SGD-Wiki - User contributions [en]

Main Page

2010-10-13T21:06:08Z

Juliep:

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

[[Image:Wiki-invite3.jpg|right]]
* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

 

==Table of Contents==

[[Methods|Protocols and Methods]]: Includes useful yeast protocols and methods posted by researchers.

[[Reagents|Reagents]]: Includes links to plasmid collections and other useful reagents, such as antibodies.

[[Strains|Strains]]: Includes information about strain collections and the major yeast strain backgrounds.

[[Software|Software]]: Includes software that may be of use to S. cerevisiae researchers

[[General_Topics|General Topics]]: A collection of information about the general biology of S. cerevisiae and other fungi, including educational resources.

[[Career_Resources|Career Resources]]: Includes links to job opportunities posted by researchers.

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

[http://www.openhelix.com/sgd Online SGD Tutorial] developed by [http://www.openhelix.com/ OpenHelix]: describes navigation of SGD and many features of the database.

[[Specification for New Interactions and Phenotype FTP files]]

[http://refnucl.atlas.bx.psu.edu/ Yeast nucleosome map]: A compiled and systematic reference map of nucleosome positions across the ''Saccharomyces'' genome

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>

General Topics

2009-07-14T23:05:50Z

Juliep: /* Educational resources */

This page has replaced the Virtual Library.
=General S. cerevisiae information=

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about wine making, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml list] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

*[http://www.nature.com/scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

*[http://www.fgsc.net/ The Fungal Genetics Stock Center]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

General Topics

2009-07-14T22:45:38Z

Juliep: /* Educational resources */

This page has replaced the Virtual Library.
=General S. cerevisiae information=

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about wine making, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml list] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

*[http://www.nature.com/scitable Scitable] A free library of overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

*[http://www.fgsc.net/ The Fungal Genetics Stock Center]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

YGR198W

2007-08-17T19:05:44Z

Juliep: /* Community Commentary */

{{PageTop}}
<protect>
{|{{Prettytable}} align = 'right' width = '200px'
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003430 YGR198W]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''YPP1 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||'' ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr VII:894698..897151
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID''' || S000003430
|}
 
'''Description of YGR198W:''' Cargo-transport protein involved in endocytosis; may interact with ribosomes, based on co-purification experiments; GFP-fusion protein localizes to the cytoplasm; YGR198W is an essential gene<ref name='S000119076'>Flower T, et al. (2006) The Yeast Endocytosis Gene YGR198w (YPP1) Suppresses A30P Alpha-Synuclein Toxicity Nat Cell Biol () {{SGDpaper|S000119076}} PMID </ref><ref name='S000115662'>Fleischer TC, et al. (2006) Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev 20(10):1294-307 {{SGDpaper|S000115662}} PMID 16702403</ref><ref name='S000074185'>Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 {{SGDpaper|S000074185}} PMID 14562095</ref><ref name='S000047842'>Rodriguez-Pena JM, et al. (1998) The deletion of six ORFs of unknown function from Saccharomyces cerevisiae chromosome VII reveals two essential genes: YGR195w and YGR198w. Yeast 14(9):853-60
{{SGDpaper|S000047842}} PMID 9818723</ref>
 
 
 
 
 
</protect>
__TOC__
==Community Commentary==
{{CommentaryHelp}}

GFP-tag is more effective at the n-terminal end. Adding an epitope tag at the C-terminus makes the strain somewhat sick and lowers PI4P levels, however, it seems to localize correctly.




<protect>

==References==

{{RefHelp}}
</protect>

File:Wiki-invite3.jpg

2007-08-16T18:49:32Z

Juliep:

File:Wiki-invite.jpg

2007-08-16T18:46:48Z

Juliep:

File:Wiki img.jpg

2007-08-16T18:36:00Z

Juliep:

Polymerase targets

2007-08-10T21:10:34Z

Juliep:

{| border="1" cellpadding="10" cellspacing="0"

|-

! Polymerase

! genes

|-

| PolI

| 18S, 5.8S, and 25S rRNAs

|-

| PolII
| all nuclear protein coding genes
|-
|
| all snoRNAs except for snr52
|-
|
| U1, U2, U4, U5 spliceosomal RNAs
|-
| PolIII
| all nuclear tRNAs <ref name = 'PMID:16600899'>Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35</ref>
|-
|
| snr52 snoRNA <ref name = 'PMID:16600899'>Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35</ref>
|-
|
| U6 spliceosomal RNA <ref name = 'PMID:16600899'>Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35</ref>
|-
|
| SCR1 non-coding RNA <ref name = 'PMID:16600899'>Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35</ref>
|-
|
| RPR1 non-coding RNA <ref name = 'PMID:16600899'>Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35</ref>
|-
| mitochondrial polymerase
| all genes encoded by the mitochondrial chromosome
|}

==References==
1. Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35

Polymerase targets

2007-08-10T21:08:00Z

Juliep: New page: {| border="1" cellpadding="10" cellspacing="0" |- ! Polymerase ! genes |- | PolI | 18S, 5.8S, and 25S rRNAs |- | PolII | all nuclear protein coding genes |- | | all snoRNAs except ...

General Topics

2007-08-10T20:46:16Z

Juliep: /* General S. cerevisiae information */

=General S. cerevisiae information=

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*A [[Polymerase_targets|table]] describing the gene targets of the different polymerases in S. cerevisiae.

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies.

*An updated version the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml list] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://alces.med.umn.edu/Candida.html Candida albicans] information server from University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubbii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

=Biology related career resources=

Following is a list of sites that post biology related job openings. Please note that this is not a comprehensive list. Some of these sites may be free (may require registration) for job seekers, job posters or both.

*[http://genetics.faseb.org/genetics/g-gsa/open_positions.shtml Open positions] offered by [http://www.genetics-gsa.org/ Genetics Society of America]

*[http://www.ascb.org/careers/ Career Services] offered by [http://www.ascb.org/ American Society for Cell Biology]

*[http://www.healthecareers.com/site_templates/ASM/index.asp?aff=ASM&SPLD=ASM ASM Career Connections] offered by [http://www.asm.org/index.asp American Society for Microbiology]

*[http://www.faseb.org/careers/careerresources.htm Career Resources] offered by [http://www.faseb.org FASEB]

*[http://www.sdbonline.org/career/jobs.php Job Openings] offered by [http://www.sdbonline.org Society for Developmental Biology]

*[http://recruit.sciencemag.org Science Careers] and [http://nextwave.sciencemag.org Science Next Wave] offered by [http://www.scienceonline.org Science Magazine Online]

*[http://www.nature.com/naturejobs/ Nature Jobs] offered by [http://www.nature.com Nature Online]

*[http://www.biospace.com Career Center] offered by [http://www.biospace.com Biospace.com]

Commonly used strains

2007-07-24T19:47:48Z

Juliep:

This page describes some of the most commonly used yeast lab strains. Much of the information is taken from [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html F. Sherman (2002)] Getting started with yeast, Methods Enzymol. 350, 3-41. Other useful papers for strain background information include:

* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000050744 Mortimer and Johnston] (1986) Genetics 113:35-43 - thoroughly describes the genealogy of strain S288C
* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079648 van Dijken et al.] (2000) Enzyme Microb Technol 26:706-714 - compares various characteristics of commonly used lab strains
* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080159 Winzeler et al.] (2003) Genetics 163:79-89 - uses SFP (single-feature polymorphisms) analysis to study genetic identity between common lab strains

=S288C=
'''Genotype:''' ''MAT''α ''SUC2 gal2 mal mel flo1 flo8-1 hap1''

'''Notes:''' Strain used in the systematic sequencing project, the sequence stored in SGD. S288C does not form pseudohyphae. In addition, since it has a mutated copy of [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004246 ''HAP1''], it is not a good strain for mitochondrial studies. S288C strains are ''gal''2- and they do not use galactose anaerobically.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000050744 Mortimer and Johnston] (1986) Genetics 113:35-43.

'''Sources:'''[http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204508 ATCC:204508]

==BY4743==
'''Genotype:''' ''MAT''a/α ''his3''Δ''1/his3''Δ''1 leu2''Δ''0/leu2''Δ''0 lys2''Δ''0/LYS2 MET15/met15''Δ''0 ura3''Δ''0/ura3''Δ''0''

'''Notes:'''Strain used in the [http://www-sequence.stanford.edu/group/yeast_deletion_project/project_desc.html systematic deletion project], generated from a cross between BY4741 and BY4742, which are derived from S288C. See Brachmann et al. reference for details.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al.] (1998) Yeast 14:115-32.

