BSGatlas

xynC

BSGatlas-gene-2136

BSGatlas

Description	Information
Coordinates	1942714..1943982
Genomic Size	1269 bp
Name	xynC
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	xynC
	xynC
	ynfF
Category	SW 2 Metabolism
	SW 2.2 Carbon metabolism
	SW 2.2.2 Utilization of specific carbon sources
	SW 2.2.2.27 Utilization of other polymeric carbohydrates
	SW 6 Groups of genes
	SW 6.12 Secreted proteins
Description	endo-xylanase, preference for methylglucurono-xylan
Enzyme Classifications	EC 3.2.1.136: glucuronoarabinoxylan endo-1,4-beta-xylanase
Function	xylan degradation
Is essential?	no
Isoelectric point	9.08
Locus Tag	BSU_18150
Molecular weight	47.1747
Name	xynC
Product	endo-xylanase

RefSeq

Description	Information
Alternative Locus Tag	BSU18150
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 17028274, 25355936,26559526, 28330222; Product type e: enzyme
Enzyme Classifications	EC 3.2.1.136: glucuronoarabinoxylan endo-1,4-beta-xylanase
Functions	16.11: Scavenge (Catabolism)
Locus Tag	BSU_18150
Name	xynC
Title	secreted endo-xylanase
Type	CDS

BsubCyc

Description	Information
Alternative Name	ynfF
Citation	Rhee MS;Wei L;Sawhney N;Kim YS;Rice JD;Preston JF Metabolic potential of Bacillus subtilis 168 for the direct conversion of xylans to fermentation products. Appl Microbiol Biotechnol 100(3);1501-10 (2016) PUBMED: 26559526
	Rhee MS;Wei L;Sawhney N;Rice JD;St John FJ;Hurlbert JC;Preston JF Engineering the xylan utilization system in Bacillus subtilis for production of acidic Xylooligosaccharides. Appl Environ Microbiol 80(3);917-27 (2014) PUBMED: 24271172
	St John FJ;Dietrich D;Crooks C;Pozharski E;Gonzalez JM;Bales E;Smith K;Hurlbert JC A novel member of glycoside hydrolase family 30 subfamily 8 with altered substrate specificity. Acta Crystallogr D Biol Crystallogr 70(Pt 11);2950-8 (2014) PUBMED: 25372685
Comment	The cell wall of \|FRAME: TAX-4577\| contains a feruloylated arabinoxylan polymer known as feraxan. The polymer's backbone often contains additional side chains composed of 4-methyl-glucutonate residues, forming \|FRAME: Glucuronoarabinoxylans\|. Three β-xylan xylanohydrolases capable of dissociating Zea mays ferulated arabinoxylan were purified from a \|FRAME: TAX-1423\| industrial enzyme preparation \|CITS: [16666240]\|. All three enzymes exhibited optimum activities between pH 6.5 and 7.0 and had common molecular weights of 45 kDa. The ebzymes liberated oligomeric fragments that accounted for 76% of the ferulic acid, 96% of the arabinose, 71% of the xylose, 27% of the galactose, 50% of the uronic acid, and 4% of the glucose of the feraxan \|CITS: [16666240]\|, and about 20% (dry weight basis) of the total maize wall preparation \|CITS: [16667004]\|. They did not degrade larch arabinoxylan and Rhodymenia xylan \|CITS: [16666240]\|. Another study reported a \|FRAME: TAX-1423\| enzyme that cleaved \|FRAME: Glucuronoxylans glucuronoxylans\| derived from Vigna cell walls as well as \|FRAME: Glucuronoarabinoxylans glucuronoarabinoxylans\| derived from maize cell walls. The enzyme recognized glucuronosyl moieties inserted as monomeric side chains along the xylan backbone, and mediated the hydrolysis of the beta-(1→4)-xylosyl linkage on the reducing side of an adjacent unsubstituted xylosyl residue, forming products containing a single glucuronosyl side chain and a single unsubstituted β 1→4Xyl pendant terminal \|CITS: [1901062]\|. In a much later study, the \|FRAME: BSU18150\| gene of \|FRAME: TAX-224308\|, which encodes a glycosyl hydrolase family 5 (GH5) protein, was cloned as an N-terminal His tag fusion, overexpressed in E. coli and purified \|CITS: [17028274]\|. The purified recombinant protein catalyzed the same reaction as the one described above, i.e. the exclusive cleavage of a β-1,4-xylosidic bond penultimate to that linking carbon one of the xylose residue that is substituted with α-1,2-linked 4-methyl-glucuronate. Thus the \|FRAME: BSU18150\| gene most likely encodes the protein characterized by \|CITS: [1901062]\|.
Description	glucuronoarabinoxylan endo-1,4-β-xylanase
Enzyme Classifications	EC 3.2.1.136: glucuronoarabinoxylan endo-1,4-beta-xylanase
Gene Ontology	GO:0000272 polysaccharide catabolic process
	GO:0004348 glucosylceramidase activity
	GO:0005576 extracellular region
	GO:0005975 carbohydrate metabolic process
	GO:0006665 sphingolipid metabolic process
	GO:0008152 metabolic process
	GO:0016787 hydrolase activity
	GO:0016798 hydrolase activity, acting on glycosyl bonds
	GO:0033940 glucuronoarabinoxylan endo-1,4-beta-xylanase activity
	GO:0045493 xylan catabolic process
Locus Tag	BSU18150
Molecular weight	47.337
Name	xynC

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU15450, new_2886135_2886266_c, BSU_tRNA_30, new_3849617_3849712_c, new_343495_343573, BSU33330, BSU12850, new_1240279_1240355, BSU37500, new_1255867_1256041_c
Expression pos. correlated with	new_1943983_1944112_c, BSU18160, new_1945655_1945976_c, BSU26890, BSU17690, BSU20580, new_1269672_1269732_c, BSU26930, BSU26920, BSU18370
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].
	(BI) 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].
	(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 .
	(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 .
	(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].
	(Sw) Exponentially growing cells were spotted on 1 % agar LB plates and incubated at 37°C. Swarming cells were collected after 16 hours.
	(T1.30H) 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].
	(T2.0H) 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].
	(T2.30H) 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].
Lowely expressed condition	(Cold) 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].
	(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].
	(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].
	(Glucon) 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.
	(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
	(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-0.2) 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.
	(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.
Name	xynC

Fullscreen (Open in UCSC browser US | EU )