Agnès GROISILLIER-SEBART
Ingénieure de recherche CNRS
BAP A
Projets
Parcours universitaire
* 1995 : Diplôme d’Etudes Approfondies Œnologie-Ampélologie (Faculté d’Œnologie, Université Victor Segalen, Bordeaux I)
* 1995-1999: Doctorat Sciences Biologiques et Médicales, option Œnologie-Ampélologie (Faculté d’Œnologie, Université Victor Segalen, Bordeaux II)
Publications
1 publication
Timothée, Chaumier; Yang, Feng; Manirakiza, Eric; Ait-Mohamed, Ouardia; Wu, Yue; Chandola, Udita; Jesus, Bruno; Piganeau, Gwenael; Groisillier, Agnès; Tirichine, Leila
Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum Article de journal
Dans: ISME Communications, vol. 4, iss. 1, p. ycad008, 2024.
@article{Timothée2024,
title = {Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum},
author = {Chaumier Timothée and Feng Yang and Eric Manirakiza and Ouardia Ait-Mohamed and Yue Wu and Udita Chandola and Bruno Jesus and Gwenael Piganeau and Agnès Groisillier and Leila Tirichine},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833087/},
doi = {10.1093/ismeco/ycad008},
year = {2024},
date = {2024-01-10},
urldate = {2024-01-10},
journal = {ISME Communications},
volume = {4},
issue = {1},
pages = {ycad008},
abstract = {Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
1 publication
Hoguin, Antoine; Yang, Feng; Groisillier, Agnès; Bowler, Chris; Genovesio, Auguste; Ait-Mohamed, Ouardia; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases Article de journal
Dans: Communications Biology, vol. 6, iss. 1, no. 1, p. 253, 2023, ISSN: 23993642.
@article{Hoguin2023,
title = {The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases},
author = {Antoine Hoguin and Feng Yang and Agnès Groisillier and Chris Bowler and Auguste Genovesio and Ouardia Ait-Mohamed and Fabio Rocha Jimenez Vieira and Leila Tirichine},
editor = {Nature},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9998398/
hal-04024906v1 },
doi = {10.1038/s42003-023-04629-0 },
issn = {23993642},
year = {2023},
date = {2023-03-09},
urldate = {2023-03-09},
journal = {Communications Biology},
volume = {6},
number = {1},
issue = {1},
pages = {253},
abstract = {Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.
1 publication
Strat, Yoran Le; Tonon, Thierry; Leblanc, Catherine; Groisillier, Agnès
Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases Article de journal
Dans: 2022.
@article{nokey,
title = {Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases},
author = {Yoran Le Strat and Thierry Tonon and Catherine Leblanc and Agnès Groisillier},
url = {https://doi.org/10.3390/phycology3010001
https://hal.science/hal-04256946v1
hal-04256946v1},
doi = {10.3390/phycology3010001},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
abstract = {Citation: Le Strat, Y.; Tonon, T.; Leblanc, C.; Groisillier, A. Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases. Phycology 2023, 3, 1-12. https:// Abstract: Macroalgae (seaweeds) are key primary producers in marine coastal habitats and largely contribute to global ocean carbon fluxes. They also represent attractive renewable feedstock for the production of biofuels, food, feed, and bioactive. Brown algae are seaweeds that produce alginates and fucose containing sulfated polysaccharides in their cell wall and laminarin and mannitol for carbon storage. The availability of genomes of the kelp Saccharina japonica and of the filamentous Ectocarpus sp. paved the way for the biochemical characterization of recombinant enzymes involved in their polysaccharide and carbohydrates synthesis, including, notably, mannitol. Brown algal mannitol biosynthesis starts with the conversion of fructose-6-phospate into mannitol-1-phosphate (mannitol-1P), and this intermediate is hydrolysed by a haloacid dehalogenase phosphatase (M1Pase) to produce mannitol. We report here the biochemical characterization of a second M1Pase in Ectocarpus sp. (EsM1Pase1). Both Ectocarpus M1Pases were redox-sensitive enzymes, with EsM1Pase1 active only in presence of the reducing agent. Such catalytic properties have not been observed for any M1Pases yet. EsM1Pases were specific to mannitol-1-P, in contrast to S. japonica M1Pases that could act on other phosphorylated sugars. Finally, brown algal M1Pases formed two well-supported clades, with possible distinct subcellular localization and physiological role(s) under diverse environmental conditions and/or life cycle stages.},