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1050|Open Biosystems:YSC1050]

==FY1679==
'''Genotype:''' ''MAT''a/α ''ura3-52/ura3-52 trp1''Δ''63/TRP1 leu2''Δ''1/LEU2 his3''Δ''200/HIS3 GAL2/GAL''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

'''References:'''[http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000047446 Winston et al.] (1995) Yeast 11:53-55.

'''Sources:''' [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/data/fy1679.html EUROSCARF:10000D]

==AB972==
'''Genotype:''' ''MAT''α'' X2180-1B trp10 [rho 0]''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD. AB972 is an ethidium bromide-induced rho- derivative of the strain X2180-1B-''trp1''.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000057090 Olson MV et al.] (1986) Proc. Natl. Acad. Sci. USA 83:7826-7830.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204511 ATCC:204511]

==A364A==
'''Genotype:''' ''MAT''a'' ade1 ade2 ura1 his7 lys2 tyr1 gal1 SUC mal cup''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079649 Hartwell] (1967) J. Bacteriol. 93:1662-1670.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=208526 ATCC:208526]

==XJ24-24a==
'''Genotype:''' ''MAT''a ''ho HMa HMα ade6 arg4-17 trp1-1 tyr7-1 MAL2''

'''Notes:''' Derived from, but not isogenic to S288C

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000055409 Strathern et al.] (1979) Cell 18:309-319

==DC5==
'''Genotype:''' ''MAT''a'' leu2-3,112 his3-11,15 can1-11''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000054242 Broach et al.] (1979) Gene 8:121-133

==YNN216==
'''Genotype:''' ''MAT''a/α ''ura3-52/ura3-52 lys2-801amber/lys2-801amber ade2-101ochre/ade2-101ochre''

'''Notes:''' Congenic to S288C (see Sikorski and Hieter). Used to derive YSS and CY strains (see Sobel and Wolin).

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862.
==YPH499==
'''Genotype:''' ''MAT''a ''ura3-52 lys2-801_amber ade2-101_ochre trp1-''Δ''63 his3-''Δ''200 leu2-''Δ''1''

'''Notes:''' Contains nonrevertible (deletion) auxotrophic mutations that can be used for selection of vectors. Note that ''trp1-''Δ''63'', unlike ''trp1-''Δ''1'', does not delete adjacent ''GAL3'' UAS sequence and retains homology to ''TRP1'' selectable marker. ''gal2-'', does not use galactose anaerobically. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204679 ATCC:204679]

==YPH500==
'''Genotype:''' ''MAT''α ''ura3-52 lys2-801_amber ade2-101_ochre trp1-''Δ''63 his3-''Δ''200 leu2-''Δ''1''

'''Notes:'''''MAT''α strain isogenic to [http://staff.yeastgenome.org/index.php/straintable#yph499 YPH499] except at mating type locus. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204680 ATCC:204680]

==YPH501==
'''Genotype:''' ''MAT''a/''MAT''α ''ura3-52/ura3-52 lys2-801_amber/lys2-801_amber ade2-101_ochre/ade2-101_ochre trp1-''Δ''63/trp1-''Δ''63 his3-''Δ''200/his3-''Δ''200 leu2-''Δ''1/leu2-''Δ''1''

'''Notes:'''a/α diploid isogenic to [http://staff.yeastgenome.org/index.php/straintable#yph499 YPH499] and [http://staff.yeastgenome.org/index.php/straintable#yph500 YPH500]. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204681 ATCC:204681]

=Sigma 1278B=

'''Notes:'''Used in pseudohyphal growth studies. [[History_of_Sigma|Detailed notes]] about the sigma strains have been kindly provided by Cora Styles.

