BSGatlas

yfkS

BSGatlas-gene-945

BSGatlas

Description	Information
Coordinates	847282..847482
Genomic Size	201 bp
Name	yfkS
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	yfkS
Category	SW 4 Lifestyles
	SW 4.2 Sporulation
	SW 4.2.5 Germination/ based on similarity
	SW 4.3 Coping with stress
	SW 4.3.1 General stress proteins (controlled by SigB)
	SW 4.3.8 Resistance against oxidative and electrophile stress
	SW 6 Groups of genes
	SW 6.2 Membrane proteins
Description	D protein for the [[protein\|7CE0CAF27B1C0F507E783B8B80622270B00634FD]]-[[protein\|B7EEC1910715507596734540D24B3C93B4B7065F]]-[[protein\|7A62875A659B9F0967C392F38895D9E15A29D559]] germinant receptor of unknown specificity, general stress protein, survival of ethanol and paraquat stresses
Function	germination, survival of of stress conditions
Is essential?	no
Isoelectric point	10.01
Locus Tag	BSU_07770
Molecular weight	7.6654
Name	yfkS
Product	D protein for the [[protein\|7CE0CAF27B1C0F507E783B8B80622270B00634FD]]-[[protein\|B7EEC1910715507596734540D24B3C93B4B7065F]]-[[protein\|7A62875A659B9F0967C392F38895D9E15A29D559]] germinant receptor

RefSeq

Description	Information
Alternative Locus Tag	BSU07770
Description	Evidence 3: Putative function from multiplecomputational evidences; PubMedId: 23625846; Product typerc: receptor
Locus Tag	BSU_07770
Name	yfkS
Title	putative spore germination D protein
Type	CDS

BsubCyc

Description	Information
Citation	Ramirez-Peralta A;Gupta S;Butzin XY;Setlow B;Korza G;Leyva-Vazquez MA;Christie G;Setlow P Identification of New Proteins that Modulate the Germination of Spores of Bacillus Species. J Bacteriol (2013) PUBMED: 23625846
	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
Description	hypothetical protein
Gene Ontology	GO:0000303 response to superoxide
	GO:0016020 membrane
	GO:0016021 integral component of membrane
Locus Tag	BSU07770
Molecular weight	7.801
Name	yfkS

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU22720, BSU36250, BSU31410, BSU40970, BSU31400, BSU40960, BSU14080, new_1482096_1482247, BSU18800, new_3809370_3809496_c
Expression pos. correlated with	BSU07760, BSU07780, BSU07790, BSU35810, BSU35820, BSU33070, BSU25730, BSU37200, BSU38440, BSU33060
Highly 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.
	(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].
	(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.
	(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	(GM+15) 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+150) 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+45) 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+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.
	(HPh) 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].
	(MG-0.1) 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.
	(MG+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.
	(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.
	(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.
	(T-3.40H) 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	yfkS

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