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Citation: Le Strat, Y.; Tonon, T.; Leblanc, C.; Groisillier, A. Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases. Phycology 2023, 3, 1-12. https:// Abstract: Macroalgae (seaweeds) are key primary producers in marine coastal habitats and largely contribute to global ocean carbon fluxes. They also represent attractive renewable feedstock for the production of biofuels, food, feed, and bioactive. Brown algae are seaweeds that produce alginates and fucose containing sulfated polysaccharides in their cell wall and laminarin and mannitol for carbon storage. The availability of genomes of the kelp Saccharina japonica and of the filamentous Ectocarpus sp. paved the way for the biochemical characterization of recombinant enzymes involved in their polysaccharide and carbohydrates synthesis, including, notably, mannitol. Brown algal mannitol biosynthesis starts with the conversion of fructose-6-phospate into mannitol-1-phosphate (mannitol-1P), and this intermediate is hydrolysed by a haloacid dehalogenase phosphatase (M1Pase) to produce mannitol. We report here the biochemical characterization of a second M1Pase in Ectocarpus sp. (EsM1Pase1). Both Ectocarpus M1Pases were redox-sensitive enzymes, with EsM1Pase1 active only in presence of the reducing agent. Such catalytic properties have not been observed for any M1Pases yet. EsM1Pases were specific to mannitol-1-P, in contrast to S. japonica M1Pases that could act on other phosphorylated sugars. Finally, brown algal M1Pases formed two well-supported clades, with possible distinct subcellular localization and physiological role(s) under diverse environmental conditions and/or life cycle stages.
1 publication
Rathor, Pramod; Borza, Tudor; Liu, Yanhui; Qin, Yuan; Stone, Sophia; Zhang, Junzeng; Hui, Joseph P M; Berrue, Fabrice; Groisillier, Agnès; Tonon, Thierry; Yurgel, Svetlana; Potin, Philippe; Prithiviraj, Balakrishnan
Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance Article de journal
Dans: Plants, vol. 9, no. 11, 2020, ISSN: 2223-7747.
@article{plants9111508,
title = {Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance},
author = {Pramod Rathor and Tudor Borza and Yanhui Liu and Yuan Qin and Sophia Stone and Junzeng Zhang and Joseph P M Hui and Fabrice Berrue and Agnès Groisillier and Thierry Tonon and Svetlana Yurgel and Philippe Potin and Balakrishnan Prithiviraj},
url = {https://www.mdpi.com/2223-7747/9/11/1508},
doi = {10.3390/plants9111508},
issn = {2223-7747},
year = {2020},
date = {2020-01-01},
journal = {Plants},
volume = {9},
number = {11},
abstract = {Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3-52.7 nmol g−1 fresh weight of mannitol, which was sufficient to impart salinity and temperature stress tolerance. Transcriptomics revealed significant differences in the expression of numerous genes, in standard and salinity stress conditions, including genes involved in K+ homeostasis, ROS signaling, plant development, photosynthesis, ABA signaling and secondary metabolism. These results suggest that the improved tolerance to salinity stress observed in transgenic plants producing mannitol in µM range is achieved by the activation of a significant number of genes, many of which are involved in priming and modulating the expression of genes involved in a variety of functions including hormone signaling, osmotic and oxidative stress, and ion homeostasis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3–52.7 nmol g−1 fresh weight of mannitol, which was sufficient to impart salinity and temperature stress tolerance. Transcriptomics revealed significant differences in the expression of numerous genes, in standard and salinity stress conditions, including genes involved in K+ homeostasis, ROS signaling, plant development, photosynthesis, ABA signaling and secondary metabolism. These results suggest that the improved tolerance to salinity stress observed in transgenic plants producing mannitol in µM range is achieved by the activation of a significant number of genes, many of which are involved in priming and modulating the expression of genes involved in a variety of functions including hormone signaling, osmotic and oxidative stress, and ion homeostasis.
