NEW YORK (GenomeWeb News) – An international team reported in the early, online edition of Nature Biotechnology this week that they have created and started analyzing a genome-wide deletion library for the fission yeast model organism Schizosaccharomyces pombe.
The researchers created a set of more than 4,800 heterozygous diploid fission yeast deletion mutants representing more than 98 percent of known fission yeast protein-coding genes. Their analyses of these mutants have already started turning up key similarities and differences between the fission yeast and the budding yeast Saccharomyces cerevisiae — suggesting, for instance, that more fission yeast than budding yeast genes are essential.
"Fission and budding yeast are not closely related and differ in a number of aspects including organization of the cell cycle, heterochromatin, complexity of centromeres and DNA replication origins, and the prevalence of introns," senior author Kwang-Lae Hoe, a researcher with the Korea Research Institute of Bioscience and Biotechnology's Integrative Omics Research and Bioevaluation Centres, and colleagues wrote, "which makes their comparison valuable for defining genes and processes required more generally in eukaryotes."
Libraries of budding yeast mutants in which genes have been systematically deleted across the genome have contributed to an improved understanding of eukaryote biology, the researchers explained. But making similar genome-wide deletion sets is more challenging in many other eukaryotes, they added, and gene knockdown by RNA interference is often used instead.
To create a second eukaryotic gene deletion strain set, Hoe and his collaborators used a homologous recombination-based method, generating 4,836 heterozygous diploid fission yeast deletion strains representing 98.4 percent of the yeast's annotated protein-coding genes. They also created strains missing a handful of Tf2 transposons, a few dozen suspected genes, and another 48 pseudogenes.
The mutant strains were bar-coded using computationally created sequences so deletion strains can be tracked during future experiments using microarrays or PCR.
The team has already started examining the effects of these gene deletions. For instance, in the new paper, they describe the results of experiments aimed at determining how many of the deleted genes are essential for fission yeast viability.
They found that at least more than a quarter of fission yeast genes — 26.1 percent — are essential, compared with 17.8 percent in budding yeast. And though S. pombe yeast has fewer genes overall than budding yeast, the team noted, fission yeast still has more essential genes overall.
In their subsequent analyses, the researchers explored the characteristics of the essential versus non-essential fission yeast genes, looking at everything from their position in the genome and ORF localization to their intron content, uniqueness, and proposed function.
In addition, they were able to compare these results with data on essential genes in budding yeast and determine which essential genes are conserved between the two yeast species and in other eukaryotes.
Through comparisons with budding yeast, combined with additional experiments using slow-growing mutants, the researchers also teased apart roles for some fission yeast genes in processes such as cell division, transcription, and translation.
"The availability of a near complete, genome-wide deletion collection for fission yeast provides a useful tool for the functional studies of eukaryotic molecular and cell biology and for biotechnological applications," the researchers concluded.
South Korean firm Bioneer said that it has provided around $7 million to help fund work on developing the S. pombe genome-wide deletion library. Additional information on the project is available on the firm's website.