References of "Baurain, Denis"
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See detailHigh-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

in Archives of Virology (in press)

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in ... [more ▼]

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in genomic regions encompassing partial coding sequences for non-structural (NS) 1-2, NS5, NS6, NS7 proteins within open reading frame (ORF) 1. In a region encoding a portion of the major capsid protein (VP1) within ORF2 (also including the ORF4 region) and a portion of the minor structural protein (VP2), the mutation rates were estimated to be at least one order of magnitude higher. The VP2 coding region was found to have the highest mutation rate. [less ▲]

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See detailThe BCCM/ULC collection to conserve the biodiversity and study the secondary metabolites of Polar cyanobacteria
Lara, Yannick ULg; Durieu, Benoit ULg; Renard, Marine ULg et al

Poster (2016, November 16)

In the Polar Regions, Cyanobacteria are the key primary producers and main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in ... [more ▼]

In the Polar Regions, Cyanobacteria are the key primary producers and main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in lakes and soil crusts. Their success in these harsh cold conditions can probably be explained by particular adaptations to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other environmental stresses. The BCCM/ULC public collection is funded by the Belgian Science Policy Office since 2011. It has obtained the ISO9001 certification for deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. This collection aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic mats, soil crusts, cryoconites, endoliths,….) and make it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, pigments, and genomic make-up. It presently includes 226 cyanobacterial strains, of which 119 are of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). As shown by morphological identification, the strains belong to five orders (Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales). The 16S rRNA and ITS sequences of the strains are being characterized. The first 85 Antarctic strains already studied are distributed into 25 Operational Taxonomic Units (OTUs = groups of sequences with > 97,5% 16S rRNA similarity), and thus, represent a quite large diversity. Moreover, strains identified as members of the genera Leptolyngbya or Phormidium appear in several lineages. This supports the idea that there is a need to revise the taxonomy of these polyphyletic genera with a simple filamentous morphology. To better understand the functioning, metabolism and adaptative strategies of cyanobacteria in the extreme Antarctic environment, the genome sequencing of 11 strains has been started. Pair-read data from illumina MiSeq runs were obtained and submitted to a bioinformatic pipeline dedicated to the assembly of genomes and search of sequences involved in the biosynthesis of secondary metabolites. Gene cluster prediction analysis allowed to characterize 20 clusters of NRPS, PKS and hybrid NRPS-PKS from 2 to 66kb. Surprisingly, none of the characterized operons had previously been described in the literature. [less ▲]

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See detailPREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool
Tocquin, Pierre ULg; Naomé, Aymeric ULg; Jourdan, Samuel ULg et al

E-print/Working paper (2016)

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their ... [more ▼]

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/. [less ▲]

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See detailThe BCCM/ULC collection to conserve the biodiversity and explore the applied potential of Polar cyanobacteria
Becker, Pierre; SZTERNFELD, P; ANDJELKOVIC, M et al

Poster (2016, October 28)

In the Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial ... [more ▼]

In the Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They may present interesting features to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other stresses. The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic mats, soil crusts, cryoconites, endoliths…). It makes it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up. It presently includes 226 cyanobacterial strains, with 119 being of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). An ISO 9001 certificate was obtained for the public deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. The morphological identification shows that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. The 16S rRNA and ITS sequences of the strains are being characterized. Our results show that the Antarctic strains are positioned into 25 OTUs (sequences with > 97,5% 16S rRNA similarity), and thus, represent a quite large diversity. In addition, cyanobacteria are known to produce a wide range of secondary metabolites (e.g. alkaloids, cyclic and linear peptides, polyketides) with bioactive potential. Among these bioactive metabolites, some display antibiotic, anticancer or antifungal effects. In collaboration with the BCCM/IHEM collection of biomedical fungi, a screening of cyanobacterial strains from BCCM/ULC was performed in order to discover potential new antifungal drugs. The analysis of a first set of methanol extracts from 15 different strains put in evidence the antifungal activity of a Phormidium priestleyi isolate. The latter remains active up to 0.5% (v/v) of fungal culture and was able to inhibit the growth of various fungal species among Candida, Cryptococcus, Aspergillus, and Penicillium. The raw extract was subjected to HPLC and a fraction containing the active molecule was obtained. This molecule appeared to be a thermostable hydrophobic compound. Moreover, in vitro toxicological analyses suggest that the compound has a general cytotoxic effect that could be inhibited by the mammalian metabolism. Further analyses are needed to identify the molecule and to determine if it could be a candidate for a new antifungal drug. In summary, the BCCM/ULC public collection serves as a Biological Resource Centre to conserve ex situ and document the biodiversity of polar cyanobacteria, as well as a repository for discovery of novel bioactive compounds. [less ▲]

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See detailThe BCCM/ULC collection to conserve and study the biodiversity of Polar cyanobacteria
Wilmotte, Annick ULg; Renard, Marine ULg; Lara, Yannick ULg et al

Poster (2016, September)

The BCCM/ULC public collection of Cyanobacteria has been funded since 2011 by the Belgian Science Policy Office. BCCM/ULC is currently holding 226 cyanobacterial strains, with 119 being of Antarctic ... [more ▼]

The BCCM/ULC public collection of Cyanobacteria has been funded since 2011 by the Belgian Science Policy Office. BCCM/ULC is currently holding 226 cyanobacterial strains, with 119 being of Antarctic origin (including 3 from the sub-Antarctic). The cyanobacteria constitute the bacterial phylum with the largest morphological diversity and their taxonomy is still a work in progress. In Polar Regions, Cyanobacteria represent key primary producers and are important drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build extensive benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They have adapted to their environment, and may present interesting features to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other stresses. In this poster, we present the results of the 16S rRNA phylogenetic analysis for 76 Antarctic strains. This allows us to illustrate the diversity present in the collection, to detect lineages for which no genome has yet been sequenced, and to pinpoint taxonomic problems that should be addressed in a more comprehensive study. [less ▲]

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See detailThe BCCM/ULC collection: a Biological Ressource Center to give access to the Antarctic cyanobacterial diversity
Wilmotte, Annick ULg; Renard, Marine ULg; Lara, Yannick ULg et al

Poster (2016, August)

On the Antarctic continent, Cyanobacteria represent the key primary producers and the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic ... [more ▼]

On the Antarctic continent, Cyanobacteria represent the key primary producers and the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They may present interesting features to survive freeze/thaw cycles, sea-sonally contrasted light intensities, high UV radiations, dessication and other stresses. The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.). It makes it available for researchers to study the taxonomy, evolu-tion, adaptations to harsh environmental conditions, and genomic make-up. It pres-ently includes 226 cyanobacterial strains, with 119 being of Antarctic origin (cata-logue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The morphological identification shows that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. We present here the molecular datasets showing the diversity of the BCCM/ULC strains, studied on the basis of the 16S rRNA gene. A selection of strains was also characterized by sequencing of rpoC1, recA, and gyrA genes after amplification with newly designed primers. Our results mainly show that 25 OTUs included strains of Antarctic origin. Moreo-ver, strains identified as members of the genera Leptolyngbya or Phormidium ap-pear in several lineages. This supports the need to revise these polyphyletic genera with a simple filamentous morphology. A certain divergence of some Antarctic strains from related strains isolated from other regions can also be observed. It suggests that a portion of the Antarctic cyanobacterial flora may have evolved in-dependently from the cyanobacteria in other continents. [less ▲]

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See detailUsing Next Generation Sequencing to characterize species diets: a study case with faeces of wild boar in the Spanish Pyrenees
Mouton, Alice ULg; Espelta, Jose Maria; Baurain, Denis ULg et al

Poster (2016)

The genomic era offer an exciting opportunity to establish biodiversity assessment for plants and animals. More specifically, DNA metabarcoding can be used as a proxy for the biodiversity existing in a ... [more ▼]

The genomic era offer an exciting opportunity to establish biodiversity assessment for plants and animals. More specifically, DNA metabarcoding can be used as a proxy for the biodiversity existing in a sample (soil, water, faeces,..) and therefore it represents a powerful and a non invasive tool to answer concerns regarding ecological questions (conservation, restoration). To illustrate such prospect, we conducted a study on the expanding wild boar populations in the Spanish Pyrenees. Over the last decades, the populations of wild boar are growing in the Iberian peninsula mainly due to their high adaptability to new environments, new climates, varied diets and high reproduction rates. Despite the economic interest of the species in the Peninsula, this expansion cause many damage on ecosystems, humans and farming practices. By moving higher in altitude, it has been suggested that the wild boar populations might be responsible for the rapid decline of the endangered capercaillie (Tetrao urogallus) populations in the Pyrenees. By searching for food, they come accross the ground nesting bird nest and gobble the eggs. The aim of this study was therefore to analyze the diet of the wild boar populations in higher altitude in the Spanish Pyrenees. 81 faecal samples collected during summer and autumn 2014 in the Aigues Tortes National Park have been extracted, amplified and sequenced using the Illumina Technology. With this method, a precise estimation of the animal prey existing in the wild boar faeces was possible and will eventually allow wild life managers to apply concrete management measures for this expanding species. [less ▲]

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See detailCoding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle.
Kadri, Naveen Kumar ULg; Harland, Chad ULg; Faux, Pierre ULg et al

in Genome Research (2016)

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events ... [more ▼]

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for approximately 10% of the genetic variance in males. [less ▲]

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See detailGram-Negative Bacteria: "Inner" vs. "Cytoplasmic" or "Plasma Membrane": A Question of Clarity rather than Vocabulary
Baurain, Denis ULg; Wilmotte, Annick ULg; Frère, Jean-Marie ULg

in Journal of Microbial and Biochemical Technology (2016), 8(4), 325-326

In this short commentary, we show that the utilisation of the term “inner membrane” to characterize the cytoplasmic or plasma membrane of Gram-negative bacteria can be a source of confusion and we propose ... [more ▼]

In this short commentary, we show that the utilisation of the term “inner membrane” to characterize the cytoplasmic or plasma membrane of Gram-negative bacteria can be a source of confusion and we propose that it should be completely abandoned. [less ▲]

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See detailON THE USE OF HIGH-THROUGHPUT SEQUENCING FOR THE STUDY OF CYANOBACTERIAL DIVERSITY IN ANTARCTIC AQUATIC MATS 1
Stelmach Pessi, Igor ULg; De Carvalho Maalouf, Pedro; Laughinghouse, Haywood Dail et al

in Journal of Phycology (2016), 52

The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better ... [more ▼]

The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better understanding of microbial distribution in the environment, but its application is hampered by several methodological and analytical challenges. In this work we explored the use of HTS as a tool for the study of cyanobacterial diversity in Antarctic aquatic mats. Our results highlight the importance of using artificial communities to validate the parameters of the bioinformatics procedure used to analyse natural communities, since pipeline-dependent biases had a strong effect on the observed community structures. Analysis of microbial mats from five Antarctic lakes and an aquatic biofilm from the Sub-Antarctic showed that HTS is a valuable tool for the assessment of cyanobacterial diversity. The majority of the OTUs retrieved were related to filamentous taxa such as Leptolyngbya and Phormidium, which are common genera in Antarctic lacustrine microbial mats. However, other phylotypes related to different taxa such as Geitlerinema, Pseudanabaena, Synechococcus and Chamaesiphon, Calothrix and Coleodesmium were also found. Results revealed a much higher diversity than what had been reported using traditional methods and also highlighted remarkable differences between the cyanobacterial communities of the studied lakes. The aquatic biofilm from the Sub-Antarctic had a distinct cyanobacterial community in comparison to the studied Antarctic lakes, which, in turn, displayed a salinity-dependent community-structure at the phylotype level. [less ▲]

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See detailOn the LZ distance for dereplicating redundant prokaryotic genomes
Léonard, Raphaël ULg; Baurain, Denis ULg; Kerff, Frédéric ULg et al

Poster (2015, December 07)

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a prob- lem when trying to assemble broadly sampled genome sets for phylogenomics and ... [more ▼]

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a prob- lem when trying to assemble broadly sampled genome sets for phylogenomics and comparative genomics. Indeed, most of the new genomes belong to the same subset of hyper-sampled phyla, such as Proteobacteria and Firmicutes, or even to single species, such as Escherichia coli (almost 2000 genomes as of Sept 2015), while the continuous flow of newly discovered phyla prompts for regular updates. This situation makes it difficult to maintain sets of representative genomes combining lesser known phyla, for which only few species are available, and sound subsets of highly abundant phyla. An automated straightforward method is required but none are publicly available. The LZ distance, in conjunction with the quality of the annotations, can be used to create an automated approach for selecting a subset of represen- tative genomes without redundancy. We are planning to release this tool on a website that will be made publicly available. [less ▲]

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See detailThe BCCM/ULC culture collection to conserve, document and explore the polar cyanobacterial diversity
Wilmotte, Annick ULg; Renard, Marine ULg; Kleinteich, Julia et al

Poster (2015, September 07)

In Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they form benthic microbial mats ... [more ▼]

In Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they form benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They have adapted to their environment, and may present interesting features to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other environmental stresses. The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.). The collection is available for researchers to study the taxonomy, evolution, adaptations to extreme environmental conditions, and genomic make-up. It presently includes 200 cyanobacterial strains, with 123 being of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The morphological identification shows that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. The large diversity is also supported by the phylogenetic analyses based on the 16S rRNA sequences. This broad distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. To this end, the sequencing of the complete genome of 16 selected strains is currently under way. In addition, cyanobacteria produce a wide range of secondary metabolites (e.g. alkaloides, cyclic and linear peptides, polyketides) with different bioactive potential (e.g. antibiotic, antiviral, anticancer, cytotoxic, genotoxic). Bioassays have shown antifungal activities of the cell extracts from strains Plectolyngbya hodgsonii ULC009 and Phormidium priestleyi ULC026. The potential of the polar strains to produce cyanotoxins and other secondary metabolites is currently being studied by ELISA, LC-MS and the detection of genes involved in their production. Due to the geographic isolation and the strong environmental stressors of the habitat, the exploration of these metabolites in Antarctic cyanobacterial strains seems promising for biotechnology or biomedical applications (Biondi et al. 2008). In summary, the BCCM/ULC public collection could serve as a Biological Resource Centre (OECD 2001) to conserve and document the biodiversity of polar cyanobacteria, as well as a repository for discovery of novel bioactive compounds. REFERENCES Biondi, N., Tredici, M., Taton, A., Wilmotte, A., Hodgson, D., Losi, D., & Marinelli, F. (2008) : Cyanobacteria from benthic mats of Antarctic lakes as a source of new bioactivities. Journal of Applied Microbiology, 105(1) : 105- 115 OECD (2001) Biological Resource Centres : Underpinning the Future of Life Sciences and Biotechnology. http://www.oecd.org/science/biotech/2487422.pdf [less ▲]

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See detailGenome sequencing of an endemic filamentous Antarctic cyanobacterium
Lara, Yannick ULg; Verlaine, Olivier ULg; Kleinteich, Julia et al

Poster (2015, August 03)

The strain Phormidium priestleyi ULC007 was isolated from a benthic mat located in a shallow freshwater pond in the Larsemann Hills (69°S), Western Antarctica. This strain belongs to a cyanobacterial ... [more ▼]

The strain Phormidium priestleyi ULC007 was isolated from a benthic mat located in a shallow freshwater pond in the Larsemann Hills (69°S), Western Antarctica. This strain belongs to a cyanobacterial cluster that appeared as potentially endemic (Taton et al. 2006). After obtaining an axenic isolate, we sequenced the genome of this strain in the frame of the BELSPO CCAMBIO project, in order to better understand the functioning, metabolism and adaptative strategies of cyanobacteria to the extreme Antarctic environment. [less ▲]

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See detailThe BCCM/ULC collection : a Biological Ressource Center for polar cyanobacteria
Wilmotte, Annick ULg; Renard, Marine ULg; Lara, Yannick ULg et al

Poster (2015, August 03)

In this study, during the 2013 MicroFun expedition, we sampled 72 locations around Svalbard including diverse biotopes such as glacial forefields, tundra soils, hot springs, soil crusts, microbial mats ... [more ▼]

In this study, during the 2013 MicroFun expedition, we sampled 72 locations around Svalbard including diverse biotopes such as glacial forefields, tundra soils, hot springs, soil crusts, microbial mats, wet walls, cryoconites, plankton and periphyton, in order to (1) assess the biodiversity of cyanobacteria around Svalbard, (2) verify the existence of biogeographical trends around the archipelago, and (3) compare these data with other polar (cold) areas, especially Antarctica. We used a pyrosequencing approach targeting cyanobacteria-specific 16S rRNA gene sequences to deeply study the cyanobacterial communities. [less ▲]

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See detailThe hidden face of the human macrophage chitotriosidase: taking a new look at this enzyme based on the biochemical and phylogenomic analysis of its chitin binding domain
Crasson, Oscar ULg; Legrand, François; Léonard, Raphaël ULg et al

Poster (2015, August)

Carbohydrates recognition is a critical process involved in numerous aspects of the cell biology such as inflammation, innate immune responses and proliferation. Chitin is an homopolysaccharide composed ... [more ▼]