2020
Dittami, Simon M; Corre, Erwan; Brillet-Guéguen, Loraine; Lipinska, Agnieszka P; Pontoizeau, Noé; Aite, Meziane; Avia, Komlan; Caron, Christophe; Cho, Chung Hyun; Collén, Jonas; Cormier, Alexandre; Delage, Ludovic; Doubleau, Sylvie; Frioux, Clémence; Gobet, Angélique; González-Navarrete, Irene; Groisillier, Agnès; Hervé, Cécile; Jollivet, Didier; KleinJan, Hetty; Leblanc, Catherine; Liu, Xi; Marie, Dominique; Markov, Gabriel V; Minoche, André E; Monsoor, Misharl; Pericard, Pierre; Perrineau, Marie-Mathilde; Peters, Akira F; Siegel, Anne; Siméon, Amandine; Trottier, Camille; Yoon, Hwan Su; Himmelbauer, Heinz; Boyen, Catherine; Tonon, Thierry
The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga Article de journal
Dans: Marine Genomics, vol. 52, p. 100740, 2020, ISSN: 1874-7787.
@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}
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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.
2019
Michel, Gurvan; Guillouzo, Alexia; Massé, Bertille; Génicot, Sabine; Groisillier, Agnès
Novel Ulvan lyase and use thereof for cleaving polysaccharides Patent
US20190323048A1, 2019, (US Patent App. 16/333,207).
@patent{michel2019novel,
title = {Novel Ulvan lyase and use thereof for cleaving polysaccharides},
author = {Gurvan Michel and Alexia Guillouzo and Bertille Massé and Sabine Génicot and Agnès Groisillier},
url = {https://patents.google.com/patent/US20190323048A1/en},
year = {2019},
date = {2019-10-24},
number = {US20190323048A1},
publisher = {Google Patents},
location = {Centre National de la Recherche Scientifique CNRS, Sorbonne Universite},
abstract = {Some embodiments are directed to a novel ulvan lyase, a nucleic acid sequence coding for said enzyme, a vector comprising said coding sequence, a method for manufacturing said ulvan lyase, and a method for producing ulvan oligosaccharides with biological activity using said enzyme},
note = {US Patent App. 16/333,207},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
Some embodiments are directed to a novel ulvan lyase, a nucleic acid sequence coding for said enzyme, a vector comprising said coding sequence, a method for manufacturing said ulvan lyase, and a method for producing ulvan oligosaccharides with biological activity using said enzyme
2018
Groisillier, Agnès
Cloning and expression strategies for the post-genomic analysis of brown algae Chapitre d'ouvrage
Dans: Charrier, Bénédicte; Wichard, Thomas; Reddy, C R K (Ed.): Protocols for Macroalgae Research, Chapitre 30, p. 453–468, CRC Press, 2018, ISBN: 9781498796422.
@inbook{groisillier2018cloning,
title = {Cloning and expression strategies for the post-genomic analysis of brown algae},
author = {Agnès Groisillier},
editor = {Bénédicte Charrier and Thomas Wichard and C R K Reddy},
doi = {https://doi.org/10.1201/b21460},
isbn = {9781498796422},
year = {2018},
date = {2018-01-01},
booktitle = {Protocols for Macroalgae Research},
journal = {Protocols for macroalgae research},
pages = {453--468},
publisher = {CRC Press},
chapter = {30},
abstract = {The production of stable and soluble proteins is one of the most important steps before structural and functional studies of biological importance. An alternative to obtaining native enzymes is the purification of recombinant enzymes after expression of genes of interest in a heterologous host, in particular the bacteria Escherichia coli. One of the advantages of this approach is to quickly produce bacterial biomass likely to contain the proteins of interest. This protocol describes the different steps to cloning, expression, and purification of protein identified in the brown alga Ectocarpus siliculosus.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
The production of stable and soluble proteins is one of the most important steps before structural and functional studies of biological importance. An alternative to obtaining native enzymes is the purification of recombinant enzymes after expression of genes of interest in a heterologous host, in particular the bacteria Escherichia coli. One of the advantages of this approach is to quickly produce bacterial biomass likely to contain the proteins of interest. This protocol describes the different steps to cloning, expression, and purification of protein identified in the brown alga Ectocarpus siliculosus.
2016
Groisillier, Agnès; Tonon, Thierry
Determination of Recombinant Mannitol-1-phosphate Dehydrogenase Activity from Ectocarpus sp. Article de journal
Dans: BIO-PROTOCOL, vol. 6, no. 21, 2016.
