Responsable : Leila TIRICHINE
Les microalgues sont à la base de la chaîne alimentaire de l’écosystème marin. Elles jouent un rôle primordial dans l’équilibre de notre planète grâce à leur fonction de photosynthèse qui fait d’elle le premier producteur d’oxygène et un véritable puits de carbone. Au-delà de leur importance écologique, elles représentent une source importante de composés bioactifs utilisés dans les industries pharmaceutiques, agroalimentaires, cosmétiques et de l’énergie.
Malgré leur importance écologique et économique, les bases moléculaires impliquées dans la réponse des microalgues à leur environnement et l’impact des changements que connaît notre planète sur leur devenir et évolution sont très peu connus. Nous étudions les mécanismes moléculaires en particulier épigénétiques, notamment la méthylation de l’ADN et les modifications post-traductionnelles des histones impliquées dans la réponse des micro-algues aux facteurs biotiques et abiotiques de l’environnement. Nous utilisons des approches multi-échelles, de la cellule entière/génome aux gènes, combinées à de la bioinformatique intégrative pour comprendre la biologie des modèles/systèmes étudiés en tant qu’entité et dans un contexte plus globale. Nous nous intéressons plus particulièrement à un groupe dominant des micro-algues, les diatomées et utilisons des espèces modèles ainsi que des approches moléculaires pluridisciplinaires pour comprendre comment les diatomées répondent aux contraintes biotiques et abiotiques des océans actuels. Nous utilisons des espèces modèles et non modèles pour étudier les interactions des diatomées avec les bactéries en particulier de type diazotrophe.
Mots-clés : bactéries, bioinformatique, diatomées, épigénétique, épigénomique, microalgues, microbiologie
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3 publications
Bourdareau, Simon; Tirichine, Leila; Lombard, Bérangère; Loew, Damarys; Scornet, Delphine; Wu, Yue; Coelho, Susana M; Cock, Mark J Histone modifications during the life cycle of the brown alga Ectocarpus Article de journal Genome Biology, 22 (1), 2021, ISSN: 1474760X. @article{Bourdareau2021, title = {Histone modifications during the life cycle of the brown alga Ectocarpus}, author = {Simon Bourdareau and Leila Tirichine and Bérangère Lombard and Damarys Loew and Delphine Scornet and Yue Wu and Susana M Coelho and Mark J Cock}, url = {https://pubmed.ncbi.nlm.nih.gov/33397407/}, doi = {10.1186/s13059-020-02216-8}, issn = {1474760X}, year = {2021}, date = {2021-12-01}, journal = {Genome Biology}, volume = {22}, number = {1}, publisher = {BioMed Central Ltd}, abstract = {Background: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes. |
Hoguin, Antoine; Rastogi, Achal; Bowler, Chris; Tirichine, Leila Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum Article de journal Scientific Reports, p. 1–10, 2021, ISSN: 2045-2322. @article{Hoguin2021, title = {Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum}, author = {Antoine Hoguin and Achal Rastogi and Chris Bowler and Leila Tirichine}, url = {https://doi.org/10.1038/s41598-021-82529-1}, doi = {10.1038/s41598-021-82529-1}, issn = {2045-2322}, year = {2021}, date = {2021-01-01}, journal = {Scientific Reports}, pages = {1--10}, publisher = {Nature Publishing Group UK}, abstract = {Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions. |
Rahmani, Alexandra; Delavat, François; Lambert, Christophe; Goic, Nelly Le; Dabas, Eric; Paillard, Christine; Pichereau, Vianney Frontiers in Cellular and Infection Microbiology, 11 , p. 634427, 2021, ISSN: 2235-2988. @article{rahmani_implication_2021, title = {Implication of the Type IV Secretion System in the Pathogenicity of Vibrio tapetis, the Etiological Agent of Brown Ring Disease Affecting the Manila Clam Ruditapes philippinarum}, author = {Alexandra Rahmani and François Delavat and Christophe Lambert and Nelly Le Goic and Eric Dabas and Christine Paillard and Vianney Pichereau}, url = {https://www.frontiersin.org/articles/10.3389/fcimb.2021.634427/full}, doi = {10.3389/fcimb.2021.634427}, issn = {2235-2988}, year = {2021}, date = {2021-01-01}, urldate = {2021-04-29}, journal = {Frontiers in Cellular and Infection Microbiology}, volume = {11}, pages = {634427}, abstract = {Vibrio tapetis is a