editing. Genetics 212(2):377-385 (2019)

Durand E, Gagnon-Arsenault I, Hallin I, Nielly-Thibault L, Namy O & CR Landry, The high 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)

Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn L, Anderson J, Landry CR. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nature Communications 10, Article number: 923 (2019)


Bleuven C, Dubé AK, N’guyen GQ, Gagnon-Arsenault I, Martin H & Landry CR,
A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology. MicrobiologyOpen accepted (2018)

N’guyen GQ, Martin N, Jain M, Lagace L, Landry CR & Filteau M, A systems biology approach to explore the impact of maple tree dormancy release on sap variation and maple syrup quality. Scientific Reports, 8:14658 (2018)

Despres PC, Dube AK, Nielly-Thibault L, Yachie N & Landry CR, Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast. G3 

Dionne U, Chartier FJM, de los Santos YL, Lavoie N, Bernard DN,  Banerjee SL, Otis F, Jacquet K, Tremblay MG, Jain M, Bourassa S, Gish GD, Gagné JP, Poirier GG, Laprise P, Voyer N, Landry CR, Doucet N & Bisson N, Direct phosphorylation of SRC Homology 3 domains by tyrosine kinase receptors disassembles ligand-induced signalling networks. Molecular Cell 70:1-13 (2018)

Wolters JF, Charron G, Gaspary A, Landry CR, Fiumera AC & Fiumera HI, Mitochondrial recombination reveals mito-mito epistasis in yeast. Genetics 209:307-319 (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)


Hénault M*, Eberlein C*, Charron G, Durand E, Nielly-Thibault L, Martin H & Landry CR, Yeast population genomics goes wild: the case of Saccharomyces paradoxus. In: Polz M, Rajora OP (eds) Population genomics: microorganisms. Springer (2017)

Samandi S, Roy AV, Delcourt V, Lucier JF, Gagnon J, Beaudoin MC, Vanderperre B, Breton MA, Motard J, Jacques JF, Brunelle M, Gagnon-Arsenault I, Fournier I, Ouangraoua A, Hunting DJ, Cohen AA, Landry CR, Scott MS & Roucou X, Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. eLife 6:e27860 (2017)

Landry CR & Diss G, Molecular dependency impacts on the compensating ability of paralogs: a response to Veitia. Trends in Genetics 33:657-658 (2017)

Leducq JB*, Henault M*, Charron G, Nielly-Thibault L, Terrat Y, Fiumera HL, Shapiro BJ & Landry CR, Mitochondrial recombination and introgression during speciation by hybridization. Molecular Biology and Evolution 34:1947-1959 (2017)

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

Charron G & Landry CR, No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system. Biology Letters 13:20170197 (2017)

Marsit S, Leducq JB, Durand E, Marchant A, Filteau M & Landry CR, Evolutionary biology through the lens of budding yeast comparative genomics. Nature Reviews Genetics 18:581-598 (2017)

Peris D, Moriarty RV, Alexander WG, Baker EC, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK & Hittinger CT, Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnology for Biofuels 10:78 (2017)

Diss G, Gagnon-Arsenault I, Dion-Coté AM, Vignaud H, Ascencio DI, Berger CM & Landry CR, Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 355:630-634 (2017)

Hébert FO, Grambauer S, Barber I, Landry CR & Aubin-Horth N, Major host transitions are modulated through transcriptome-wide reprogramming events in Schistocephalus solidus, a threespine stickleback parasite. Molecular Ecology 26:1118–1130 (2017)

Xia W, Nielly-Thibault L, Charron G, Landry CR, Kasimer D, Anderson JB & Kohn LM, Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland. Molecular Ecology 26:995–1007 (2017)

Hénault M & CR Landry. When nuclear-encoded proteins and mitochondrial RNAs do not get along, species split apart. EMBO Reports 18:8–10 (2017)


Caron D, Byrne DP, Thebault P, Soulet D, Landry CR, Eyers PA & Elowe S, Mitotic phosphotyrosine network analysis reveals that tyrosine phosphorylation regulates Polo-like kinase 1 (PLK1). Science Signaling 9:rs14 (2016)

Filteau M, Charron G & Landry CR, Identification of the fitness determinants of budding yeast on a natural substrate. The ISME Journal 11:959–971 (2016)

Bleuven C & Landry CR, Molecular and cellular bases of adaptation to a changing environment in microorganisms. Proceedings of the Royal Society B 283:20161458 (2016)

Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D & Hittinger CT, Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus. PLoS Genetics 12:e1006155 (2016)