@article{EQ5:Groisillier:2016,
title = {Determination of Recombinant Mannitol-1-phosphate Dehydrogenase Activity from Ectocarpus sp.},
author = {Agnès Groisillier and Thierry Tonon},
url = {https://doi.org/10.21769/bioprotoc.1982},
doi = {10.21769/bioprotoc.1982},
year = {2016},
date = {2016-01-01},
journal = {BIO-PROTOCOL},
volume = {6},
number = {21},
publisher = {Bio-Protocol, LLC},
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pubstate = {published},
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Groisillier, Agnès; Tonon, Thierry
Determination of Recombinant Mannitol-1-phosphatase Activity from Ectocarpus sp. Article de journal
Dans: BIO-PROTOCOL, vol. 6, no. 16, 2016.
@article{EQ5:Groisillier:2016b,
title = {Determination of Recombinant Mannitol-1-phosphatase Activity from Ectocarpus sp.},
author = {Agnès Groisillier and Thierry Tonon},
url = {https://doi.org/10.21769%2Fbioprotoc.1896},
doi = {10.21769/bioprotoc.1896},
year = {2016},
date = {2016-01-01},
journal = {BIO-PROTOCOL},
volume = {6},
number = {16},
publisher = {Bio-Protocol, LLC},
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2015
Bonin, Patricia; Groisillier, Agnès; Raimbault, Alice; Guibert, Anaïs; Boyen, Catherine; Tonon, Thierry
Molecular and biochemical characterization of mannitol-1-phosphate dehydrogenase from the model brown alga Ectocarpus sp Article de journal
Dans: Phytochemistry, vol. 117, p. 509-520, 2015.
@article{EQ5:Groisillier:2015c,
title = {Molecular and biochemical characterization of mannitol-1-phosphate dehydrogenase from the model brown alga Ectocarpus sp},
author = {Patricia Bonin and Agnès Groisillier and Alice Raimbault and Anaïs Guibert and Catherine Boyen and Thierry Tonon},
doi = {10.1016/j.phytochem.2015.07.015},
year = {2015},
date = {2015-09-01},
journal = {Phytochemistry},
volume = {117},
pages = {509-520},
abstract = {The sugar alcohol mannitol is important in the food, pharmaceutical, medical and chemical industries. It is one of the most commonly occurring polyols in nature, with the exception of Archaea and animals. It has a range of physiological roles, including as carbon storage, compatible solute, and osmolyte. Mannitol is present in large amounts in brown algae, where its synthesis involved two steps: a mannitol-1-phosphate dehydrogenase (M1PDH) catalyzes a reversible reaction between fructose-6-phosphate (F6P) and mannitol-1-phosphate (M1P) (EC 1.1.1.17), and a mannitol-1-phosphatase hydrolyzes M1P to mannitol (EC 3.1.3.22). Analysis of the model brown alga Ectocarpus sp. genome provided three candidate genes for M1PDH activities. We report here the sequence analysis of Ectocarpus M1PDHs (EsM1PDHs), and the biochemical characterization of the recombinant catalytic domain of EsM1PDH1 (EsM1PDH1cat). Ectocarpus M1PDHs are representatives of a new type of modular M1PDHs among the polyol-specific long-chain dehydrogenases/reductases (PSLDRs). The N-terminal domain of EsM1PDH1 was not necessary for enzymatic activity. Determination of kinetic parameters indicated that EsM1PDH1cat displayed higher catalytic efficiency for F6P reduction compared to M1P oxidation. Both activities were influenced by NaCl concentration and inhibited by the thioreactive compound pHMB. These observations were completed by measurement of endogenous M1PDH activity and of EsM1PDH gene expression during one diurnal cycle. No significant changes in enzyme activity were monitored between day and night, although transcription of two out of three genes was altered, suggesting different levels of regulation for this key metabolic pathway in brown algal physiology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The sugar alcohol mannitol is important in the food, pharmaceutical, medical and chemical industries. It is one of the most commonly occurring polyols in nature, with the exception of Archaea and animals. It has a range of physiological roles, including as carbon storage, compatible solute, and osmolyte. Mannitol is present in large amounts in brown algae, where its synthesis involved two steps: a mannitol-1-phosphate dehydrogenase (M1PDH) catalyzes a reversible reaction between fructose-6-phosphate (F6P) and mannitol-1-phosphate (M1P) (EC 1.1.1.17), and a mannitol-1-phosphatase hydrolyzes M1P to mannitol (EC 3.1.3.22). Analysis of the model brown alga Ectocarpus sp. genome provided three candidate genes for M1PDH activities. We report here the sequence analysis of Ectocarpus M1PDHs (EsM1PDHs), and the biochemical characterization of the recombinant catalytic domain of EsM1PDH1 (EsM1PDH1cat). Ectocarpus M1PDHs are representatives of a new type of modular M1PDHs among the polyol-specific long-chain dehydrogenases/reductases (PSLDRs). The N-terminal domain of EsM1PDH1 was not necessary for enzymatic activity. Determination of kinetic parameters indicated that EsM1PDH1cat displayed higher catalytic efficiency for F6P reduction compared to M1P oxidation. Both activities were influenced by NaCl concentration and inhibited by the thioreactive compound pHMB. These observations were completed by measurement of endogenous M1PDH activity and of EsM1PDH gene expression during one diurnal cycle. No significant changes in enzyme activity were monitored between day and night, although transcription of two out of three genes was altered, suggesting different levels of regulation for this key metabolic pathway in brown algal physiology.
