<i>Schizosaccharomyces pombe</i> Essential Genes: A Pilot Study

Decottignies, Anabelle; Sanchez-Perez, Isabel; Nurse, Paul

doi:10.1101/gr.636103

Cited by 71 publications

(66 citation statements)

References 53 publications

(41 reference statements)

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“…However, genome-wide RNA interference of TPP2 showed that reduction of the transcript did not result in any obvious phenotypes in C. elegans, even though the gene is normally well expressed at all stages of development (Kamath et al, 2003). This nonessential nature of TPP2 is also supported by the pilot study searching for essential genes in S. pombe (Decottignies et al, 2003). In S. cerevesiae, a TPP2-type gene is notably absent from the genome.…”

Section: Discussionmentioning

confidence: 56%

Tripeptidyl Peptidase II. An Oligomeric Protease Complex from Arabidopsis

et al. 2005

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The breakdown of most nuclear and cytoplasmic proteins involves their partial cleavage by the 26S proteasome followed by further disassembly to free amino acids by the combined action of endo-and exopeptidases. In animals, one important intermediate exopeptidase is tripeptidyl peptidase (TPP)II, which digests peptide products of the 26S proteasome and other endopeptidases into tripeptides. Here, we describe the purification and characterization of TPPII from Arabidopsis (Arabidopsis thaliana). Like its animal counterparts, Arabidopsis TPPII exists as a soluble, approximately 5-to 9-MD complex. Two related species of 153 and 142 kD are present in the purified preparations that are derived from a single TPP2 gene. Sequencing by Edman degradation of the intact polypeptides and mass spectrometry of proteolytic fragments demonstrated that the 142-kD form mainly differs from the 153-kD form by a truncation at the C-terminal end. This serine protease is a member of the subtilisin superfamily and is sensitive to the inhibitors alanine-alanine-phenylalanine-chloromethylketone and butabindide, which are diagnostic for the TPPII subfamily. The Arabidopsis TPP2 gene is widely expressed in many tissue types with related genes evident in other plant genomes. Whereas the 26S proteasome is essential, TPPII appears not as important for plant physiology. An Arabidopsis T-DNA mutant defective in TPP2 expression displays no phenotypic abnormalities and is not hypersensitive to either amino acid analogs or the 26S proteasome inhibitor MG132. As a consequence, plants likely contain other intermediate exopeptidases that assist in amino acid recycling.Proteolysis serves a variety of essential functions, including the elimination of misfolded or damaged proteins, the precise removal of regulatory proteins, and the maintenance of free amino acid pools needed for continual protein synthesis (Vierstra, 1996;Tomkinson, 1999). To facilitate this breakdown, plants and animals have evolved several proteolytic mechanisms for each subcellular compartment. In the vacuole/lysosome, proteins are catabolized by a variety of proteases and peptidases following their delivery to this hydrolytic compartment via endocytic and autophagic mechanisms (Thompson and Vierstra, 2005). For nuclear and cytoplasmic proteins, as well as abnormal polypeptides transported in a retrograde fashion from the endoplasmic reticulum to the cytoplasm, a major route involves ubiquitin (Ub) and the 26S proteasome (Smalle and Vierstra, 2004). Here, proteins destined for degradation are selectively tagged by the covalent attachment of multiple Ubs.These ubiquitinated proteins are then recognized and cleaved into smaller fragments by the 26S proteasome, a self-compartmentalized ATP-dependent protease complex with broad substrate and cleavage specificity.Products of the 26S proteasome are predominantly peptides 6 to 12 amino acids in length (Wenzel et al., 1994;Kisselev et al., 1999;Voges et al., 1999). Complete recycling requires further cleavage of these peptides by intermediate...

