SubtiWiki - User contributions [en]

User:Fabian M Commichau

2011-11-04T15:24:07Z

Fabian M Commichau: Blanked the page

User:Fabian M Commichau

2011-10-25T12:23:28Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''user name'''
|Fabian M. Commichau ([mailto:fcommic1@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''nickname''' || The GODFATHER of SPINE
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || '''68-73 kg'''
|-
|style="background:#ABCDEF;" align="center"|'''shoe size''' || '''43'''
|-
|style="background:#ABCDEF;" align="center"| '''hobbies''' || Onkel Bazillus
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || Ride first, work later
|-
|style="background:#FAF8CC;" align="center"|'''collaborating with '''
|style="background:#FAF8CC;" align="center"|'''Hinz and Kunz '''
|-
|-
|}
 

[[File:Example.jpg|300px|thumb|left|]] <br/br/>

User:Fabian M Commichau

2011-10-25T12:20:36Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''user name'''
|Fabian Commichau ([mailto:fcommic1@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''nickname''' || The GODFATHER of SPINE
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || '''68-73 kg'''
|-
|style="background:#ABCDEF;" align="center"|'''shoe size''' || '''43'''
|-
|style="background:#ABCDEF;" align="center"| '''hobbies''' || Onkel Bazillus
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || Moonlighting
|-
|style="background:#FAF8CC;" align="center"|'''collaborating with '''
|style="background:#FAF8CC;" align="center"|'''Hinz and Kunz '''
|-
|-
|}
 

[[File:Example.jpg|300px|thumb|left|]] <br/br/>

SPINE

2011-10-25T12:14:42Z

Fabian M Commichau: /* The reference for the method: */

'''SPINE is a method to detect ''in vivo'' protein-protein interactions''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]

==[http://www.iba-go.com/prottools/prot_p_ppi-meth.html#spine '''See the principle''' ]==

=='''A detailed protocol to detect the interaction between [[RocG]] and [[GltC]]:''' ==

1 litre of a ''B. subtilis'' culture was grown to an OD600 of approx. 1.0 and incubated with 0.6% formaldehyde ( 4% stock solution in PBS, pH 6.5!) for 20 minutes @ 37°C on a shaker.
The cells were harvested and washed once in 1 X PBS pH 6.5.
The pellets can then be stored @ -20 °C.
The [[GltC]] protein was expressed carrying a Strep-tag and [[RocG]] expression was induced by arginine ([http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]). Expression of the Strep-tagged GltC protein allows to test the functionality of the protein.
Crude extracts (10-15 ml) were prepared by using a French Press.
After a centrifugation step for 1 h @ 27.000 g the clarified crude extracts were loaded onto a Streptactin sepharose column (0.5-1 ml matrix) to isolate the cross-linked protein complexes (the detailed procedure for protein purification is described in the IBA manual, http://www.iba-go.com/).
After the purification of the protein complexes the crosslinks can be resolved by boiling the samples in Laemmli buffer for 10-15 minutes @ 95 °C ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]).
A 12.5% SDS gel was loaded with the samples and the proteins were then visualized by silver-staining. The interaction partner/s were identified by mass spectroscopy and Western blotting.

Preparation of the formaldehyde stock solution (max. 4% in 1X PBS pH 6.5):
We use ''para''-formaldehyde (a white powder). ''para''-formaldehyde dissolves within approx. 20-30 minutes in 1 X PBS for @ 65 to 70 °C.

The sepharose matrix was purchased from the IBA company, Göttingen (http://www.iba-go.com/).

=='''Relevant plasmids:'''==

for use in ''B. subtilis'' (multicopy plasmids): [[pGP380]], [[pGP382]]

for use in ''B. subtilis'' (chromosomal integration under the control of the native promoter): [[pGP1389]]

for use in ''E. coli'': [[pGP172]], [[pGP574]]

=='''Biotin-containing proteins that are purified with the Strep-Tactin column'''==
[[PycA]], [[AccB]]

=='''The reference for the method:'''==
<pubmed> 17994626 </pubmed>

=='''SPINE for membrane proteins:'''==
<pubmed> 21472855 </pubmed>

=='''Other studies that made use of SPINE'''==
<pubmed> 17608797 19193632 20572937 20933603 21622759 21803996 21992469 </pubmed>

SPINE

2011-10-25T11:52:43Z

Fabian M Commichau: /* Other studies that made use of SPINE */

'''SPINE is a method to detect ''in vivo'' protein-protein interactions''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]

==[http://www.iba-go.com/prottools/prot_p_ppi-meth.html#spine '''See the principle''' ]==