Groisillier, Agnès; Tonon, Thierry
Determination of Fructokinase Activity from Zobellia galactanivorans Article de journal
Dans: BIO-PROTOCOL, vol. 5, no. 21, 2015.
@article{EQ5:Groisillier:2015,
title = {Determination of Fructokinase Activity from Zobellia galactanivorans},
author = {Agnès Groisillier and Thierry Tonon},
url = {https://doi.org/10.21769/bioprotoc.1633},
doi = {10.21769/bioprotoc.1633},
year = {2015},
date = {2015-01-01},
journal = {BIO-PROTOCOL},
volume = {5},
number = {21},
publisher = {Bio-Protocol, LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Groisillier, Agnès; Tonon, Thierry
Determination of Mannitol-2-dehydrogenase Activity Article de journal
Dans: BIO-PROTOCOL, vol. 5, no. 21, 2015.
@article{EQ5:Groisillier:2015b,
title = {Determination of Mannitol-2-dehydrogenase Activity},
author = {Agnès Groisillier and Thierry Tonon},
url = {https://doi.org/10.21769/bioprotoc.1634},
doi = {10.21769/bioprotoc.1634},
year = {2015},
date = {2015-01-01},
journal = {BIO-PROTOCOL},
volume = {5},
number = {21},
publisher = {Bio-Protocol, LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Groisillier, Agnès; Labourel, Aurore; Michel, Gurvan; Tonon, Thierry
The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans Article de journal
Dans: Applied and Environmental Microbiology, vol. 81, no. 5, p. 1799–1812, 2015, ISSN: 0099-2240.
@article{EQ5:Groisillier:2015d,
title = {The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans},
author = {Agnès Groisillier and Aurore Labourel and Gurvan Michel and Thierry Tonon},
editor = {H Nojiri},
url = {https://aem.asm.org/content/81/5/1799},
doi = {10.1128/AEM.02808-14},
issn = {0099-2240},
year = {2015},
date = {2015-01-01},
journal = {Applied and Environmental Microbiology},
volume = {81},
number = {5},
pages = {1799--1812},
publisher = {American Society for Microbiology Journals},
abstract = {Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans (Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K+. Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans (Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K+. Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.
Ficko-Blean, Elizabeth; Duffieux, Delphine; Rebuffet, Étienne; Larocque, Robert; Groisillier, Agnes; Michel, Gurvan; Czjzek, Mirjam
Dans: Acta Crystallographica Section D Biological Crystallography, vol. 71, no. 2, p. 209–223, 2015.
@article{EQ5:GROISILLIER:2015e,
title = {Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family},
author = {Elizabeth Ficko-Blean and Delphine Duffieux and Étienne Rebuffet and Robert Larocque and Agnes Groisillier and Gurvan Michel and Mirjam Czjzek},
url = {https://doi.org/10.1107%2Fs1399004714025024},
doi = {10.1107/s1399004714025024},
year = {2015},
date = {2015-01-01},
journal = {Acta Crystallographica Section D Biological Crystallography},
volume = {71},
number = {2},
pages = {209--223},
publisher = {International Union of Crystallography (IUCr)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2014
Collén, Pi Nyvall; Jeudy, Alexandra; Sassi, Jean-François; Groisillier, Agnès; Czjzek, Mirjam; Coutinho, Pedro M; Helbert, William
A Novel Unsaturated β-Glucuronyl Hydrolase Involved in Ulvan Degradation Unveils the Versatility of Stereochemistry Requirements in Family GH105* Article de journal
Dans: Journal of Biological Chemistry, vol. 289, no. 9, p. 6199-6211, 2014, ISSN: 0021-9258.