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Section: Discussionmentioning

confidence: 56%

Tripeptidyl Peptidase II. An Oligomeric Protease Complex from Arabidopsis

et al. 2005

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“…Among the remaining 3015 yeast genes, 342 (11.3%) gave nonviable phenotypes. This indicated that the common fungal sequences comprised a far greater proportion of essential genes than sequences which were not part of the conserved fungal set, and this was previously observed for Schizosaccharomyces pombe (Decottignies et al 2003).…”

Section: Common Fungal Genesmentioning

confidence: 64%

“…Winzeler et al (1999) created S. cerevisiae deletion mutants for 2026 ORFs and found that 17% were essential for viability on rich media, and 40% showed some growth defect. Decottignies et al (2003) examined 100 deletion mutants in S. pombe and concluded that 17.5% of the genes were essential. Giaever et al (2002) created deletion mutants for 5916 S. cerevisiae genes and found that 18.7% were essential for growth on rich glucose medium.…”

Section: Eukaryotic Homologsmentioning

confidence: 99%

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Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

Hsiang

Baillie

2005

J Mol Evol

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Abstract. The purpose of this research was to search for evolutionarily conserved fungal sequences to test the hypothesis that fungi have a set of core genes that are not found in other organisms, as these genes may indicate what makes fungi different from other organisms. By comparing 6355 predicted or known yeast (Saccharomyces cerevisiae) genes to the genomes of 13 other fungi using Standalone TBLASTN at an e-value <1E-5, a list of 3340 yeast genes was obtained with homologs present in at least 12 of 14 fungal genomes. By comparing these common fungal genes to complete genomes of animals (Fugu rubripes, Caenorhabditis elegans), plants (Arabidopsis thaliana, Oryza sativa), and bacteria (Agrobacterium tumefaciens, Xylella fastidiosa), a list of common fungal genes with homologs in these plants, animals, and bacteria was produced (938 genes), as well as a list of exclusively fungal genes without homologs in these other genomes (60 genes). To ensure that the 60 genes were exclusively fungal, these were compared using TBLASTN to the major sequence databases at GenBank: NR (nonredundant), EST (expressed sequence tags), GSS (genome survey sequences), and HTGS (unfinished high-throughput genome sequences). This resulted in 17 yeast genes with homologs in other fungal genomes, but without known homologs in other organisms. These 17 core, fungal genes were not found to differ from other yeast genes in GC content or codon usage patterns. More intensive study is required of these 17 genes and other common fungal genes to discover unique features of fungi compared to other organisms.

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“…They contend that the characterization of genes essential for growth in fungal pathogens is an important step in development of novel antifungal drugs, as well as providing insights into biological diversity of fungi. Decottignies et al (2003) used a PCR-based gene deletion procedure on 100 genes of S. pombe and found that 17.5% of these deletions were of essential genes. They then compared 450 proteins from two yeasts (S. cerevisiae and S. pombe) with those of Metazoa, plants and prokaryotes in the GenBank nonredundant protein database, and estimated that 80% of the essential genes of S. pombe were shared with other eukaryotes, with half of these genes also found in prokaryotes, while only 10% of essential genes were fungal specific.…”

Section: Fungal Comparative Genomics -Essential Fungal Genesmentioning

confidence: 99%

Issues in Comparative Fungal Genomics

Hsiang

Baillie

2006

Applied Mycology and Biotechnology

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Biologists face an overwhelming richness of nucleotide and protein sequence data. By the middle of 2005, there were almost 300 complete genomes that were publicly accessible. Most of these were archeal or bacterial since prokaryotic genomes are much smaller than eukaryotic genomes. Among eukaryotes, fungi, particularly yeasts, have some of the smallest genome sizes and hence represent the highest number of complete or almost complete genomes sequenced. By mid-2005, there were over 43 fungal genomes that were completely or almost completely sequenced and publicly accessible. What are the relationships among fungi and between fungi and other organisms? What type of genes and pathways are required for pathogenicity and other fungal lifestyles? Researchers are addressing these types of questions with data from high-throughput genomic sequencing. This review examines some recent uses of fungal genomic data in comparative genome analyses. Comparative genomics can facilitate research into the following areas: evolution, phylogenetics, targeted drugs, gene discovery, and gene function. Each of these is discussed as well as the availability and ownership of the genomic data, and the concepts of homology (homologs, orthologs, paralogs) and similarity.

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Schizosaccharomyces pombe Essential Genes: A Pilot Study

Cited by 71 publications

References 53 publications

Tripeptidyl Peptidase II. An Oligomeric Protease Complex from Arabidopsis

Tripeptidyl Peptidase II. An Oligomeric Protease Complex from Arabidopsis

Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

Issues in Comparative Fungal Genomics

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