Ecole doctorale "LOGIQUE DU VIVANT

Ecole Doctorale COMPLEXITE DU VIVANT – Fiche Projet CONCOURS
Nom et prénom du directeur de thèse (et si besoin du co-directeur) : J. Mark Cock / Susana M. Coelho
Le directeur de thèse et le co-directeur doivent impérativement être habilités à diriger les recherches (HDR)
Coordonnées
Coordonnées
Tel : 0298292360
Tel : 0298292360
e-mail : [email protected]
e-mail : [email protected]
Nom et prénom du co-encadrant (non HdR ) (s’il y a lieu) :
Nom et prénom du responsable de l’équipe : J. Mark Cock / Susana M. Coelho
Nombre de chercheurs et enseignants-chercheurs statutaires de l’équipe titulaires d’une HDR : 2
Nom et prénom du responsable du laboratoire : Catherine Boyen
Intitulé du laboratoire et N° d’unité : UMR 8227 CNRS-UPMC Integrative Biology of Marine Models
Spécialité : Biologie du développement, Evolution
Titre du projet de thèse :
Dissection of the genetic network that regulates life cycle transition in the brown alga Ectocarpus
Résumé du projet de thèse
The brown algae are a group of multicellular organisms that are very distantly related to both land plants and animals. As a
result of this distance, these organisms exhibit many unusual evolutionary features. Brown algae are also key components of
many marine ecosystems and are increasingly of economic importance in the aquaculture domain. The Algal Genetics
Group has been developing the filamentous alga Ectocarpus as a model system to study the biology of this group of
organisms1, a project that has included complete genome sequencing and the establishment of various genomic and genetic
tools for this species2–4. Current research projects in the Algal Genetics Group are aimed at understanding the reproductive
biology of this filamentous alga, in particular the genetic regulation of its life cycle and the mechanism of sex determination.
The life cycle of an organism is one of its most elemental features, underpinning a broad range of phenomena including
developmental processes, reproductive fitness, mode of dispersal and adaptation to the local environment. The brown algae
are a particularly interesting group to study life cycle regulation because they exhibit a broad range of different types of life
cycles5. Several Ectocarpus mutants affected in life cycle progression have been identified 6,7, including the ouroboros (oro)
mutant in which the sporophyte generation is converted into a fully functional gametophyte 6. Recent work has shown that
ouroboros and a more recently isolated mutant, samsara (sam), carry lesions in two TALE homeodomain transcription
factor genes. In the green alga Chlamydomonas, two TALE homeodomain transcription factors carried by the plus and
minus gametes form a heterodimer in the zygote, and it is this heterodimer that directs the deployment of the diploid phase
program8. Our data suggest that the system described in Chlamydomonas may be extremely ancient, dating back to the
crown radiation of the eukaryotes (i.e. the common ancestor of green and brown algae). Current work in the Algal Genetics
Group aims to further characterise the ORO/SAM regulatory system with the long term objective of making more extensive
comparisons with green algal/land plant life cycle regulatory networks and thereby understanding the evolution of these
master regulatory systems over time.
The objective of this PhD project will be to further characterise the genetic network that controls life cycle progression in
Ectocarpus by characterising genes that interact genetically with ORO and SAM. Both forward and reverse genetic
approaches will be used to identify and characterise these interacting genes. For the reverse genetic approach, a yeast twohybrid screen is currently being carried out as part of a Masters 2 project and several potential ORO and SAM interactors
have been identified and are currently being characterised. The objectives during the PhD will be to first validate candidate
interactors by determining whether the interaction is also detected in in vitro pull-down assays and then, secondly, to
characterise validated interactors by screening for mutant lines carrying genetic lesions in the genes that encode the
interacting proteins. This second approach will use a large collection of 2600 mutant lines which has recently been
established in the group for reverse genetic screens using the Targeting Local Lesions in Genomes (TILLING) method9. The
TILLING collection should allow the identification of multiple mutant lines for each gene using a PCR-based screening
strategy.
