SGD-Wiki - User contributions [en]

YDL140C

2008-04-15T08:06:06Z

Galicola: /* 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=S000002299 YDL140C]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''RPO21 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||''RPB1, RPB220, SUA8''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr IV:210562..205361
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID''' || S000002299
|}
 
'''Description of YDL140C:''' RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime<ref name='S000080886'>Cramer P (2002) Multisubunit RNA polymerases. Curr Opin Struct Biol 12(1):89-97 {{SGDpaper|S000080886}} PMID 11839495</ref><ref name='S000074163'>Geiduschek EP and Kassavetis GA (2001) The RNA polymerase III transcription apparatus. J Mol Biol 310(1):1-26 {{SGDpaper|S000074163}} PMID 11419933</ref><ref name='S000069428'>Proudfoot N (2000) Connecting transcription to messenger RNA processing. Trends Biochem Sci 25(6):290-3 {{SGDpaper|S000069428}} PMID 10838569</ref><ref name='S000058793'>Cramer P, et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640-9 {{SGDpaper|S000058793}} PMID 10784442</ref><ref name='S000058335'>Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62(2):465-503 {{SGDpaper|S000058335}} PMID 9618449</ref><ref name='S000057661'>Archambault J and Friesen JD (1993) Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57(3):703-24
{{SGDpaper|S000057661}} PMID 8246845</ref>
 
 
 
 
 
</protect>
__TOC__
==Community Commentary==
{{CommentaryHelp}}

Rpb1-1 mutation: this is a ts mutant which does not transcribe at the restrictive temperature. According to Scafe, S., Martin, C., Nonet, M., Podos, S., Okamura, S. and Young, R. (MCB 1990 vol. 10(3):1270-1275) this mutation is G->A at base 4622 (base 1 is A of ATG). However, according the Nedea, EC., Markov, D., Naryshkina, T. and Severinov, K. (J. Bact. 1999 Vol 181(8):2663-2665) the rpb1-1 mutation is equivalent to a parallel ts mutation in the E. coli RNA pol, in a conserved Glycine. According to their article, the rpb1-1 mutation is in this conserved Gly (aa 1437, or base 4310) and not Gly 1541 (base 4622 according to R. Young).
After sequencing two rpb1-1 mutants in our posession, we agree with Severinov, that the G->A mutation is at base 4310 and NOT in base 4622.




<protect>

==References==

{{RefHelp}}
</protect>

YDL140C

2008-04-15T08:05:28Z

Galicola: /* References */

{{PageTop}}
<protect>
{|{{Prettytable}} align = 'right' width = '200px'
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000002299 YDL140C]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''RPO21 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||''RPB1, RPB220, SUA8''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr IV:210562..205361
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID''' || S000002299
|}
 
'''Description of YDL140C:''' RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime<ref name='S000080886'>Cramer P (2002) Multisubunit RNA polymerases. Curr Opin Struct Biol 12(1):89-97 {{SGDpaper|S000080886}} PMID 11839495</ref><ref name='S000074163'>Geiduschek EP and Kassavetis GA (2001) The RNA polymerase III transcription apparatus. J Mol Biol 310(1):1-26 {{SGDpaper|S000074163}} PMID 11419933</ref><ref name='S000069428'>Proudfoot N (2000) Connecting transcription to messenger RNA processing. Trends Biochem Sci 25(6):290-3 {{SGDpaper|S000069428}} PMID 10838569</ref><ref name='S000058793'>Cramer P, et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640-9 {{SGDpaper|S000058793}} PMID 10784442</ref><ref name='S000058335'>Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62(2):465-503 {{SGDpaper|S000058335}} PMID 9618449</ref><ref name='S000057661'>Archambault J and Friesen JD (1993) Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57(3):703-24
{{SGDpaper|S000057661}} PMID 8246845</ref>
 
 
 
 
 
</protect>
__TOC__
==Community Commentary==
{{CommentaryHelp}}




<protect>
==References==

{{RefHelp}}
</protect>

YDL140C

2008-04-15T08:05:02Z

Galicola: /* References */

{{PageTop}}
<protect>
{|{{Prettytable}} align = 'right' width = '200px'
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000002299 YDL140C]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name''' ||''RPO21 ''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Aliases''' ||''RPB1, RPB220, SUA8''
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Feature type''' || ORF, Verified[[Category:ORF]][[Category:ORF, Verified]]
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
|nowrap| Chr IV:210562..205361
|-
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID''' || S000002299
|}
 
'''Description of YDL140C:''' RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime<ref name='S000080886'>Cramer P (2002) Multisubunit RNA polymerases. Curr Opin Struct Biol 12(1):89-97 {{SGDpaper|S000080886}} PMID 11839495</ref><ref name='S000074163'>Geiduschek EP and Kassavetis GA (2001) The RNA polymerase III transcription apparatus. J Mol Biol 310(1):1-26 {{SGDpaper|S000074163}} PMID 11419933</ref><ref name='S000069428'>Proudfoot N (2000) Connecting transcription to messenger RNA processing. Trends Biochem Sci 25(6):290-3 {{SGDpaper|S000069428}} PMID 10838569</ref><ref name='S000058793'>Cramer P, et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640-9 {{SGDpaper|S000058793}} PMID 10784442</ref><ref name='S000058335'>Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62(2):465-503 {{SGDpaper|S000058335}} PMID 9618449</ref><ref name='S000057661'>Archambault J and Friesen JD (1993) Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57(3):703-24
{{SGDpaper|S000057661}} PMID 8246845</ref>
 
 
 
 
 
</protect>
__TOC__
==Community Commentary==
{{CommentaryHelp}}




<protect>
==References==

{{RefHelp}}
</protect>

Rpb1-1 mutation: this is a ts mutant which does not transcribe at the restrictive temperature. According to Scafe, S., Martin, C., Nonet, M., Podos, S., Okamura, S. and Young, R. (MCB 1990 vol. 10(3):1270-1275) this mutation is G->A at base 4622 (base 1 is A of ATG). However, according the Nedea, EC., Markov, D., Naryshkina, T. and Severinov, K. (J. Bact. 1999 Vol 181(8):2663-2665) the rpb1-1 mutation is equivalent to a parallel ts mutation in the E. coli RNA pol, in a conserved Glycine. According to their article, the rpb1-1 mutation is in this conserved Gly (aa 1437, or base 4310) and not Gly 1541 (base 4622 according to R. Young).
After sequencing two rpb1-1 mutants in our posession, we agree with Severinov, that the G->A mutation is at base 4310 and NOT in base 4622.

Methods

2007-09-04T11:25:21Z

Galicola:

*[http://www.fhcrc.org/labs/breeden/Methods_BreedenLab.html| Yeast Lab Protocols] from the Breeden Lab, Fred Hutchinson Cancer Research Center.

*[http://www.fhcrc.org/labs/gottschling/ Yeast Lab Protocols] from the Gottschling Lab, Fred Hutchinson Cancer Research Center.

*[http://www.umanitoba.ca/faculties/medicine/biochem/gietz/Trafo.html The Definitive Yeast Transformation Homepage] from the University of Manitoba.

*[http://fangman-brewer.genetics.washington.edu/index.html DNA Replication Protocols] from the Fangman and Brewer Labs, University of Washington.

*[http://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html Interaction Trap at Work] information page from Erica Golemis's laboratory at the Fox Chase Cancer Center.

*[http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide. Version 2.0], a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.

*The [http://depts.washington.edu/yeastrc/ NCRR Yeast Resource Center] at the University of Washington facilitates the study of yeast protein complexes by providing access to techniques such as mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction.

*Full text of the paper (Erdeniz et al. (1997) Genome Res. 7:1174-1183) describing [http://www.genome.org/cgi/content/full/7/12/1174 PCR-Based Allele Replacement]. Available to the public without password restriction and at no charge, through a special arrangement with Genome Research arranged by Rodney Rothstein.

*[http://genomics.princeton.edu/dunham/chemostat.html Chemostat Manual] from Maitreya Dunham's lab, Princeton University. See her [http://genomics.princeton.edu/dunham/protocols.shtml other protocols].

*[http://www.phys.ksu.edu/gene/chapters.html A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University.