gerD
BSGatlas-gene-203
BSGatlas
Description | Information |
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Coordinates | 158515..159072 |
Genomic Size | 558 bp |
Name | gerD |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | - |
Type | CDS |
SubtiWiki
Description | Information |
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Alternative Name | gerD |
Category | SW 4 Lifestyles |
SW 4.2 Sporulation | |
SW 4.2.4 Germination | |
SW 4.2.4.2 Additional germination proteins | |
SW 6 Groups of genes | |
SW 6.2 Membrane proteins | |
Description | scaffold of the germinosome, required for clustering of germinant receptors in the spore inner membrane |
Function | germination |
Is essential? | no |
Isoelectric point | 4.86 |
Locus Tag | BSU_01550 |
Molecular weight | 20.971 |
Name | gerD |
Product | lipoprotein |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU01550 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 17122337, 10618233,10376819, 24530795; Product type f: factor |
Functions | 16.13: Shape |
16.3: Control | |
Locus Tag | BSU_01550 |
Name | gerD |
Title | lipoprotein factor mediating clustering ofgermination proteins |
Type | CDS |
BsubCyc
Description | Information |
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Citation | Chen Y;Ray WK;Helm RF;Melville SB;Popham DL Levels of Germination Proteins in Bacillus subtilis Dormant, Superdormant, and Germinating Spores. PLoS One 9(4);e95781 (2014) PUBMED: 24752279 |
Cheung HY;Cui J;Sun S Real-time monitoring of Bacillus subtilis endospore components by attenuated total reflection Fourier-transform infrared spectroscopy during germination. Microbiology 145 ( Pt 5);1043-8 (1999) PUBMED: 10376819 | |
Doona CJ;Ghosh S;Feeherry FF;Ramirez-Peralta A;Huang Y;Chen H;Setlow P High pressure germination of Bacillus subtilis spores with alterations in levels and types of germination proteins. J Appl Microbiol 117(3);711-20 (2014) PUBMED: 24891141 | |
Korza G;Setlow P Topology and Accessibility of Germination Proteins in the Bacillus subtilis Spore Inner Membrane. J Bacteriol 195(7);1484-91 (2013) PUBMED: 23335419 | |
Li Y;Jin K;Ghosh S;Devarakonda P;Carlson K;Davis A;Stewart KA;Cammett E;Rossi PP;Setlow B;Lu M;Setlow P;Hao B Structural and Functional Analysis of the GerD Spore Germination Protein of Bacillus Species. J Mol Biol 426(9);1995-2008 (2014) PUBMED: 24530795 | |
Luu S;Cruz-Mora J;Setlow B;Feeherry FE;Doona CJ;Setlow P The Effects of Heat Activation on Nutrient and High-Pressure Germination of Spores of Bacillus Species With and Without Various Germination Proteins. Appl Environ Microbiol (2015) PUBMED: 25681191 | |
Ramirez-Peralta A;Zhang P;Li YQ;Setlow P Effects of sporulation conditions on the germination and germination protein levels of Bacillus subtilis spores. Appl Environ Microbiol 78(8);2689-97 (2012) PUBMED: 22327596 | |
Stewart KA;Setlow P Numbers of individual nutrient germinant receptors and other germination proteins in spores of Bacillus subtilis. J Bacteriol 195(16);3575-82 (2013) PUBMED: 23749970 | |
Stewart KA;Yi X;Ghosh S;Setlow P Germination protein levels and rates of germination of spores of Bacillus subtilis with overexpressed or deleted genes encoding germination proteins. J Bacteriol 194(12);3156-64 (2012) PUBMED: 22493018 | |
Troiano AJ;Zhang J;Cowan AE;Yu J;Setlow P Analysis of the Dynamics of a Bacillus subtilis Spore Germination Protein Complex during Spore Germination and Outgrowth. J Bacteriol 197(2);252-61 (2015) PUBMED: 25349160 | |
Wang G;Yi X;Li YQ;Setlow P Germination of individual Bacillus subtilis spores with alterations in the GerD and SpoVA proteins, which are important in spore germination. J Bacteriol 193(9);2301-11 (2011) PUBMED: 21398556 | |
Wuytack EY;Soons J;Poschet F;Michiels CW Comparative study of pressure- and nutrient-induced germination of Bacillus subtilis spores. Appl Environ Microbiol 66(1);257-61 (2000) PUBMED: 10618233 | |
Comment | GerD is required for normal germination of B. subtilis spores in media containing nutrient germinants such as L-alanine or asparagine, glucose, and fructose |CITS: [110906][17122337]|. GerD is located in the inner membrane of B. subtilis spores |CITS: [18556788][19332816]|, most often in one discrete location per spore, and is required for clustering of germinant receptors |CITS: [21696470]|. GerD has a predicted signal sequence and lipidation site. Mutagenesis of this site reduces function of GerD |CITS: [2517635][17122337][18556788][19332816]|. One or more strains containing mutant alleles of this gene can be obtained from the Bacillus Genetic Stock Center. Click here to see the list of available strains at BGSC. |
Description | lipoprotein with a role in spores' rapid response to nutrient germinants |
Gene Ontology | GO:0005886 plasma membrane |
GO:0009847 spore germination | |
GO:0016020 membrane | |
Locus Tag | BSU01550 |
Molecular weight | 21.117 |
Name | gerD |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | BSU02120, BSU10640, BSU10630, BSU06330, new_1143506_1143576, BSU10620, BSU05000, BSU31170, BSU31400, BSU35480 |
Expression pos. correlated with | BSU05890, BSU05899, BSU06559, BSU03930, BSU03920, BSU29910, BSU08640, BSU28660, new_600145_600228_c, BSU05530 |
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]. |
(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. | |
(nit) 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. | |
(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 | (GM+10) 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. |
(GM+5) 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. | |
(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 | |
(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 . | |
(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]. | |
(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]. | |
(Mal) 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. | |
(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. | |
Name | gerD |