@article{COLLEN20146199,
title = {A Novel Unsaturated β-Glucuronyl Hydrolase Involved in Ulvan Degradation Unveils the Versatility of Stereochemistry Requirements in Family GH105*},
author = {Pi Nyvall Collén and Alexandra Jeudy and Jean-François Sassi and Agnès Groisillier and Mirjam Czjzek and Pedro M Coutinho and William Helbert},
url = {https://www.sciencedirect.com/science/article/pii/S0021925820440797},
doi = {https://doi.org/10.1074/jbc.M113.537480},
issn = {0021-9258},
year = {2014},
date = {2014-01-01},
journal = {Journal of Biological Chemistry},
volume = {289},
number = {9},
pages = {6199-6211},
abstract = {Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.
Dittami, Simon M; Barbeyron, Tristan; Boyen, Catherine; Cambefort, Jeanne; Collet, Guillaume; Delage, Ludovic; Gobet, Angélique; Groisillier, Agnès; Leblanc, Catherine; Michel, Gurvan; Scornet, Delphine; Siegel, Anne; Tapia, Javier E; Tonon, Thierry
Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae Article de journal
Dans: Frontiers in Genetics, vol. 5, p. 241, 2014, ISSN: 1664-8021.
@article{10.3389/fgene.2014.00241,
title = {Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae},
author = {Simon M Dittami and Tristan Barbeyron and Catherine Boyen and Jeanne Cambefort and Guillaume Collet and Ludovic Delage and Angélique Gobet and Agnès Groisillier and Catherine Leblanc and Gurvan Michel and Delphine Scornet and Anne Siegel and Javier E Tapia and Thierry Tonon},
url = {https://www.frontiersin.org/article/10.3389/fgene.2014.00241},
doi = {10.3389/fgene.2014.00241},
issn = {1664-8021},
year = {2014},
date = {2014-01-01},
journal = {Frontiers in Genetics},
volume = {5},
pages = {241},
abstract = {Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.
Genicot, Sabine M; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William
Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora Article de journal
Dans: Frontiers in Chemistry, vol. 2, p. 67, 2014, ISSN: 2296-2646.
@article{10.3389/fchem.2014.00067,
title = {Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora},
author = {Sabine M Genicot and Agnès Groisillier and Hélène Rogniaux and Laurence Meslet-Cladière and Tristan Barbeyron and William Helbert},
url = {https://www.frontiersin.org/article/10.3389/fchem.2014.00067},
doi = {10.3389/fchem.2014.00067},
issn = {2296-2646},
year = {2014},
date = {2014-01-01},
journal = {Frontiers in Chemistry},
volume = {2},
pages = {67},
abstract = {Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain Psc^{T}. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.
Coste, François; Garet, Gaëlle; Groisillier, Agnès; Nicolas, Jacques; Tonon, Thierry
Automated Enzyme Classification by Formal Concept Analysis Proceedings Article
Dans: Glodeanu, Cynthia Vera; Kaytoue, Mehdi; Sacarea, Christian (Ed.): Formal Concept Analysis, p. 235–250, Springer International Publishing, Cham, 2014, ISBN: 978-3-319-07248-7.
@inproceedings{10.1007/978-3-319-07248-7_17,
title = {Automated Enzyme Classification by Formal Concept Analysis},
author = {François Coste and Gaëlle Garet and Agnès Groisillier and Jacques Nicolas and Thierry Tonon},
editor = {Cynthia Vera Glodeanu and Mehdi Kaytoue and Christian Sacarea},
doi = {10.1007/978-3-319-07248-7_17},
isbn = {978-3-319-07248-7},
year = {2014},
date = {2014-01-01},
booktitle = {Formal Concept Analysis},
pages = {235--250},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {Enzymes are macro-molecules (linear sequences of linked molecules) with a catalytic activity that make them essential for any biochemical reaction. High throughput genomic techniques give access to the sequence of new enzymes found in living organisms. Guessing the enzyme's functional activity from its sequence is a crucial task that can be approached by comparing the new sequences with those of already known enzymes labeled by a family class. This task is difficult because the activity is based on a combination of small sequence patterns and sequences greatly evolved over time. This paper presents a classifier based on the identification of common subsequence blocks between known and new enzymes and the search of formal concepts built on the cross product of blocks and sequences for each class. Since new enzyme families may emerge, it is important to propose a first classification of enzymes that cannot be assigned to a known family. FCA offers a nice framework to set the task as an optimization problem on the set of concepts. The classifier has been tested with success on a particular set of enzymes present in a large variety of species, the haloacid dehalogenase superfamily.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Enzymes are macro-molecules (linear sequences of linked molecules) with a catalytic activity that make them essential for any biochemical reaction. High throughput genomic techniques give access to the sequence of new enzymes found in living organisms. Guessing the enzyme's functional activity from its sequence is a crucial task that can be approached by comparing the new sequences with those of already known enzymes labeled by a family class. This task is difficult because the activity is based on a combination of small sequence patterns and sequences greatly evolved over time. This paper presents a classifier based on the identification of common subsequence blocks between known and new enzymes and the search of formal concepts built on the cross product of blocks and sequences for each class. Since new enzyme families may emerge, it is important to propose a first classification of enzymes that cannot be assigned to a known family. FCA offers a nice framework to set the task as an optimization problem on the set of concepts. The classifier has been tested with success on a particular set of enzymes present in a large variety of species, the haloacid dehalogenase superfamily.
2013
Groisillier, Agnès; Shao, Zhanru; Michel, Gurvan; Goulitquer, Sophie; Bonin, Patricia; Krahulec, Stefan; Nidetzky, Bernd; Duan, Delin; Boyen, Catherine; Tonon, Thierry
Mannitol metabolism in brown algae involves a new phosphatase family Article de journal
Dans: Journal of Experimental Botany, vol. 65, no. 2, p. 559-570, 2013, ISSN: 0022-0957.
@article{10.1093/jxb/ert405,
title = {Mannitol metabolism in brown algae involves a new phosphatase family},
author = {Agnès Groisillier and Zhanru Shao and Gurvan Michel and Sophie Goulitquer and Patricia Bonin and Stefan Krahulec and Bernd Nidetzky and Delin Duan and Catherine Boyen and Thierry Tonon},
url = {https://doi.org/10.1093/jxb/ert405},
doi = {10.1093/jxb/ert405},
issn = {0022-0957},
year = {2013},
date = {2013-01-01},
journal = {Journal of Experimental Botany},
volume = {65},
number = {2},
pages = {559-570},
abstract = {Brown algae belong to a phylogenetic lineage distantly related to green plants and animals, and are found predominantly in the intertidal zone, a harsh and frequently changing environment. Because of their unique evolutionary history and of their habitat, brown algae feature several peculiarities in their metabolism. One of these is the mannitol cycle, which plays a central role in their physiology, as mannitol acts as carbon storage, osmoprotectant, and antioxidant. This polyol is derived directly from the photoassimilate fructose-6-phosphate via the action of a mannitol-1-phosphate dehydrogenase and a mannitol-1-phosphatase (M1Pase). Genome analysis of the brown algal model Ectocarpus siliculosus allowed identification of genes potentially involved in the mannitol cycle. Among these, two genes coding for haloacid dehalogenase (HAD)-like enzymes were suggested to correspond to M1Pase activity, and thus were named EsM1Pase1 and EsM1Pase2, respectively. To test this hypothesis, both genes were expressed in Escherichia coli. Recombinant EsM1Pase2 was shown to hydrolyse the phosphate group from mannitol-1-phosphate to produce mannitol but was not active on the hexose monophosphates tested. Gene expression analysis showed that transcription of both E. siliculosus genes was under the influence of the diurnal cycle. Sequence analysis and three-dimensional homology modelling indicated that EsM1Pases, and their orthologues in Prasinophytes, should be seen as founding members of a new family of phosphatase with original substrate specificity within the HAD superfamily of proteins. This is the first report describing the characterization of a gene encoding M1Pase activity in photosynthetic organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brown algae belong to a phylogenetic lineage distantly related to green plants and animals, and are found predominantly in the intertidal zone, a harsh and frequently changing environment. Because of their unique evolutionary history and of their habitat, brown algae feature several peculiarities in their metabolism. One of these is the mannitol cycle, which plays a central role in their physiology, as mannitol acts as carbon storage, osmoprotectant, and antioxidant. This polyol is derived directly from the photoassimilate fructose-6-phosphate via the action of a mannitol-1-phosphate dehydrogenase and a mannitol-1-phosphatase (M1Pase). Genome analysis of the brown algal model Ectocarpus siliculosus allowed identification of genes potentially involved in the mannitol cycle. Among these, two genes coding for haloacid dehalogenase (HAD)-like enzymes were suggested to correspond to M1Pase activity, and thus were named EsM1Pase1 and EsM1Pase2, respectively. To test this hypothesis, both genes were expressed in Escherichia coli. Recombinant EsM1Pase2 was shown to hydrolyse the phosphate group from mannitol-1-phosphate to produce mannitol but was not active on the hexose monophosphates tested. Gene expression analysis showed that transcription of both E. siliculosus genes was under the influence of the diurnal cycle. Sequence analysis and three-dimensional homology modelling indicated that EsM1Pases, and their orthologues in Prasinophytes, should be seen as founding members of a new family of phosphatase with original substrate specificity within the HAD superfamily of proteins. This is the first report describing the characterization of a gene encoding M1Pase activity in photosynthetic organisms.
