Seminar: "What ciliates have taught us about the origins of new genetic codes" Dr. Estienne C. Swart

Speaker: Dr. Estienne C. Swart, Institute of Cell Biology, University of Bern

Title: "What ciliates have taught us about the origins of new genetic codes"

Abstract

Consistent with an ancient, common origin, the majority of extant organisms use the standard genetic code to translate the bulk of their nuclear genes. Deviations from the use of the standard code to translate nuclear genes are sparsely scattered amongst the major eukaryotic branches, with the exception of one microbial eukaryote clade - the ciliates - which are currently known to use seven alternative genetic codes in addition to the standard one. The most common codon reassignments, including all of those observed in ciliates, are from stops to amino acids (sense). It has been a mystery why new nuclear genetic codes have evolved so often in ciliates, but infrequently in other eukaryotes. In a large collection of marine microbial eukaryote transcriptomes (MMETSP) I discovered three new genetic codes in ciliates, including two with stop/sense codons that potentially represent a snapshot of genetic code evolution in action. In these ambiguous codes the ribosome efficiently translates all the codons within protein-coding sequences, incorporating standard amino acids; upon reaching an mRNA end, the ribosome switches from translating “stop” codons to terminating at them. This suggests that the genetic code diversity found in ciliates may be due to the ability to thrive in an intermediate situation in which codons have either of two possible meanings, depending on their position. Computational analyses suggest that mRNA ends, presumably via the proteins bound to them, enable the ribosome to distinguish codons as stops. In this seminar I will also provide a taste of some of the extraordinary genomic and developmental biology of ciliates, and conclude by briefly describing how I wish to investigate such biology in future.

Biography

By training, I am a computational biologist with interests spanning genomics, molecular, cellular, and evolutionary biology. I have been fascinated by microbial eukaryotes, especially ciliates, the current subjects of my research, since my doctoral studies in the Landweber lab in the Department of Ecology and Evolutionary Biology at Princeton University (June 2012 graduation). The primary subject of my doctoral thesis was the nature and radical, fragmented architecture of the somatic genome of the ciliate Oxytricha trifallax. After graduation I joined the Nowacki lab in The Institute of Cell Biology at The University of Bern, Switzerland as a postdoctoral fellow. In Bern, I have been investigating the role of small RNAs and associated proteins in developmental genome reorganization in Paramecium, and the nature and evolution of alternative genetic codes.