Gram-negative bacterium that causes infections of mollusk bivalves and fish. The Brown Ring Disease (BRD) is an infection caused by V. tapetis that primarily affects the Manila clam Ruditapes philippinarum. Recent studies have shown that a type IV secretion system (T4SS) gene cluster is exclusively found in strains of V. tapetis pathogenic to clams. However, whether the T4SS is implicated or not during the infection process remains unknown. The aim of this study was to create and characterize a V. tapetis T4SS null mutant, obtained by a near-complete deletion of the virB4 gene, in order to determine the role of T4SS in the development of BRD. This study demonstrated that the T4SS is neither responsible for the loss of hemocyte adhesion capacities, nor for the decrease of the lysosomal activity during BRD. Nevertheless, we observed a 50% decrease of the BRD prevalence and a decrease of mortality dynamics with the DvirB4 mutant. This work demonstrates that the T4SS of V. tapetis plays an important role in the development of BRD in the Manila clam.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrio tapetis is a Gram-negative bacterium that causes infections of mollusk bivalves and fish. The Brown Ring Disease (BRD) is an infection caused by V. tapetis that primarily affects the Manila clam Ruditapes philippinarum. Recent studies have shown that a type IV secretion system (T4SS) gene cluster is exclusively found in strains of V. tapetis pathogenic to clams. However, whether the T4SS is implicated or not during the infection process remains unknown. The aim of this study was to create and characterize a V. tapetis T4SS null mutant, obtained by a near-complete deletion of the virB4 gene, in order to determine the role of T4SS in the development of BRD. This study demonstrated that the T4SS is neither responsible for the loss of hemocyte adhesion capacities, nor for the decrease of the lysosomal activity during BRD. Nevertheless, we observed a 50% decrease of the BRD prevalence and a decrease of mortality dynamics with the DvirB4 mutant. This work demonstrates that the T4SS of V. tapetis plays an important role in the development of BRD in the Manila clam. |
10 publications
Zhao, Xue; Rastogi, Achal; Deton Cabanillas, Anne Flore ; Ait Mohamed, Ouardia ; Cantrel, Catherine; Lombard, Berangère; Murik, Omer; Genovesio, Auguste; Bowler, Chris; Bouyer, Daniel; Loew, Damarys; Lin, Xin; Veluchamy, Alaguraj; Vieira, Fabio Rocha Jimenez; Tirichine, Leila Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum Article de journal New Phytologist, p. nph.17129, 2020, ISSN: 0028-646X. @article{Zhao2020b, title = {Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum}, author = {Xue Zhao and Achal Rastogi and Anne Flore {Deton Cabanillas} and Ouardia {Ait Mohamed} and Catherine Cantrel and Berangère Lombard and Omer Murik and Auguste Genovesio and Chris Bowler and Daniel Bouyer and Damarys Loew and Xin Lin and Alaguraj Veluchamy and Fabio Rocha Jimenez Vieira and Leila Tirichine}, url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17129}, doi = {10.1111/nph.17129}, issn = {0028-646X}, year = {2020}, date = {2020-12-01}, journal = {New Phytologist}, pages = {nph.17129}, publisher = {Blackwell Publishing Ltd}, abstract = {In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated. |
Ait-Mohamed, Ouardia; Novák Vanclová, Anna M G; Joli, Nathalie; Liang, Yue; Zhao, Xue; Genovesio, Auguste; Tirichine, Leila; Bowler, Chris; Dorrell, Richard G PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum Article de journal Frontiers in Plant Science, 11 , 2020, ISSN: 1664462X. @article{Ait-Mohamed2020, title = {PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum}, author = {Ouardia Ait-Mohamed and Anna M G {Novák Vanclová} and Nathalie Joli and Yue Liang and Xue Zhao and Auguste Genovesio and Leila Tirichine and Chris Bowler and Richard G Dorrell}, url = {https://pubmed.ncbi.nlm.nih.gov/33178253/}, doi = {10.3389/fpls.2020.590949}, issn = {1664462X}, year = {2020}, date = {2020-10-01}, journal = {Frontiers in Plant Science}, volume = {11}, publisher = {Frontiers Media S.A.}, abstract = {Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation. |