=SK1=
'''Genotype:''' ''MAT''a/α'' HO gal2 cupS can1R''

'''Notes:''' Commonly used for studying sporulation or meiosis. Canavanine-resistant derivative

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079650 Kane SM and Roth J.] (1974) Bacteriol. 118: 8-14

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204722 ATCC:204722]

=CEN.PK (aka CEN.PK2)=
'''Genotype:''' ''MAT''a/α'' ura3-52/ura3-52 trp1-289/trp1-289 leu2-3_112/leu2-3_112 his3 ''Δ''1/his3 ''Δ''1 MAL2-8C/MAL2-8C SUC2/SUC2''

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079648 van Dijken et al.] (2000) Enzyme Microb Technol 26:706-714

'''Sources:''' [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/data/cen.html EUROSCARF:30000D]

=W303=
'''Genotype:''' ''MAT''a/''MAT''α {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''} [''phi+'']

'''Notes:''' W303 also contains a ''bud4'' mutation that causes
haploids to bud with a mixture of axial and bipolar budding
patterns. In addition, the original W303 strain contains the
''rad5-535'' allele.

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR''). ''bud4'' info: Voth, W.P. et al. (2005) Eukaryotic Cell, in press. ''rad5-535'' info: Fan et al. (1996) Genetics 142:749

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

==W303-1A==
'''Genotype:''' ''MAT''a {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''}

'''Notes:''' W303-1A possesses a ''ybp1-1'' mutation (I7L, F328V, K343E, N571D) which abolishes Ybp1p function, increasing sensitivity to oxidative stress.

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR''). ''ybp1-1'' info: [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000073844 Veal et al.] (2003) J. Biol. Chem. 278:30896-904. 

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

==W303-1B==
'''Genotype:''' ''MAT''α {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''}

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR'').

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

=X2180-1A=
'''Genotype:''' ''MAT''a'' SUC2 mal mel gal2 CUP1''

'''References:''' Robert Mortimer, personal comm.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=204504 ATCC:204504]

=D273-10B=
'''Genotype:''' ''MAT''α ''mal''

'''Notes:''' Normal cytochrome content and respiration; low frequency of rho-. This strain and its auxotrophic derivatives were used in numerious laboratories for mitochondrial and related studies and for mutant screens. Good respirer that's relatively resistant to glucose repression.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080158 Sherman, F.] (1963) Genetics 48:375-385.

'''Sources:''' [http://www.atcc.org/catalog/numSearch/numResults.cfm?atccNum=24657 ATCC:24657]

=FL100=
'''Genotype:''' ''MAT''a

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000065623 Lacroute, F.] (1968) J. Bacteriol. 95:824-832.

YPL240C

2007-02-23T01:40:27Z

Juliep: /* Community Commentary */

{{PageTop}}
<protect>
{|{{Prettytable}} align = 'right' width = '200px'
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YPL240C YPL240C]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''HSP82 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||''HSP90''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr XVI:98625..96496
|}
 
'''Description of {{PAGENAME}}:''' Cytoplasmic chaperone (Hsp90 family) required for pheromone signaling and negative regulation of Hsf1p; docks with the mitochondrial import receptor Tom70p for preprotein delivery; interacts with co-chaperones Cns1p, Cpr6p, Cpr7p, and Sti1p<ref name='S000072572'>Young JC, et al. (2003) Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell 112(1):41-50 {{SGDpaper|S000072572}} PMID 12526792</ref><ref name='S000053355'>Prodromou C, et al. (1999) Regulation of Hsp90 ATPase activity by tetratricopeptide repeat (TPR)-domain co-chaperones. EMBO J 18(3):754-62 {{SGDpaper|S000053355}} PMID 9927435</ref><ref name='S000052578'>Louvion JF, et al. (1998) Hsp90 is required for pheromone signaling in yeast. Mol Biol Cell 9(11):3071-83 {{SGDpaper|S000052578}} PMID 9802897</ref><ref name='S000049475'>Duina AA, et al. (1998) Requirement for Hsp90 and a CyP-40-type cyclophilin in negative regulation of the heat shock response. J Biol Chem 273(30):18974-8 {{SGDpaper|S000049475}} PMID 9668076</ref><ref name='S000047783'>Marsh JA, et al. (1998) Cns1 is an essential protein associated with the hsp90 chaperone complex in Saccharomyces cerevisiae that can restore cyclophilin 40-dependent functions in cpr7Delta cells. Mol Cell Biol 18(12):7353-9 {{SGDpaper|S000047783}} PMID 9819422</ref><ref name='S000047779'>Dolinski KJ, et al. (1998) CNS1 encodes an essential p60/Sti1 homolog in Saccharomyces cerevisiae that suppresses cyclophilin 40 mutations and interacts with Hsp90. Mol Cell Biol 18(12):7344-52
{{SGDpaper|S000047779}} PMID 9819421</ref>
 
