BSGatlas

dxs

BSGatlas-gene-2849

BSGatlas

Description	Information
Coordinates	2523713..2525614
Genomic Size	1902 bp
Name	dxs
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	dxs
	dxs
	yqiE
Category	SW 2 Metabolism
	SW 2.4 Lipid metabolism
	SW 2.4.2 Biosynthesis of lipids
	SW 2.4.2.3 Biosynthesis of isoprenoids
	SW 2.6 Additional metabolic pathways
	SW 2.6.2 Biosynthesis of cofactors
	SW 2.6.2.3 Biosynthesis/ acquisition of thiamine
	SW 6 Groups of genes
	SW 6.1 Essential genes
Description	1-deoxyxylulose-5-phosphate synthase, first step in the MEP pathway of isoprenoid biosynthesis
Enzyme Classifications	EC 2.2.1.7: 1-deoxy-D-xylulose-5-phosphate synthase
Function	biosynthesis of thiamine, MEP pathway of isoprenoid biosynthesis
Is essential?	yes
Isoelectric point	6
Locus Tag	BSU_24270
Molecular weight	69.3804
Name	dxs
Product	1-deoxyxylulose-5-phosphate synthase

RefSeq

Description	Information
Alternative Locus Tag	BSU24270
Description	Evidence 2a: Function from experimental evidencesin other organisms; PubMedId: 12682299, 12882400,15292217, 17458547, 23840410, 25212876; Product type e :enzyme
Enzyme Classifications	EC 2.2.1.7: 1-deoxy-D-xylulose-5-phosphate synthase
Functions	16.2: Construct biomass (Anabolism)
Locus Tag	BSU_24270
Name	dxs
Title	1-deoxyxylulose-5-phosphate synthase
Type	CDS

BsubCyc

Description	Information
Alternative Name	yqiE
Citation	Hess BM;Xue J;Markillie LM;Taylor RC;Wiley HS;Ahring BK;Linggi B Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics. PLoS One 8(6);e66104 (2013) PUBMED: 23840410
	Kudoh K;Kubota G;Fujii R;Kawano Y;Ihara M Exploration of the 1-deoxy-d-xylulose 5-phosphate synthases suitable for the creation of a robust isoprenoid biosynthesis system. J Biosci Bioeng (2016) PUBMED: 27856234
Comment	\|FRAME: BSU24270-MONOMER\| (Dxs) catalyzes the thiamin diphosphate-dependent reaction that condenses pyruvate and D-glyceraldehyde-3-phosphate to yield \|FRAME: DEOXYXYLULOSE-5P\| \|CITS: [17458547]\|. This is the first, rate-limiting step in the \|FRAME: NONMEVIPP-PWY\| of isoprenoid biosynthesis, and is believed to feed into the pyridoxal 5-phosphate (vitamin B6) and thiamin (vitamin B1) biosynthesis pathways. Overexpression of dxs resulted in a yield of isoprene that was 40% over that produced by the wild-type strain \|CITS: [21296950]\|. A study of the \|FRAME: TAX-1423\| enzyme suggested that it may not be involved in pyridoxal 5-phosphate biosynthesis \|CITS: [12882400]\|. A linkage between Dxs and thiamin biosynthesis has been established in other organisms \|CITS: [15292217]\| but not yet in B. subtilis.
Description	1-deoxyxylulose-5-phosphate synthase
Enzyme Classifications	EC 2.2.1.7: 1-deoxy-D-xylulose-5-phosphate synthase
Gene Ontology	GO:0000287 magnesium ion binding
	GO:0003824 catalytic activity
	GO:0008152 metabolic process
	GO:0008299 isoprenoid biosynthetic process
	GO:0008661 1-deoxy-D-xylulose-5-phosphate synthase activity
	GO:0009228 thiamine biosynthetic process
	GO:0016114 terpenoid biosynthetic process
	GO:0016740 transferase activity
	GO:0030976 thiamine pyrophosphate binding
	GO:0046872 metal ion binding
	GO:0052865 1-deoxy-D-xylulose 5-phosphate biosynthetic process
Locus Tag	BSU24270
Molecular weight	69.559
Name	dxs

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU11260, new_1399409_1400187, BSU13360, new_1912142_1913240_c, BSU40280, BSU19820, BSU10610, BSU09740, BSU32850, BSU23410
Expression pos. correlated with	BSU24260, BSU17050, BSU00040, BSU28590, BSU06330, BSU06340, BSU16780, BSU40370, BSU40380, BSU08425
Highly expressed condition	(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].
	(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.
	(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
	(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 .
	(LBGtran) 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 .
	(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	(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].
	(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.
	(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.
	(T0.30H) 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].
	(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].
Name	dxs

KEGG Pathways

Description	Information
Pathway	Thiamine metabolism (ko00730)
	Terpenoid backbone biosynthesis (ko00900)
	Metabolic pathways (ko01100)
	Biosynthesis of secondary metabolites (ko01110)

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