Carraro, Nicolas; Richard, Xavier; Sulser, Sandra; Delavat, François; Mazza, Christian; van der Meer, Jan Roelof An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element Article de journal eLife, 9 , p. 1–40, 2020, ISSN: 2050084X. @article{Carraro2020, title = {An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element}, author = {Nicolas Carraro and Xavier Richard and Sandra Sulser and François Delavat and Christian Mazza and Jan Roelof van der Meer}, doi = {10.7554/eLife.57915}, issn = {2050084X}, year = {2020}, date = {2020-07-01}, journal = {eLife}, volume = {9}, pages = {1--40}, publisher = {eLife Sciences Publications Ltd}, abstract = {Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an ‘upstream' cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modeling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or ‘analog') input to bistable (subpopulation-specific or ‘digital') output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the ‘downstream' functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma-and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an ‘upstream' cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modeling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or ‘analog') input to bistable (subpopulation-specific or ‘digital') output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the ‘downstream' functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma-and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements. |
Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leila Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies Book Chapter The molecular life of diatoms, Springer Nature Switzerland AG, 2020. @inbook{cEQ5:ZHAO_TIRICHINE:2020, title = {Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies}, author = {Xue Zhao and Antoine Hoguin and Timothée Chaumier and Leila Tirichine}, year = {2020}, date = {2020-04-01}, booktitle = {The molecular life of diatoms}, publisher = {Springer Nature Switzerland AG}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } |
Sato, Shinya; Nanjappa, Deepak; Dorrell, Richard G; Vieira, Fabio Rocha Jimenez; Kazamia, Elena; Tirichine, Leila; Veluchamy, Alaguraj; Heilig, Roland; Aury, Jean Marc; Jaillon, Olivier; Wincker, Patrick; Fussy, Zoltan; Obornik, Miroslav; ñ, Sergio Mu A; Mann, David G; Bowler, Chris; Zingone, Adriana Scientific Reports, 10 (1), p. 1–12, 2020, ISSN: 20452322. @article{Sato2020, title = {Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal}, author = {Shinya Sato and Deepak Nanjappa and Richard G Dorrell and Fabio Rocha Jimenez Vieira and Elena Kazamia and Leila Tirichine and Alaguraj Veluchamy and Roland Heilig and Jean Marc Aury and Olivier Jaillon and Patrick Wincker and Zoltan Fussy and Miroslav Obornik and Sergio A Mu{ñ}oz-Gómez and David G Mann and Chris Bowler and Adriana Zingone}, doi = {10.1038/s41598-020-65941-x}, issn = {20452322}, year = {2020}, date = {2020-01-01}, journal = {Scientific Reports}, volume = {10}, number = {1}, pages = {1--12}, abstract = {Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence. |
Rastogi, Achal; Vieira, Fabio Rocha Jimenez; Deton-Cabanillas, Anne-Flore; Veluchamy, Alaguraj; Cantrel, Catherine; Wang, Gaohong; Vanormelingen, Pieter; Bowler, Chris; Piganeau, Gwenael; Hu, Hanhua; Others, A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum Article de journal The ISME journal, 14 (2), p. 347–363, 2020. @article{rastogi2020genomics, title = {A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum}, author = {Achal Rastogi and Fabio Rocha Jimenez Vieira and Anne-Flore Deton-Cabanillas and Alaguraj Veluchamy and Catherine Cantrel and Gaohong Wang and Pieter Vanormelingen and Chris Bowler and Gwenael Piganeau and Hanhua Hu and Others}, doi = {https://doi.org/10.1038/s41396-019-0528-3}, year = {2020}, date = {2020-01-01}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {347--363}, publisher = {Nature Publishing Group}, abstract = {Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A–D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A–D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species. |