The forward genetic approach, which will be carried out in parallel, will involve screening for mutations that suppress the
phenotypes of the oro and sam mutations. As mentioned above, the oro and sam mutations cause the sporophyte generation
to be converted into a gametophyte. One of the marked difference between the sporophyte and gametophyte generations is
that the former is firmly attached to the substratum whereas the gametophyte adheres poorly and floats off into the medium.
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Ecole Doctorale COMPLEXITE DU VIVANT – Fiche Projet CONCOURS
The suppressor mutation screen will therefore involve screening for individuals that have regained the ability to anchor to
the substratum, indicating that they have reverted to the sporophyte generation. Reversion will then be verified by
determining whether the individuals have sporophyte morphology, produce spores instead of gametes and exhibit other
typical sporophyte features. Suppressor mutations will then be characterised genetically and the genetic lesion identified
using a cloning-by-sequencing approach. Note that the relative effort expended on the forward and reverse genetic
approaches will be continuously reviewed during the project, taking into account factors such as problems encountered and
the potential interest of the genes or phenotypes identified.
Together these two strategies are expected to identify new genetic components of the system that regulates life cycle
progression in Ectocarpus and improve our understanding of how the master regulators ORO and SAM mediate this
transition.
References
1. Cock, J. M., Peters, A. F. & Coelho, S. M. Brown algae. Curr Biol 21, R573–5 (2011).
2. Cock, J. M. et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465,
617–21 (2010).
3. Heesch, S. et al. A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly
of the genome sequence. New Phytol 188, 42–51 (2010).
4. Coelho, S. M. et al. Ectocarpus: A model organism for the brown algae. Cold Spring Harb. Protoc 2012, 193–198
(2012).
5. Cock, J. M., Godfroy, O., Macaisne, N., Peters, A. F. & Coelho, S. M. Evolution and regulation of complex life cycles: a
brown algal perspective. Curr Opin Plant Biol 17, 1–6 (2013).
6. Coelho, S. M. et al. OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the
brown alga Ectocarpus. Proc Natl Acad Sci USA 108, 11518–11523 (2011).
7. Peters, A. F. et al. Life-cycle-generation-specific developmental processes are modified in the immediate upright mutant
of the brown alga Ectocarpus siliculosus. Development 135, 1503–12 (2008).
8. Lee, J. H., Lin, H., Joo, S. & Goodenough, U. Early sexual origins of homeoprotein heterodimerization and evolution of
the plant KNOX/BELL family. Cell 133, 829–40 (2008).
9. Tsai, H., Ngo, K., Lieberman, M., Missirian, V. & Comai, L. Tilling by sequencing. Methods Mol Biol 1284, 359–80
(2015).
Thèses actuellement en cours dans l’équipe
Nom et Prénom du doctorant
Mignerot, Laure
Bourdareau, Simon
Nom du directeur de thèse
Année de 1ere
inscription et
Ecole Doctorale
Susana M. Coelho / J.
Mark Cock
J. Mark Cock / Susana M.
Coelho
Financement pendant la thèse
2015
ERC and Région Bretagne
2014
Bourse CdV
Trois publications récentes du directeur de thèse (du co-directeur ou du co-encadrant s’il y a lieu).Mettre en gras le nom
du directeur de thèse.
Luthringer, R., Lipinska, A., Cormier, A., Peters, A.F., Roze, D., Cock, J. M. and Coelho, S.M. (2015). The
pseudoautosomal region of the Ectocarpus UV sex chromosome. Molecular Biology and Evolution, 32, 2973-2985.
Tarver, J., Cormier, A. Pinzon, N., Taylor, R., Carré, W., Strittmatter, M., Seitz, H., Coelho, S.M. and Cock, J.M. (2015).
microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in
the brown alga Ectocarpus. Nucleic Acids Research, 43, 6384-6398.
Ahmed, S.*, Cock, J.M.*, Pessia, E.*, Luthringer, R., Cormier, A., Robuchon, M. Sterck, L., Peters, A.F., Dittami, S.M.,
Corre, E., Valero, M., Aury, J.-M., Roze, D., Van de Peer, Y., Bothwell, J., Marais, G.A.B., Coelho, S.M. (2014). A haploid
system of sex determination in the brown alga Ectocarpus sp. Current Biology, 24, 1-13. *joint first authors.
