BSGatlas

trmFO

BSGatlas-gene-1901

BSGatlas

Description	Information
Coordinates	1685812..1687119
Genomic Size	1308 bp
Name	trmFO
Outside Links	SubtiWiki
	BsubCyc
Strand	+
Type	CDS

SubtiWiki

Description	Information
Alternative Name	gid
	trmFO
	trmFO
	ylyC
Category	SW 3 Information processing
	SW 3.3 Protein synthesis, modification and degradation
	SW 3.3.1 Translation
	SW 3.3.1.8 tRNA modification and maturation
Description	flavoprotein, tRNA:m(5)U-54 methyltransferase, glucose-inhibited division protein
Enzyme Classifications	EC 2.1.1.74: methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase
Function	tRNA modification
Is essential?	no
Isoelectric point	5.77
Locus Tag	BSU_16130
Molecular weight	47.8991
Name	trmFO
Product	tRNA:m(5)U-54 methyltransferase

RefSeq

Description	Information
Alternative Locus Tag	BSU16130
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 16027442, 21561081,23095745, 23157377, 27825927, 28745052; Product type e :enzyme
Enzyme Classifications	EC 2.1.1.74: methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase
Functions	16.2: Construct biomass (Anabolism)
	16.6: Maintain
Locus Tag	BSU_16130
Name	trmFO
Title	tRNA:m(5)U-54 methyltransferase
Type	CDS

BsubCyc

Description	Information
Alternative Name	gid
	ylyC
Citation	Hamdane D;Bou-Nader C;Cornu D;Hui-Bon-Hoa G;Fontecave M Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry 54(28);4354-64 (2015) PUBMED: 26120776
	Hamdane D;Bruch E;Un S;Field M;Fontecave M Activation of a unique flavin-dependent tRNA-methylating agent. Biochemistry 52(49);8949-56 (2013) PUBMED: 24228791
	Hamdane D;Skouloubris S;Myllykallio H;Golinelli-Pimpaneau B Expression and purification of untagged and histidine-tagged folate-dependent tRNA:m5U54 methyltransferase from Bacillus subtilis. Protein Expr Purif 73(1);83-9 (2010) PUBMED: 20412857
Comment	TrmFO catalyzes the C5-methylation of uridine at position 54 in the TΨC loop of tRNAs using 5,10-methylenetetrahydrofolate (CH₂THF) as the methyl group donor and FADH₂ as a reducing agent \|CITS: [16027442]\|. Catalysis proceeds via an air-stable FADH· radical intermediate \|CITS: [21561081]\|. Cys226 attacks the C6 atom of the uridine and Cys53 plays the role of the general base abstracting the C5 proton \|CITS: [21846722]\|.
Description	tRNA:m⁵U-54 methyltransferase
Enzyme Classifications	EC 2.1.1.74: methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase
Gene Ontology	GO:0005737 cytoplasm
	GO:0008033 tRNA processing
	GO:0008168 methyltransferase activity
	GO:0016740 transferase activity
	GO:0030488 tRNA methylation
	GO:0030698 5,10-methylenetetrahydrofolate-dependent tRNA (m5U54) methyltransferase activity
	GO:0032259 methylation
	GO:0047151 methylenetetrahydrofolate-tRNA-(uracil-5-)-methyltransferase (FADH2-oxidizing) activity
	GO:0050660 flavin adenine dinucleotide binding
Locus Tag	BSU16130
Molecular weight	48.063
Name	trmFO

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU11860, BSU11850, BSU11840, BSU35310, BSU21750, BSU29140, BSU04990, BSU29120, BSU02090, BSU06310
Expression pos. correlated with	BSU16710, BSU15220, BSU14630, new_942230_942320_c, new_1591418_1591539, BSU16700, BSU16140, BSU22150, BSU09840, BSU37490
Highly expressed condition	(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.
	(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].
	(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
	(LBGexp) 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 .
	(Oxctl) 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
	(Paraq) 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
	(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.
Lowely 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].
	(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].
	(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].
	(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.
	(Sw) Exponentially growing cells were spotted on 1 % agar LB plates and incubated at 37°C. Swarming cells were collected after 16 hours.
	(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].
	(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].
	(T3.0H) 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	trmFO

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