SGD Quarterly Newsletter

Posted November 8, 2007

In this issue:

  1. Gene Focus: S. cerevisiae PEXs and Human PBDs
  2. Computational predictions added to SGD
  3. New links added: GI numbers, Ortholog resources, an Organelle database, and a new microarray search tool
  4. Antibodies list started in Wiki
  5. SGD respects your privacy
  6. 81 new Summary Paragraphs
  7. 3 sequence/annotation changes made to the systematic sequence of S. cerevisiae
  8. Upcoming Conferences and Courses
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About this Newsletter

This is the November 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You have received it because you are listed as a contact for SGD in our database.

  1. Gene Focus: S. cerevisiae PEXs and Human PBDs

    The GO consortium is currently working on a project to collectively annotate all model organism genes with homologs involved in human diseases. As part of this project, SGD curators have recently revised and updated our annotations on yeast PEX genes. From yeast to man, the biogenesis of peroxisomes requires a group of conserved "peroxin" protein factors encoded by the PEX genes. In humans, failure to properly develop or maintain peroxisomes leads to peroxisome biogenesis disorders (PBDs), a group of rare, genetically heterogeneous diseases characterized by severe mental retardation, neuronal, hepatic and renal abnormalities, and death in early infancy. In many cases, the genetic defects underlying PBDs have been identified. These mutations fall into at least 14 different complementation groups, and all affect the import of one or more classes of peroxisomal proteins. This cellular phenotype is shared by yeast pex mutants, and the study of pex mutants and peroxisome biogenesis in S. cerevisiae has enhanced our understanding of how the human orthologs function. For complete references and many more details, please see the individual locus pages for these genes (listed in the following table).

    Gene Function S. cerevisiae Gene (links to SGD) Human Gene
    (links to OMIM)    		 Associated Human Disease PBD group
    Peroxisomal membrane protein import PEX3 PEX3 Zellweger syndrome spectrum ^ 12
    None PEX16 Zellweger syndrome spectrum ^ 9
    PEX19 PXF Zellweger syndrome spectrum ^ 14
    Receptor for Peroxisomal Targeting Sequence 1 (PTS1) PEX5 PEX5
    (aka PTS1R or PXR1)    		 Zellweger syndrome spectrum ^ 2
    Receptor for Peroxisomal Targeting Sequence 2 (PTS2) PEX7 PEX7 rhizomelic chondrodysplasia punctata, type 1 11
    PTS2 receptor accessory factor PEX18 None; Pex5pL may be functional equivalent  ---   --- 
    PEX21 None; Pex5pL may be functional equivalent  ---   --- 
    Docking complex component PEX13 PEX13 Zellweger syndrome spectrum ^ 13
    PEX14 PEX14 Zellweger syndrome spectrum ^  
    PEX17 None  ---   --- 
    Translocation complex component PEX2 PXMP3 Zellweger syndrome spectrum ^ 5, 10
    PEX10 PEX10 Zellweger syndrome spectrum ^ 7
    PEX12 PEX12 Zellweger syndrome spectrum ^ 3
    Association between the docking complex and the translocation complex PEX8 None  ---   --- 
    Receptor recycling PEX1 PEX1 Zellweger syndrome spectrum ^ 1
    PEX4 None  ---   --- 
    PEX6 PEX6 Zellweger syndrome spectrum ^ 4, 6
    PEX15 None  ---   --- 
    PEX22 None  ---   --- 
    None PEX26 Zellweger syndrome spectrum ^ 8
    Peroxisome proliferation PEX11 PEXllA
    PEX11B
    PEX11G    		 None  --- 
    PEX25 None  ---   --- 
    PEX27 None  ---   --- 

    ^Clinical features of patients with these genetic defects vary and are usually classified as one or more of three diseases with overlapping features (Zellweger syndrome, neonatal adrenoleukodystrophy, or infantile Refsum disease) sometimes collectively referred to as "Zellweger syndrome spectrum."

  2. Computational predictions added to SGD

    SGD has incorporated computational GO annotations for S. cerevisiae proteins from the GO Annotation (GOA) project at EBI. These annotations are identified by the 'Annotation Method: Computational' and the evidence code 'IEA' on both the GO evidence and references page and the GO term page. To better present these annotations, slight changes have been made in the formats of the Locus Summary Page (e.g. TPS1), the GO evidence and references page (e.g. TPS1) and the GO term page (e.g. spindle pole body). In addition, the annotation method formerly called 'Core' is now called 'Manually curated' to better describe the process used to make these GO annotations.

    Annotations assigned from published literature (Manually curated and High-throughput) will continue to be the primary set of GO annotations for S. cerevisiae gene products. Computational annotations are not queried by the GO Term Finder and GO Slim Mapper tools, nor are they included in SGD's gene_association.sgd file containing GO annotations for S. cerevisiae gene products.