Docteurs encadrés par le directeur de thèse ayant soutenu après septembre 2010 et publications relatives à leur sujet de thèse.
Mettre en gras le nom du directeur de thèse et celui du docteur.
Nom Prénom : Alexandre Cormier
Date de soutenance : 16/11/2015
Durée de thèse (en mois): 36
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Ecole Doctorale COMPLEXITE DU VIVANT – Fiche Projet CONCOURS
Publications :
Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O, Lipinska, A.,
Perrineau, M.-M., Van De Peer, Y., Hitte, C., Corre, E., Coelho, S.M. and Cock, J.M. (2016). Re-annotation, improved
large-scale assembly and establishment of a catalogue of non-coding loci for the genome of the model brown alga
Ectocarpus. In preparation
Luthringer, R., Lipinska, A., Cormier, A., Peters, A.F., Roze, D., Cock, J. M. and Coelho, S.M. (2015). The
pseudoautosomal region of the Ectocarpus UV sex chromosome. Molecular Biology and Evolution (I.F. 14.3), 32:
2973-2985.
Tarver, J., Cormier, A. Pinzon, N., Taylor, R., Carré, W., Strittmatter, M., Seitz, H., Coelho, S.M., Cock, J.M. (2015).
microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs
in the brown alga Ectocarpus. Nucleic Acids Research, 43, 6384-6398.
Lipinska, A.*, Cormier, A.*, Luthringer, R., Peters, A.F., Corre, E., Gachon, C.M.M., Cock, J.M. and Coelho, S.M.
(2015). Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga Ectocarpus. Molecular
Biology and Evolution, 32, 1581-1597. *joint first authors.
Ahmed, S., Cock, J.M., Pessia, E., Luthringer, R., Cormier, A., Robuchon, M. Sterck, L., Peters, A.F., Dittami, S.M.,
Corre, E., Valero, M., Aury, J.-M., Roze, D., Van de Peer, Y., Bothwell, J., Marais, G.A.B., Coelho, S.M. (2014). A
haploid system of sex determination in the brown alga Ectocarpus sp. Current Biology, 24, 1-13.
Luthringer, R., Cormier, A., Ahmed, S., Peters, A.F., Cock, J.M. and Coelho, S.M. (2014). Sexual dimorphism in the
brown algae. Perspectives in Phycology, 1, 11-25.
Nom Prénom : Rémy Luthringer
Date de soutenance : 10/2012
Durée de thèse (en mois): 36
Publications :
Luthringer, R.*, Lipinska, A.*, Cormier, A., Peters, A.F., Roze, D., Cock, J. M. and Coelho, S.M. (2015). The
pseudoautosomal region of the Ectocarpus UV sex chromosome. Molecular Biology and Evolution, 32: 2973-2985.
*joint first authors.
Ahmed, S., Cock, J.M., Pessia, E., Luthringer, R., Cormier, A., Robuchon, M. Sterck, L., Peters, A.F., Dittami, S.M.,
Corre, E., Valero, M., Aury, J.-M., Roze, D., Van de Peer, Y., Bothwell, J., Marais, G.A.B., Coelho, S.M. (2014). A
haploid system of sex determination in the brown alga Ectocarpus sp. Current Biology, 24, 1-13.
Luthringer, R., Cormier, A., Ahmed, S., Peters, A.F., Cock, J.M. and Coelho, S.M. (2014). Sexual dimorphism in the
brown algae. Perspectives in Phycology, 1, 11-25.
Lipinska, A., Cormier, A., Luthringer, R., Peters, A.F., Corre, E., Gachon, C.M.M., Cock, J.M. and Coelho, S.M.
(2015). Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga Ectocarpus. Molecular
Biology and Evolution, 32, 1581-1597.
