Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

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We demonstrate that in Saccharomyces cerevisiae, the tandem array of ribosomal RNA genes [RDNl) is a target for integration of the Tyl retrotransposon that resuhs in silencing of Tyl transcription and transposition. Tyl elements transpose into random rDNA repeat units and are mitotically stable. In addition, we have found that mutation of several putative modifiers of RDNl chromatin structure abolishes silencing of Tyl elements in the rDNA array. Disruption of SIR2, which elevates recombination in RDNl, or TOPI, which increases psoralen accessibility in rDNA, or HTAl-HTBl, which reduces histone H2A-H2B levels and causes localized chromatin perturbations, abolishes transcriptional silencing of Tyl elements in RDNl. Furthermore, deletion of the gene for the ubiquitin conjugating enzyme Ubc2p, which ubiquitinates histones in vitro, derepresses not only Tyl transcription but also mitotic recombination in RDNl. On the basis of these results, we propose that a specialized chromatin structure exists in RDNl that silences transcription of the Tyl retrotransposon.

The yeast retrotransposon Ty) has been tagged with a reporter gene that allows selection of RNA-mediated transposition events and is applicable to the study of retroelements in other organisms. The reporter gene is a yeast HIS3 gene interrupted by an artificial intron (AI) in the antisense orientation. The HIS3AI sequences were inserted into a Ty) element such that the intron is on the sense strand of the Ty) element; therefore, splicing and retrotransposition of marked Tyl transcripts can give rise to His' cells. Fusion of the Tyl-H3mHIS3AI element to the inducible GAL] promoter resulted in a high frequency of histidine prototrophs upon galactose induction. Moreover, spontaneous His+ revertants derived from strains containing genomic TymfIIS3AI elements are a result of retrotransposition. By using this assay, we estimated the Ty) transposition rate to be between 3 x 10-7 and 1 x 10-5 transpositions per Ty) element per generation.Variations in the transposition rate of individual Ty) elements are correlated with the relative abundance of their transcripts.

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Saccharomyces cerevisiae and Saccharomyces paradoxus lack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. Glutathione Stransferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation. IMPORTANCERetrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both "host and parasite." To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication.

A computer model of the metabolism of glutamate, glutamine, γ-aminobutyrate, and the tricarboxylic acid cycle in mouse brain has been constructed in terms of 39 reactions among 19 substances or groups of substances (permitting manipulation of 30 independent variables). The model is divided into two compartments, in conformity with previous models based on indirect evidence, and it is found that this compartmentation is indeed the same as that indicated directly with specifically 14C-labelled acetate and glucose. The movement of materials between the large and small compartments has been studied; glutamine appears to flow from the small to the large compartment, γ-aminobutyrate in the reverse direction.