Fan, Xiao; Han, Wentao; Teng, Linhong; Jiang, Peng; Zhang, Xiaowen; Xu, Dong; Li, Chang; Pellegrini, Matteo; Wu, Chunhui; Wang, Yitao; Kaczurowski, Michelle Joyce Slade; Lin, Xin; Tirichine, Leila; Mock, Thomas; Ye, Naihao Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants Article de journal New Phytologist, 225 (1), p. 234–249, 2020, ISSN: 14698137. @article{Fan2020, title = {Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants}, author = {Xiao Fan and Wentao Han and Linhong Teng and Peng Jiang and Xiaowen Zhang and Dong Xu and Chang Li and Matteo Pellegrini and Chunhui Wu and Yitao Wang and Michelle Joyce Slade Kaczurowski and Xin Lin and Leila Tirichine and Thomas Mock and Naihao Ye}, doi = {10.1111/nph.16125}, issn = {14698137}, year = {2020}, date = {2020-01-01}, journal = {New Phytologist}, volume = {225}, number = {1}, pages = {234--249}, abstract = {Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae. |
Zhao, Xue; Deton Cabanillas, Anne Flore ; Veluchamy, Alaguraj; Bowler, Chris; Vieira, Fabio Rocha Jimenez; Tirichine, Leila Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae Article de journal Frontiers in Marine Science, 7 , p. 189, 2020, ISSN: 2296-7745. @article{10.3389/fmars.2020.00189, title = {Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae}, author = {Xue Zhao and Anne Flore {Deton Cabanillas} and Alaguraj Veluchamy and Chris Bowler and Fabio Rocha Jimenez Vieira and Leila Tirichine}, url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00189}, doi = {10.3389/fmars.2020.00189}, issn = {2296-7745}, year = {2020}, date = {2020-01-01}, journal = {Frontiers in Marine Science}, volume = {7}, pages = {189}, abstract = {Polycomb (PcG) and Trithorax (TrxG) complexes are two evolutionarily conserved epigenetic regulatory components that act antagonistically to regulate the expression of genes involved in cell differentiation and development in multicellular organisms. The absence of PcG in both yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that polycomb proteins might have evolved together with the emergence of multicellular organisms. However, high throughput sequencing of several microalgal genomes and transcriptomes reveals an unprecedented abundance and diversity of genes encoding the components of these complexes. We report here the diversity of genes encoding PcG and TrxG proteins in microalgae from the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) and detected at broad scale in Tara Oceans genomics datasets using a highly sensitive method called eDAF (enhanced Domain Architecture Filtering). Further, we explored the correlation between environmental factors measured during the Tara Oceans expedition and transcript levels of PcG and TrxG components. PcG and TrxG are responsible for the deposition of a number of histone marks among which a TrxG associated mark, H3K4me3 which we profiled genome wide in the model diatom Phaeodactylum tricornutum to understand its role in microalgae and revisited the previously published histone code and co-occurrence with other histone marks including the antagonizing Polycomb deposited mark H3K27me3.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Polycomb (PcG) and Trithorax (TrxG) complexes are two evolutionarily conserved epigenetic regulatory components that act antagonistically to regulate the expression of genes involved in cell differentiation and development in multicellular organisms. The absence of PcG in both yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that polycomb proteins might have evolved together with the emergence of multicellular organisms. However, high throughput sequencing of several microalgal genomes and transcriptomes reveals an unprecedented abundance and diversity of genes encoding the components of these complexes. We report here the diversity of genes encoding PcG and TrxG proteins in microalgae from the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) and detected at broad scale in Tara Oceans genomics datasets using a highly sensitive method called eDAF (enhanced Domain Architecture Filtering). Further, we explored the correlation between environmental factors measured during the Tara Oceans expedition and transcript levels of PcG and TrxG components. PcG and TrxG are responsible for the deposition of a number of histone marks among which a TrxG associated mark, H3K4me3 which we profiled genome wide in the model diatom Phaeodactylum tricornutum to understand its role in microalgae and revisited the previously published histone code and co-occurrence with other histone marks including the antagonizing Polycomb deposited mark H3K27me3. |
