gabR
BSGatlas-gene-477
BSGatlas
Description | Information |
---|---|
Coordinates | 440025..441464 |
Genomic Size | 1440 bp |
Name | gabR |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | - |
Type | CDS |
SubtiWiki
Description | Information |
---|---|
Alternative Name | gabR |
gabR | |
ycnF | |
Category | SW 2 Metabolism |
SW 2.3 Amino acid/ nitrogen metabolism | |
SW 2.3.2 Utilization of amino acids | |
SW 2.3.2.10 Utilization of gamma-amino butyric acid | |
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 | |
Description | transcription activator of [[gene|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B]]-[[gene|A0BEB92D54799956A4ADE106A1388E5710141069]], repressor of [[gene|gabR ]]([SW|MocR/ GabR family]) |
Function | regulation of gamma-amino butyric acid utilization |
Is essential? | no |
Isoelectric point | 6.71 |
Locus Tag | BSU_03890 |
Molecular weight | 54.9994 |
Name | gabR |
Product | transcription regulator |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU03890 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 15223311, 24127574,25388514, 27640111, 28348215, 28412355; Product type r :regulator |
Locus Tag | BSU_03890 |
Name | gabR |
Title | transcriptional regulator (GntR/MocR family)with PLP binding site (GabR-GABA-PLP aldimine) |
Type | CDS |
BsubCyc
Description | Information |
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Alternative Name | ycnF |
Citation | Al-Zyoud WA;Hynson RM;Ganuelas LA;Coster AC;Duff AP;Baker MA;Stewart AG;Giannoulatou E;Ho JW;Gaus K;Liu D;Lee LK;Bocking T Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Res 44(3);1411-20 (2016) PUBMED: 26681693 |
Amidani D;Tramonti A;Canosa AV;Campanini B;Maggi S;Milano T;di Salvo ML;Pascarella S;Contestabile R;Bettati S;Rivetti C Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor. Biochim Biophys Acta 1861(1 Pt A);3474-3489 (2017) PUBMED: 27640111 | |
Belitsky BR;Sonenshein AL GabR, a member of a novel protein family, regulates the utilization of gamma-aminobutyrate in Bacillus subtilis. Mol Microbiol 45(2);569-83 (2002) PUBMED: 12123465 | |
Belitsky BR Bacillus subtilis GabR, a protein with DNA-binding and aminotransferase domains, is a PLP-dependent transcriptional regulator. J Mol Biol 340(4);655-64 (2004) PUBMED: 15223311 | |
Okuda K;Kato S;Ito T;Shiraki S;Kawase Y;Goto M;Kawashima S;Hemmi H;Fukada H;Yoshimura T Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator. Mol Microbiol 95(2);245-57 (2015) PUBMED: 25388514 | |
Comment | GabR regulates transcription of the gabTD operon in response to the availability of GABA and PLP and negatively autoregulates its own expression |CITS: [12123465][15223311]|. Crystal structures of apo-GabR and GabR in a complex with PLP show that the protein forms a head-to-tail domain-swapped homodimer with an N-terminal winged-helix DNA-binding domain and a C-terminal type 1 aminotransferase-like domain that binds PLP |CITS: [24127574]|. Dimerization via the C-terminal domain appears to enable DNA-binding by the N-terminal domain |CITS: [25911692]|. The DNA binding mechanism of GabR was further investigated by SAXS, suggesting a role for the shape of the bridging sequence between the two cognate binding sites |CITS: [26681693]|. GabR binding causes an 80° bend in DNA |CITS: [27640111]|. Activation of gabTD transcription is likely due to a rearrangement of GabR promoter binding that is due to a conformational change when GABA forms an external aldimine with PLP in GabR |CITS: [25388514]|. |
Description | transcriptional dual regulator GabR (GntR/MocR family) |
Gene Ontology | GO:0000984 bacterial-type RNA polymerase regulatory region sequence-specific DNA binding |
GO:0000986 bacterial-type proximal promoter sequence-specific DNA binding | |
GO:0003677 DNA binding | |
GO:0003700 DNA-binding transcription factor activity | |
GO:0003824 catalytic activity | |
GO:0006351 transcription, DNA-templated | |
GO:0006355 regulation of transcription, DNA-templated | |
GO:0008483 transaminase activity | |
GO:0009058 biosynthetic process | |
GO:0016740 transferase activity | |
GO:0030170 pyridoxal phosphate binding | |
GO:0042803 protein homodimerization activity | |
GO:0044374 sequence-specific DNA binding, bending | |
GO:0045892 negative regulation of transcription, DNA-templated | |
GO:0045893 positive regulation of transcription, DNA-templated | |
GO:0051171 regulation of nitrogen compound metabolic process | |
Locus Tag | BSU03890 |
Molecular weight | 55.166 |
Name | gabR |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | BSU22520, new_2459114_2459288, new_1077024_1077320_c, BSU21950, new_1569226_1569349_c, BSU15090, BSU28110, new_2329450_2329514_c, BSU06920, BSU25120 |
Expression pos. correlated with | BSU05260, BSU08250, BSU24180, BSU38370, BSU40350, new_574025_574105_c, BSU10880, BSU23990, BSU05280, BSU04040 |
Highly expressed condition | (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 | |
(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]. | |
(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]. | |
(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 . | |
(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]. | |
(MG+60) 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. | |
(S1) 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. | |
(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. | |
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]. | |
(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]. | |
(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 . | |
(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]. | |
(Pyr) 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. | |
(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. | |
(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. | |
Name | gabR |