SGD Quarterly Newsletter, Fall 2007

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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.

Contents

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
PEX 19 PXF Zellweger syndrome spectrum 14
Receptor for Peroxisomal Targeting Sequence 1 (PTS1) PEX 5 PEX5

(aka PTS1R or PXR1)

Zellweger syndrome spectrum 2
Receptor for Peroxisomal Targeting Sequence 2 (PTS2) PEX 7 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  ---   --- 

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

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

  • NCBI protein GI numbers (GenInfo identifiers) have been added to the "All Associated sequences" option of the "Retrieve Sequences" pulldown menu for all verified and uncharacterized protein-coding locus pages. The GI identifiers are hyperlinked to NCBI's protein pages. The NCBI protein GI identifiers are also listed in the dbxref.tab file, on SGD's FTP site. For more information about NCBI protein GI identifiers, please see the Sequence Identifiers documentation at NCBI.
  • Links to the Fungal Orthogroups Repository have been added to the "Comparison Resources" pulldown menu on the Locus Summary pages of 5,780 protein-coding genes. The Fungal Orthogroups Repository is a database of orthology groups among protein-coding genes of 17 Ascomycete fungi, maintained by the Regev group at the Broad Institute, MIT. Orthology groups were determined by the SYNERGY method, as described in the publication Wapinski et al., 2007.
  • Ortholog Search (P-POD) links have been added to the "Comparison Resources" pulldown menu for all protein-coding locus pages. These links lead to ortholog family pages at the Princeton Protein Orthology Database (P-POD) developed by the Genome Databases Group at Princeton. The P-POD resource displays families of predicted orthologs from selected organisms, with an emphasis on providing information about disease-related genes and experimental confirmation of orthology from the literature. For more information on P-POD, see the recent publication by Heinicke et al., 2007.
  • Organelle DB links have been added to the "Localization Resources" pulldown menu on the Locus Summary pages of 2,279 protein-coding genes. Organelle DB, established by the Kumar lab at the LIfe Sciences Institute, University of Michigan, contains localization information and images for this set of S. cerevisiae proteins as well as protein localization data for 138 eukaryotic organisms, with an emphasis on the constituents of organelles and protein complexes. Organelle DB is described in Wiwatwattana et al., 2007. Links will be added to additional SGD Locus Summary pages as more localization information is added to Organelle DB.
  • Links to the SPELL (Serial Pattern of Expression Levels Locator) resource have been added to the "Functional Analysis" pulldown menu on the Locus Summary pages of all open reading frames. SPELL searches large gene expression microarray compendia to identify datasets relevant to a gene or set of genes, and then identifies genes in those datasets whose expression is similar to that of the query set. SPELL is described in Hibbs et al., 2007

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 theCommunity Wiki to allow uses 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" ink at the top of the page.

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.

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/YLR295C ATP2/YJR121W AUR1/YKL004W CSG2/YBR036C CYC7/YEL039C
DAL1/YIR027C DAL2/YIR029W DAL3/YIR032C DPL1/YDR294C DUR1,2/YBR208C
FDH1/YOR388C FHL1/YPR104C GAD1/YMR250W GDH1/YOR375C GDH3/YAL062W
GLN1/YPR035W GLT1/YDL171C HEM1/YDR232W HEM2/YGL040C HEM3/YDL205C
HEM4/YOR278W IPT1/YDR072C LAC1/YKL008C LAG1/YHL003C LCB1/YMR296C
LCB2/YDR062W LCB3/YJL134W LCB4/YOR171C LCB5/YLR260W LIP1/YMR298W
LYS1/YIR034C LYS12/YIL094C LYS2/YBR115C LYS20/YDL182W LYS21/YDL131W
LYS4/YDR234W LYS9/YNR050C MCM2/YBL023C MCM3/YEL032W MCM4/YPR019W
MCM5/YLR274W MCM6/YGL201C MCM7/YBR202W MET1/YKR069W MET8/YBR213W
ORC1/YML065W ORC2/YBR060C ORC3/YLL004W ORC4/YPR162C ORC5/YNL261W
ORC6/YHR118C PDR1/YGL013C PDR3/YBL005W PDR5/YOR153W RAD2/YGR258C
RAD27/YKL113C RAD3/YER171W RFA1/YAR007C RFA2/YNL312W RFA3/YJL173C
SCS7/YMR272C SEC61/YLR378C SEN1/YLR430W SFA1/YDL168W SSL2/YIL143C
SSS1/YDR086C STE5/YDR103W SUR1/YPL057C SUR2/YDR297W TRR1/YDR353W
TRR2/YHR106W TRX1/YLR043C TRX2/YGR209C TRX3/YCR083W TSC10/YBR265W
UGA1/YGR019W UGA2/YBR006W YDC1/YPL087W YPC1/YBR183W YSR3/YKR053C
YJL068C

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.

Chromosome Sequence/Annotation Changes New Features Added
I None None
II None None
III MSH3/YCR092C None
IV None None
V None None
VI None None
VII None None
VIII None None
IX None None
X None None
XI YKR005C None
XII None None
XIII None None
XIV LSM7/YNL147W None
XV None None
XVI None None
Mito None None

Upcoming Conferences and Courses

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

  • 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: mahoney@genetics-gsa.org
  • Plant & Fungal Cytoskeleton
Il Ciocco, Lucca (Barga), Italy
August 3 - 8, 2008
Application Deadline: July 13, 2008


asterisks indicate attendance by SGD.*

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