SubtiWiki - User contributions [en]

Rny

2009-11-23T09:49:57Z

Putzer: /* Extended information on the protein */

* '''Description:''' [[RNase]] Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] Y
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates [[S-box]] [[riboswitch]] RNA turnover, required for the processing of the ''[[gapA]]'' operon mRNA, depletion of [[RNase]] Y increases bulk mRNA stability.
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16960

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' [[RNase]] Y cleaves [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro''; preference for 5' monophosphorylated substrate ''in vitro'', endonucleolytic cleavage [http://www.ncbi.nlm.nih.gov/pubmed/19779461]; required for the processing of the ''[[gapA]]'' operon mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed], cleavage activity appears sensitive to downstream secondary structure.

* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions, [http://www.ncbi.nlm.nih.gov/pubmed/19779461]

* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure, [http://www.ncbi.nlm.nih.gov/pubmed/19779461]

* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cell membrane, single-pass membrane protein {{PubMed|18763711,17005971,19820159}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there

=Biological materials =

* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.

* '''Expression vector:'''
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
**Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs

=Labs working on this gene/protein=

[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>18763711,19193632,17005971 19779461 19820159 </pubmed>

[[Category:Protein-coding genes]]

Rny

2009-11-23T09:48:33Z

Putzer: /* Basic information/ Evolution */

* '''Description:''' [[RNase]] Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] Y
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates [[S-box]] [[riboswitch]] RNA turnover, required for the processing of the ''[[gapA]]'' operon mRNA, depletion of [[RNase]] Y increases bulk mRNA stability.
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16960

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' [[RNase]] Y cleaves [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro''; preference for 5' monophosphorylated substrate ''in vitro'', endonucleolytic cleavage [http://www.ncbi.nlm.nih.gov/pubmed/19779461]; required for the processing of the ''[[gapA]]'' operon mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed], cleavage activity appears sensitive to downstream secondary structure.

* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions

* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure

* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cell membrane, single-pass membrane protein {{PubMed|18763711,17005971,19820159}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there

=Biological materials =

* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.

* '''Expression vector:'''
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
**Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs

=Labs working on this gene/protein=

[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>18763711,19193632,17005971 19779461 19820159 </pubmed>

[[Category:Protein-coding genes]]

Rny

2009-10-05T14:20:10Z

Putzer:

* '''Description:''' RNase Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase Y
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates S-box riboswitch RNA turnover, required for the processing of the ''[[gapA]]'' operon mRNA, depletion of RNase Y increases bulk mRNA stability.
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16960

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNase Y cleaves S-box riboswitch RNAs ''in vivo'' and ''in vitro''; preference for 5' monophosphorylated substrate ''in vitro'', endonucleolytic cleavageNucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate (according to Swiss-Prot) required for the processing of the ''[[gapA]]'' operon mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed], cleavage activity appears sensitive to downstream secondary structure.

* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot) 2',3' cyclic nucleotide phosphodiesterase family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions

* '''Effectors of protein activity:''' appeares sensitive to downstream secondary structure

* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cell membrane (according to Swiss-Prot), Single-pass membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there

=Biological materials =

* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.

* '''Expression vector:'''
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
**Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs

=Labs working on this gene/protein=

[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>18763711,19193632,17005971 19779461 </pubmed>

[[Category:Protein-coding genes]]