BSGatlas

rpoE

BSGatlas-gene-4331

BSGatlas

Description	Information
Coordinates	3812542..3813063
Genomic Size	522 bp
Name	rpoE
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	rpoE
Category	SW 3 Information processing
	SW 3.2 RNA synthesis and degradation
	SW 3.2.1 Transcription
	SW 3.2.1.1 RNA polymerase
Description	[[protein\|RNA polymerase]] delta subunit, affects the regulation of [SW\|RNA polymerase] by the concentration of the initiating nucleoside triphosphate (iNTP)
Enzyme Classifications	EC 2.7.7.6: DNA-directed RNA polymerase
Function	[SW\|transcription]
Is essential?	no
Isoelectric point	3.65
Locus Tag	BSU_37160
Molecular weight	20.254
Name	rpoE
Product	[SW\|RNA polymerase] delta subunit

RefSeq

Description	Information
Alternative Locus Tag	BSU37160
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 189250, 9795209,10336502, 10438769, 10672039, 10910724, 11029421,23543716, 26546673, 27679485; Product type f: factor
Functions	16.3: Control
Locus Tag	BSU_37160
Name	rpoE
Title	RNA polymerase (delta subunit) andtranscriptional repressor
Type	CDS

BsubCyc

Description	Information
Citation	Demo G;Papoušková V;Komarek J;Kadeřávek P;Otrusinova O;Srb P;Rabatinova A;Krasny L;Zidek L;Sklenař V;Wimmerova M X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase. J Struct Biol 187(2);174-86 (2014) PUBMED: 24937760
	Doherty GP;Fogg MJ;Wilkinson AJ;Lewis PJ Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition. Microbiology 156(Pt 12);3532-43 (2010) PUBMED: 20724389
	Motackova V;Novacek J;Zawadzka-Kazimierczuk A;Kazimierczuk K;Zidek L;Sanderova H;Krasny L;Kozminski W;Sklenar V Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR 48(3);169-77 (2010) PUBMED: 20890634
	Novacek J;Zawadzka-Kazimierczuk A;Papouskova V;Zidek L;Sanderova H;Krasny L;Kozminski W;Sklenar V 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomol NMR 50(1);1-11 (2011) PUBMED: 21424579
	Papouskova V;Kadeřávek P;Otrusinova O;Rabatinova A;SSanderova H;Novacek J;Krasny L;Sklenař V;Žídek L Structural study of the partially disordered full-length δ subunit of RNA polymerase from Bacillus subtilis. Chembiochem 14(14);1772-9 (2013) PUBMED: 23868186
	Prajapati RK;Sengupta S;Rudra P;Mukhopadhyay J Bacillus subtilis δ Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation. J Biol Chem 291(3);1064-75 (2016) PUBMED: 26546673
	Prajapati RK;Sur R;Mukhopadhyay J A Novel Function of δ Factor from Bacillus subtilis as a Transcriptional Repressor. J Biol Chem 291(46);24029-24035 (2016) PUBMED: 27679485
	Rabatinova A;Sanderova H;Jirat Matějčková J;Korelusova J;Sojka L;Barvik I;Papouskova V;Sklenar V;Žídek L;Krasny L The δ subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell. J Bacteriol 195(11);2603-11 (2013) PUBMED: 23543716
	Zawadzka-Kazimierczuk A;Kozminski W;Billeter M TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra. J Biomol NMR 54(1);81-95 (2012) PUBMED: 22806130
	Zawadzka-Kazimierczuk A;Kozminski W;Sanderova H;Krasny L High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins. J Biomol NMR 52(4);329-37 (2012) PUBMED: 22350953
Comment	16.3: Control
Description	RNA polymerase (delta subunit)
Gene Ontology	GO:0001000 bacterial-type RNA polymerase core enzyme binding
	GO:0001131 transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding
	GO:0003899 DNA-directed 5'-3' RNA polymerase activity
	GO:0006351 transcription, DNA-templated
	GO:0006355 regulation of transcription, DNA-templated
	GO:0016740 transferase activity
	GO:0016779 nucleotidyltransferase activity
	GO:2000142 regulation of DNA-templated transcription, initiation
Locus Tag	BSU37160
Molecular weight	20.399
Name	rpoE

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU18350, BSU17690, BSU22580, BSU18360, BSU10860, BSU26890, BSU26370, BSU18370, BSU40310, BSU21520
Expression pos. correlated with	new_3813064_3813166_c, BSU37500, new_3849617_3849712_c, new_1535752_1535847_c, new_1255867_1256041_c, BSU33350, new_2792102_2792210_c, BSU36270, BSU14630, BSU22890
Highly expressed condition	(dia0) 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].
	(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].
	(G180) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(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].
	(HPh) 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].
	(LBexp) Cells were grown in Luria-Bertani medium (Sigma) [LB] 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 .
	(LBGexp) 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 .
	(Oxctl) 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
	(Paraq) 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
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].
	(B60) 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].
	(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].
	(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].
	(Gly) A 5 ml aliquot of LB medium was inoculated using frozen culture stocks. After a few hours growth at 37°C, precultures were prepared by inoculating 5 ml of M9 with this LB culture at several different dilutions usually ranging from 500- to 2000-fold. The dilution range was chosen so that one of these precultures had grown to and OD600 of 0.5 - 1.0 after overnight inculation. The chosen M9 medium precultures [at OD600 of 0.5 - 1.0] were used to inoculate 100 mL of M9 medium in 500 mL non-baffled shake flasks to an OD600 of 0.02. Filter-sterilized carbon sources were added separately to the medium M9 at following concentration: D-Glucose 3g/L[Glu], L-Malic acid 4.5g/L[Mal], L-Malic acid + D-Glucose 3 and 2g/L[M+G], D-Fructose 3g/L[Fru], D-Gluconate 4g/L[Glucon], Pyruvate 6g/L[Pyr], Glycerol 6g/L[Gly], Glutamic acid + Succinic acid 2 and 2g/L[G+S]. Where necessary, carbon source solutions were pH neutralized with 4 M NaOH prior to addition to the medium. Cells were harvested during the exponential growth phase.
	(LBstat) Cells were grown in Luria-Bertani medium (Sigma) [LB] 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 .
	(M0t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90].
	(M40t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90].
	(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].
Name	rpoE

KEGG Pathways

Description	Information
Pathway	RNA polymerase (ko03020)

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