Personne : Tremblay, Denise
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Université Laval. Faculté des sciences et de génie. Département de biochimie
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- PublicationAccès libreComplete genome sequence of Escherichia coli Siphophage BRET(American Society for Microbiology, 2019-01-31) Ngazoa-Kakou, Solange; Tremblay, Denise; Moineau, Sylvain; Plante, Pier-Luc; Addablah, Audrey A.; Lemire, Nicolas; Corbeil, Jacques; Hutinet, Geoffrey; Rousseau, Geneviève M.; Shao, Yuyu; Koudou, Aristide; Soro, Benjamin K.; Coulibaly, David N.; Aoussi, Serge; Dosso, MireilleThe lytic Escherichia coli siphophage BRET was isolated from a chicken obtained at a local market in Abidjan, Côte d’Ivoire. Its linear genome sequence consists of 59,550 bp (43.4% GC content) and contains 88 predicted genes, including 4 involved in archaeosine biosynthesis. Phage BRET is related (95% nucleotide identity) to Enterobacteria phage JenK1
- PublicationRestreintDiversity of streptococcus thermophilus phages in a large-production cheese factory in Argentina(Elsevier Inc., 2006-10-01) Luján Quiberoni, Andrea del; Tremblay, Denise; Moineau, Sylvain; Ackermann, Hans-W.; Reinheimer, Jorge AlbertoPhage infections still represent a serious risk to the dairy industry, in which Streptococcus thermophilus is used in starter cultures for the manufacture of yogurt and cheese. The goal of the present study was to analyze the biodiversity of the virulent S. thermophilus phage population in one Argentinean cheese plant. Ten distinct S. thermophilus phages were isolated from cheese whey samples collected in a 2-mo survey. They were then characterized by their morphology, host range, and restriction patterns. These phages were also classified within the 2 main groups of S. thermophilus phages (cos- and pac-type) using a newly adapted multiplex PCR method. Six phages were classified as cos-type phages, whereas the 4 others belonged to the pac-type group. This study illustrates the phage diversity that can be found in one factory that rotates several cultures of S. thermophilus. Limiting the number of starter cultures is likely to reduce phage biodiversity within a fermentation facility.
- PublicationAccès librePhages of lactic acid bacteria : from genomics to industrial applications(American Society for Microbiology, 2002-08-01) Tremblay, Denise; Labrie, Steve; Moineau, SylvainBacteriophage research has received considerable attention in recent years due to an outburst of studies and editorials about the potential use of phages in treating bacterial infections (see ASM News, September 2001). This research work is fueled by the pressing need to find alternative strategies to antibiotics. Conversely, dairy microbiologists have been trying intensively to get rid of bacteriophages for more than seventy years!
- PublicationAccès libreComplete genome sequence of Brevibacterium linens SMQ-1335(American Society for Microbiology, 2016-11-10) Dumaresq, Jeannot; Tremblay, Denise; Moineau, Sylvain; Roberts, Richard J.; Labrie, Simon; Gonçalves de Melo, AlessandraBrevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% GC content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.
- PublicationAccès librePhage-host interactions in Streptococcus thermophilus : genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array(Nature Publishing Group, 2017-03-06) Achigar, Rodrigo; Tremblay, Denise; Moineau, Sylvain; Magadán, Alfonso H.; Pianzzola, María JuliaThree cos-type virulent Streptococcus thermophilus phages were isolated from failed mozzarella production in Uruguay. Genome analyses showed that these phages are similar to those isolated elsewhere around the world. The CRISPR1 and CRISPR3 arrays of the three S. thermophilus host strains from Uruguay were also characterized and similarities were noted with previously described model strains SMQ-301, LMD-9 and DGCC7710. Spontaneous bacteriophage-insensitive S. thermophilus mutants (BIMs) were obtained after challenging the phage-sensitive wild-type strain Uy02 with the phage 128 and their CRISPR content was analyzed. Analysis of 23 BIMs indicated that all of them had acquired at least one new spacer in their CRISPR1 array. While 14 BIMs had acquired spacer at the 5′-end of the array, 9 other BIMs acquired a spacer within the array. Comparison of the leader sequence in strains Uy02 and DGCC7710 showed a nucleotide deletion at position -1 in Uy02, which may be responsible for the observed ectopic spacer acquisition. Analysis of the spacer sequences upstream the newly acquired ectopic spacer indicated presence of a conserved adenine residue at position -2. This study indicates that natural strains of S. thermophilus can also acquire spacers within a CRISPR array. Introductio
- PublicationAccès libreCharacterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex(Blackwell Science, 2018-09-24) Tremblay, Denise; Fraleon de Almeida, Juliana Cristina; Moineau, Sylvain; Gonçalves de Melo, Alessandra; Rousseau, Geneviève M.; Reis de Rezende, Rafael; Alfenas-Zerbini, PolianeClustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR‐Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR‐Cas systems in plant‐pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR‐Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR‐Cas types I‐E and II‐C were found, with I‐E being the most common. The presence of the same CRISPR‐Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I‐E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage‐insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR‐Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer‐protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR‐Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy.
- PublicationAccès libreMachine learning assisted design of highly active peptides for drug discovery(Public Library of Science, 2015-04-07) Tremblay, Denise; Biron, Éric; Giguère, Sébastien; Moineau, Sylvain; Laviolette, François; Liang, Xinxia; Marchand, Mario; Corbeil, JacquesThe discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning approaches can greatly assist in the process and even partly replace expensive laboratory experiments by learning a predictor with existing data or with a smaller amount of data generation. Unfortunately, once the model is learned, selecting peptides having the greatest predicted bioactivity often requires a prohibitive amount of computational time. For this combinatorial problem, heuristics and stochastic optimization methods are not guaranteed to find adequate solutions. We focused on recent advances in kernel methods and machine learning to learn a predictive model with proven success. For this type of model, we propose an efficient algorithm based on graph theory, that is guaranteed to find the peptides for which the model predicts maximal bioactivity. We also present a second algorithm capable of sorting the peptides of maximal bioactivity. Extensive analyses demonstrate how these algorithms can be part of an iterative combinatorial chemistry procedure to speed up the discovery and the validation of peptide leads. Moreover, the proposed approach does not require the use of known ligands for the target protein since it can leverage recent multi-target machine learning predictors where ligands for similar targets can serve as initial training data. Finally, we validated the proposed approach in vitro with the discovery of new cationic antimicrobial peptides.
- PublicationAccès libreVariability in the durability of CRISPR-Cas immunity(Royal Society of London, 2019-03-25) Chabas, Hélène; Tremblay, Denise; Nicot, Antoine; Moineau, Sylvain; Meaden, Sean; Westra, Edze R.; Pradier, Léa; Lion, Sébastien; Gandon, SylvainThe durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology.
- PublicationAccès libreLong-term bacteriophage preservation(2004-01-01) Tremblay, Denise; Moineau, Sylvain; Ackermann, Hans-W.
- PublicationAccès libreVirulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.(Nature Publishing Group, 2020-01-17) Mathieu, Aurélie; Tremblay, Denise; Dion, Moïra; Moncaut, Elisabeth; Shah, Shiraz A.; Krogfelt, Karen A.; Susanne, Schjørring; Bisgaard, Hans; Nielsen, Dennis Sandris; Petit, Marie-AgnèsBacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics.