@article{EQ5:GROISILLIER:2020,

title = {The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga},

author = {Simon M Dittami and Erwan Corre and Loraine Brillet-Guéguen and Agnieszka P Lipinska and Noé Pontoizeau and Meziane Aite and Komlan Avia and Christophe Caron and Chung Hyun Cho and Jonas Collén and Alexandre Cormier and Ludovic Delage and Sylvie Doubleau and Clémence Frioux and Angélique Gobet and Irene González-Navarrete and Agnès Groisillier and Cécile Hervé and Didier Jollivet and Hetty KleinJan and Catherine Leblanc and Xi Liu and Dominique Marie and Gabriel V Markov and André E Minoche and Misharl Monsoor and Pierre Pericard and Marie-Mathilde Perrineau and Akira F Peters and Anne Siegel and Amandine Siméon and Camille Trottier and Hwan Su Yoon and Heinz Himmelbauer and Catherine Boyen and Thierry Tonon},

url = {http://www.sciencedirect.com/science/article/pii/S1874778720300015},

doi = {https://doi.org/10.1016/j.margen.2020.100740},

issn = {1874-7787},

year  = {2020},

date = {2020-08-01},

journal = {Marine Genomics},

volume = {52},

pages = {100740},

abstract = {Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus KÛtzing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Belcour2020,

title = {Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift},

author = {Arnaud Belcour and Jean Girard and Méziane Aite and Ludovic Delage and Camille Trottier and Charlotte Marteau and Cédric Leroux and Simon M Dittami and Pierre Sauleau and Erwan Corre and Jacques Nicolas and Catherine Boyen and Catherine Leblanc and Jonas Collén and Anne Siegel and Gabriel V Markov},

url = {https://www.sciencedirect.com/science/article/pii/S2589004220300328},

doi = {10.1016/J.ISCI.2020.100849},

issn = {2589-0042},

year  = {2020},

date = {2020-02-01},

journal = {iScience},

volume = {23},

number = {2},

pages = {100849},

publisher = {Elsevier},

abstract = {Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as “metabolic pathway drift,” is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Frioux2018,

title = {Scalable and exhaustive screening of metabolic functions carried out by microbial consortia},

author = {Clémence Frioux and Enora Fremy and Camille Trottier and Anne Siegel},

url = {https://academic.oup.com/bioinformatics/article/34/17/i934/5093211},

doi = {10.1093/bioinformatics/bty588},

issn = {1367-4803},

year  = {2018},

date = {2018-09-01},

journal = {Bioinformatics},

volume = {34},

number = {17},

pages = {i934--i943},

publisher = {Oxford University Press},

abstract = {Motivation. The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far. 

Results. We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria. 

Availability and implementation. Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Aite2018,

title = {Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models},

author = {Méziane Aite and Marie Chevallier and Clémence Frioux and Camille Trottier and Jeanne Got and Maria Paz Cortés and Sebastiàn N Mendoza and Grégory Carrier and Olivier Dameron and Nicolas Guillaudeux and Mauricio Latorre and Nicolàs Loira and Gabriel V Markov and Alejandro Maass and Anne Siegel},

editor = {Jens Nielsen},

url = {http://dx.plos.org/10.1371/journal.pcbi.1006146},

doi = {10.1371/journal.pcbi.1006146},

issn = {1553-7358},

year  = {2018},

date = {2018-05-01},

journal = {PLOS Computational Biology},

volume = {14},

number = {5},

pages = {e1006146},

publisher = {Public Library of Science},

abstract = {Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from “à la carte” pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thiriet-Rupert2018,

title = {Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea},

author = {S Thiriet-Rupert and G Carrier and Camille Trottier and D Eveillard and B Schoefs and G Bougaran and J -P Cadoret and B Chénais and B Saint-Jean},

doi = {10.1016/j.algal.2017.12.011},

issn = {22119264},

year  = {2018},

date = {2018-01-01},

journal = {Algal Research},

volume = {30},

abstract = {Microalgae are an outstanding source of high value products with applications in food, feed or biofuel production. Among these promising organisms, the haptophyte Tisochrysis lutea is commonly used as a feed for shellfish and shrimps in aquaculture. Its capacity to produce high amounts of docosahexanoic acid and storage lipids is also of economic interest for nutrition and energy production. Consequently, understanding its lipid accumulation under nitrogen deprivation is of major interest. Here, we aimed to identify Transcription Factors (TFs) involved in the establishment of the mutant phenotype of the 2Xc1 strain of T. lutea, which accumulates double the quantity of storage lipids under nitrogen deprivation than the wild type strain (WTc1). Strains were grown in chemostats and subjected to different nitrogen availability (limitation, repletion and depletion). Using RNA-seq data, the differentially expressed genes (DEGs) between strains were identified and summarized as a co-expression network to pinpoint putative major TFs in mutant phenotypes. This analysis was followed by a complementary Weighted Gene Correlation Network Analysis in order to classify genes based on their relative importance to mutant phenotype features, regardless of annotation biases due to the lack of functional annotation of the Tisochrysis lutea draft genome. This network-like strategy allowed the identification of seven TF candidates related to key functions in the mutant strain compared with WTc1. In particular, MYB-2R_14 and NF-YB_2 TFs are related to photosynthesis, oxidative stress response and triacylglycerol synthesis. GATA_2, MYB-rel_11 and MYB-2R_20 TFs are likely to be related to nitrogen uptake or carbon and nitrogen recycling, feeding carbohydrate synthesis in the form of chrysolaminarin. Finally, a q-RT-PCR approach further characterized the role of MYB-rel_11 and MYB-2R_20, revealing an expression pattern dependent on nitrogen availability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Laniau2017,