=='''A detailed protocol to detect the interaction between [[RocG]] and [[GltC]]:''' ==

1 litre of a ''B. subtilis'' culture was grown to an OD600 of approx. 1.0 and incubated with 0.6% formaldehyde ( 4% stock solution in PBS, pH 6.5!) for 20 minutes @ 37°C on a shaker.
The cells were harvested and washed once in 1 X PBS pH 6.5.
The pellets can then be stored @ -20 °C.
The [[GltC]] protein was expressed carrying a Strep-tag and [[RocG]] expression was induced by arginine ([http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]). Expression of the Strep-tagged GltC protein allows to test the functionality of the protein.
Crude extracts (10-15 ml) were prepared by using a French Press.
After a centrifugation step for 1 h @ 27.000 g the clarified crude extracts were loaded onto a Streptactin sepharose column (0.5-1 ml matrix) to isolate the cross-linked protein complexes (the detailed procedure for protein purification is described in the IBA manual, http://www.iba-go.com/).
After the purification of the protein complexes the crosslinks can be resolved by boiling the samples in Laemmli buffer for 10-15 minutes @ 95 °C ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]).
A 12.5% SDS gel was loaded with the samples and the proteins were then visualized by silver-staining. The interaction partner/s were identified by mass spectroscopy and Western blotting.

Preparation of the formaldehyde stock solution (max. 4% in 1X PBS pH 6.5):
We use ''para''-formaldehyde (a white powder). ''para''-formaldehyde dissolves within approx. 20-30 minutes in 1 X PBS for @ 65 to 70 °C.

The sepharose matrix was purchased from the IBA company, Göttingen (http://www.iba-go.com/).

=='''Relevant plasmids:'''==

for use in ''B. subtilis'' (multicopy plasmids): [[pGP380]], [[pGP382]]

for use in ''B. subtilis'' (chromosomal integration under the control of the native promoter): [[pGP1389]]

for use in ''E. coli'': [[pGP172]], [[pGP574]]

=='''Biotin-containing proteins that are purified with the Strep-Tactin column'''==
[[PycA]], [[AccB]]

=='''The reference for the method:'''==
<pubmed> 17994626 </pubmed>

=='''Other studies that made use of SPINE'''==
<pubmed> 17608797 19193632 20572937 20933603 21622759 21803996 21992469 </pubmed>

RnjA

2011-10-22T18:01:38Z

Fabian M Commichau: /* Original publications */

* '''Description:''' [[RNase]] J1 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rnjA ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykqC''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] J1
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA processing
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/RnjA RNase J1]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.902
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1665 bp, 555 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[adeC]]'', ''[[ykzG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13326]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ykqC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[Rnases]]}},
{{SubtiWiki category|[[essential genes]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14530

===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+BG11813]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' endonuclease and 5'-3' exonuclease

* '''Protein family:''' RNase J subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[RnjB]]

=== RNAs affected by ''rnjA'' ===

* ''[[hbs]]''
* ''[[thrS]]''
* ''[[yhxA]]-[[glpP]]'' (in a RppH-dependent manner) {{PubMed|21925382}}

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** part of the [[RNA degradosome]] {{PubMed|19193632}}
** [[RnjA]]-[[RnjB]] {{PubMed|19193632,20025672}}
** [[RnjA]]-[[PfkA]] {{PubMed|19193632}}
** [[RnjA]]-[[PnpA]] {{PubMed|19193632}}
** [[RnjA]]-[[Rny]] {{PubMed|19193632,21803996}}
** [[RnjA]]-[[CshA]] {{PubMed|20572937}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do;jsessionid=8B071C0C81B11ADEBA3DDC3FF3395811?structureId=3BK1 3BK1] (RNase J from ''Thermus thermophilus'') [http://www.pdb.org/pdb/explore/explore.do?structureId=3BK2 3BK2] (RNase J from ''Thermus thermophilus'', complex with UMP)

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45493 Q45493]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14530]

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

=== Additional information===
* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
* required for ''[[thrS]]'' RNA processing, involved in maturation of the 5’-end of the16S rRNA

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]

=Biological materials =

* '''Mutant:''' GP41 (''rnjA'' under control of p(xyl)), available in [[Stülke]] lab; SSB342 (''rnjA'' under pspac), cat, available in [[Harald Putzer]] lab

* '''Expression vector:'''
** for chromosomal expression of RNase J1-Strep (spc): GP1034, available in [[Jörg Stülke]]'s lab
** for chromosomal expression of RNase J1-Strep (cat): GP1042, available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' pGP418 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1020 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

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

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]

=Your additional remarks=

=References=
==Reviews==
'''Additional reviews:''' {{PubMed|21957024}}
<pubmed>20458164 21334965 21893280</pubmed>

==Original publications==
'''Additional publications:''' {{PubMed|21893285,21893286,21908660}}
<pubmed>18079181, 19553197, 17981983, 19458035, 15831787, 18204464, 18713320, 19193632, 17005971, 18445592, 17512403, 17229210, 17576666, 19210617 19633085 19638340 19850915 19880604 20025672 20418391 20572937 ,21803996 21862575 21925382 </pubmed>
[[Category:Protein-coding genes]]

RnjA

2011-10-22T17:57:54Z

Fabian M Commichau: /* Original publications */

GltB

2009-03-12T09:30:27Z

Fabian M Commichau: /* References */

* '''Description:''' small subunit of glutamate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (small subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54.6 kDa, 7.69
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1479 bp, 493 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[yogA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltB_nucleotide.txt Gene sequence (+200bp) corrected ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltB_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:gltB_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2007785 - 2009263

===Phenotypes of a mutant ===

auxotrophic for glutamate

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12594]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH

* '''Protein family:''' glutamate synthase family.

* '''Paralogous protein(s):''' none

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** nucleotide binding domain (NADP) (299–313)

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34399]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18440]

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.4.1.13]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltA]]-[[gltB]]''

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

* '''Regulation:''' see ''[[gltA]]''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP736 (spc), available in [[Stülke]] lab

* '''Expression vector:''' pGP1119 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[gltA]]''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of ''Bacillus subtilis'' glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in ''Bacillus subtilis'': Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]

GltB

2009-03-12T09:29:49Z

Fabian M Commichau: /* References */

* '''Description:''' small subunit of glutamate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (small subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54.6 kDa, 7.69
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1479 bp, 493 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[yogA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltB_nucleotide.txt Gene sequence (+200bp) corrected ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltB_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:gltB_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2007785 - 2009263

===Phenotypes of a mutant ===

auxotrophic for glutamate

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12594]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH

* '''Protein family:''' glutamate synthase family.

* '''Paralogous protein(s):''' none

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** nucleotide binding domain (NADP) (299–313)

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34399]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18440]

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.4.1.13]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltA]]-[[gltB]]''

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

* '''Regulation:''' see ''[[gltA]]''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP736 (spc), available in [[Stülke]] lab

* '''Expression vector:''' pGP1119 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[gltA]]''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in "Bacillus subtilis": Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]

User:Fabian M Commichau

2009-03-12T09:28:17Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 68-76 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 43
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || Moonlighting
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''Hinz and Kunz '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:27:42Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 68-76 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 43
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' ||
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''Hinz and Kunz '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:27:31Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 68-76 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 43
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' ||
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''Hinz and Co '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:26:58Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 68-76 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 43
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' ||
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:26:23Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || Amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 68-76 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 43
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:25:57Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|300px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:25:19Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || amber
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|200px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:24:31Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Dr. π
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|200px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:24:07Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|200px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:23:52Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg|400px|thumb|left|]]

User:Fabian M Commichau

2009-03-12T09:22:14Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg]]

User:Fabian M Commichau

2009-03-12T09:21:57Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----
|" align="center"|-
[[File:Example.jpg]]

User:Fabian M Commichau

2009-03-12T09:21:20Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----
|-
[[File:Example.jpg]]

User:Fabian M Commichau

2009-03-12T09:20:42Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 

----

[[File:Example.jpg]]

User:Fabian M Commichau

2009-03-12T09:18:14Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}
 
[[File:Example.jpg]]

User:Fabian M Commichau

2009-03-12T09:17:48Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Fabian Commichau ([mailto:Fcommic@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Pimp
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fabsi
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || red
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 34 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 49
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Tante Yersinia
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || to plesure women
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[]] and [[]] '''
|-
|-
|}

User:Heilers

2009-03-12T09:17:12Z

Fabian M Commichau: /* Main research interests */

= Lab head: [[Jörg Stülke]] =
'''Additional information'''
* [mailto:heilers@gwdg.de send mail]
* location: Göttingen, Germany
* Homepage: [http://wwwuser.gwdg.de/~genmibio/stuelke.html link]
[[image:Heilers.jpg]]
= Publications =
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=%22Eilers%2BH%22+AND+stulke&log$=activity Pubmed]

Since I have no publication as a first author, i´m at least the inventor of Sroppel´s nickname [[Fips]]

= Main research interests =
Gene expression, Flight13 records, regulatory mechanisms and signal transduction in ''M. pneumoniae'' [http://www.genome.ad.jp/kegg-bin/show_organism?org=mpn link], protein-DNA interactions, moonlighting proteins, SPICE und anderen geilen Scheiß!

= Open positions =

Trainees are always welcome!

User:Heilers

2009-03-12T09:16:33Z

Fabian M Commichau: /* Main research interests */

= Lab head: [[Jörg Stülke]] =
'''Additional information'''
* [mailto:heilers@gwdg.de send mail]
* location: Göttingen, Germany
* Homepage: [http://wwwuser.gwdg.de/~genmibio/stuelke.html link]
[[image:Heilers.jpg]]
= Publications =
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=%22Eilers%2BH%22+AND+stulke&log$=activity Pubmed]

Since I have no publication as a first author, i´m at least the inventor of Sroppel´s nickname [[Fips]]

= Main research interests =
Gene expression, regulatory mechanisms and signal transduction in ''M. pneumoniae'' [http://www.genome.ad.jp/kegg-bin/show_organism?org=mpn link], protein-DNA interactions, moonlighting proteins, SPICE und anderen geilen Scheiß!

= Open positions =

Trainees are always welcome!

User:Heilers

2009-03-12T09:16:21Z

Fabian M Commichau: /* Main research interests */

= Lab head: [[Jörg Stülke]] =
'''Additional information'''
* [mailto:heilers@gwdg.de send mail]
* location: Göttingen, Germany
* Homepage: [http://wwwuser.gwdg.de/~genmibio/stuelke.html link]
[[image:Heilers.jpg]]
= Publications =
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=%22Eilers%2BH%22+AND+stulke&log$=activity Pubmed]

Since I have no publication as a first author, i´m at least the inventor of Sroppel´s nickname [[Fips]]

= Main research interests =
Gene expression, regulatory mechanisms and signal transduction in ''M. pneumoniae'' [http://www.genome.ad.jp/kegg-bin/show_organism?org=mpn link], protein-DNA interactions, moonlighting proteins, SPICE und anderen geilen Scheiß

= Open positions =

Trainees are always welcome!

Sroppel

2009-03-12T09:14:42Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Sebastian Roppel ([mailto:sroppel@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || Genetix
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fipsy
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || steel brown
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 190 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 47
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Onkel Bacillus
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || Schreibmaschine
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[User:Aschmei|Aschmei]] and [[User:CLammers|CLammers]] '''
|-
|-
|}

Sroppel

2009-03-12T09:14:04Z

Fabian M Commichau:

{| align="left" border="5" cellpadding="5"
|-
|style="background:#ABCDEF;" align="center"|'''Username'''
|Sebastian Roppel ([mailto:sroppel@gwdg.de send mail])
|-
|style="background:#ABCDEF;" align="center"| '''Status''' || genetiker
|-
|style="background:#ABCDEF;" align="center"| '''Nick-name''' || Fipsy
|-
|style="background:#ABCDEF;" align="center"| '''hair color''' || steel brown
|-
|style="background:#ABCDEF;" align="center"| '''weight''' || 190 kg
|-
|style="background:#ABCDEF;" align="center"|'''schoesize''' || 44
|-
|style="background:#ABCDEF;" align="center"| '''Hobbies''' || Onkel Bacillus
|-
|style="background:#ABCDEF;" align="center"|'''dedication''' || Schreibmaschine
|-
|style="background:#FAF8CC;" align="center"|'''colaborating with '''
|style="background:#FAF8CC;" align="center"|'''[[User:Aschmei|Aschmei]] and [[User:CLammers|CLammers]] '''
|-
|-
|}

User:Fabian M Commichau

2009-03-12T09:13:06Z

Fabian M Commichau:

User:Fabian M Commichau

2009-03-12T09:07:07Z

Fabian M Commichau:

Username FMC (send mail)
Status diplomastudent
Nick-name Dr. π
hair color brown
weight 70 - 76 kg
schoesize 43
Hobbies unknown
dedication SubtiWiki

User:Fabian M Commichau

2009-03-12T09:06:27Z

Fabian M Commichau:

Username Sebastian Roppel (send mail)
Status diplomastudent
Nick-name Dr. π
hair color brown
weight 70 - 76 kg
schoesize 43
Hobbies unknown
dedication SubtiWiki
collaborating with Aschmei and CLammers

User:Fabian M Commichau

2009-03-12T09:02:16Z

Fabian M Commichau:

