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Reconstructing the origins of animal multicellularity using experimental evolution

Periodic Reporting for period 1 - MULTICELLEXPEVO (Reconstructing the origins of animal multicellularity using experimental evolution)

Reporting period: 2018-09-01 to 2020-08-31

All living animals evolved from a single-celled ancestor. Understanding how this ancestor evolved to become the first multicellular animal is crucial to trace our origins. To date comparative genomic and phylogenetic comparisons of meta-zoans genomes with their closest unicellular relatives was the unique research strategy to unravel animal origins of mul-ticellularity. Phylogenomic analyses have shown that animals are closely related to three unicellular lineages: choanoflagellates, filastereans and ichthyosporeans, which together form the Holozoa clade. Each lineage uses a distinct developmental mode that includes transient simple multicellular forms. Choanoflagellates undergo colo-nial clonal development; the filasterean Capsaspora owczarzaki has an aggregative multicellular stage; and most ichthyosporeans form multinucleated coenocytes. To date, it is still unknown from which developmental mode animals emerged. Both choanoflagellates and filastereans are highly studied and genetic tools are currently in development in order to answer this question. However, ichthyosporeans have received less attention despite their attractive coenocytic lifecycle. This developmental mode comprises a growth stage in which nuclei divide synchronously within a common cytoplasm. The coenocyte then undergoes plasma membrane cleavage followed by release of new-born cells. By better understanding the cell biology of these interesting organisms, we were hoping to better understand how ancestral developmental mechanisms first evolved and how these compare with animal developmental processus.
Such project is important for society because it would allow us better to understand the evolution of animals inclduing us humans. It would also allow us to unravel the ancestral mechanism of transition between unicellular organisms and multicellular ones.
More specifically, the MULTICELLEXPEVO project aimed to better understand requirements needed for the unicellular to multicellular transition. It clearly focused on investigating the role of actin and microtubule cytoskeletons in the formation of the aggregative stage as well as the development of genetic tools through experimental evolution and random mutagenesis using Capsaspora owczarzaki as a model.
Despite being focalized on Capsaspora owczarzaki , many aspects of this project were done using the ichthyosporean Sphaeroforma arctica for several technical reasons explained below. However, our project concluded in general that unicellular holozoan use similar morphological processes during their transient multicellular stage. More specifically, we showed that S. arctica undergo cellularization using plasma membrane invagination forming a transinet epithelium-like layer of cells. Such cellularization ressembled the cellularization of the Drosophila embryo.
In my research proposal I had planned to use the experimental evolution approach to evolve multicellular forms in the filasterean Capsaspora owczarzaki. The experimental procedure did not change, the used specie was however ex-changed to the Ichthyosporean Sphaeroforma arctica. This change was mainly due, to the incapacity to select for C. owczarzaki aggregate as they float rather than sediment. Moreover, the growth medium of C. owczarzaki is highly rich in nutrient and thus very susceptible to contamination, which is extremely troublesome during long-term selection.

To summarize, the project yielded 1 peer-reviewed and published manuscript as well as a second publication in preparation. Here i will briefly summarize the different projects and the main outcome.
- Cell-cycle and Cellularization regulation in S. arctica :
Prior to the Marie-curie fund, I've been involved in a project published in Current Biology in which we characterise with Andrej Ondracka the cell cycle of Sphaeroforma arctica and discover that nuclear division cycles are under the control of a timer which is a unique feature among unicellular organisms. We further showed that the timer mechanisms is decoupled from cell size regulation. Such discovery show interesting cell biological similarities between insect early embryo and Ichthyosporean development. This was the stepping stone for my Marie-Curie project in which we analyzed the cellularization of S. arctica. Indeed, we further investigated the cell-cycle of Sphaeroforma arctica using Microscopy, RNAseq and chemical inhibition. Our results show that Sphaeroforma arctica undergoes a sophisticated cell division process also known as cellularization. This process allows the multi-nucleated coenocyte to undergo division to generate hundreds of uninucleated newborn cells. This process involved coordinated plasma membrane invaginations relying on an extensive actomyosin network. We also show that an intermediary stage of cellularization represents a self-organized, clonally-generated, polarized layer of cells resembling the animal epithelium. We further show that this cell stage is associated with distinct gene expression of cell adhesion proteins including catenins and integrins, both known as major regulators of cell-cell and cell-matrix adhesion in animals. This work has been published in eLife and featured in another eLife paper written by Prof. Mukund Thathai.
Finally, although not yet published, I've obtained Sphaeroforma arctica mutants using experimental evolutions. These mutants show distinct clonal multicellularity and are and will be further investigated to better understand how they acquired these novel traits.
In other projects , I've been involved in better characterising the cell cycle of C. owczarzaki and the dynamics of microtubule cytoskeleton during this cycle. I also been involved in characterising the role of actin-dependent filopodia in establishing integral-mediated adhesion in C. owczarzaki. Both projects will soon be published.
Overall, the MULTICELLEXPEVO project established Sphaeroforma arctica, an organism that was previously almost completely uncharacterised, as a promising novel model system for evolutionary cell biology, and has produced one high-level scientific publication in a top journals. Several other publications are being finalised. Furthermore, this project and the Marie-curie funding allowed me to obtain an Ambizione fellowship from the Swiss national fund (FNS) to start my own research lab in the EPFL, Lausanne, Switzerland. Altogether, this project enabled me to further develop my scientific and personal skills and opened a serious door toward establishing myself as an independent researcher in a top-ranked institution (EPFL).
Cellularization in Sphaeroforma arctica