Nom Prénom : Alok Arun
Date de soutenance : 10/2012
Durée de thèse (en mois): 36
Publications :
Arun, A., Peters, N., Scornet, D., Peters, A.F., Cock, J.M. and Coelho, S.M. (2013). Non-cell autonomous regulation
of the switch between the gametophyte and sporophyte generations of the brown alga Ectocarpus. New Phytologist,
197, 503-510.
Bogaert, K.A., Arun, A., Coelho, S.M. and De Clerck O. (2013). Brown algae as a model for plant organogenesis. In:
Plant Methods in Molecular Biology - Plant Organogenesis. De Smet I. (ed.) Springer Verlag. 959, 97-125.
Collén, J., Porcel, B., Carré, W., Ball, S., Chaparro, C., Tonon, T., Barbeyron, T., Michel, G., Noel, B., Valentin, K.,
Elias, M., Artiguenave, F., Arun, A., Aury, J.-M., Barbosa-Neto, J.F., Bothwell, J.H., Bouget, F.-Y., Brillet, L.,
Cabello-Hurtado, F., Capella-Gutíerrez, S., Charrier, B., Cladière, L., Cock, J.M., Coelho, S.M., Colleoni, C., Czjzek,
M., Da Silva, C., Delage, L., Denoeud, F., Deschamps, P., Dittami, S.M., Gabaldón, T., Gachon, C.M.M., Groisillier, A.
Hervé, C., Jabbari, K., Katinka, M., Kloareg, B., Kowalczyk, N., Labadiec, K., Leblanc, C., Lopez, P.J., McLachlan, D.,
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Ecole Doctorale COMPLEXITE DU VIVANT – Fiche Projet CONCOURS
Meslet-Cladiere, L., Moustafa, A., Nehr, Z., Nyvall Collén, P., Panaud, O., Partensky, F., Poulain, J., A. Rensing, S.A.,
Rousvoal, S., Samson, G., Symeonidi, A., Weissenbach, J., Zambounis, A., Wincker, P. and Boyen C. (2013). Genome
structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.
Proc. Natl. Acad. Sci. USA, 110, 5247-5252.
Cock, J.M., Arun, A., Godfroy, O., Macaisne, N., Strittmatter, M., Peters, A.F. and Coelho, S.M. (2012). Genomics of
brown algae: current advances and future prospects. Genes and Genomics, 34, 1-5.
Cock, J.M., Sterck, L., Ahmed, S., Allen, A.E., Amoutzias, G., Anthouard, V., Artiguenave, F., Arun, A., Aury, J.-M.,
Badger, J.H., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J.H., Bowler, C., Boyen, C., Brownlee, C., Carrano, C.J.,
Charrier, B., Cho, G.Y., Coelho, S.M., Collén, J., Le Corguillé, G., Corre, E., Dartevelle, L., Da Silva, C., Delage, L.,
Delaroque, N., Dittami, S.M., Doulbeau, S., Elias, M., Farnham, G., Gachon, C.M.M., Godfroy, O., Gschloessl, B.,
Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Luthringer,
R., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P.J., Macaisne, N., Martens, C., Maumus, F., Michel, G., MirandaSaavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C.A., Nelson, D.R., Nyvall-Collén, P.,
Peters, A.F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S.,
Samanta, M., Samson, G., Schroeder, D.C., Scornet, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J.W.,
Valentin, K., von Dassow, P., Yamagishi, T., Rouzé, P., Van de Peer, Y., Wincker, P. (2012) The Ectocarpus genome
and brown algal genomics. In: Genomic insights into the biology of algae. Piganeau, G. (ed) Advances in Botanical
Research (special issue), 64, 141-184.
Coelho, S.M., Godfroy, O., Arun, A., Le Corguillé, G., Peters, A.F. and Cock, J.M. (2011). OUROBOROS is a master
regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus. Proc. Natl. Acad. Sci.
USA, 108, 11518-11523.
Coelho, S.M., Godfroy, O., Arun, A., Le Corguillé, G., Peters, A.F. and Cock, J.M. (2011). Genetic regulation of life
cycle transitions in the brown alga Ectocarpus siliculosus. Plant Signaling and Behavior, 6, 1858-1860
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