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 Plants, 9 (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. |
Strat, Yoran Le; Tonon, Thierry; Leblanc, Catherine; Groisillier, Agnès Characterization of redox sensitive algal mannitol-1-phosphatases of the haloacid dehalogenase superfamily of proteins Article de journal bioRxiv, 2020. @article{LeStrat2020.07.01.179531, title = {Characterization of redox sensitive algal mannitol-1-phosphatases of the haloacid dehalogenase superfamily of proteins}, author = {Yoran Le Strat and Thierry Tonon and Catherine Leblanc and Agnès Groisillier}, url = {https://www.biorxiv.org/content/early/2020/07/01/2020.07.01.179531}, doi = {10.1101/2020.07.01.179531}, year = {2020}, date = {2020-01-01}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Macroalgae (or seaweeds) are the dominant primary producers in marine vegetated coastal habitats and largely contribute to global ocean carbon fluxes. They also represent attractive renewable production platforms for biofuels, food, feed, and bioactives, notably due to their diverse and peculiar polysaccharides and carbohydrates. Among seaweeds, brown algae produce alginates and sulfated fucans as constituents of their cell wall, and the photoassimilates laminarin and mannitol for carbon storage. Availability of brown algal genomes, including those of the kelp Saccharina japonica and the filamentous Ectocarpus sp., has paved the way for biochemical characterization of recombinant enzymes involved in their polysaccharide and carbohydrates synthesis, notably mannitol. Biosynthesis of mannitol in brown algae starts from fructose-6-phospate, which is converted into mannitol-1-phosphate (M1P), and this intermediate is then hydrolysed by a haloacid dehalogenase type M1P phosphatase (M1Pase) to produce mannitol. We report here the biochemical characterization of a second M1Pase in Ectocarpus sp after heterologous expression in Escherichia coli. (EsM1Pase1). Our results show that both Ectocarpus M1Pases were redox sensitive, with EsM1Pase1 being active only in presence of reducing agent. Such catalytic properties have not been observed for any of the M1Pase characterized so far. EsM1Pases were specific to mannitol, in contrast to S. japonica M1Pases that can use other phosphorylated sugars as substrates. Finally, brown algal M1Pases grouped into two well-supported clades, with potential different subcellular localization and physiological role(s) under diverse environmental conditions and/or stages of life cycle.Competing Interest StatementThe authors have declared no competing interest.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Macroalgae (or seaweeds) are the dominant primary producers in marine vegetated coastal habitats and largely contribute to global ocean carbon fluxes. They also represent attractive renewable production platforms for biofuels, food, feed, and bioactives, notably due to their diverse and peculiar polysaccharides and carbohydrates. Among seaweeds, brown algae produce alginates and sulfated fucans as constituents of their cell wall, and the photoassimilates laminarin and mannitol for carbon storage. Availability of brown algal genomes, including those of the kelp Saccharina japonica and the filamentous Ectocarpus sp., has paved the way for biochemical characterization of recombinant enzymes involved in their polysaccharide and carbohydrates synthesis, notably mannitol. Biosynthesis of mannitol in brown algae starts from fructose-6-phospate, which is converted into mannitol-1-phosphate (M1P), and this intermediate is then hydrolysed by a haloacid dehalogenase type M1P phosphatase (M1Pase) to produce mannitol. We report here the biochemical characterization of a second M1Pase in Ectocarpus sp after heterologous expression in Escherichia coli. (EsM1Pase1). Our results show that both Ectocarpus M1Pases were redox sensitive, with EsM1Pase1 being active only in presence of reducing agent. Such catalytic properties have not been observed for any of the M1Pase characterized so far. EsM1Pases were specific to mannitol, in contrast to S. japonica M1Pases that can use other phosphorylated sugars as substrates. Finally, brown algal M1Pases grouped into two well-supported clades, with potential different subcellular localization and physiological role(s) under diverse environmental conditions and/or stages of life cycle.Competing Interest StatementThe authors have declared no competing interest. |
