BSGatlas

tnrA

BSGatlas-gene-1582

BSGatlas

Description	Information
Coordinates	1397411..1397743
Genomic Size	333 bp
Name	tnrA
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	scgR
	tnrA
	tnrA
Category	SW 2 Metabolism
	SW 2.3 Amino acid/ nitrogen metabolism
	SW 2.3.1 Biosynthesis/ acquisition of amino acids
	SW 2.3.1.1 Biosynthesis/ acquisition of glutamate/ glutamine/ ammonium assimilation
	SW 3 Information processing
	SW 3.4 Regulation of gene expression
	SW 3.4.2 Transcription factors and their control
	SW 3.4.2.5 Transcription factors/ other
	SW 3.4.5 Regulators of core metabolism
Description	transcriptional pleiotropic regulator ([SW\|MerR family]) involved in global nitrogen regulation
Function	regulation of nitrogen assimilation
Is essential?	no
Isoelectric point	10.23
Locus Tag	BSU_13310
Molecular weight	12.9864
Name	tnrA
Product	transcription activator/ repressor ([SW\|MerR family])

RefSeq

Description	Information
Alternative Locus Tag	BSU13310
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 10231480, 12823818,15916606, 16547045, 17085574, 17183219, 21435182,23535029, 26635369; Product type r: regulator
Functions	16.3: Control
Locus Tag	BSU_13310
Name	tnrA
Title	nitrogen sensing transcriptional regulator
Type	CDS

BsubCyc

Description	Information
Alternative Name	scgR
Citation	Fedorova K;Kayumov A;Woyda K;Ilinskaja O;Forchhammer K Transcription factor TnrA inhibits the biosynthetic activity of glutamine synthetase in Bacillus subtilis. FEBS Lett 587(9);1293-8 (2013) PUBMED: 23535029
	Fedorova KP;Sharafutdinov IS;Turbina Elu;Bogachev MI;Il'inskaia ON;Kaiumov AR [The C-terminus of transcription factor TnrA from Bacillus subtilis controls DNA-binding domain activity but is not required for dimerization]. Mol Biol (Mosk) 47(2);331-7 (2013) PUBMED: 23808168
	Fujita Y;Satomura T;Tojo S;Hirooka K CcpA-Mediated Catabolite Activation of the Bacillus subtilis ilv-leu Operon and Its Negation by Either CodY- or TnrA-Mediated Negative Regulation. J Bacteriol 196(21);3793-806 (2014) PUBMED: 25157083
	Groot Kormelink T;Koenders E;Hagemeijer Y;Overmars L;Siezen RJ;de Vos WM;Francke C Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics 13;191 (2012) PUBMED: 22607086
	Gunka K;Commichau FM Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation. Mol Microbiol 85(2);213-24 (2012) PUBMED: 22625175
	Hauf K;Kayumov A;Gloge F;Forchhammer K The Molecular Basis of TnrA Control by Glutamine Synthetase in Bacillus subtilis. J Biol Chem 291(7);3483-95 (2016) PUBMED: 26635369
	Kaiumov AR;Fedorova KP;Il'inskaia ON;Sharipova MR [The amount and localization of regulatory proteins TnrA and GlnK in Bacillus subtilis cells under nitrogen starvation conditions]. Mol Biol (Mosk) 44(4);743-5 (2010) PUBMED: 20873235
	Kayumov A;Heinrich A;Fedorova K;Ilinskaya O;Forchhammer K Interaction of the general transcription factor TnrA with the PII-like protein GlnK and glutamine synthetase in Bacillus subtilis. FEBS J 278(10);1779-89 (2011) PUBMED: 21435182
	Mirouze N;Bidnenko E;Noirot P;Auger S Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis. Microbiologyopen 4(3);423-35 (2015) PUBMED: 25755103
	Schumacher MA;Chinnam NB;Cuthbert B;Tonthat NK;Whitfill T Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis. Genes Dev 29(4);451-64 (2015) PUBMED: 25691471
Comment	One or more strains containing mutant alleles of this gene can be obtained from the Bacillus Genetic Stock Center. Click here to see the list of available strains at BGSC. ChIP-Chip data: \|CITS: [25755103]\| Evidence 1a: Function experimentally demonstrated in the studied strain; PubMedId: 10231480, 12823818, 15916606, 16547045, 17085574, 17183219; Product type r : regulator1 6.3: Control
Description	nitrogen sensing transcriptional regulator
Gene Ontology	GO:0000166 nucleotide binding
	GO:0003677 DNA binding
	GO:0005515 protein binding
	GO:0006351 transcription, DNA-templated
	GO:0006355 regulation of transcription, DNA-templated
Locus Tag	BSU13310
Molecular weight	13.126
Name	tnrA

