Life with 6000 Genes

Department of Biochemistry, Stanford University, Palo Alto, California, United States
Science (Impact Factor: 33.61). 11/1996; 274(5287):546, 563-7. DOI: 10.1126/science.274.5287.546
Source: PubMed


The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential
protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275
transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's
16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent
genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate
the biological functions of all of these genes.

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    • "The LSO1 gene (YJR005C-A) was not found in the initial study (Shakoury-Elizeh et al. 2004) and is the most increased by BPS with an over 200-fold increase in the mRNA (Table 2). LSO1 was not known during that original study because it was " late-annotated small open reading frame " as the LSO1 encodes a small 93 amino acid gene product not annotated in the original yeast genome project (Goffeau et al. 1996; Cliften et al. 2003; Kastenmayer et al. 2006). LSO1 was annotated after being found by homology with the genome of the filamentous fungus Ashbya gossypii (Brachat et al. 2003). "
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    ABSTRACT: We have identified a new downstream target gene of the Aft1/2-regulated iron regulon in budding yeast Saccharomyces cerevisiae, the late-annotated small open reading frame LSO1. LSO1 transcript is among the most highly induced from a transcriptome analysis of a fet3-1 mutant grown in the presence of the iron chelator bathophenanthrolinedisulfonic acid. LSO1 has a paralog, LSO2, which is constitutively expressed and not affected by iron availability. In contrast, we find that the LSO1 promoter region contains three consensus binding sites for the Aft1/2 transcription factors and that an LSO1-lacZ reporter is highly induced under low-iron conditions in a Aft1-dependent manner. The expression patterns of the Lso1 and Lso2 proteins mirror those of their mRNAs. Both proteins are localized to the nucleus and cytoplasm, but become more cytoplasmic upon iron deprivation consistent with a role in iron transport. LSO1 and LSO2 appear to play overlapping roles in the cellular response to iron starvation since single lso1 and lso2 mutants are sensitive to iron deprivation and this sensitivity is exacerbated when both genes are deleted.
    MicrobiologyOpen 10/2015; DOI:10.1002/mbo3.303 · 2.21 Impact Factor
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    • "In most of these, the PCMT gene has been predicted but little efforts have been directed towards their isolation and characterization. Sequencing and subsequent annotation revealed that the genome of Saccharomyces cerevisiae lacked a PCMT gene or its homolog [17] [18]. In contrast, a PCMT homolog, Pcm2, has been identified in fission yeast Schizosaccharomyces pombe [19]. "
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    ABSTRACT: Backgrounds: Spontaneous deamidation and isoaspartate (IsoAsp) formation contributes to aging and reduced longevity in cells. A protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT) is responsible for minimizing IsoAsp moieties in most organisms. Methods: PCMT was purified in its native form from yeast Candida utilis. The role of the native PCMT in cell survival and protein repair was investigated by manipulating intracellular PCMT levels with Oxidized Adenosine (AdOx) and Lithium Chloride (LiCl). Proteomic Identification of possible cellular targets was carried out using 2-dimensional gel electrophoresis, followed by on-Blot methylation and mass spectrometric analysis. Results: The 25.4. kDa native PCMT from C. utilis was found to have a Km of 3.5. μM for AdoMet and 33.36. μM for IsoAsp containing Delta Sleep Inducing Peptide (DSIP) at pH 7.0. Native PCMT comprises of 232 amino acids which is coded by a 698. bp long nucleotide sequence. Phylogenetic comparison revealed the PCMT to be related more closely with the prokaryotic homologs. Increase in PCMT levels in vivo correlated with increased cell survival under physiological stresses. PCMT expression was seen to be linked with increased intracellular reactive oxygen species (ROS) concentration. Proteomic identification of possible cellular substrates revealed that PCMT interacts with proteins mainly involved with cellular housekeeping. PCMT effected both functional and structural repair in aged proteins in vitro. General significance: Identification of PCMT in unicellular eukaryotes like C. utilis promises to make investigations into its control machinery easier owing to the familiarity and flexibility of the system.
    08/2015; 4. DOI:10.1016/j.bbrep.2015.08.015
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    • "However, this is hardly ever the case: most of the genome sequences published are called ''unfinished'' as they are heavily fragmented, whereas the number of truly ''finished'' genomes remains remarkably low. Only the small, compact genomes of a few so-called ''model'' organisms have been fully assembled until now, mostly bacteria (such as Haemophilus influenzae and Escherichia coli [4] [5]) and fungi (e.g., Saccharomyces cerevisiae [6]) along with a single metazoan to date, the nematode Caenorhabditis elegans [7]. All other sequences consist of ''drafts'' of varying quality, including the human genome that still contains numerous gaps but is nevertheless the most complete mammalian reference assembly available [8] [9]. "
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    ABSTRACT: High-throughput DNA sequencing technologies are fuelling an accelerating trend to assemble de novo or resequence the genomes of numerous species as well as to complete unfinished assemblies. While current DNA sequencing technologies remain limited to reading stretches of a few hundreds or thousands of base pairs, experimental and computational methods are continuously improving with the goal of assembling entire genomes from large numbers of short DNA sequences. However, the algorithms that piece together DNA strands face important limitations due, notably, to the presence of repeated sequences or of multiple haplotypes within one genome, thus leaving many assemblies incomplete. Recently, the realization that the physical contacts experienced by a portion of a DNA molecule could be used as a robust and quantitative assay to determine its genomic position has led to the emerging field of contact genomics, which promises to revolutionize current genome assembly approaches by exploiting the flexible polymer properties of chromosomes. Here we review the current applications of contact genomics to genome scaffolding, haplotyping and metagenomic assembly, then outline the future developments we envision. Copyright © 2015. Published by Elsevier B.V.
    FEBS letters 04/2015; 40(20). DOI:10.1016/j.febslet.2015.04.034 · 3.17 Impact Factor
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