Yeast Ribosomal RNA Genes Boost Genome Stability

Genes coding for ribosomal RNA help to maintain the stability of yeast genomes, according to a study appearing online today in Science.

By comparing four Saccharomyces cerevisiae strains with different ribosomal RNA gene copy numbers, a Japanese research team found that that the strains with fewer ribosomal genes or rDNA were more sensitive to DNA damage caused by chemicals or ultraviolet light. This sensitivity seems to be due to a role for rDNA genes in recombination repair and sister chromatid cohesion. As such, the findings suggest rDNA amplification systems may have evolved in eukaryotic cells to maintain genome stability.

"The extra rDNA copies facilitate condensin association and sister-chromatid cohesion, thereby facilitating recombinatorial repair" senior author Takehiko Kobayashi, a researcher affiliated with Japan's Graduate University for Advanced Studies and the National Institute of Genetics, and co-authors wrote.

Organisms often have multiple sequences coding for rRNA and other RNA products, the researchers explained. In yeast, for example, tandem repeat sequences of rDNA genes are often found in clusters along chromosomes — past research suggests chromosome 12 houses some 150 copies of rDNA genes.

A gene amplification system in yeast and other eukaryotes seems to prop up the number of rDNA genes, despite gene loss through recombination. And although some rDNA is transcribed into rRNA, at least half of the copies of yeast rDNA aren't. A similar pattern has been reported in other organisms, including plants, the team noted, which seem to have thousands of untranscribed rDNA copies.

In an effort to explore what extra copies of rDNA genes are doing in the yeast genome, the researchers examined four S. cerevisiae strains that had 20, 40, 80, or 110 copies of rDNA genes.

Each of the strains produced typical levels of rRNA and grew well under normal conditions. But when the yeast strains were exposed to ultraviolet light or to the chemical methyl methanesulfonate, the strains with fewer rDNA copies were more sensitive to these DNA damaging agents.

By curbing rDNA transcription in the strain with the greatest number of rDNA copies by removing RNA polymerase I genes, the team showed that they could make this strain as sensitive to DNA damage as the low copy strain.

Their subsequent experiments suggest the S. cerevisiae strain with just 20 copies of rDNA apparently undergoes increased rDNA recombination following DNA damage compared with strains that had more rDNA copies.

And, the team noted, this strain also had more chromosomal damage and replication problems — particularly involving chromosome 12 — than the high copy strain.

When they screened yeast mutants looking for mutations that eliminated the rDNA copy number-related sensitivity to DNA damage, the researchers identified several genes involved in recombination repair.

Based on such findings, they propose that yeast stains with fewer rDNA copies may be less able to repair recombination changes to rDNA because so many of the genes are tied up in the process of transcription.

In addition, their experiments suggest low copy rDNA strains have problems with cohesion between sister chromatids, adding to their DNA damage sensitivity.

"Our results suggest that multiple copies of rDNA are required to reduce rDNA transcription and allow efficient replication-coupled recombination repair by facilitating condensin association and sister-chromatid cohesion," the team wrote.

And because bacteria have far fewer rDNA copies than eukaryotic cells — and lack the rDNA amplification system found in these cells — they argued that rDNA copy number evolution might correspond to the advent of organisms with larger cells.

"Bigger cells needed more ribosomes and rDNA transcription," the researchers concluded. "This increased rDNA transcription would have been toxic due to greater sensitivity to DNA damage caused by environmental factors … selecting for cells that can maintain multiple rDNA copies, and resulting in the evolution of the rDNA amplification system."