SubtiWiki - User contributions [en]

Jan Willem Veening

2015-02-10T14:11:17Z

Jwveening: /* Open positions */

[[File:JW-Office-color-crop-2.jpg ]]

==Jan-Willem Veening==
*Current institution: University of Groningen, Molecular Genetics Group, [http://http://www.rug.nl/staff/j.w.veening/ Veening lab]
*Contact: j.w.veening@rug.nl [mailto:j.w.veening@rug.nl send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.rug.nl/staff/j.w.veening/ Associate Professor at Groningen]
*[http://www.molgenrug.nl/ Molecular Genetics Group]

==Open positions==
Contact [mailto:j.w.veening@rug.nl me] for info.

[[File:GrouppictureAugust2014small.jpg]]
Veening lab, August 2014

= '''Back to [[Labs working on Bacillus]]''' =

Jan Willem Veening

2015-02-10T14:10:59Z

Jwveening: /* Open positions */

File:GrouppictureAugust2014small.jpg

2015-02-10T14:10:21Z

Jwveening:

Jan Willem Veening

2015-02-10T14:09:26Z

Jwveening:

File:JW-Office-color-crop-2.jpg

2015-02-10T14:09:08Z

Jwveening:

File:JW-Office-color-crop.jpg

2015-02-10T14:06:36Z

Jwveening:

Jan Willem Veening

2015-02-10T14:04:57Z

Jwveening: /* Homepages */

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: University of Groningen, Molecular Genetics Group, [http://http://www.rug.nl/staff/j.w.veening/ Veening lab]
*Contact: j.w.veening@rug.nl [mailto:j.w.veening@rug.nl send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.rug.nl/staff/j.w.veening/ Associate Professor at Groningen]
*[http://www.molgenrug.nl/ Molecular Genetics Group]

==Open positions==
Contact [mailto:j.w.veening@rug.nl me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Jan Willem Veening

2015-02-10T14:03:03Z

Jwveening: /* Jan-Willem Veening */

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: University of Groningen, Molecular Genetics Group, [http://http://www.rug.nl/staff/j.w.veening/ Veening lab]
*Contact: j.w.veening@rug.nl [mailto:j.w.veening@rug.nl send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen]
*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
Contact [mailto:j.w.veening@rug.nl me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Sda

2009-07-29T13:05:33Z

Jwveening:

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not initiate sporulation Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || developmental checkpoint protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of

sporulation (phosphorylation of Spo0A) to the function

of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAE01463]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_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:''' BSU25690

===Phenotypes of a mutant ===
*sporulates at a higher frequency
*will sporulate in the presence of replication stress

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[KinB]]-[[Sda]], [[KinA]]-[[Sda]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from Geobacillus stearothermophilus, complex with KinB), [http://www.rcsb.org/pdb/explore.do?structureId=1PV0 1PV0]

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q7WY62 Q7WY62]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25690]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''sda''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' [[DnaA]]
** repressed when no DNA damage is present ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Regulatory mechanism:''' Probably activated by [[DnaA]] under replication stress
** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

Bill Burkholder http://burkholder.stanford.edu/

=Your additional remarks=

=References=

<pubmed>11207367, 16267290, 19465772, 15023339 </pubmed>

[[Category:Protein-coding genes]]

Sda

2009-07-29T13:04:12Z

Jwveening: /* Labs working on this gene/protein */

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not iniate sporulation Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || developmental checkpoint protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of

sporulation (phosphorylation of Spo0A) to the function

of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAE01463]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_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:''' BSU25690

===Phenotypes of a mutant ===
*sporulates at a higher frequency
*will sporulate in the presence of replication stress

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[KinB]]-[[Sda]], [[KinA]]-[[Sda]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from Geobacillus stearothermophilus, complex with KinB), [http://www.rcsb.org/pdb/explore.do?structureId=1PV0 1PV0]

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q7WY62 Q7WY62]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25690]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''sda''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' [[DnaA]]
** repressed when no DNA damage is present ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Regulatory mechanism:''' Probably activated by [[DnaA]] under replication stress
** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

Bill Burkholder http://burkholder.stanford.edu/

=Your additional remarks=

=References=

<pubmed>11207367, 16267290, 19465772, 15023339 </pubmed>

[[Category:Protein-coding genes]]

Sda

2009-07-29T13:03:14Z

Jwveening: /* References */

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not iniate sporulation Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || developmental checkpoint protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of

sporulation (phosphorylation of Spo0A) to the function

of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAE01463]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_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:''' BSU25690

===Phenotypes of a mutant ===
*sporulates at a higher frequency
*will sporulate in the presence of replication stress

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[KinB]]-[[Sda]], [[KinA]]-[[Sda]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from Geobacillus stearothermophilus, complex with KinB), [http://www.rcsb.org/pdb/explore.do?structureId=1PV0 1PV0]

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q7WY62 Q7WY62]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25690]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''sda''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' [[DnaA]]
** repressed when no DNA damage is present ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Regulatory mechanism:''' Probably activated by [[DnaA]] under replication stress
** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>11207367, 16267290, 19465772, 15023339 </pubmed>

[[Category:Protein-coding genes]]

Jan Willem Veening

2009-07-29T13:01:34Z

Jwveening: /* Open positions */

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: University of Groningen, Department of Genetics, [http://http://molgen.biol.rug.nl/molgen/index.php Molecular Genetics Group]
*Contact: j.w.veening@rug.nl [mailto:j.w.veening@rug.nl send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen]
*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
Contact [mailto:j.w.veening@rug.nl me] for info.