    For more information on SGD's incorporation of computational GO annotations, see the publication by Hong et al., 2007.

  3. New links added: GI numbers, Ortholog resources, an Organelle database, and a new microarray search tool

  4. Antibodies list started in Wiki

    Periodically, SGD curators are asked if we know of a resource that lists antibodies that recognize S. cerevisiae proteins. In response, we have created a page in the Community Wiki to allow users to generate this resource. An Antibodies list has been started; it is linked from the Reagents section of the wiki. Please add information about antibodies to this list by clicking the "edit" link at the top of the page.

  5. SGD respects your privacy

    In response to concerns about displaying email addresses, the Colleague Submission and Update forms have been updated to allow you to choose whether or not your email address is displayed on your colleague page. If you do not want your email address shown, click "N" in the option provided on the form.

  6. 81 new Summary Paragraphs

    Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter (August - October 2007), new summary paragraphs for the following 81 features have been added to their respective Locus Summary pages.

    List of Summary Paragraphs Added During the Last Quarter
    ATP14/YLR295CATP2/YJR121WAUR1/YKL004WCSG2/YBR036CCYC7/YEL039C
    DAL1/YIR027CDAL2/YIR029WDAL3/YIR032CDPL1/YDR294CDUR1,2/YBR208C
    FDH1/YOR388CFHL1/YPR104CGAD1/YMR250WGDH1/YOR375CGDH3/YAL062W
    GLN1/YPR035WGLT1/YDL171CHEM1/YDR232WHEM2/YGL040CHEM3/YDL205C
    HEM4/YOR278WIPT1/YDR072CLAC1/YKL008CLAG1/YHL003CLCB1/YMR296C
    LCB2/YDR062WLCB3/YJL134WLCB4/YOR171CLCB5/YLR260WLIP1/YMR298W
    LYS1/YIR034CLYS12/YIL094CLYS2/YBR115CLYS20/YDL182WLYS21/YDL131W
    LYS4/YDR234WLYS9/YNR050CMCM2/YBL023CMCM3/YEL032WMCM4/YPR019W
    MCM5/YLR274WMCM6/YGL201CMCM7/YBR202WMET1/YKR069WMET8/YBR213W
    ORC1/YML065WORC2/YBR060CORC3/YLL004WORC4/YPR162CORC5/YNL261W
    ORC6/YHR118CPDR1/YGL013CPDR3/YBL005WPDR5/YOR153WRAD2/YGR258C
    RAD27/YKL113CRAD3/YER171WRFA1/YAR007CRFA2/YNL312WRFA3/YJL173C
    SCS7/YMR272CSEC61/YLR378CSEN1/YLR430WSFA1/YDL168WSSL2/YIL143C
    SSS1/YDR086CSTE5/YDR103WSUR1/YPL057CSUR2/YDR297WTRR1/YDR353W
    TRR2/YHR106WTRX1/YLR043CTRX2/YGR209CTRX3/YCR083WTSC10/YBR265W
    UGA1/YGR019WUGA2/YBR006WYDC1/YPL087WYPC1/YBR183WYSR3/YKR053C
    YJL068C



  7. 3 sequence/annotation changes made to the systematic sequence of S. cerevisiae

    As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. During the last quarter (August - November 2007), annotation changes were made affecting 3 features and 0 new features were added.

    ChromosomeSequence/Annotation ChangesNew Features Added
    INoneNone
    IINoneNone
    IIIMSH3/YCR092CNone
    IVNoneNone
    VNoneNone
    VINoneNone
    VIINoneNone
    VIIINoneNone
    IXNoneNone
    XNoneNone
    XIYKR005CNone
    XIINoneNone
    XIIINoneNone
    XIVLSM7/YNL147WNone
    XVNoneNone
    XVINoneNone
    MitoNoneNone

  8. Upcoming Conferences and Courses

    *asterisks indicate attendance by SGD
    Genetic Analysis: Model Organisms to Human Biology Meeting
    Town and Country Resort & Conference Center, San Diego, CA
    January 5 - 9, 2008
    Abstract Deadline: November 14, 2007

    6th International Meeting on Yeast Apoptosis
    Leuven, Belgium
    April 30 - May 4, 2008
    Abstract Deadline: February 1, 2008

    Cellular & Molecular Fungal Biology
    Holderness School, Plymouth, NH
    June 29 - July 4, 2008
    Application Deadline: June 8, 2008

    Yeast Genetics and Molecular Biology Meeting*
    University of Toronto, Toronto, Ontario, Canada
    July 22-27, 2008
    Abstract Deadline: TBA
    For more information contact:

    Plant & Fungal Cytoskeleton
    Il Ciocco, Lucca (Barga), Italy
    August 3 - 8, 2008
    Application Deadline: July 13, 2008

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CONTACT SGD: yeast-curator@yeastgenome.org
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