4 publications
Murik, Omer; Tirichine, Leila; Prihoda, Judit; Thomas, Yann; ú, Wagner Ara L; Allen, Andrew E; Fernie, Alisdair R; Bowler, Chris Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom Article de journal New Phytologist, 221 (3), p. 1303–1316, 2019, ISSN: 14698137. @article{Murik2019, title = {Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom}, author = {Omer Murik and Leila Tirichine and Judit Prihoda and Yann Thomas and Wagner L Ara{ú}jo and Andrew E Allen and Alisdair R Fernie and Chris Bowler}, doi = {10.1111/nph.15479}, issn = {14698137}, year = {2019}, date = {2019-01-01}, journal = {New Phytologist}, volume = {221}, number = {3}, pages = {1303--1316}, abstract = {Diatom dominance in contemporary aquatic environments indicates that they have developed unique and effective mechanisms to cope with the rapid and considerable fluctuations that characterize these environments. In view of their evolutionary history from a secondary endosymbiosis, inter-organellar regulation of biochemical activities may be of particular relevance. Diatom mitochondrial alternative oxidase (AOX) is believed to play a significant role in supplying chloroplasts with ATP produced in the mitochondria. Using the model diatom Phaeodactylum tricornutum we generated AOX knockdown lines, and followed sensitivity to stressors, photosynthesis and transcriptome and metabolome profiles of wild-type and knockdown lines. We show here that expression of the AOX gene is upregulated by various stresses including H 2 O 2 , heat, high light illumination, and iron or nitrogen limitation. AOX knockdown results in hypersensitivity to stress. Knockdown lines also show significantly reduced photosynthetic rates and their chloroplasts are more oxidized. Comparisons of transcriptome and metabolome profiles suggest a strong impact of AOX activity on gene expression, which is carried through to the level of the metabolome. Our data provide evidence for the involvement of mitochondrial AOX in processes central to the cell biology of diatoms, revealing that cross-talk between mitochondria and chloroplasts is crucial for maintaining sensitivity to changing environments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diatom dominance in contemporary aquatic environments indicates that they have developed unique and effective mechanisms to cope with the rapid and considerable fluctuations that characterize these environments. In view of their evolutionary history from a secondary endosymbiosis, inter-organellar regulation of biochemical activities may be of particular relevance. Diatom mitochondrial alternative oxidase (AOX) is believed to play a significant role in supplying chloroplasts with ATP produced in the mitochondria. Using the model diatom Phaeodactylum tricornutum we generated AOX knockdown lines, and followed sensitivity to stressors, photosynthesis and transcriptome and metabolome profiles of wild-type and knockdown lines. We show here that expression of the AOX gene is upregulated by various stresses including H 2 O 2 , heat, high light illumination, and iron or nitrogen limitation. AOX knockdown results in hypersensitivity to stress. Knockdown lines also show significantly reduced photosynthetic rates and their chloroplasts are more oxidized. Comparisons of transcriptome and metabolome profiles suggest a strong impact of AOX activity on gene expression, which is carried through to the level of the metabolome. Our data provide evidence for the involvement of mitochondrial AOX in processes central to the cell biology of diatoms, revealing that cross-talk between mitochondria and chloroplasts is crucial for maintaining sensitivity to changing environments. |