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU03610, BSU03600, BSU22410, BSU03590, BSU00550, BSU13030, BSU18500, BSU09790, BSU19230, BSU29470
Expression pos. correlated with	BSU03320, BSU13299, new_1397771_1398159_c, BSU03310, new_2829529_2830447_c, BSU36510, BSU33140, new_1277495_1278195_c, BSU07580, BSU21700
Highly expressed condition	(BT) A fresh colony grown on an LB plate was used to inoculate 10 ml of LB and grown for 10 hoursat 30°C. This culture wasused to inoculate 10 ml of MSgg medium (S.S. Branda et al., J Bacteriol 186, 3970, Jun, 2004) and incubated with vigorous shaking. The cultures in MSgg were diluted to the same extent in 96 wells microtiterplates (5 μl for 1.5 ml of medium) and incubated without shaking at 30°C. Cells from the control cultures were harvested after 24 hours of incubation [BT]. Biofilms were harvested from 96 well plates after incubation for 36 hours [B36] and 60 hours [B60].
	(Cold) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha].
	(T-0.40H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T-1.10H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T-1.40H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T0.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T0.30H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T1.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T1.30H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T2.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
Lowely expressed condition	(B36) A fresh colony grown on an LB plate was used to inoculate 10 ml of LB and grown for 10 hoursat 30°C. This culture wasused to inoculate 10 ml of MSgg medium (S.S. Branda et al., J Bacteriol 186, 3970, Jun, 2004) and incubated with vigorous shaking. The cultures in MSgg were diluted to the same extent in 96 wells microtiterplates (5 μl for 1.5 ml of medium) and incubated without shaking at 30°C. Cells from the control cultures were harvested after 24 hours of incubation [BT]. Biofilms were harvested from 96 well plates after incubation for 36 hours [B36] and 60 hours [B60].
	(dia15) Diamide was added to an exponentially growing culture (OD600 approx. 0.6) at a sub-lethal concentration(0.5 mM) and growth continued at 37°C with vigorous shaking. Samples were collected 0, 5 and 15 minutes after diamide addition [dia0, dia5 and dia15].
	(Diami) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(Etha) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha].
	(H2O2) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(Heat) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha].
	(LBGstat) Cells were grown in Luria-Bertani medium (Sigma) supplemented with glucose 0.3 % [LBG] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle .
	(LPh) Cells were harvested (i) during exponential growth in high phosphate defined medium [HPh]; (ii) during exponential growth in low phosphate defined medium [LPh] (J. P. Muller, Z. An, T. Merad, I. C. Hancock, C. R. Harwood, Microbiology 143, 947, Mar, 1997);and (iii) at three hours after the outset of the phosphate-limitation induced stationary phase [LPhT].
	(Salt) Cells were grown in Spizizen’s minimal medium (SMM) at 37 °C with vigorous shaking. Salt was added, to a final concentration of 0.4 M to an exponentially growing culture of cells at OD500 of 0.4. Samples were harvested before [SMM] and 10 minutes after [Salt] NaCl addition.
Name	tnrA

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