Hébert FO, Grambauer S, Barber I, Landry CR & Aubin-Horth N, Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. GigaScience 5:24 (2016)

Leducq JB*, Nielly-Thibault L*, Charron G*, Eberlein C, Verta JP, Samani P, Sylvester K, Hittinger CT, Bell G & Landry CR, Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nature Microbiology 1:15003 (2016)

Landry CR, Analysis of biological systems. Invited book review for The Quarterly Review of Biology (2016)

Verta JP, Landry CR & Mackay J, Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations. New Phytologist 211:159–171 (2016)

Barbosa R, Almeida P, Safar SVB, Santos RO, Morais PB, Nielly-Thibault L, Leducq JB, Landry CR, Gonçalves P, Rosa CA & Sampaio JP, Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae. Genome Biology and Evolution 18:317–329 (2016)

Filteau M, Hamel V & Landry CR,  La levure à vin – Modèle d’étude des gènes et des maladies humaines dans un contexte personnalisé. Médecine/Sciences 32:332–334 (2016)

Michnick SW, Landry CR, Levy ED, Diss G, Ear PH, Kowarzyk J, Malleshaiah MK, Messier V & Tchekanda E, Protein-fragment complementation assays for large-scale analysis, functional dissection, and spatiotemporal dynamic studies of protein-protein interactions in living cells. Cold Spring Harbor Protocol (2016)

Michnick SW, Levy ED, Landry CR, Kowarzyk J & Messier V, The dihydrofolate reductase protein-fragment complementation assay: a survival-selection assay for large-scale analysis of protein-protein interactions. Cold Spring Harbor Protocol (2016)

Diss G & Landry CR, Combining the dihydrofolate reductase protein-fragment complementation assay with gene deletions to establish genotype-to-phenotype maps of protein complexes and interaction networks. Cold Spring Harbor Protocol (2016)


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)

Filteau M, Vignaud H, Rochette S, Diss G, Chrétien AE, Berger CM & Landry CR, Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps. Briefings in Functional Genomics 15:130–137 (2015)

Eberlein C, Leducq JB & Landry CR, The genomics of wild yeast populations sheds lights on the domestication of man’s best (micro) friend. Molecular Ecology 24:5309-5311 (2015)

Nigg M, Laroche J, Landry CR & Bernier L, RNAseq analysis highlights specific transcriptome signatures of yeast and mycelial growth phases in the Dutch elm disease fungus Ophiostoma novo-ulmi. G3: Genes|Genomes|Genetics 5:2487-2495 (2015)

Torres-Quiroz F, Filteau M & Landry CR, Feedback regulation between autophagy and PKA. Autophagy 11:1181-1183 (2015)

Freel KC, Charron G, Leducq JB, Landry CR & Schacherer J, Lachancea quebecensis sp. nov., a yeast species consistently isolated from the tree bark in the Canadian province of Quebec. International Journal of Systematic and Evolutionary Microbiology 65:3392-3399 (2015)

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

Hebert FO, Phelps L, Samonte I, Panchal M, Grambauer S, Barber I, Kalbe M, Landry CR & Aubin-Horth N, Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes. Parasites & Vectors 8:225 (2015)

Landry CR, Zhong X, Nielly-Thibault L & Roucou X, Found in translation: functions and evolution of a recently discovered alternative proteome. Current Opinion in Structural Biology 32:74–80 (2015)

Boutchueng-Djidjou M, Collard-Simard G, Fortier S, Hébert SS, Kelly I, Landry CR & Faure RL, The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signalling and the Golgi/endosomes protein network. Molecular and Cellular Proteomics 14:1079-1092 (2015)

Stockwell SR, Landry CR & Rifkin SA, The yeast galactose network as a quantitative model for cellular memory. Molecular BioSystems 11:28-37 (2015)

Samani P, Low-Decarie E, McKelvey K, Bell T, Burt A, Koufopanou V, Landry CR & Bell G, Metabolic variation in natural populations of wild yeast. Ecology and Evolution 5:722-732 (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 Visualized Experiments 97:e52255 (2015)


Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR & Moses AM, Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Computational Biology 12:e1003977 (2014)

Charron G*, Leducq JB* & Landry CR, Chromosomal variation segregates within incipient species and correlates with reproductive isolation. Molecular Ecology 23:4362-4372 (2014)

Landry CR, Freschi L, Zarin T & Moses AM, Turnover of protein phosphorylation evolving under stabilizing selection. Frontiers in Genetics 5:245 (2014)

