Schizosaccharomyces pombe comparative genomics; from sequence to systems

Abstract

The fission yeast Schizosaccharomyces pombe is becoming increasingly important as a model for the characterization and study of many globally conserved genes, second only in importance to the budding yeast Saccharomyces cerevisiae. This chapter provides an updated inventory of gene number and genome contents for fission yeast compared to budding yeast. Functional and comparative genomics studies, and the insights these have provided into how the different genome contents of these two yeasts are manifested in their individual biologies are reviewed. Phylogenetic analysis, comparative genomics and experimental research support the choice of S. pombe as a model for the dissection of many biological processes, which are often more similar to the analogous processes in higher eukaryotes than those of the Saccharomytina. The review underlines the advantages of exploiting this organism through the integration of bench science, functional genomics, phylogenomics and systems biology in order to identify and interpret the minimal requirements for a eukaryotic cell.

Sterol Regulatory Element Binding Protein Is a Principal Regulator of Anaerobic Gene Expression in Fission Yeast

“…Significant anaerobically induced genes (boldface type), significant anaerobically repressed genes (underlined), and significant Sre1p-dependent genes (boxed) are shown. The S. pombe ergosterol synthesis pathway is modeled after S. cerevisiae using the S. pombe ortholog table and has not been determined experimentally (22,37 was upregulated. Finally, many anaerobically induced genes have not been assigned functions.…”

“…Significant anaerobically induced genes (boldface type) and significant Sre1p-dependent genes (boxed) are shown. The S. pombe heme synthesis pathway is modeled after S. cerevisiae using the S. pombe ortholog table and has not been determined experimentally (30,37). Abbreviations: ␦-ALA, 5-aminolevulinate; PBG, porphobilinogen; Preurogen, hydroxymethylbilane; Urogen, uroporphyrinogen; Coprogen, coproporphryinogen; Protogen, protoporphyrinogen; Proto, protoporphyrin.…”

Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%

“…The substantial coverage reported here shows that the majority of gene products have at least some minimal functional information attached to them, whether from experiment, sequence similarity or high-throughput studies. However, coverage is only one measure of annotation progress and curation necessarily requires long-term investment to make (Lespinet et al, 2002;Wood, 2006). For these genes, fission yeast is frequently an important model, providing functional insights for human orthologues (Wood, 2006).…”

Big Data Supervised Pairwise Ortholog Detection in Yeasts

“…All methodologies including the proposed supervised big data approach generally declined their performance for ortholog detection in S. cerevisiae -S. pombe datasets, probably because of S. pombe is a distant relative of S. cerevisiae [23]. The supervised classifiers performance was also negatively affected by differences in data distribution between the train and test sets [42].…”

“…These species bring about experimental models for many essential processes of eukaryotes since most of their genes have been predicted as homologs to multicellular eukaryotes ones. Specifically, S. pombe genes are more similar to mammals' genes than S. cerevisiae ones [23]. However, S. pombe is a distant relative of S. cerevisiae, accordingly, ortholog detection between them is a difficult task due to the divergence of sequences [13].…”