Tetrahymena thermophila is a ciliated eukaryotic unicellular organism belonging to the regnum of protozoa and bearing two nuclei, a transcriptionally silent, diploid germline micronucleus (MIC) and a transcriptionally active, polyploid somatic macronucleus (MAC)[1]. In 1923, when Nobel Laureate Andre Lwoff succeeded in growing Tetrahymena in pure culture, the basis for exploiting this alveolate as a model organism was laid. Milestone discoveries made in T. thermophila are the discovery of dynein motors[2], telomeres[3], RNA-mediated catalysis[4], telomerase[ 5] and the function of histone acetyltransferases in transcription regulation[6]. Within the last decades molecular biological techniques have been developed to alter T. thermophila’s genome and proteome: DNA transfection methods range from microinjection[7] and electroporation[ 8] into the MAC to biolistic bombardment of MIC and MAC[9]. Episomal plasmids based on an rDNAreplicon are available[10], as well as knock out/-in techniques based on homologous recombination[11,12].