sigF
BSGatlas-gene-2757
BSGatlas
Description | Information |
---|---|
Coordinates | 2443429..2444196 |
Genomic Size | 768 bp |
Name | sigF |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | - |
Type | CDS |
SubtiWiki
Description | Information |
---|---|
Alternative Name | sigF |
sigF | |
spoIIAC | |
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 4.2 Sporulation | |
SW 4.2.1 Sporulation proteins | |
SW 4.2.1.4 Sporulation proteins/ other | |
Description | [SW|RNA polymerase] forespore-specific (early) [SW|sigma factor] SigF |
Function | transcription of [SW|sporulation] genes (early forespore) |
Is essential? | no |
Isoelectric point | 5.08 |
Locus Tag | BSU_23450 |
Molecular weight | 29.2227 |
Name | sigF |
Product | [SW|RNA polymerase] forespore-specific (early) [SW|sigma factor] SigF |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU23450 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 9891799, 15187183,15205417, 15819616, 16045607, 22115775, 23169620,24067622, 26506528; Product type cp: cell process |
Functions | 16.3: Control |
16.5: Explore | |
Locus Tag | BSU_23450 |
Name | sigF |
Title | RNA polymerase sporulation-specific sigma factor(sigma-F) |
Type | CDS |
BsubCyc
Description | Information |
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Alternative Name | spoIIAC |
Citation | Bradshaw N;Losick R Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase. Elife 4 (2015) PUBMED: 26465112 |
Fengos G;Iber D Prediction stability in a data-based, mechanistic model of σF regulation during sporulation in Bacillus subtilis. Sci Rep 3;2755 (2013) PUBMED: 24067622 | |
Fimlaid KA;Shen A Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. Curr Opin Microbiol 24;88-95 (2015) PUBMED: 25646759 | |
Iber D Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case. Adv Bioinformatics 2011;124062 (2011) PUBMED: 22312331 | |
Narula J;Devi SN;Fujita M;Igoshin OA Ultrasensitivity of the Bacillus subtilis sporulation decision. Proc Natl Acad Sci U S A 109(50);E3513-22 (2012) PUBMED: 23169620 | |
Overkamp W;Kuipers OP Transcriptional Profile of Bacillus subtilis sigF-Mutant during Vegetative Growth. PLoS One 10(10);e0141553 (2015) PUBMED: 26506528 | |
Serrano M;Real G;Santos J;Carneiro J;Moran CP;Henriques AO A negative feedback loop that limits the ectopic activation of a cell type-specific sporulation sigma factor of Bacillus subtilis. PLoS Genet 7(9);e1002220 (2011) PUBMED: 21935351 | |
Comment | 16.5: Explore 16.3: Control |
Description | RNA polymerase sporulation-specific sigma factor (sigma-F) |
Gene Ontology | 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:0016987 sigma factor activity | |
GO:0030435 sporulation resulting in formation of a cellular spore | |
Locus Tag | BSU23450 |
Molecular weight | 29.372 |
Name | sigF |
Nicolas et al. predictions
Description | Information |
---|---|
Expression neg. correlated with | new_613552_613640, BSU05680, BSU38540, BSU03250, new_3105044_3105139_c, BSU11180, BSU37570, BSU37580, BSU03240, new_1868453_1868560 |
Expression pos. correlated with | BSU23460, BSU23470, BSU08670, new_3032370_3032416_c, BSU29630, BSU22280, BSU38080, BSU02240, BSU15320, BSU24360 |
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]. |
(M9stat) Cells were grown in M9 supplemented with glucose (0.3 %) at 37°C with vigorous shaking. The composition of the M9 minimal medium is (per liter): 8.5 g Na2HPO4.2H20, 3 g KH2PO4, 1 g NH4Cl and 0.5 g NaCl. The following solutions were individually sterilized and added (volumes per liter of medium): 1 ml 0.1 M CaCl2.2H2O, 1 ml 1 M MgSO4.7H2O, 1 ml 50 mM Fe-Citrate. Also added was 10 ml of a trace salts solution containing (per liter): 170 mg ZnCl2, 100 mg MnCl2.4H2O, 60 mg CoCl2.6H2O, 60 mg Na2MoO4.2H2O and 43 mg CuCl2.2H2O. Overnight cultures were diluted 2000-fold in pre-warmed M9 medium and samples were harvested during exponential growth [M9exp], at the transition phase [M9tran] and during stationary phase [M9stat]. | |
(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. | |
(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. | |
(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. | |
(T4.0H) 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]. | |
(T5.0H) 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 | (C30) Cellsgrown overnight on LB agar plates at 30°Cwere harvested and used to inoculate pre-warmed minimal medium at OD600 of 0.5 (D. Dubnau, R. Davidoff-Abelson, J Mol Biol 56, 209, Mar 14, 1971). After growth at 37°C with vigorous shaking, cells were diluted ten times in fresh pre-warmed minimal medium and samples were harvested after a period of 30 minutes [C30] , i.e. before maximal induction of competence, and after a period of 90 minutes [C90], i.e. when competence induction was maximal. |
(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 | |
(G135) 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]. | |
(G150) 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]. | |
(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 | |
(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 | |
Name | sigF |