Collén, Jonas; Porcel, Betina; Carré, Wilfrid; Ball, Steven G; Chaparro, Cristian; Tonon, Thierry; Barbeyron, Tristan; Michel, Gurvan; Noel, Benjamin; Valentin, Klaus; Elias, Marek; Artiguenave, François; Arun, Alok; Aury, Jean-Marc; Barbosa-Neto, José F; Bothwell, John H; Bouget, François-Yves; Brillet, Loraine; Cabello-Hurtado, Francisco; Capella-Gutiérrez, Salvador; Charrier, Bénédicte; Cladière, Lionel; Cock, Mark J; Coelho, Susana M; Colleoni, Christophe; Czjzek, Mirjam; Silva, Corinne Da; Delage, Ludovic; Denoeud, France; Deschamps, Philippe; Dittami, Simon M; Gabaldón, Toni; Gachon, Claire M M; Groisillier, Agnès; Hervé, Cécile; Jabbari, Kamel; Katinka, Michael; Kloareg, Bernard; Kowalczyk, Nathalie; Labadie, Karine; Leblanc, Catherine; Lopez, Pascal J; McLachlan, Deirdre H; Meslet-Cladiere, Laurence; Moustafa, Ahmed; Nehr, Zofia; Collén, Pi Nyvall; Panaud, Olivier; Partensky, Frédéric; Poulain, Julie; Rensing, Stefan A; Rousvoal, Sylvie; Samson, Gaelle; Symeonidi, Aikaterini; Weissenbach, Jean; Zambounis, Antonios; Wincker, Patrick; Boyen, Catherine
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida Article de journal
Dans: Proceedings of the National Academy of Sciences, vol. 110, no. 13, p. 5247–5252, 2013, ISSN: 0027-8424.
@article{Collén5247,
title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida},
author = {Jonas Collén and Betina Porcel and Wilfrid Carré and Steven G Ball and Cristian Chaparro and Thierry Tonon and Tristan Barbeyron and Gurvan Michel and Benjamin Noel and Klaus Valentin and Marek Elias and François Artiguenave and Alok Arun and Jean-Marc Aury and José F Barbosa-Neto and John H Bothwell and François-Yves Bouget and Loraine Brillet and Francisco Cabello-Hurtado and Salvador Capella-Gutiérrez and Bénédicte Charrier and Lionel Cladière and Mark J Cock and Susana M Coelho and Christophe Colleoni and Mirjam Czjzek and Corinne Da Silva and Ludovic Delage and France Denoeud and Philippe Deschamps and Simon M Dittami and Toni Gabaldón and Claire M M Gachon and Agnès Groisillier and Cécile Hervé and Kamel Jabbari and Michael Katinka and Bernard Kloareg and Nathalie Kowalczyk and Karine Labadie and Catherine Leblanc and Pascal J Lopez and Deirdre H McLachlan and Laurence Meslet-Cladiere and Ahmed Moustafa and Zofia Nehr and Pi Nyvall Collén and Olivier Panaud and Frédéric Partensky and Julie Poulain and Stefan A Rensing and Sylvie Rousvoal and Gaelle Samson and Aikaterini Symeonidi and Jean Weissenbach and Antonios Zambounis and Patrick Wincker and Catherine Boyen},
url = {https://www.pnas.org/content/110/13/5247},
doi = {10.1073/pnas.1221259110},
issn = {0027-8424},
year = {2013},
date = {2013-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {110},
number = {13},
pages = {5247--5252},
publisher = {National Academy of Sciences},
abstract = {Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.