Biology of Nucleic Acids in Ciliates

Estienne Swart

EstienneSwart FacPage Nov17
  • PhD 2006-2012, Princeton University
  • Postdoctoral fellow 2012-2017, University of Bern
  • Group leader at the MPI for Developmental Biology since 2017

Research Interest

Currently I'm pursuing two main research directions. In the first direction, I wish to determine the key molecules involved during developmental, genome-wide DNA elimination in ciliates, a major group of microbial eukaryotes. This DNA elimination process, which transforms germline genomes into somatic ones, involves domesticated transposases assisted by other proteins and small RNAs. To investigate this, a combination of functional genomic approaches in model ciliates (e.g. Paramecium) and comparative genomic approaches between model and non-model ciliates will be employed. This will allow determination of which molecular components involved in the DNA elimination are functionally conserved, how they came to be, and how they cooperate.

The second research direction involves investigation of how translation and translation-associated processes operate, in the context of non-standard genetic codes. In a few recently discovered non-standard genetic codes, "stop" codons are either translated or serve as proper stops, but how this is achieved remains to be experimentally demonstrated. For this, ciliates belonging to the same taxonomic class, but with different genetic codes are the focal organisms (e.g. Stentor uses the standard code, whereas as Condylostoma and Blepharisma use non-standard codes).

  • Fig1 Swart
    click to enlarge

Fig 1. Ciliates have dimorphic nuclei within each cell. Changes made to the DNA as a germline nucleus develops into a new somatic nucleus in ciliates like Oxytricha trifallax and Stylonychia lemnae are shown. The challenge is to work out the transformation mechanisms. Image copyright: 3Swart et al. 2013 (CC BY).

  • Fig2 Swart
    click to enlarge

Fig 2. A model for translation elongation and termination in Condylostoma magnum. In this ciliate's genetic code "stop" codons are translated within coding sequences, but terminate translation close to the transcript end, possibly due to interactions with proteins there. Image copyright: 2Swart et al. 2016 (CC BY).

Available PhD Projects

Investigation of the genomes and genome editing in the ciliate Blepharisma japonicum.

Selected Reading

1 Swart EC, Denby Wilkes C, Sandoval PY, Hoehener C, Singh A, et al. (2017) Identification and analysis of functional associations among natural eukaryotic genome editing components. F1000Research. doi: 10.12688/f1000research.12121.1

2 Swart EC, Serra V, Petroni G, Nowacki M. (2016) Genetic codes with no dedicated stop codon: context dependent translation termination. Cell. 166: 1-12. doi: 10.1016/j.cell.2016.06.020.

3 Swart EC, Bracht J, Magrini V, Minx P, Chen X, et al. (2013) The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLOS Biology. 11(1): e1001473. doi: 10.1371/journal.pbio.1001473