Jan Willem Veening

2009-07-29T13:01:03Z

Jwveening: /* Homepages */

Jan Willem Veening

2009-07-29T13:00:17Z

Jwveening: /* Jan-Willem Veening */

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: University of Groningen, Department of Genetics, [http://http://molgen.biol.rug.nl/molgen/index.php Molecular Genetics Group]
*Contact: j.w.veening@rug.nl [mailto:j.w.veening@rug.nl send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen (from June 2009)]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
Contact [mailto:j.w.veening@ncl.ac.uk me] for info.

SirA

2009-04-07T09:08:36Z

Jwveening:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yneE or sirA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yoxF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 7.353
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 444 bp, 148 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tkt]]'', ''[[yneF]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yneE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yneE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:yneE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

yneE was renamed to sirA.

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yneEF.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11248]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17900]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

sirA ('''s'''porulation '''i'''nhibitor of '''r'''eplication) is activated by Spo0A~P and inhibits DNA replication during sporulation.

=References=

PMID 19329632

# Rahn-Lee L, Gorbatyuk B, Skovgaard O & Losick R.(2009) The Conserved Sporulation Protein YneE inhibits DNA replication in Bacillus subtilis ''J Bact.'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 19329632]

Jan Willem Veening

2009-03-30T15:04:18Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: Newcastle University, [http://www.ncl.ac.uk/camb/cbcb/ Centre for Bacterial Cell Biology]
*Contact: j.w.veening@ncl.ac.uk [mailto:j.w.veening@ncl.ac.uk send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen (from June 2009)]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
Contact [mailto:j.w.veening@ncl.ac.uk me] for info.

Jan Willem Veening

2009-03-13T18:18:13Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: Newcastle University, [http://www.ncl.ac.uk/camb/cbcb/ Centre for Bacterial Cell Biology]
*Contact: j.w.veening@ncl.ac.uk [mailto:j.w.veening@ncl.ac.uk send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen (from June 2009)]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
*We currently have an open PhD position and are looking for a highly motivated student with affinity for microbiology (microbiological experience not necessarily required). Contact [mailto:j.w.veening@ncl.ac.uk me] for more info.

Sda

2009-03-13T18:16:24Z

Jwveening:

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not iniate sporulation Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || developmental checkpoint protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of

sporulation (phosphorylation of Spo0A) to the function

of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===
*sporulates at a higher frequency
*will sporulate in the presence of replication stress

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
monocistron
* '''Sigma factor:'''
SigA
* '''Regulation:'''
DnaA
* '''Regulatory mechanism:'''
Probably activated by DnaA under replication stress
* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Jan Willem Veening

2009-03-13T18:12:26Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: Newcastle University, [http://www.ncl.ac.uk/camb/cbcb/ Centre for Bacterial Cell Biology]
*Contact: j.w.veening@ncl.ac.uk [mailto:j.w.veening@ncl.ac.uk send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen (from June 2009)]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
*We currently have an open PhD position and am looking for a highly motivated student with affinity for microbiology (microbiological experience not necessarily required). Contact [mailto:j.w.veening@ncl.ac.uk me] for more info.

File:CIMG1375.JPG

2009-03-13T15:38:31Z

Jwveening:

Main Page

2009-03-13T13:49:01Z

Jwveening:

Welcome to Subtiwiki!

This Wiki is in an early stage of development.

To try how it works, go to the [[playground]]!

If you have any suggestions, please add them to the [[Wish List]]!

Pages for all genes are now available, but the information is not complete. To get an idea of how it could look like, visit one of the pages below:

