BSGatlas

sigB

BSGatlas-gene-573

BSGatlas

Description	Information
Coordinates	522862..523650
Genomic Size	789 bp
Name	sigB
Outside Links	SubtiWiki
	BsubCyc
Strand	+
Type	CDS

SubtiWiki

Description	Information
Alternative Name	rpoF
	sigB
	sigB
Category	SW 3 Information processing
	SW 3.2 RNA synthesis and degradation
	SW 3.2.1 Transcription
	SW 3.2.1.2 Sigma factors
	SW 3.4 Regulation of gene expression
	SW 3.4.1 Sigma factors and their control
	SW 3.4.1.1 Sigma factors
	SW 4 Lifestyles
	SW 4.3 Coping with stress
	SW 4.3.1 General stress proteins (controlled by SigB)
Description	[SW\|RNA polymerase] [SW\|sigma factor] [[protein\|580011DE5DC40EC9E7E0512791D328FAA010DCB8]]
Function	general stress response, biocontrol of fungal growth
Is essential?	no
Isoelectric point	5.42
Locus Tag	BSU_04730
Molecular weight	29.9946
Name	sigB
Product	[SW\|RNA polymerase] [SW\|sigma factor] [[protein\|580011DE5DC40EC9E7E0512791D328FAA010DCB8]]

RefSeq

Description	Information
Alternative Locus Tag	BSU04730
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 15312768, 15805528,16077134, 16267279, 16321960, 17158665, 28271471; Producttype r: regulator
Functions	16.3: Control
	16.8: Protect
Locus Tag	BSU_04730
Name	sigB
Title	RNA polymerase sigma-37 factor (sigma(B))
Type	CDS

BsubCyc

Description	Information
Alternative Name	rpoF
Citation	Blom EJ;Ridder AN;Lulko AT;Roerdink JB;Kuipers OP Time-Resolved Transcriptomics and Bioinformatic Analyses Reveal Intrinsic Stress Responses during Batch Culture of Bacillus subtilis. PLoS One 6(11);e27160 (2011) PUBMED: 22087258
	Kuo HH;Huang WC;Lin TF;Yeh HY;Liou KM;Chang BY The core-independent promoter-specific binding of Bacillus subtilis σB. FEBS J 282(7);1307-18 (2015) PUBMED: 25652417
	Liebal UW;Sappa PK;Millat T;Steil L;Homuth G;Volker U;Wolkenhauer O Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis. Mol Biosyst 8(6);1806-14 (2012) PUBMED: 22511268
	Locke JC;Young JW;Fontes M;Hernandez Jimenez MJ;Elowitz MB Stochastic pulse regulation in bacterial stress response. Science 334(6054);366-9 (2011) PUBMED: 21979936
	Mars RA;Mendonca K;Denham EL;van Dijl JM The reduction in small ribosomal subunit abundance in ethanol-stressed cells of Bacillus subtilis is mediated by a SigB-dependent antisense RNA. Biochim Biophys Acta 1853(10 Pt A);2553-9 (2015) PUBMED: 26115952
	Nannapaneni P;Hertwig F;Depke M;Hecker M;Mader U;Volker U;Steil L;van Hijum SA Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. Microbiology 158(Pt 3);696-707 (2012) PUBMED: 22174379
	Narula J;Tiwari A;Igoshin OA Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks. PLoS Comput Biol 12(12);e1005267 (2016) PUBMED: 27977677
	Reder A;Hoper D;Gerth U;Hecker M Contributions of individual σB-dependent general stress genes to oxidative stress resistance of Bacillus subtilis. J Bacteriol 194(14);3601-10 (2012) PUBMED: 22582280
	Ringus DL;Gaballa A;Helmann JD;Wiedmann M;Boor KJ Fluoro-phenyl-styrene-sulfonamide, a novel inhibitor of σB activity, prevents the activation of σB by environmental and energy stresses in Bacillus subtilis. J Bacteriol 195(11);2509-17 (2013) PUBMED: 23524614
	Waters SM;Robles-Martinez JA;Nicholson WL Exposure of Bacillus subtilis to low pressure (5 kilopascals) induces several global regulons, including those involved in the SigB-mediated general stress response. Appl Environ Microbiol 80(16);4788-94 (2014) PUBMED: 24878601
	Young JW;Locke JC;Elowitz MB Rate of environmental change determines stress response specificity. Proc Natl Acad Sci U S A 110(10);4140-5 (2013) PUBMED: 23407164
	Yu WB;Ye BC Transcriptional Profiling Analysis of Bacillus subtilis in Response to High Levels of Fe(3.). Curr Microbiol 72(6);653-62 (2016) PUBMED: 26858131
Comment	16.8: Protect 16.3: Control
Description	RNA polymerase sigma-37 factor (sigma(B))
Gene Ontology	GO:0000303 response to superoxide
	GO:0003677 DNA binding
	GO:0003700 DNA-binding transcription factor activity
	GO:0006351 transcription, DNA-templated
	GO:0006352 DNA-templated transcription, initiation
	GO:0006355 regulation of transcription, DNA-templated
	GO:0006950 response to stress
	GO:0016987 sigma factor activity
	GO:0042542 response to hydrogen peroxide
	GO:0043620 regulation of DNA-templated transcription in response to stress
Locus Tag	BSU04730
Molecular weight	29.901
Name	sigB

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU22000, BSU29930, BSU27420, BSU22900, BSU13400, new_2396720_2396797_c, new_1525061_1525238_c, BSU13410, BSU32340, new_2310988_2311968
Expression pos. correlated with	BSU04720, BSU04740, BSU04710, BSU39810, BSU08570, BSU37240, new_929322_929389, BSU07750, BSU02830, BSU04340
Highly 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].
	(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].
	(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.
	(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].
	(LoTm) 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].
	(LPhT) 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.
	(Sw) Exponentially growing cells were spotted on 1 % agar LB plates and incubated at 37°C. Swarming cells were collected after 16 hours.
Lowely expressed condition	(ferm) Cells were grown in a synthetic medium (E. Härtig, A. Hartmann, M. Schätzle, A. M. Albertini, D. Jahn, Appl Environ Microbiol 72, 5260, 2006) at 37 °C. For aerobic growth, an overnight culture was used to inoculate 100 ml of the synthetic medium to a starting OD578 of 0.05. The culture was then incubated in a 500 ml baffled flask with shaking at 250 rpm [aero]. Anaerobic growth was carried out (i) in the presence of 10 mM potassium nitrate (nitrate respiration) [nit]; or (ii) in the absence of 10 mM postassium nitrate (fermentative growth) [ferm]. The procedure for anaerobic growth was: medium was inoculated to an OD578 nm of 0.1 in flasks completely filled with medium and sealed with rubber stoppers. They were shaken at 100 rpm to minimize cell aggregation. These cultures were inoculated aerobically with an aerobically grown overnight culture. Anaerobic conditions were achieved in the stoppered flasks after a short time through the consumption of residual oxygen. Cells were harvested during the exponential growth phase.
	(S3) 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.
	(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.
	(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	sigB

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