June 1 2006
12:00 LSB 2320

Dr. Cliff Brunk
UCLA Ecology and Evolutionary Biology

Unusual Molecular Evolution of Tetrahymena



An examination of all available actin genes clearly indicates that the actin genes found in ciliates are significantly more divergent from non-ciliate actin genes than non-ciliate actin genes are from each other. It is also evident that the ciliate actins are as divergent from one another as they are from non-ciliate actins. This unusually high divergence among ciliate proteins suggests that these species accumulate mutations at an unusually high rate. The rate of mutation accumulation for a species can be adjusted and is certainly under selective pressure.

The unusual dual nuclear system characterizing the ciliates might predispose it to select for a higher average mutation rate. These ciliates have a multiploid somatic macronucleus that is responsible for all gene expression during the vegetative life of the cells and a silent germinal micronucleus, which permits a high mutation rate. During the vegetative phase each macronucleus drifts toward a haploid status, phenotypic assortment. During macronuclear anlagen development following conjugation chromosome fragmentation and macronuclear recombination so thoroughly disrupts linkage groups that all of the genes assort virtually independently.

This unusual genetic system has profound implications for the mutation rate that can be tolerated. During vegetative growth, the micronuclear genome is not under selective pressure. Thus, a high mutation rate can be readily accommodated, which in turn allows pairs (or sets) of mutations to accumulate. Although these mutations may be independently deleterious, yet in combinations they can confer a selective advantage. This process dramatically expands the different protein sequences available for the action of selection at the next conjugation.

The nature of the ciliate macronuclear genome and the aspects of the genetic system also make it inherently tolerant to a high mutation rate.

Given the highly divergent nature of the genes in Tetrahymena thermophila identifying the genes and control regions is very challenging. It is abundantly clear that the most accurate and efficient identification of genes and control elements in the genome of an organism can be achieved by “phylogenetic foot-printing”, in which closely related genomes are compared for conserved regions. We have an excellent draft of the Tetrahymena thermophila genome available, but little is know about the genes and control regions. Prior to adding a second Tetrahymena species to the list of eukaryotic genomes to be sequenced, we must first determine the Tetrahymena species that is an optimal evolutionary distance from T. thermophila. T. malaccensis is closest related species to T. thermophila, while T. ellioti is the next closest. We can readily align random genomic sequences from T. malaccensis with the T. thermophila genome, but only a few of the T. ellioti sequences can be accurately aligned with the T. thermophila genome.

We have determined the complete mitochondrial genome sequence from several species of Tetrahymena; T. thermophila, T. malaccensis, T. pigmentosa and T. paravorax. With the published mitochondrial genome of T. pyriformis we have five complete Tetrahymena mitochondrial genomes for comparison. All of the genomes are highly conserved relative to one another. In spite of conservation among the Tetrahymena species, of the 44 mitochondrial protein only 22 are sufficiently similar to proteins found in GenBank to allow an identification of homologues.

While the Tetrahymena mitochondrial genes appear to be divergent relative to non-Tetrahymena mitochondrial genes they are similar to each other. In contrast the Tetrahymena nuclear genes are divergent relative to other Tetrahymena species as well as non-Tetrahymena genes.

Brunk, C. F., Lee, L. C., Tran, A. B. and Li, J., Complete Sequence of the Mitochondrial genome of Tetrahymena thermophila and comparative methods for Identifying Highly Divergent Genes. Nucleic Acid Res. 31: 1673-1682, 2003.

Sadler, L. A. and Brunk, C. F., Phylogenetic Relationships and Unusual Diversity in Histone H4 Proteins within the Tetrahymena pyriformis Complex. Mol. Biol. Evolution 9: 70-84, 1992.

Brunk, C. F. and Sadler, L. A., Characterization of the Promoter Region of Tetrahymena Gene. Nuc. Acids Res. 18: 323-329, 1990.

Kellis, M., Patterson, N., Endrizzi, M, Birren, B. and Lander, E. S., Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements. Nature 423: 241-254, 2003.

General Reference:
Asai, D. J. and Forney, J. D., Tetrahymena thermophila, Methods in Cell Biology, Volume 62, Academic Press N.Y. 2000.