Fabian M. Commichau

File:Example.jpg

2009-03-12T09:01:40Z

Fabian M Commichau:

User:Fabian M Commichau

2009-03-12T09:01:25Z

Fabian M Commichau: Created page with 'File:Example.jpg'

[[File:Example.jpg]]

RocG

2009-03-12T08:59:08Z

Fabian M Commichau: /* Phenotypes of a mutant */

* '''Description:''' catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rocG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of GltC
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_nucleotide.txt Gene sequence (+200bp) corrected ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:rocG_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3879765 - 3881036

===Phenotypes of a mutant ===

Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family

* '''Paralogous protein(s):''' [[GudB]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''gltAB'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''rocG''

* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]

* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])

* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression

* '''Additional information:'''
Activation by RocR requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]

=Biological materials =

* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab

* '''Expression vector:''' pGP902 (in [[pGP172]], N-terminal Strep-tag), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

'''Enzymatic activity of RocG'''
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
# Khan, M. I., K. Ito, H. Kim, H. Ashida, T. Ishikawa, H. Shibata, and Y. Sawa. 2005. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-1870. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16244435 PubMed]
# Stillman TJ, Baker PJ, Britton KL, Rice DW Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 1993, 234:1131-1139. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8263917 PubMed]

'''Function in the control of [[GltC]] activity'''
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
# Belitsky BR, Sonenshein AL (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186:3399-3407 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150225 PubMed]

'''Expression of ''rocG'''''
# Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the ''rocG-rocA'' intergenic region in ''Bacillus subtilis''. Microbiology 149: 739-750. [http://www.ncbi.nlm.nih.gov/sites/entrez/12634342 PubMed]
# Belitsky BR, Sonenshein, AL: An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA 1999, 96:10290-10295. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
# Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150224 PubMed]

GltC

2009-03-12T08:55:29Z

Fabian M Commichau: /* Extended information on the protein */

* '''Description:''' Transcriptional activator of the ''gltAB'' operon. Activates expression of the operon in the absence of arginine. 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || No
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation of the glutamate synthase operon (''gltAB'')
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_nucleotide.txt Gene sequence (+200bp) corrected ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:gltC_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2013989 - 2014888

===Phenotypes of a mutant ===
''gltC'' mutants are auxotrophic for glutamate.

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activation of the ''gltAB'' operon [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Protein family:''' LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37

* '''Modification:'''

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

* '''Effectors of protein activity:''' 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]

* '''Interactions:'''
** GltC-[[RocG]], This interaction takes place in the presence of glutamate. It prevents the transcription activation of the ''gltAB'' operon. Note that [[RocG]] expression is strongly regulated by carbon and nitrogen sources, respectively. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20668 P20668]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18460 KEGG]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltC]]''

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

* '''Regulation:''' autoregulation by GltC

* '''Regulatory mechanism:''' autorepression

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]

* ''' Additional information:'''

=Biological materials =

* '''Mutant:''' GP344 (erm), GP738 (spc) (available in [[Stülke]] lab)

* '''Expression vector:''' pGP903 (in [[pWH844]], N-terminal His-tag) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in Stülke lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
# Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8257110 PubMed]

GltC

2009-03-12T08:55:08Z

Fabian M Commichau: /* Extended information on the protein */

* '''Description:''' Transcriptional activator of the ''gltAB'' operon. Activates expression of the operon in the absence of arginine. 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || No
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation of the glutamate synthase operon (''gltAB'')
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_nucleotide.txt Gene sequence (+200bp) corrected ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:gltC_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2013989 - 2014888

===Phenotypes of a mutant ===
''gltC'' mutants are auxotrophic for glutamate.

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activation of the ''gltAB'' operon [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Protein family:''' LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37

* '''Modification:'''

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

* '''Effectors of protein activity:''' 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]

* '''Interactions:'''
** GltC-[[RocG]], This interaction takes place in the presence of glutamate. It prevents the transcription activation of the ''gltAB'' operon. Note that [[RocG]] expression is strongly regulated by carbon and nitrogen source, respectively. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20668 P20668]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18460 KEGG]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltC]]''

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

* '''Regulation:''' autoregulation by GltC

* '''Regulatory mechanism:''' autorepression

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]

* ''' Additional information:'''

=Biological materials =

* '''Mutant:''' GP344 (erm), GP738 (spc) (available in [[Stülke]] lab)

* '''Expression vector:''' pGP903 (in [[pWH844]], N-terminal His-tag) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in Stülke lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
# Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8257110 PubMed]

File:Fmc.jpg

2009-03-12T08:45:11Z

Fabian M Commichau: