BSGatlas

degU

BSGatlas-gene-4142

BSGatlas

Description	Information
Coordinates	3644607..3645296
Genomic Size	690 bp
Name	degU
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	degU
	degU
	iep
	sacU
Category	SW 3 Information processing
	SW 3.4 Regulation of gene expression
	SW 3.4.2 Transcription factors and their control
	SW 3.4.2.1 Two-component system response regulators
	SW 4 Lifestyles
	SW 4.1 Exponential and early post-exponential lifestyles
	SW 4.1.2 Biofilm formation
	SW 4.1.2.4 Regulation
	SW 6 Groups of genes
	SW 6.4 Phosphoproteins
	SW 6.4.2 Phosphorylation on an Asp residue
Description	two-component response regulator, regulation of degradative enzyme expression, [SW\|genetic competence], [SW\|biofilm formation], capsule biosynthesis (together with [[protein\|5D479874B43F521DB52EDC2C27CDE4967F22DE47]]), non-phosphorylated DegU is required for swarming motility
Function	regulation of degradative enzymes, [SW\|genetic competence], and other adaptive responses
Is essential?	no
Isoelectric point	5.6
Locus Tag	BSU_35490
Molecular weight	25.7186
Name	degU
Product	two-component response regulator

RefSeq

Description	Information
Alternative Locus Tag	BSU35490
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 10908654, 11557812,12471443, 12950930, 14563871, 15342569, 15598897,17590234, 17827323, 21736639, 22677979, 24847778,25288929, 25880922, 25887289, 27920766; Product type r :regulator
Functions	16.3: Control
Locus Tag	BSU_35490
Name	degU
Title	two-component response regulator
Type	CDS

BsubCyc

Description	Information
Alternative Name	iep
	sacU
Citation	Belas R When the swimming gets tough, the tough form a biofilm. Mol Microbiol 90(1);1-5 (2013) PUBMED: 23927648
	Bridier A;Le Coq D;Dubois-Brissonnet F;Thomas V;Aymerich S;Briandet R The Spatial Architecture of Bacillus subtilis Biofilms Deciphered Using a Surface-Associated Model and In Situ Imaging. PLoS One 6(1);e16177 (2011) PUBMED: 21267464
	Cairns LS;Marlow VL;Bissett E;Ostrowski A;Stanley-Wall NR A mechanical signal transmitted by the flagellum controls signalling in Bacillus subtilis. Mol Microbiol 90(1);6-21 (2013) PUBMED: 23888912
	Cairns LS;Martyn JE;Bromley K;Stanley-Wall NR An alternate route to phosphorylating DegU of Bacillus subtilis using acetyl phosphate. BMC Microbiol 15(1);78 (2015) PUBMED: 25887289
	Davidson FA;Seon-Yi C;Stanley-Wall NR Selective Heterogeneity in Exoprotease Production by Bacillus subtilis. PLoS One 7(6);e38574 (2012) PUBMED: 22745669
	Gupta M;Rao KK Phosphorylation of DegU is essential for activation of amyE expression in Bacillus subtilis. J Biosci 39(5);747-52 (2014) PUBMED: 25431404
	Hsueh YH;Cozy LM;Sham LT;Calvo RA;Gutu AD;Winkler ME;Kearns DB DegU-phosphate activates expression of the anti-sigma factor FlgM in Bacillus subtilis. Mol Microbiol 81(4);1092-108 (2011) PUBMED: 21736639
	Ishii H;Tanaka T;Ogura M The Bacillus subtilis response regulator gene degU is positively regulated by CcpA and by catabolite-repressed synthesis of ClpC. J Bacteriol 195(2);193-201 (2013) PUBMED: 23123903
	Kobayashi K Plant methyl salicylate induces defense responses in the rhizobacterium Bacillus subtilis. Environ Microbiol 17(4);1365-76 (2015) PUBMED: 25181478
	Kovacs AT Bacterial differentiation via gradual activation of global regulators. Curr Genet 62(1);125-8 (2016) PUBMED: 26458398
	Marlow VL;Cianfanelli FR;Porter M;Cairns LS;Dale JK;Stanley-Wall NR The prevalence and origin of exoprotease-producing cells in the Bacillus subtilis biofilm. Microbiology 160(Pt_1);56-66 (2014) PUBMED: 24149708
	Marlow VL;Porter M;Hobley L;Kiley TB;Swedlow JR;Davidson FA;Stanley-Wall NR Phosphorylated DegU Manipulates Cell Fate Differentiation in the Bacillus subtilis Biofilm. J Bacteriol 196(1);16-27 (2014) PUBMED: 24123822
	Miras M;Dubnau D A DegU-P and DegQ-Dependent Regulatory Pathway for the K-state in Bacillus subtilis. Front Microbiol 7;1868 (2016) PUBMED: 27920766
	Mordini S;Osera C;Marini S;Scavone F;Bellazzi R;Galizzi A;Calvio C The Role of SwrA, DegU and PD3 in fla/che Expression in B. subtilis. PLoS One 8(12);e85065 (2013) PUBMED: 24386445
	Ogura M;Tsukahara K SwrA regulates assembly of Bacillus subtilis DegU via its interaction with N-terminal domain of DegU. J Biochem 151(6);643-55 (2012) PUBMED: 22496484
	Ogura M;Yoshikawa H;Chibazakura T Regulation of the response regulator gene degU through the binding of SinR/SlrR and exclusion of SinR/SlrR by DegU in Bacillus subtilis. J Bacteriol 196(4);873-81 (2014) PUBMED: 24317403
	Ploss TN;Reilman E;Monteferrante CG;Denham EL;Piersma S;Lingner A;Vehmaanpera J;Lorenz P;van Dijl JM Homogeneity and heterogeneity in amylase production by Bacillus subtilis under different growth conditions. Microb Cell Fact 15;57 (2016) PUBMED: 27026185
	Tanaka K;Iwasaki K;Morimoto T;Matsuse T;Hasunuma T;Takenaka S;Chumsakul O;Ishikawa S;Ogasawara N;Yoshida K Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis. BMC Microbiol 15(1);43 (2015) PUBMED: 25880922
Comment	16.3: Control
Description	DegU two-component response regulator, phosphorylated;DegU two-component response regulator
Gene Ontology	GO:0000156 phosphorelay response regulator activity
	GO:0000160 phosphorelay signal transduction system
	GO:0003677 DNA binding
	GO:0003700 DNA-binding transcription factor activity
	GO:0005737 cytoplasm
	GO:0005829 cytosol
	GO:0006351 transcription, DNA-templated
	GO:0006355 regulation of transcription, DNA-templated
	GO:0035556 intracellular signal transduction
Locus Tag	BSU35490
Molecular weight	25.867
Name	degU

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	new_2701783_2703117, new_1253669_1254769, new_4159457_4159757_c, new_3153832_3153982_c, new_4194210_4195441_c, BSU13050, BSU17750, new_3421635_3422223_c, new_525021_528076_c, new_3154077_3154734_c
Expression pos. correlated with	BSU40960, new_3645297_3645378_c, BSU40970, BSU15290, BSU15280, BSU29610, BSU38860, BSU18990, BSU16960, BSU36250
Highly expressed condition	(BC) Cultures were inoculated from frozen glycerol stocks and grown overnight in LB at 37°C. These cultures were thendiluted, plated onto LB plates, and incubated for 16 h at 37°C. Cells were harvested from plates containing individual colonies [BI] andfrom plates with confluen growth [BC].
	(BI) Cultures were inoculated from frozen glycerol stocks and grown overnight in LB at 37°C. These cultures were thendiluted, plated onto LB plates, and incubated for 16 h at 37°C. Cells were harvested from plates containing individual colonies [BI] andfrom plates with confluen growth [BC].
	(HiOs) Cells were grown in Spizizen’s minimal medium (SMM) (C. Anagnostopoulos, J. Spizizen, J Bacteriol 81, 741, May, 1961) with vigorous agitation. The control culture was grown at 37 °C [SMMPr]. For growth at high or low temperatures, pre-cultures were grown at 37 °C, diluted to an OD578nm of 0.1 and subsequently transferred to 51 °C [HiTm] and 16 °C [LoTm], respectively. For the growth at high salinity, the salinity of the medium was adjusted by adding NaCl (5 M stock solution) to produce a final concentration of 1.2 M [HiOs].
	(HiTm) Cells were grown in Spizizen’s minimal medium (SMM) (C. Anagnostopoulos, J. Spizizen, J Bacteriol 81, 741, May, 1961) with vigorous agitation. The control culture was grown at 37 °C [SMMPr]. For growth at high or low temperatures, pre-cultures were grown at 37 °C, diluted to an OD578nm of 0.1 and subsequently transferred to 51 °C [HiTm] and 16 °C [LoTm], respectively. For the growth at high salinity, the salinity of the medium was adjusted by adding NaCl (5 M stock solution) to produce a final concentration of 1.2 M [HiOs].
	(LBtran) 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].
	(M40t45) 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].
	(MG+120) A culture of LB medium was inocualted from a frozen glycerol stock of B. subtilis. After few hours at 37oC when the culture was growing exponentially, this culture was used to inoculate M9 minimal medium at several different dilutions usually in the range of 500- to 2000-fold. The dilution range was chosen to ensure that at least one of these M9 precultures had reached an OD600 between 0.5 - 1.0 after overnight incubation. These precultures were then used to inoculate 2.5 L of M9 medium in a 3.1 L KLF bioreactor (Bioengineering AG, Wald, Switzerland) to a starting OD600 of 0.03 – 0.05. Condiions in the bioreactor were rigorously controlled as follows: temperature was controlled at 37 °C; the pH was maintained at exactly 7.2 by automatic titration with 2.0 M KOH and 2.0 M H2SO4, and the dissolved oxygen tension was maintained above 50%. In each nutritional shift experiment cells were grown on the single substrate until the OD600 reached 0.50, at which point the second substrate was added instantaneously (4 g/L L-malate or 3 g/L glucose). The nutrient shifts performed were from glucose to glucose+malate [GM] and from malate to malate+glucose [MG] (Buescher et al., accompanying paper). Cell growth during the course was monitored throughout the experiment by measuring OD600.
	(S2) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
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].
	(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].
	(dia5) 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
	(S4) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S5) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S6) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S7) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S8) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
Name	degU

KEGG Pathways

Description	Information
Pathway	Two-component system (ko02020)
	Quorum sensing (ko02024)

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