Carbohydrates recognition is a critical process involved in numerous aspects of the cell biology such as inflammation, innate immune responses and proliferation. Chitin is an homopolysaccharide composed of β-1,4-linked N-acetylglucosamine (GlcNAc) units that is an abundant structural component of various infectious organisms like protozoans, nematodes and fungi. As there is no endogenous chitin produced by mammals, this polymer appeared to be a strategic target for innate immune agents which is why various carbohydrate binding proteins, associated or not with catalytic domains, are synthetized by plants and animals and are known to play a crucial role in innate immunity. The macrophage chitotriosidase (HCHT) is one of the three active chitinases synthetized by humans and has triggered significant attention recently due to its association with various inflammatory disorders. HCHT belongs to the Glycosyl Hydrolase family 18 (GH18) and is known to be involved in innate immunity. Nevertheless, its precise physiological function remains unclear. As numerous GHs, HCHT is a modular protein composed of a catalytic domain (GH18) associated to a Carbohydrate Binding Module (CBM) which is essential to hydrolyse crystalline chitin. If the catalytic domain GH18 is highly common in other GHs from animals, plants, fungi, bacteria, archea and viruses, its CBM (named ChBD) is much less conserved which makes the association between these two domains particularly intriguing. This work aims to demystify HCHT’s physiological function. Firstly, using competitive inhibition assays, we have highlighted the ability of ChBD to interact with chitooligosaccharides (GlcNAc1-2-4-6) which suggests that ChBD can potentially act as a lectin domain. Secondly, to better understand the molecular basis for chitin recognition, we have used homology modelling to build, with high confidence, the 3D structure model of ChBD. Based on this model, a specific set of residues has been selected for alanine scan mutagenesis which has allowed us to define the minimum chitin binding interface of the protein. Thirdly, Phylogenomic studies were performed to analyse the evolutionary history of the isolated catalytic and ChBD domains and understand how these domains were combined. Based on all these results, we discuss a new way of looking at HCHT where its ChBD would be the key determinant that has guided the catalytic domain from a basic metabolic function to a critical component of innate immunity in human. Finally, we propose a mechanism that explains how this enzyme could act at the molecular level to defend us against chitin-containing pathogens. [less ▲]

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See detailPinpointing the origin of plastids using phylogenomics
Baurain, Denis ULg

Scientific conference (2015, April 17)

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See detailRooting the tree of life: the phylogenetic jury is still out.
Gouy, Richard ULg; Baurain, Denis ULg; Philippe, Herve

in Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2015), 370(1678), 20140329

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue ... [more ▼]

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework. [less ▲]

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See detailThe mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae.
Perez, Emilie ULg; Lapaille, Marie; Degand, Herve et al

in Mitochondrion (2014), 19 Pt B

The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential ... [more ▼]

The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologs to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native- and SDS-PAGE to both confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa. [less ▲]

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See detailEvolution des eucaryotes : l'éclairage de la phylogénie moléculaire
Baurain, Denis ULg

Conference (2014, October 23)

Ce cours-conférence propose d'examiner l'origine et l'évolution des eucaryotes au travers de la biologie, la géologie et la paléontologie. Les eucaryotes forment un des trois domaines de la vie, et ... [more ▼]

Ce cours-conférence propose d'examiner l'origine et l'évolution des eucaryotes au travers de la biologie, la géologie et la paléontologie. Les eucaryotes forment un des trois domaines de la vie, et comprennent les animaux (dont les êtres humains), les plantes et les champignons, mais surtout une énorme majorité de protistes (eucaryotes unicellulaires) dont la diversité reste encore en partie à explorer. De grandes questions restent à élucider quant à l'origine du domaine Eucarya, sa position au sein de l'arbre de la vie, et les modalités et conditions de diversification et d'évolution depuis au moins 1,8 milliards d'années. La première leçon abordera l'origine de la cellule eucaryote, en discutant les différentes hypothèses existantes et la nature de LECA (Last Eucaryotic Common Ancestor). Comment tester ces hypothèses avec de nouvelles approches ? Comment révéler la diversité actuelle des eucaryotes encore en partie inexplorée et quelles réponses peut-elle apporter ? La seconde leçon présentera d'abord l'éclairage de la phylogénie moléculaire : comment utiliser les informations conservées dans le matériel génétique, pour mieux comprendre l'évolution des eucaryotes ? Quelles sont les possibilités et les limitations de la phylogénomique et des horloges moléculaires ? On présentera ensuite les informations enregistrées dans le registre fossile du Précambrien. Comment reconnaitre les eucaryotes fossiles, les étudier, et reconstruire leur évolution et diversification dans les conditions paléoenvironnementales depuis au moins 1,8 milliards d'années ? Ces deux leçons donneront donc un aperçu de l'état des connaissances, des nouvelles méthodes utilisées, et des grandes énigmes à résoudre à propos de notre domaine Eucarya. [less ▲]

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