BSGatlas

ytvA

BSGatlas-gene-3546

BSGatlas

Description	Information
Coordinates	3106210..3106995
Genomic Size	786 bp
Name	ytvA
Outside Links	SubtiWiki
	BsubCyc
Strand	+
Type	CDS

SubtiWiki

Description	Information
Alternative Name	ytvA
Category	SW 3 Information processing
	SW 3.4 Regulation of gene expression
	SW 3.4.1 Sigma factors and their control
	SW 3.4.1.2 Control of sigma factors
Description	blue light sensor, positive regulation of [[protein\|580011DE5DC40EC9E7E0512791D328FAA010DCB8]] activity under conditions of blue light
Function	control of [[protein\|580011DE5DC40EC9E7E0512791D328FAA010DCB8]] activity
Is essential?	no
Isoelectric point	4.69
Locus Tag	BSU_30340
Molecular weight	29.044
Name	ytvA
Product	blue light receptor, flavoprotein

RefSeq

Description	Information
Alternative Locus Tag	BSU30340
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 11964249, 16923906,16923909, 17200735, 17443319, 17575448, 19948797,21259411, 21851109, 23416074, 24171435, 25211155,27203230, 28502782, 28632317; Product type rc: receptor
Functions	16.12: Sense
	16.3: Control
Locus Tag	BSU_30340
Name	blrA
Title	blue light GTP-binding receptor
Type	CDS

