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Helene Carrere – One of the best experts on this subject based on the ideXlab platform.

Nicholas D. Gold – One of the best experts on this subject based on the ideXlab platform.

  • Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii.
    PloS one, 2018
    Co-Authors: Yu Zhan, Christophe H. Marchand, Alexandre Maes, Adeline Mauries, Yi Sun, James S. Dhaliwal, James Uniacke, Simon Arragain, Heng Jiang, Nicholas D. Gold
    Abstract:

    Organelles are intracellular compartments which are themselves compartmentalized. Biogenic and metabolic processes are localized to specialized domains or microcompartments to enhance their efficiency and suppress deleterious side reactions. An example of intra-organellar compartmentalization is the pyrenoid in the chloroplasts of algae and hornworts. This microcompartment enhances the photosynthetic CO2-fixing activity of the Calvin-Benson cycle enzyme Rubisco, suppresses an energetically wasteful oxygenase activity of Rubisco, and mitigates limiting CO2 availability in aquatic environments. Hence, the pyrenoid is functionally analogous to the carboxysomes in cyanobacteria. However, a comprehensive analysis of pyrenoid functions based on its protein composition is lacking. Here we report a proteomic characterization of the pyrenoid in the green algaalga Chlamydomonas reinhardtii. Pyrenoid-enriched fractions were analyzed by quantitative mass spectrometry. Contaminant proteins were identified by parallel analyses of pyrenoid-deficient mutants. This pyrenoid proteome contains 190 proteins, many of which function in processes that are known or proposed to occur in pyrenoids: e.g. the carbon concentrating mechanism, starch metabolism or RNA metametabolism and translation. Using radioisotope pulse labeling experiments, we show that pyrenoid-associated ribosomes could be engaged in the localized synthesis of the large subunit of Rubisco. New pyrenoid functions are supported by proteins in tetrapyrrole and chlorophyll synthesis, carotenoid metabolism or amino acid metabolism. Hence, our results support the long-standing hypothesis that the pyrenoid is a hub for metabolism. The 81 proteins of unknown function reveal candidates for new participants in these processes. Our results provide biochemical evidence of pyrenoid functions and a resource for future research on pyrenoids and their use to enhance Agricultural Plant productivity. Data are available via ProteomeXchange with identifier PXD004509.

Abdellatif Barakat – One of the best experts on this subject based on the ideXlab platform.

  • Impact of xylan structure and lignin-xylan association on methane production from C5-sugars.
    Biomass & Bioenergy, 2014
    Co-Authors: Abdellatif Barakat, Amal Kadimi, Jean-philippe Steyer, Helene Carrere
    Abstract:

    Xylan biopolymers are the dominant hemicelluloses present in Agricultural Plant materials which have potential use in various biotechnological processes including methane production. Hence, the effect of lignin content and the structural features of xylan on anaerobic digestion were studied by using synthetic assemblies consisting of xylans and lignin models (dehydrogenation polymers). The ramification by arabinose and uronic acid was shown to be a key factor in low methane potential (BMP) from xylans and xylan–lignin assemblies. Indeed, BMP increased when xylose content was increased, and decreased when arabinose and uronic acid contents were increased. Lignin content and molecular weight were found to be the most influential parameters on the anaerobic digestion rate. Digestion rate decreased when the lignin content and molecular mass increased.

  • Impact of xylan structure and lignine-xylan association on methane production from C5-sugars
    Biomass and Bioenergy, 2014
    Co-Authors: Abdellatif Barakat, Amal Kadimi, Jean-philippe Steyer, Helene Carrere
    Abstract:

    Xylan biopolymers are the dominant hemicelluloses present in Agricultural Plant materials which have potential use in various biotechnological processes including methane production. Hence, the effect of lignin content and the structural features of xylan on anaerobic digestion were studied by using synthetic assemblies consisting of xylans and lignin models (dehydrogenation polymers). The ramification by arabinose and uronic acid was shown to be a key factor in low methane potential (BMP) from xylans and xylanelignin assemblies. Indeed, BMP increased when xylose content was increased, and decreased when arabinose and uronic acid contents were increased. Lignin content and molecular weight were found to be the most influential parameters on the anaerobic digestion rate. Digestion rate decreased when the lignin content and molecular mass increased.

Michael Katinka – One of the best experts on this subject based on the ideXlab platform.

  • The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants
    PLoS genetics, 2014
    Co-Authors: Betina M. Porcel, Fred R. Opperdoes, Benjamin Noel, Mohammed-amine Madoui, Tansy C. Hammarton, Mark C. Field, Corinne Da Silva, Arnaud Couloux, Julie Poulain, Michael Katinka
    Abstract:

    Members of the family Trypanosomatidae infect many organisms, including animals, Plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of Plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict Plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two Plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of Agricultural Plant disease.

Yu Zhan – One of the best experts on this subject based on the ideXlab platform.

  • Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii.
    PloS one, 2018
    Co-Authors: Yu Zhan, Christophe H. Marchand, Alexandre Maes, Adeline Mauries, Yi Sun, James S. Dhaliwal, James Uniacke, Simon Arragain, Heng Jiang, Nicholas D. Gold
    Abstract:

    Organelles are intracellular compartments which are themselves compartmentalized. Biogenic and metabolic processes are localized to specialized domains or microcompartments to enhance their efficiency and suppress deleterious side reactions. An example of intra-organellar compartmentalization is the pyrenoid in the chloroplasts of algae and hornworts. This microcompartment enhances the photosynthetic CO2-fixing activity of the Calvin-Benson cycle enzyme Rubisco, suppresses an energetically wasteful oxygenase activity of Rubisco, and mitigates limiting CO2 availability in aquatic environments. Hence, the pyrenoid is functionally analogous to the carboxysomes in cyanobacteria. However, a comprehensive analysis of pyrenoid functions based on its protein composition is lacking. Here we report a proteomic characterization of the pyrenoid in the green alga Chlamydomonas reinhardtii. Pyrenoid-enriched fractions were analyzed by quantitative mass spectrometry. Contaminant proteins were identified by parallel analyses of pyrenoid-deficient mutants. This pyrenoid proteome contains 190 proteins, many of which function in processes that are known or proposed to occur in pyrenoids: e.g. the carbon concentrating mechanism, starch metabolism or RNA metabolism and translation. Using radioisotope pulse labeling experiments, we show that pyrenoid-associated ribosomes could be engaged in the localized synthesis of the large subunit of Rubisco. New pyrenoid functions are supported by proteins in tetrapyrrole and chlorophyll synthesis, carotenoid metabolism or amino acid metabolism. Hence, our results support the long-standing hypothesis that the pyrenoid is a hub for metabolism. The 81 proteins of unknown function reveal candidates for new participants in these processes. Our results provide biochemical evidence of pyrenoid functions and a resource for future research on pyrenoids and their use to enhance Agricultural Plant productivity. Data are available via ProteomeXchange with identifier PXD004509.

  • Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii
    'Public Library of Science (PLoS)', 2018
    Co-Authors: Yu Zhan, Yi Sun, Marchand, Christophe H., Maes Alexandre, Mauriès Adeline, Dhaliwal James, Uniacke James, Arragain Simon, Jiang Heng, Gold Nicholas
    Abstract:

    International audienceOrganelles are intracellular compartments which are themselves compartmentalized. Bio-genic and metabolic processes are localized to specialized domains or microcompartments to enhance their efficiency and suppress deleterious side reactions. An example of intra-organellar compartmentalization is the pyrenoid in the chloroplasts of algae and hornworts. This microcompartment enhances the photosynthetic CO 2-fixing activity of the Calvin-Ben-son cycle enzyme Rubisco, suppresses an energetically wasteful oxygenase activity of Rubisco, and mitigates limiting CO 2 availability in aquatic environments. Hence, the pyre-noid is functionally analogous to the carboxysomes in cyanobacteria. However, a comprehensive analysis of pyrenoid functions based on its protein composition is lacking. Here we report a proteomic characterization of the pyrenoid in the green algaalga Chlamydomonas rein-hardtii. Pyrenoid-enriched fractions were analyzed by quantitative mass spectrometry. Contaminant proteins were identified by parallel analyses of pyrenoid-deficient mutants. This pyrenoid proteome contains 190 proteins, many of which function in processes that are known or proposed to occur in pyrenoids: e.g. the carbon concentrating mechanism, starch metabolism or RNA metametabolism and translation. Using radioisotope pulse labeling experiments , we show that pyrenoid-associated ribosomes could be engaged in the localized synthesis of the large subunit of Rubisco. New pyrenoid functions are supported by proteins in tetrapyrrole and chlorophyll synthesis, carotenoid metabolism or amino acid metabolism. Hence, our results support the long-standing hypothesis that the pyrenoid is a hub for metabolism. The 81 proteins of unknown function reveal candidates for new participants in these processes. Our results provide biochemical evidence of pyrenoid functions and a resource for future research on pyrenoids and their use to enhance Agricultural Plant productivity. Data are available via ProteomeXchange with identifier PXD004509