title = {Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks},

author = {J Laniau and C Frioux and J Nicolas and C Baroukh and M-P Cortes and J Got and Camille Trottier and D Eveillard and A Siegel},

doi = {10.7717/peerj.3860},

issn = {21678359},

year  = {2017},

date = {2017-01-01},

journal = {PeerJ},

volume = {2017},

number = {10},

abstract = {Background. The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions. In both approaches, this analysis is generally centered on the outcome of the network and considers all metabolic compounds to be equivalent in this respect. As in the case of genes and reactions, about which the concept of essentiality has been developed, it seems, however, that some metabolites play crucial roles in system responses, due to the cell structure or the internal wiring of the metabolic network. Results. We propose a classification of metabolic compounds according to their capacity to influence the activation of targeted functions (generally the growth phenotype) in a cell. We generalize the concept of essentiality to metabolites and introduce the concept of the phenotypic essential metabolite (PEM) which influences the growth phenotype according to sustainability, producibility or optimal-efficiency criteria. We have developed and made available a tool, Conquests, which implements a method combining graph-based and flux-based analysis, two approaches that are usually considered separately. The identification of PEMs is made effective by using a logical programming approach. Conclusion. The exhaustive study of phenotypic essential metabolites in six genomescale metabolic models suggests that the combination and the comparison of graph, stoichiometry and optimal flux-based criteria allows some features of the metabolic network functionality to be deciphered by focusing on a small number of compounds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thiriet-Rupert2016,

title = {Transcription factors in microalgae: genome-wide prediction and comparative analysis},

author = {Stanislas Thiriet-Rupert and Grégory Carrier and Benoît Chénais and Camille Trottier and Gaël Bougaran and Jean-Paul Cadoret and Benoît Schoefs and Bruno Saint-Jean},

url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2610-9},

doi = {10.1186/s12864-016-2610-9},

issn = {1471-2164},

year  = {2016},

date = {2016-12-01},

journal = {BMC Genomics},

volume = {17},

number = {1},

pages = {282},

publisher = {BioMed Central},

abstract = {Studying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features. In this study we performed the first genome-wide TF identification and comparison between haptophytes and other algal lineages. For TF identification and classification, we created a comprehensive pipeline using a combination of BLAST, HMMER and InterProScan software. The accuracy evaluation of the pipeline shows its applicability for every alga, plant and cyanobacterium, with very good PPV and sensitivity. This pipeline allowed us to identify and classified the transcription factor complement of the three haptophytes Tisochrysis lutea, Emiliania huxleyi and Pavlova sp.; the two stramenopiles Phaeodactylum tricornutum and Nannochloropsis gaditana; the chlorophyte Chlamydomonas reinhardtii and the rhodophyte Porphyridium purpureum. By using T. lutea and Porphyridium purpureum, this work extends the variety of species included in such comparative studies, allowing the detection and detailed study of lineage-specific features, such as the presence of TF families specific to the green lineage in Porphyridium purpureum, haptophytes and stramenopiles. Our comprehensive pipeline also allowed us to identify fungal and cyanobacterial TF families in the algal nuclear genomes. This study provides examples illustrating the complex evolutionary history of algae, some of which support the involvement of a green alga in haptophyte and stramenopile evolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Richard2009,

title = {Submersion time, depth, substrate type and sampling method as variation sources of marine periphyton},

author = {M Richard and Camille Trottier and M C J Verdegem and J M E Hussenot},

url = {https://www.sciencedirect.com/science/article/pii/S004484860900619X},

doi = {10.1016/J.AQUACULTURE.2009.07.005},

issn = {0044-8486},

year  = {2009},

date = {2009-10-01},

journal = {Aquaculture},

volume = {295},

number = {3-4},

pages = {209--217},

publisher = {Elsevier},

abstract = {Periphyton is an additional food source in African and Asian brackish and freshwater fish ponds. The present study was a preliminary assessment of periphyton development on artificial substrates in temperate marine ponds. The effects of submersion time, substrate type, water depth, and total or partial sampling methods on the quantity and quality of periphyton collected, were evaluated. Four types of substrate (W: wooden poles, S: smooth fiber-glass strips, m: mosquito screen (1mm-mesh) and M: garden netting (5mm-mesh)) were deployed in a marine pond, and periphyton was collected 15 and 30days later. The total amount of periphyton per substrate unit was collected as one sample or as 5 sub-samples. Results showed that (i) periphyton biomass in a marine pond increased between day 15 and day 30, (ii) more periphyton was collected on mosquito screen than on wooden poles, fiberglass strips and garden netting, (iii) periphyton biomass increased with submersion depth, (iv) sub-sampling leads to an underestimate compared to whole unit sampling, and (v) a correction of periphyton weight must be carried out considering the dissolved inorganic salts present in periphyton samples from marine and brackish ponds. Whole substrate unit sampling using a tube and stopper is recommended to avoid underestimation of periphyton development. Finally, the autotrophic fraction in the periphyton communities was very low compared to periphyton developed on biodegradable substrates in fertilized tropical ponds. Studies on fertilization and use of biodegraded substrates (i.e. long-time submerged wood) are recommended to further optimize periphyton development in temperate marine ponds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}