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

Aslett, Martin; Wood, Valerie

doi:10.1002/yea.1420

Cited by 47 publications

(43 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…3 and 5). Of the eight helicases that localize to S. pombe mitochondria (32), six are likely RNA helicases (2). Therefore, Pfh1p may be one of the (or even the only) replicative helicase for S. pombe mtDNA.…”

Section: Discussionmentioning

confidence: 99%

The Schizosaccharomyces pombe Pfh1p DNA Helicase Is Essential for the Maintenance of Nuclear and Mitochondrial DNA

Pinter

Aubert

Zakian

2008

Molecular and Cellular Biology

107

View full text Add to dashboard Cite

Schizosaccharomyces pombe Pfh1p is an essential member of the Pif family of 5-3 DNA helicases. The two Saccharomyces cerevisiae homologs, Pif1p and Rrm3p, function in nuclear DNA replication, telomere length regulation, and mitochondrial genome integrity. We demonstrate here the existence of multiple Pfh1p isoforms that localized to either nuclei or mitochondria. The catalytic activity of Pfh1p was essential in both cellular compartments. The absence of nuclear Pfh1p resulted in G 2 arrest and accumulation of DNA damage foci, a finding suggestive of an essential role in DNA replication. Exogenous DNA damage resulted in localization of Pfh1p to DNA damage foci, suggesting that nuclear Pfh1p also functions in DNA repair. The absence of mitochondrial Pfh1p caused rapid depletion of mitochondrial DNA. Despite localization to nuclei and mitochondria in S. pombe, neither of the S. cerevisiae homologs, nor human PIF1, suppressed the lethality of pfh1⌬ cells. However, the essential nuclear function of Pfh1p could be supplied by Rrm3p. Expression of Rrm3p suppressed the accumulation of DNA damage foci but not the hydroxyurea sensitivity of cells depleted of nuclear Pfh1p. Together, these data demonstrate that Pfh1p has essential roles in the replication of both nuclear and mitochondrial DNA.The founding member of the Pif family of 5Ј-3ЈDNA helicases is Saccharomyces cerevisiae Pif1p (ScPif1p) . The genomes of most multicellular animals contain a single Pif1-like gene, but several single-celled eukaryotes, including S. cerevisiae, encode two Pif1-like proteins. Although ScPif1p and ScRrm3p are ϳ40% identical in the helicase domain and both unwind double-stranded DNA with 5Ј-3Ј polarity (22, 28), these paralogs have largely nonoverlapping functions (6).ScPif1p was first identified because of its role in the repair and recombination of mitochondrial DNA (mtDNA) (15, 16). In the nucleus, ScPif1p is a catalytic inhibitor of telomerase that acts by removing telomerase from DNA ends (5, 44, 60). As a result, cells lacking ScPif1p have long telomeres. ScPif1p has additional, less well characterized roles in the replication (8, 23) and recombination (56) of chromosomal DNA. In vitro, ScPif1p preferentially unwinds RNA/DNA hybrids (7) and branched substrates (27). ScRRM3 was first identified as a suppressor of recombination in the ribosomal DNA (rDNA) (25). ScRrm3p moves with the replication fork (3) and facilitates its progression past stable, non-histone protein-DNA complexes (21, 51). ScRrm3p-sensitive sites, which are found throughout the genome (3), include tRNA genes, telomeres, centromeres, inactive replication origins, silent mating type loci, and multiple sites within rDNA (21)(22)(23). In the absence of ScRrm3p, replication forks stall and sometimes break at ScRrm3p-sensitive sites, leading to intra-S-phase checkpoint activation (21, 51) and dependency on replication fork restart activities for viability (40,43,50,52). In the rDNA, which is particularly dependent on ScRrm3p to prevent replication fork stalling, ScPif1p a...

show abstract

Section: Discussionmentioning

confidence: 99%

The Schizosaccharomyces pombe Pfh1p DNA Helicase Is Essential for the Maintenance of Nuclear and Mitochondrial DNA

Pinter

Aubert

Zakian

2008

Molecular and Cellular Biology

107

View full text Add to dashboard Cite

show abstract

“…We used the full GO 63 annotations provided for the five organisms [64][65][66][67][68] , and mapped them onto the generic slim ontology definitions provided by GOC, except in the case of AT where the plant slim ontology definitions were used. The distance between a pair of GO terms was defined to be the sum of the distances of the two terms on the GO graph from their least common ancestor.…”

Section: Methodsmentioning

confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

View full text Add to dashboard Cite

It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

show abstract

“…To determine whether any particular biological process was affected in gcn5⌬, ada2⌬, and ada3⌬ mutants, genes whose expression was significantly altered in all three mutants were analyzed for enrichment of Gene Ontology (GO) categories (Aslett and Wood 2006) or transcriptional modules (Tanay et al 2005). Among the genes with decreased mRNA levels, there was no significant enrichment for any category.…”

Section: Transcriptome Analysis Of the Saga Hat Module Suggests A Rolmentioning

confidence: 99%

The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8

Helmlinger¹,

Marguerat²,

Villén³

et al. 2008

Genes Dev.

122

View full text Add to dashboard Cite

The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we performed biochemical and genetic analyses of SAGA in the fission yeast, Schizosaccharomyces pombe. Purification of the S. pombe SAGA complex showed that its subunit composition is identical to that of Saccharomyces cerevisiae. Analysis of S. pombe SAGA mutants revealed that SAGA has two opposing roles regulating sexual differentiation. First, in nutrient-rich conditions, the SAGA histone acetyltransferase Gcn5 represses ste11 + , which encodes the master regulator of the mating pathway. In contrast, the SAGA subunit Spt8 is required for the induction of ste11 + upon nutrient starvation. Chromatin immunoprecipitation experiments suggest that these regulatory effects are direct, as SAGA is physically associated with the ste11 + promoter independent of nutrient levels. Genetic tests suggest that nutrient levels do cause a switch in SAGA function, as spt8⌬ suppresses gcn5⌬ with respect to ste11 + derepression in rich medium, whereas the opposite relationship, gcn5⌬ suppression of spt8⌬, occurs during starvation. Thus, SAGA plays distinct roles in the control of the switch from proliferation to differentiation in S. pombe through the dynamic and opposing activities of Gcn5 and Spt8.[Keywords: S. pombe; transcription; differentiation; SAGA; Gcn5; Ste11] Supplemental material is available at http://www.genesdev.org.

show abstract

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

Cited by 47 publications

References 8 publications

The Schizosaccharomyces pombe Pfh1p DNA Helicase Is Essential for the Maintenance of Nuclear and Mitochondrial DNA

The Schizosaccharomyces pombe Pfh1p DNA Helicase Is Essential for the Maintenance of Nuclear and Mitochondrial DNA

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8

Contact Info

Product

Resources

About