Huang, Ruiping; Ding, Jiancheng; Gao, Kunshan; de Carvalho, Maria Helena; Tirichine, Leila; Bowler, Chris; Lin, Xin A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum Article de journal Frontiers in Microbiology, 9 , p. 3342, 2019, ISSN: 1664-302X. @article{10.3389/fmicb.2018.03342, title = {A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum}, author = {Ruiping Huang and Jiancheng Ding and Kunshan Gao and Maria Helena de Carvalho and Leila Tirichine and Chris Bowler and Xin Lin}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03342}, doi = {10.3389/fmicb.2018.03342}, issn = {1664-302X}, year = {2019}, date = {2019-01-01}, journal = {Frontiers in Microbiology}, volume = {9}, pages = {3342}, abstract = {Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification. |
Shao, Zhanru; Thomas, Yann; Hembach, Lea; Xing, Xiaohui; Duan, Delin; Moerschbacher, Bruno M; Bulone, Vincent; Tirichine, Leila; Bowler, Chris New Phytologist, 221 (4), p. 1890–1905, 2019, ISSN: 14698137. @article{Shao2019, title = {Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms}, author = {Zhanru Shao and Yann Thomas and Lea Hembach and Xiaohui Xing and Delin Duan and Bruno M Moerschbacher and Vincent Bulone and Leila Tirichine and Chris Bowler}, doi = {10.1111/nph.15510}, issn = {14698137}, year = {2019}, date = {2019-01-01}, journal = {New Phytologist}, volume = {221}, number = {4}, pages = {1890--1905}, abstract = {Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc 5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc 5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs. |
Caputi, L; Carradec, Q; Eveillard, D; Kirilovsky, A; Pelletier, E; Karlusich, Pierella J J; Vieira, Rocha Jimenez F; Villar, E; Chaffron, S; Malviya, S; Scalco, E; Acinas, S G; Alberti, A; Aury, J -M; Benoiston, A -S; Bertrand, A; Biard, T; Bittner, L; Boccara, M; Brum, J R; Brunet, C; Busseni, G; Carratalà, A; Claustre, H; Coelho, L P; Colin, S; Daniello, S; Silva, Da C; Core, Del M; Doré, H; Gasparini, S; Kokoszka, F; Jamet, J -L; Lejeusne, C; Lepoivre, C; Lescot, M; Lima-Mendez, G; Lombard, F; Lukeš, J; Maillet, N; Madoui, M -A; Martinez, E; Mazzocchi, M G; Néou, M B; Paz-Yepes, J; Poulain, J; Ramondenc, S; Romagnan, J -B; Roux, S; Manta, Salvagio D; Sanges, R; Speich, S; Sprovieri, M; Sunagawa, S; Taillandier, V; Tanaka, A; Tirichine, Leila; Trottier, Camille; Uitz, J; Veluchamy, A; Veselá, J; Vincent, F; Yau, S; Kandels-Lewis, S; Searson, S; Dimier, C; Picheral, M; Bork, P; Boss, E; de Vargas, C; Follows, M J; Grimsley, N; Guidi, L; Hingamp, P; Karsenti, E; Sordino, P; Stemmann, L; Sullivan, M B; Tagliabue, A; Zingone, A; Garczarek, L; DÓrtenzio, F; Testor, P; Not, F; DÁlcalà, M R; Wincker, P; Bowler, C; Iudicone, D Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Article de journal Global Biogeochemical Cycles, 33 (3), 2019, ISSN: 19449224. @article{Caputi2019, title = {Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems}, author = {L Caputi and Q Carradec and D Eveillard and A Kirilovsky and E Pelletier and J J Pierella Karlusich and F Rocha Jimenez Vieira and E Villar and S Chaffron and S Malviya and E Scalco and S G Acinas and A Alberti and J -M Aury and A -S Benoiston and A Bertrand and T Biard and L Bittner and M Boccara and J R Brum and C Brunet and G Busseni and A Carratalà and H Claustre and L P Coelho and S Colin and S Daniello and C Da Silva and M Del Core and H Doré and S Gasparini and F Kokoszka and J -L Jamet and C Lejeusne and C Lepoivre and M Lescot and G Lima-Mendez and F Lombard and J Lukeš and N Maillet and M -A Madoui and E Martinez and M G Mazzocchi and M B Néou and J Paz-Yepes and J Poulain and S Ramondenc and J -B Romagnan and S Roux and D Salvagio Manta and R Sanges and S Speich and M Sprovieri and S Sunagawa and V Taillandier and A Tanaka and Leila Tirichine and Camille Trottier and J Uitz and A Veluchamy and J Veselá and F Vincent and S Yau and S Kandels-Lewis and S Searson and C Dimier and M Picheral and P Bork and E Boss and C de Vargas and M J Follows and N Grimsley and L Guidi and P Hingamp and E Karsenti and P Sordino and L Stemmann and M B Sullivan and A Tagliabue and A Zingone and L Garczarek and F DÓrtenzio and P Testor and F Not and M R DÁlcalà and P Wincker and C Bowler and D Iudicone}, doi = {10.1029/2018GB006022}, issn = {19449224}, year = {2019}, date = {2019-01-01}, journal = {Global Biogeochemical Cycles}, volume = {33}, number = {3}, abstract = {Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. |