Goldman A, Roy J, Bodenmiller B, Wanka S, Landry CR, Aebersold R & Cyert MS, The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity.  Molecular Cell 55:422-435 (2014)

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 281:20132472 (2014)

Freschi L, Osseni M & Landry CR, Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PLoS Genetics 10:e1004062 (2014)

Landry CR & Aubin-Horth N, Recent advances in ecological genomics: from phenotypic plasticity to convergent and adaptive evolution and speciation. In: Landry C, Aubin-Horth N (eds) Ecological Genomics. Advances in Experimental Medicine and Biology, 781. Springer, Dordrecht (2014)

Rochette S, Gagnon-Arsenault I, Diss G & Landry CR, Modulation of the yeast protein interactome in response to DNA damage. Journal of Proteomics 100:25-36 (2014)

Diss G, Ascencio D, DeLuna A & Landry CR, Molecular mechanisms of paralogous compensation and the robustness of cellular networks. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322:488-499 (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)


Landry CR*, Levy ED*, Abd Rabbo D, Tarassov K & Michnick SW, Extracting insight from noisy cellular networks. Cell 155:983–989 (2013)

Diss G, Dubé AK, Boutin J, Gagnon-Arsenault I & Landry CR, A systematic approach for the genetic dissection of protein complexes in living cells. Cell Reports 3:2155–2167 (2013)
See also Nature Methods 10:821 (2013)

Diss G, Filteau M, Freschi L, Leducq JB, Rochette S, Torres-Quiroz F & Landry CR, Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Current Opinion in Biotechnology 24:775-783 (2013)

Verta JP, Landry CR & Mackay JJ, Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce. Molecular Ecology 22:23692379 (2013)

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


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

Goyette G*, Boulais J*, Carruthers NJ, Landry CR, Jutras I, Duclos S, Dermine JF, Michnick SW, LaBoissière S, Lajoie G, Barreiro L, Thibault P & Desjardins M, Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution. Molecular & Cellular Proteomics 11:1365-1377 (2012)

Pavey SA, Bernatchez L, Aubin-Horth N & Landry CR, What is needed for next-generation ecological and evolutionary genomics? Trends in Ecology and Evolution 27:673-678 (2012)

Landry CR & Rifkin SA, The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary. In: Soyer O (eds) Evolutionary Systems Biology. Advances in Experimental Medicine and Biology, 751. Springer, New York (2012)

Diss G, Freschi L & Landry CR, Where do phosphosites come from and where do they go after gene duplication? International Journal of Evolutionary Biology 2012:843167 (2012)

Levy ED, Michnick SW & Landry CR, Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information. Philosophical Transactions of The Royal Society B Biological Sciences 367:2594-606 (2012)

Lee S, Thebault P, Freschi L, Beaufils S, Blundell TL, Landry CR, Bolanos-Garcia VM & Elowe S, Characterization of spindle checkpoint kinase Mps1 reveals a domain with functional and structural similarities to tetratricopeptide repeat motifs of the Bub1 and BubR1 checkpoint kinases. The Journal of Biological Chemistry 287:5988-6001 (2012)


Landry CR, A cellular roadmap for the plant kingdom. Science 333:532-533 (2011)

Freschi L, Courcelles M, Thibault P, Michnick SW & Landry CR, Phosphorylation network rewiring by gene duplication. Molecular Systems Biology 7:504 (2011)

Michnick SW, Ear PH, Landry C, Malleshaiah MK & Messier V, Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein-protein interactions in living cells. In: Luttrell L, Ferguson S (eds) Signal transduction protocols. Methods in Molecular Biology 756. Humana Press, Totowa NJ (2011)

2001 - 2010


Landry CR & Rifkin SA, Chromatin regulators shape the genotype-phenotype map. Molecular Systems Biology 6:434 (2010)

Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, Soldati T, Michnick SW, Thibault P & Desjardins M, Molecular characterization of the evolution of phagosomes. Molecular Systems Biology 6:423 (2010)

Landry CR & Aubin-Horth N, Gene network architecture as a canvas for the interpretation of ecological genomics investigations. Molecular Ecology 19:5084-5085 (2010)

Moses AM & Landry CR, Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends in Genetics 26:462-467 (2010)

Di Poi C, Diss G & Freschi L, Biodiversity matters in a changing world. Biology Letters 7:4-6 (2010) **Student initiative**

Levy ED*, Landry CR* & Michnick SW, Signaling through cooperation. Science 328:983-984 (2010)