BsubCyc

Description	Information
Citation	Diensthuber RP;Bommer M;Gleichmann T;Moglich A Full-length structure of a sensor histidine kinase pinpoints coaxial coiled coils as signal transducers and modulators. Structure 21(7);1127-36 (2013) PUBMED: 23746806
	Dorn M;Jurk M;Wartenberg A;Hahn A;Schmieder P LOV Takes a Pick: Thermodynamic and Structural Aspects of the Flavin-LOV-Interaction of the Blue-Light Sensitive Photoreceptor YtvA from Bacillus subtilis. PLoS One 8(11);e81268 (2013) PUBMED: 24278408
	Engelhard C;Raffelberg S;Tang Y;Diensthuber RP;Moglich A;Losi A;Gartner W;Bittl R A structural model for the full-length blue light-sensing protein YtvA from Bacillus subtilis, based on EPR spectroscopy. Photochem Photobiol Sci 12(10);1855-63 (2013) PUBMED: 23900620
	Jurk M;Dorn M;Kikhney A;Svergun D;Gartner W;Schmieder P The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study. J Mol Biol 403(1);78-87 (2010) PUBMED: 20800068
	Jurk M;Dorn M;Schmieder P Blue flickers of hope: secondary structure, dynamics, and putative dimerization interface of the blue-light receptor YtvA from Bacillus subtilis. Biochemistry 50(38);8163-71 (2011) PUBMED: 21851109
	Jurk M;Schramm P;Schmieder P The blue-light receptor YtvA from Bacillus subtilis is permanently incorporated into the stressosome independent of the illumination state. Biochem Biophys Res Commun 432(3);499-503 (2013) PUBMED: 23416074
	Lee R;Gam J;Moon J;Lee SG;Suh YG;Lee BJ;Lee J A critical element of the light-induced quaternary structural changes in YtvA-LOV. Protein Sci (2015) PUBMED: 26402155
	Losi A;Gartner W;Raffelberg S;Cella Zanacchi F;Bianchini P;Diaspro A;Mandalari C;Abbruzzetti S;Viappiani C A photochromic bacterial photoreceptor with potential for super-resolution microscopy. Photochem Photobiol Sci 12(2);231-5 (2013) PUBMED: 23047813
	Mansurova M;Scheercousse P;Simon J;Kluth M;Gartner W Chromophore Exchange in the Blue Light-Sensitive Photoreceptor YtvA from Bacillus subtilis. Chembiochem 12(4);641-6 (2011) PUBMED: 21259411
	Mansurova M;Simon J;Salzmann S;Marian CM;Gartner W Spectroscopic and theoretical study on electronically modified chromophores in LOV domains: 8-bromo- and 8-trifluoromethyl-substituted flavins. Chembiochem 14(5);645-54 (2013) PUBMED: 23456923
	Mukherjee A;Walker J;Weyant KB;Schroeder CM Characterization of flavin-based fluorescent proteins: an emerging class of fluorescent reporters. PLoS One 8(5);e64753 (2013) PUBMED: 23741385
	Nakasone Y;Hellingwerf KJ On the binding of BODIPY-GTP by the photosensory protein YtvA from the common soil bacterium Bacillus subtilis. Photochem Photobiol 87(3);542-7 (2011) PUBMED: 21388385
	Pennacchietti F;Abbruzzetti S;Losi A;Mandalari C;Bedotti R;Viappiani C;Zanacchi FC;Diaspro A;Gartner W The Dark Recovery Rate in the Photocycle of the Bacterial Photoreceptor YtvA Is Affected by the Cellular Environment and by Hydration. PLoS One 9(9);e107489 (2014) PUBMED: 25211155
	Raffelberg S;Gutt A;Gartner W;Mandalari C;Abbruzzetti S;Viappiani C;Losi A The amino acids surrounding the flavin 7a-methyl group determine the UVA spectral features of a LOV protein. Biol Chem 394(11);1517-28 (2013) PUBMED: 23828427
	Raffelberg S;Mansurova M;Gartner W;Losi A Modulation of the photocycle of a LOV domain photoreceptor by the hydrogen-bonding network. J Am Chem Soc 133(14);5346-56 (2011) PUBMED: 21410163
	Silva MR;Mansurova M;Gartner W;Thiel W Photophysics of structurally modified flavin derivatives in the blue-light photoreceptor YtvA: a combined experimental and theoretical study. Chembiochem 14(13);1648-61 (2013) PUBMED: 23940057
	Song SH;Madsen D;van der Steen JB;Pullman R;Freer LH;Hellingwerf KJ;Larsen DS Primary Photochemistry of the Dark- and Light-Adapted States of the YtvA Protein from Bacillus subtilis. Biochemistry 52(45);7951-63 (2013) PUBMED: 24171435
	Song X;Wang Y;Shu Z;Hong J;Li T;Yao L Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method. PLoS Comput Biol 9(7);e1003129 (2013) PUBMED: 23861663
	van der Steen JB;Avila-Perez M;Knippert D;Vreugdenhil A;van Alphen P;Hellingwerf KJ Differentiation of function among the RsbR paralogs in the general stress response of Bacillus subtilis with regard to light perception. J Bacteriol 194(7);1708-16 (2012) PUBMED: 22287516
	van der Steen JB;Hellingwerf KJ Activation of the General Stress Response of Bacillus subtilis by Visible Light. Photochem Photobiol 91(5);1032-45 (2015) PUBMED: 26189730
	van der Steen JB;Nakasone Y;Hendriks J;Hellingwerf KJ Modeling the functioning of YtvA in the general stress response in Bacillus subtilis. Mol Biosyst 9(9);2331-43 (2013) PUBMED: 23817467
Comment	A recent publication shows that while YtvA interacts with the fluorescent GTP analog BODIPY-GTP, it does not bind GTP \|CITS: [22247770]\|. 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. From GenBank annotation: Evidence 1a: Function experimentally demonstrated in the studied strain; PubMedId: 11964249, 16923906, 16923909, 17200735, 17443319, 17575448; Product type rc : receptor
Description	blue light receptor
Gene Ontology	GO:0000155 phosphorelay sensor kinase activity
	GO:0000160 phosphorelay signal transduction system
	GO:0004871 NA
	GO:0006351 transcription, DNA-templated
	GO:0006355 regulation of transcription, DNA-templated
	GO:0007165 signal transduction
	GO:0009881 photoreceptor activity
	GO:0018106 peptidyl-histidine phosphorylation
	GO:0018298 protein-chromophore linkage
	GO:0023014 signal transduction by protein phosphorylation
	GO:0050896 response to stimulus
Locus Tag	BSU30340
Molecular weight	29.195
Name	ytvA

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU27860, BSU27870, BSU27850, new_2845839_2845914_c, new_2844574_2844638_c, new_300503_300693_c, BSU30210, new_2491949_2492028_c, BSU30220, BSU27840
Expression pos. correlated with	new_3106142_3106209, new_3106996_3107052, BSU23640, BSU08620, new_4186449_4186607, BSU31480, BSU40790, BSU35870, BSU29980, BSU10260
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].
	(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].
	(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
	(HiOs) 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].
	(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.
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].
	(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.
	(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.
	(M+G) 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.
	(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.
	(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.
	(S0) 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-5.40H) 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	ytvA

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