Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis

The S. cerevisiae genome is the most well-characterized eukaryotic genome and one of the simplest in terms of identifying open reading frames (ORFs), yet its primary annotation has been updated continually in the decade since its initial release in 1996 (Goffeau et al., 1996). The Saccharomyces Genome Database (SGD; www.yeastgenome.org) (Hirschman et al., 2006), the community-designated repository for this reference genome, strives to ensure that the S. cerevisiae annotation is as accurate and useful as possible. At SGD, the S. cerevisiae genome sequence and annotation are treated as a working hypothesis, which must be repeatedly tested and refined. In this paper, in celebration of the tenth anniversary of the completion of the S. cerevisiae genome sequence, we discuss the ways in which the S. cerevisiae sequence and annotation have changed, consider the multiple sources of experimental and comparative data on which these changes are based, and describe our methods for evaluating, incorporating and documenting these new data.

blm3-1 Is an Allele of UBP3, a Ubiquitin Protease that Appears to Act During Transcription of Damaged DNA

Yeast Blm10 and mammalian PA200 proteins share significant sequence similarity and both cap the ends of 20 S proteasomes and enhance degradation of some peptide substrates. Blm10 was identified as a suppressor of the yeast blm3-1 mutation, and initially was thought to be the Blm3 protein. Both the blm3-1 and blm10-Delta mutations were reported to cause sensitivity to bleomycin and other forms of DNA damage, suggesting a role for Blm10/PA200-proteasome complexes in DNA repair. We have been unable to observe significant DNA damage sensitivity in blm10-Delta mutants in several genetic backgrounds, and we have therefore further investigated the relationship between BLM10 and blm3-1. We find that blm3-1 is a nonsense mutation in the ubiquitin protease gene UBP3. Deleting UBP3 causes phenotypes similar to those caused by blm3-1, but neither causes a general defect in DNA repair. Ubp3 has several known functions, and genetic interaction data presented here suggest an additional role in transcriptional elongation. The phenotypes caused by blm3-1 and ubp3-Delta mutations are not suppressed by over-expression of BLM10, nor are they affected by deletion of BLM10. These results remove key components of the previously reported connection between Blm10/PA200-proteasome complexes and DNA repair, and they suggest a novel way to interpret sensitivity to bleomycin as resulting from defects in transcription elongation.

The HEAT repeat protein Blm10 regulates the yeast proteasome by capping the core particle

Proteasome activity is fine-tuned by associating the proteolytic core particle (CP) with stimulatory and inhibitory complexes. Although several mammalian regulatory complexes are known, knowledge of yeast proteasome regulators is limited to the 19-subunit regulatory particle (RP), which confers ubiquitin-dependence on proteasomes. Here we describe an alternative proteasome activator from Saccharomyces cerevisiae, Blm10. Synthetic interactions between blm10Delta and other mutations that impair proteasome function show that Blm10 functions together with proteasomes in vivo. This large, internally repetitive protein is found predominantly within hybrid Blm10-CP-RP complexes, representing a distinct pool of mature proteasomes. EM studies show that Blm10 has a highly elongated, curved structure. The near-circular profile of Blm10 adapts it to the end of the CP cylinder, where it is properly positioned to activate the CP by opening the axial channel into its proteolytic chamber.

Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii

BACKGROUND

The recently sequenced genome of the filamentous fungus Ashbya gossypii revealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiae both at the level of homology and synteny (conservation of gene order). Thus, it became possible to reinvestigate the S. cerevisiae genome in the syntenic regions leading to an improved annotation.

RESULTS

We have identified 23 novel S. cerevisiae open reading frames (ORFs) as syntenic homologs of A. gossypii genes; for all but one, homologs are present in other eukaryotes including humans. Other comparisons identified 13 overlooked introns and suggested 69 potential sequence corrections resulting in ORF extensions or ORF fusions with improved homology to the syntenic A. gossypii homologs. Of the proposed corrections, 25 were tested and confirmed by resequencing. In addition, homologs of nearly 1,000 S. cerevisiae ORFs, presently annotated as hypothetical, were found in A. gossypii at syntenic positions and can therefore be considered as authentic genes. Finally, we suggest that over 400 S. cerevisiae ORFs that overlap other ORFs in S. cerevisiae and for which no homolog can be detected in A. gossypii should be regarded as spurious.

CONCLUSIONS

Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, we have shown that it still benefits substantially from comparison to the completed sequence and syntenic gene map of A. gossypii, an evolutionarily related fungus. This type of approach will strongly support the annotation of more complex genomes such as the human and murine genomes.