Michnick SW, Ear PH, Landry CR, Malleshaiah MK & Messier V, A toolkit of protein-fragment complementation assays for studying and dissecting large-scale and dynamic protein-protein interactions in living cells. In: Weissman J, Guthrie C, Fink G (eds.) Guide to yeast genetics: functional genomics, proteomics and other systems analysis. Methods in Enzymology 470. Elsevier Press, New York USA (2010)

Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C & Hartl DL, Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Molecular Ecology 19:212–227 (2010)



Landry CR*, Levy ED* & Michnick SW, Weak functional constraints on phosphoproteomes. Trends in Genetics 25:193-197 (2009)

Levy ED*, Landry CR* & Michnick SW, How perfect can protein interactomes be? Science Signalling 2:pe11 (2009)

Landry CR, Systems biology spins off a new model for the study of canalization. Trends in Ecology and Evolution 24:63-66 (2009)



Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR & Winston F, Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PloS Biology 6:e277 (2008)

Tarassov K*, Messier V*, Landry CR*, Radinovic S*, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H & Michnick SW, An in vivo map of the yeast protein interactome. Science 320:1465-1479 (2008)

Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL & Thomas WK, A Genome-wide view of the spectrum of spontaneous mutations in yeast. Proceedings of the National Academy of Sciences of the United States of America 105:9272-9277 (2008)

Brown KM, Landry CR, Hartl DL & Cavalieri D, Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Molecular Ecology 17:2985-2997 (2008)



Stefan E, Aquin S, Berger N, Landry CR, Nyfeler B, Bouvier M & Michnick SW, Quantification of dynamic protein complexes using Renilla luciferase-fragment complementation applied to protein kinase A activities in vivo. Proceedings of the National Academy of Sciences of the United States of America 104:16916-16921 (2007)

Landry CR*, Lemos B*, Rifkin SA, Dickinson WJ & Hartl DL, Genetic properties influencing the evolvability of gene expression. Science 317:118-121 (2007)

Landry CR, Castillo-Davis CI, Ogura A, Liu JS & Hartl DL, Systems-level analysis and evolution of the Drosophila phototransduction cascade. Proceedings of the National Academy of Sciences of the United States of America 104:3283-3288 (2007)

Landry CR & Aubin-Horth N, Ecological annotation of genes and genomes through ecological genomics. Molecular Ecology 16:4419-4421 (2007)

Landry CR, Hartl DL & Ranz JM, Genome clashes in hybrids: insights from gene expression. Heredity 99:483-493 (2007)

Lemos B, Landry CR, Fontanillas P, Renn SP, Kulathinal R, Brown KM & Hartl DL, Evolution of Genomic Expression. In Pagel M, Pomiankowski A (eds) Evolutionary genomics and proteomics. Sinauer Associates, Sunderland, MA (2007)

Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G & Queitsch C, Indel array: an affordable alternative for genotyping. Plant Journal 51:727-737 (2007)



Landry CR, Townsend JP, Hartl DL & Cavalieri D, Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 15:575-591 (2006)

Landry CR, Oh J, Hartl DL & Cavalieri D, Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 366:343-351 (2006)



Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG & Hartl DL, Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822 (2005)

Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A & Bazzicalupo M, Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 6: 158 (2005)

Aubin-Horth N, Landry CR, Letcher BH & Hofmann HA, Alternative life-histories shape brain gene expression profiles in males of the same population. Proceedings of the Royal Society B 272:1655-1662 (2005)



Landry C, Geyer LB, Arakaki Y, Uehara T & Palumbi SR, Recent speciation in the Indo-West Pacific: rapid evolution of gamete recognition and sperm morphology in cryptic species of sea urchin. Proceedings of the Royal Society B 270:1839-1847 (2003)

Bernatchez L & Landry C, MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology 16:363-377 (2003)



Landry C & Bernatchez L, Comparative analysis of population structure across environments and geographic scales at major histocompatibility complex and microsatellite Atlantic salmon (Salmo salar). Molecular Ecology 10:2525-2540 (2001)

Landry C, Garant D, Duchesne P & Bernatchez L, “Good genes as heterozygosity”: the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar). Proceedings of the Royal Society B 268:1279-1285 (2001)

The lab

The Landry lab is located at the Institut de Biologie Intégrative et des Systèmes (IBIS) of Université Laval and is part of the Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO). IBIS and PROTEO offer very stimulating training environments and cutting edge technologies. The Landry lab is an international team of about 30 students, PDFs and research associates from different backgrounds (microbiology, biology, bioinformatics, biochemistry) addressing questions in evolutionary cell and systems biology.

The lab