* [[gltA]]
* [[gltB]]
* [[gltC]]
* [[rocG]]
* [[rocR]]
* [[ahrC]]
* [[ccpA]]
* [[crh]]
* [[glcT]]
* [[ptsG]]
* [[ptsH]]
* [[ptsI]]
* [[pckA]]
* [[rny]]
* [[ymdB]]
* [[sigL]]
* [[pgi]]
* [[pfkA]]
* [[fbaA]]
* [[tpi]]
* [[gapA]]
* [[gapB]]
* [[pgk]]
* [[pgm]]
* [[eno]]
* [[pyk]]
* [[cggR]]
* [[sr1]]
* [[ccpN]]
* [[yqfL]]
* [[spx]]
* [[Alessandra Albertini]]
* [[Arthur Aronson]]
* [[Stephane Aymerich]]
* [[Imrich Barak]]
* [[David Bechhofer]]
* [[Sabine Brantl]]
* [[Richard Brennan]]
* [[Ciaran Condon]]
* [[Simon Cutting]]
* [[Isabel de Sa-Nogueira]]
* [[Nathalie Declerck]]
* [[Kevin Devine]]
* [[Susan Fisher]]
* [[Elisabeth Härtig]]
* [[Josef Deutscher]]
* [[Jan Maarten van Dijl]]
* [[Yasutaro Fujita]]
* [[Anne Galinier]]
* [[Boris Görke]]
* [[Leendert Hamoen]]
* [[Colin Harwood]]
* [[Michael Hecker]]
* [[Lars Hederstedt]]
* [[John Helmann]]
* [[Tina Henkin]]
* [[Adriano Henriques]]
* [[Wolfgang Hillen]]
* [[Laurent Janniere]]
* [[Mark J. Jedrzejas]]
* [[Oscar Kuipers]]
* [[Rick Lewis]]
* [[Thorsten Mascher]]
* [[Ivan Mijakovic]]
* [[Philippe Noirot]]
* [[Naotake Ogasawara]]
* [[Harald Putzer]]
* [[Milton H. Saier]]
* [[Margarita Salas]]
* [[Wolfgang Schumann]]
* [[Linc Sonenshein]]
* [[Jörg Stülke]]
* [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Jwveening Jan-Willem Veening]
* [[Uwe Völker]]
* [[Claes von Wachenfeldt]]
* [[Wade Winkler]]
* [[Peter Zuber]]
* [[pGP380]]
* [[pGP382]]
* [[pBQ200]]
* [[pAC5]]
* [[pAC6]]
* [[pAC7]]
* [[pGP172]]
* [[pGP570]]
* [[pGP574]]
* [[pWH844]]
* [[BACTH]]
* [[template]]
* [[templatelab]]
* [[templatelit]]
* [[templateplasmid]]

Sda

2009-03-13T13:44:59Z

Jwveening:

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not iniate sporulation Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' ||
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of sporulation (phosphorylation of Spo0A) to the function of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Sda

2009-03-13T13:43:09Z

Jwveening:

* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of KinA (and likely KinB as well). This in its turn results in reduced levels of Spo0A~P. Thus, replication stressed cells will not iniate sporulation Sda is rapidly turned over by the ClpX/P system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sda''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' ||
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of sporulation (phosphorylation of Spo0A) to the function of replication initiation proteins
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sda_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:sda_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Jan Willem Veening

2009-03-13T13:35:48Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

==Jan-Willem Veening==
*Current institution: Newcastle University, [http://www.ncl.ac.uk/camb/cbcb/ Centre for Bacterial Cell Biology]
*Contact: j.w.veening@ncl.ac.uk [mailto:j.w.veening@ncl.ac.uk send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability
*Synthetic biology
*Bacillus subtilis
*Streptococcus pneumoniae

==Publications==
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity Pubmed]

==Homepages==

*[http://www.ncl.ac.uk/camb/staff/profile/j.w.veening Post doc at Newcastle]
*[http://molgen.biol.rug.nl/molgen/index.php Assistant Professor at Groningen (from June 2009)]
*[http://2008.igem.org/Team:Newcastle_University iGEM 2008]
*[http://2009.igem.org/Team:Newcastle iGEM 2009]

==Open positions==
*I currently have an open PhD position and am looking for a highly motivated student with affinity for microbiology (microbiological experience not necessarily required). Contact [mailto:j.w.veening@ncl.ac.uk me] for more info.

Jan Willem Veening

2009-03-13T13:21:13Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

Also see http://www.ncl.ac.uk/camb/staff/profile/j.w.veening

==Jan-Willem Veening==
*Institution: Newcastle University
*Contact:-
**j.w.veening@ncl.ac.uk [mailto:j.w.veening@ncl.ac.uk send mail]

==Research Interests==
*Cell-cycle regulation
*Sporulation
*Chromosome segregation
*Phenotypic bi-stability

==Publications==
Pubmed http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity

Jan Willem Veening

2009-03-13T13:16:18Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

Contact Info
Dr. Jan-Willem Veening
Centre for Bacterial Cell Biology
Institute for Cell and Molecular Biosciences
Medical School
Newcastle University
Cookson Building
Framlington Place
Newcastle upon Tyne
NE2 4HH, United Kingdom
E-mail: j.w.veening@ncl.ac.uk

Also see http://www.ncl.ac.uk/camb/staff/profile/j.w.veening

http://openwetware.org/wiki/User:Jan-willem_Veening

Publications:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=veening+jw&log$=activity

Jan Willem Veening

2009-03-13T13:15:19Z

Jwveening:

Jan Willem Veening

2009-03-13T13:13:23Z

Jwveening:

[[File:JW_lab.jpg‎ ]]

http://openwetware.org/wiki/User:Jan-willem_Veening

File:JW lab.jpg

2009-03-13T13:12:43Z

Jwveening:

Jan Willem Veening

2009-03-13T13:11:30Z

Jwveening: Created page with 'http://openwetware.org/wiki/User:Jan-willem_Veening'

http://openwetware.org/wiki/User:Jan-willem_Veening