 
 
 
 
</protect>
__TOC__
==Community Commentary==
{{CommentaryHelp}}
=== Interactions ===
[[Category:Topic:Interactions]]
==== Physical ====
[[Category:Topic:Interactions:Physical]]
Physical interaction with cns1 [[Category:Physical Interactions with cns1]] 

Cns1 binds both to Hsp90 and to the yeast Hsp70 protein Ssa1 with comparable affinities. This is reminiscent of Sti1, another TPR-containing co-chaperone. <ref name='S000076436'>Hainzl O, et al. (2004) Cns1 is an activator of the Ssa1 ATPase activity. J Biol Chem 279(22):23267-73 {{SGDpaper|S000076436}} PMID 15044454</ref> <ref name = 'CAset9598-2004-07-15'>submitted by [http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch?id=9598 Dr. Harald Wegele] on 2004-07-15</ref>

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==References==

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YPL240C

2007-02-23T01:30:38Z

Juliep: /* Community Commentary */

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{|{{Prettytable}} align = 'right' width = '200px'
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YPL240C YPL240C]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''HSP82 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||''HSP90''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr XVI:98625..96496
|}
 
'''Description of {{PAGENAME}}:''' Cytoplasmic chaperone (Hsp90 family) required for pheromone signaling and negative regulation of Hsf1p; docks with the mitochondrial import receptor Tom70p for preprotein delivery; interacts with co-chaperones Cns1p, Cpr6p, Cpr7p, and Sti1p<ref name='S000072572'>Young JC, et al. (2003) Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell 112(1):41-50 {{SGDpaper|S000072572}} PMID 12526792</ref><ref name='S000053355'>Prodromou C, et al. (1999) Regulation of Hsp90 ATPase activity by tetratricopeptide repeat (TPR)-domain co-chaperones. EMBO J 18(3):754-62 {{SGDpaper|S000053355}} PMID 9927435</ref><ref name='S000052578'>Louvion JF, et al. (1998) Hsp90 is required for pheromone signaling in yeast. Mol Biol Cell 9(11):3071-83 {{SGDpaper|S000052578}} PMID 9802897</ref><ref name='S000049475'>Duina AA, et al. (1998) Requirement for Hsp90 and a CyP-40-type cyclophilin in negative regulation of the heat shock response. J Biol Chem 273(30):18974-8 {{SGDpaper|S000049475}} PMID 9668076</ref><ref name='S000047783'>Marsh JA, et al. (1998) Cns1 is an essential protein associated with the hsp90 chaperone complex in Saccharomyces cerevisiae that can restore cyclophilin 40-dependent functions in cpr7Delta cells. Mol Cell Biol 18(12):7353-9 {{SGDpaper|S000047783}} PMID 9819422</ref><ref name='S000047779'>Dolinski KJ, et al. (1998) CNS1 encodes an essential p60/Sti1 homolog in Saccharomyces cerevisiae that suppresses cyclophilin 40 mutations and interacts with Hsp90. Mol Cell Biol 18(12):7344-52
{{SGDpaper|S000047779}} PMID 9819421</ref>
 
 
 
 
 
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==Community Commentary==
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=== Interactions ===
[[Category:Topic:Interactions]]
==== Physical ====
[[Category:Topic:Interactions:Physical]]
Physical interaction with cns1 [[Category:Physical Interactions with cns1]] 

Cns1 binds both to Hsp90 and to the yeast Hsp70 protein Ssa1 with comparable affinities. This is reminiscent of Sti1, another TPR-containing co-chaperone. <ref name='S000076436'>Hainzl O, et al. (2004) Cns1 is an activator of the Ssa1 ATPase activity. J Biol Chem 279(22):23267-73 {{SGDpaper|S000076436}} PMID 15044454</ref> <ref name = 'CAset9598-2004-07-15'>submitted by [http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch?id=9598 Dr. Harald Wegele] on 2004-07-15</ref>

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==References==

{{RefHelp}}
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