Diatom functional genomics

Diatoms are major component of the eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes and novel combinations of genes acquired from bacterial, animal and plant ancestors. 

Diatoms are major components of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. The recent availability of whole genome sequences from representative diatom species has revealed distinct features in their genomes and novel combinations of genes acquired from bacterial, animal and plant ancestors. Major objective of our research is to fully exploit the novel available genetic tools and genomic information to identify the mechanisms controlling diatom growth and distribution in the marine environment. Because light is a key environmental signal for photosynthetic organisms, we are performing a comprehensive characterization of diatom light responses, by studying:

  • the blue-light Cryprochrome and red/far-red light Phytochrome photoreceptors, their signaling pathways and their function;
  • the diatom response to light stress, dissecting key photoprotection mechanisms;
  • the light regulated rhythmic processes and their unknown regulators.
  • the small non-coding RNAs and gene silencing pathways and their regulatory role in diatoms.

    In parallel, we are generating novel genetic resources in the molecular model species Phaeodactylumtricornutum.

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  • The diatom light sensors: We are characterizing the blue-light Cryprochromes and red/far-red light Phytochrome photoreceptors, their spectral properties, signalling pathways and functions in vivo. We are also studying the gene regulatory networks connecting light perception to the cell physiology.
  • The regulators of chloroplast activity: We are studying the dynamic responses of the diatom photosynthetic apparatus to changing light conditions, by characterizing the LHCX family and the regulators of the Xanthophyll cycle. These approaches are also instrumental for finding new strategies to enhance biomass yield and lipid production.
  • The diatom circadian clock: By performing a high-resolution transcriptomic and functional analysis of all the Transcription Factors encoded in the genome we have recently identified previously unknown circadian clock components and we are assessing their function in circadian rhythm regulation.
  • The small non-coding RNAs and gene silencing pathways: We have recently performed a comprehensive characterization of the P. tricornutum sRNAs and their correlation with genomic and epigenomic information. We revealed the existence of diversified sRNA pathways and the existence of complex and interconnected networks of ncRNA pathways.
  • Novel genetic resources in diatoms: Within the Network ASSEMBLE (EU-FP7) project, we are generating 20,000 P. tricornutum mutated lines by Activation Tagging (gain-of-function mutations through gene over-expression). In the context of the EMBRC (European Marine Biological Resource Centre) consortium, we systematically inactivate each of the 200 diatom transcription factors. Moreover, we have recently demonstrated targeted and stable modifications of the genome of P. tricornutum, using both meganucleases and TALE nucleases. 

Highlights

Marine diatoms possess sophisticated strategies for detecting and responding to environmental light variations. We have recently identified novel photoreceptors such as the AUREOCHROMEs and novel photoreceptor variants of the Cryprochromes and Phytochrome families. Their characterization raises novel hypotheses on the role of these proteins in controlling growth and adaptive responses in a marine context.

The recent characterization of the diatom small ncRNAs also unveiled that the diatom P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of the diatom sRNA populations and previously unappreciated features such as a well-defined and unprecedented 180 nt-long periodic distribution of smallRNAs at several highly methylated regions, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Future directions

We will further explore the molecular bases of diatom light responses combining physiological and molecular studies with genetic and genomic approaches in the model species P. tricornutum. Novel environmental genomic data and the analysis of the marine microbial eukaryote transcriptomes will also help to address the function and distribution of these light regulators in marine environment.

By benefiting from the participation in different research networks, we will continue to improve the diatom genetic resources. Long term goal of the team is to generate a large collection of diatom strains with marked modifications of metabolic processes as support to our research and for biotechnology. 

Collaborations

International collaborations

  • Prof. Wolfgang R. Hess (Genetics & Experimental Bioinformatics, University Freiburg
  • Institute of Biology, Freiburg, Germany).
  • Dr. Maurizio Ribera D’Alcalà & Dr. Daniele Iudicone, Stazione Zoologica A. Dohrn of Naples, Italy.
  • Dr. Thomas Mock, School of Environmental Sciences, University of East Anglia, Norwich, UK.
  • Dr K. Tessmar-Raible, Dpt of Micobiology Immunobiology and Genetics, Max F. Perutz Laboratory, University of Vienna (Austria).
  • Dr. Paola Olivieri, Dept. Genetics, Evolution and Environment, University College London, UK.
  • Prof. Takeshi Todo and Dr. Tomoko Ishikawa, Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Japan.
  • Prof. Oliver Ebenhoeh, University Court of The University of Aberdeen, United Kindom and 12 partners of the EU Funded Marie Curie Initial Training Network “AccliPhot”, 2012-2016.
  • Dr. Markus Teige, Max F. Perutz Laboratory, University of Vienna (Austria) and 11 parteners of EU Funded Marie Curie Initial Training Network “CALIPSO” 2013-2017

National collaborations:

  • Alessandra Carbone and Hugues Richard, Analytical Genomics team, Laboratoire de Biologie Computationnelle et Quantitative, UMR 7238 CNRS-Université Pierre et Marie Curie, Paris, FR.
  • Dr. Giovanni Finazzi and Dr. Eric Maréchal, Laboratoire de Physiologie Végétale et Cellulaire, CNRS, CEA, Grenoble, FR.
  • Dr. Chris Bowler, Institut de Biologie de l'École Normale Supérieure, Paris, France.
  • Dr. Lionel Navarro, Institut de Biologie de l'École Normale Supérieure, Paris, France.