Skip to main content

Investigating adaptation of phase separation to environment in the control of germline specification

Supervisor: René Ketting

Co-Supervisor: Miguel Andrade


Scientific Background:
In many species the specification of germ cells during embryonic development is driven by maternally provided cytoplasmic material, also known as germ plasm. Well known examples of this manner of germ cell specification are found in the nematode C. elegans, the fruitfly Drosophila melanogaster and also in the vertebrate Danio rerio (zebrafish). Interestingly, germ plasm is in fact a so-called condensate of RNA and protein, meaning that it forms through a process known as phase separation. Phase separation is now known to play many different roles in cell biology, and one of its features is that it is in principle very sensitive to environmental conditions such as temperature. Combined with the fact that the above-named species are all ectotherms, it can be anticipated that the factors that drive germ plasm formation need to be adapted to the general temperatures at which these species reproduce. However, this aspect of germ plasm biology has not been well studied, and the extent to which temperature-mediated control of germ plasm plays a role in the activation of the germ cell gene expression program is unclear. Similarly, adaption of phase-separating proteins to temperatures is also an aspect that still requires intense research.

Coming from our general interest in small RNA biology in germ cells, which intimately connects to germ plasm, we have recently detected an interesting novel germ plasm-residing protein in the zebrafish. This protein, named Buc2l, is a homolog of the well-described germplasm protein Buc, and we found Buc and Buc2l to interact both in vivo, as well as in an heterologous cell culture setting. Interestingly, zebrafish Buc2l contains six copies of a strongly conserved stretch of about 70 amino acids, and the copy-number this repeat varies amongst different fish species: three in Cyprinus carpio, five in Carassius auratus, four in Anabarilius graham, and apparent absence of the repeat in other species, such as Pangasianodon hypophthalmus and Pygocentrus nattereri. Since it has been well-established that repeated domains often have important roles in phase separation, we hypothesize that the repeat length variance in Buc2l affects germ plasm properties and that it may have a role in adjusting to the different temperatures in which different fish species reproduce. Additionally, we hypothesize that this may affect to what extent the germ cell-resident small RNA pathways can associate with germ plasm.


PhD project: Investigating adaptation of phase separation to environment in the control of germline specification
To achieve this, we will study the relevance of this repeat in germ plasm formation using already available zebrafish mutants. We will also study the effect of repeat length on Buc2l phase separation properties, using purified proteins as well as a well a heterologous cell culture system in our group (BmN4 cells: ovary derived germ cells from the silk moth). This project connects to our first GenEvo project in C. elegans, in the sense that the new project will probe small RNA pathway adaptation to environment, whereas the first project addressed potential small RNA pathway adaptation to varying transposon targets. For this project, a collaboration with Miguel Andrade is planned, in order to be better able to analyse how the identified repeat sequence evolved in different fish lineages.


Publications relevant to this project
Dodson AE, Kennedy S. Phase Separation in Germ Cells and Development. (2020) Dev Cell. 12;55(1):4-17.
Boke et al. Amyloid-like Self-Assembly of a Cellular Compartment.(2016) Cell 166(3):637-650.
Roovers et al. Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification. (2018) Dev. Cell 46(3):285-301.
Skugor et al. Multiplicity of Buc copies in Atlantic salmon contrasts with loss of the germ cell determinant in primates, rodents and axolotl. BMC Evolutionary Biology (2016) 16:232.