In a paper selected for an editorial highlight in the journal Genetics, NIEHS researchers and their collaborators reported that the enzyme RNaseH2 (see sidebar) is essential for maintaining the integrity of DNA in yeast. The new findings may help advance understanding of the mechanisms underlying certain neurodegenerative and autoimmune disorders.
Collaboration leads to discovery
“This collaboration began with the discovery that a large number of ribonucleotides are incorporated into the nuclear genome of budding yeast,” explained Jessica Williams, Ph.D., a staff scientist in the NIEHS DNA Replication Fidelity Group, led by Tom Kunkel, Ph.D. “These ribonucleotides are very efficiently removed by the RNase H2 enzyme, and failure to remove them causes mutations and other forms of genome instability,” Williams said.
Scientists in Kunkel’s lab collaborated with Lucas Argueso, Ph.D., and his team at Colorado State University (CSU). Kunkel’s group conducted genome-wide sequence analyses of yeast strains carrying the enzyme DNA polymerase epsilon in a mutated form that causes more ribonucleotides to be incorporated into the DNA strand. The researchers then modified the mutant strains so that they did not express the gene that codes for RNase H2.
“In one of our strains lacking RNase H2, more of the mutations associated with chromosome recombination were observed, compared to a strain containing RNase H2,” Kunkel said.
This observation prompted Argueso’s group in Colorado to conduct detailed analyses using experimental strategies they had developed previously to quantify recombination in yeast. They constructed yeast strains carrying the same mutant forms of the DNA polymerases studied in the Kunkel lab. Argueso and his team found that, consistent with the genome-wide analysis, strains with mutated DNA polymerase epsilon and deficient RNase H2 showed elevated rates of large mutations involving many nucleotides. They also found that increased recombination depended upon the presence of the topoisomerase 1 enzyme.
Implications for human diseases
Mutations in human RNase H2 are associated with diseases that include the neurodegenerative disorder Aicardi Goutieres Syndrome (AGS), which affects the brain, skin, and the immune system, and systemic lupus erythrematosus (SLE), an autoimmune disorder.
Scott Lujan, Ph.D., an NIEHS bioinformatics contractor and another of the paper’s co-authors, compared DNA replication to typing. He compared ribonucleotides incorporated into the strand with text typed in the wrong font. “RNase H2 is the enzyme that corrects the font,” he said, pointing out that, similar to how Find and Replace functions may miss text in the wrong font, these mutations may not be repaired.
Extend discoveries to mouse and human cells
As a simple organism with a small genome and fast growth rate, yeast has long been used to study molecular processes that are similar among many other organisms, including humans. “The same problem happens in humans, carrots, butterflies, or yeast cells, [which are] the model organism used in our lab,” Argueso said, on the CSU website SOURCE. “The same yeast that is used to bake bread and to brew beer is an incredibly useful biomedical research model.”
In future studies, Kunkel’s team plans to extend their findings in yeast by studying mutations triggered by ribonucleotides in mouse and human cells, to learn how they might contribute to human disease.
Citation: Conover HN, Lujan SA, Chapman MJ, Cornelio DA, Sharif R, Williams JS, Clark AB, Camilo F, Kunkel TA, Argueso JL. 2015. Stimulation of Chromosomal Rearrangements by Ribonucleotides. Genetics 201(3):951-961.
(Qing Xu is a biologist in the NIEHS Metabolism, Genes, and Environment Group.)