BSGatlas

rnjA

BSGatlas-gene-1723

BSGatlas

Description	Information
Coordinates	1523118..1524785
Genomic Size	1668 bp
Name	rnjA
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	rnjA
	rnjA
	ykqC
Category	SW 3 Information processing
	SW 3.2 RNA synthesis and degradation
	SW 3.2.4 RNases
	SW 3.2.4.1 Exoribonucleases
	SW 6 Groups of genes
	SW 6.1 Essential genes
Description	RNase J1, important for the degradation of RNA fragments containing transcription terminators, resolves stalled transcription complexes
Function	RNA processing
Is essential?	no
Isoelectric point	5.9
Locus Tag	BSU_14530
Molecular weight	61.3447
Name	rnjA
Product	RNase J1

RefSeq

Description	Information
Alternative Locus Tag	BSU14530
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 12682299, 15831787,17005971, 17229210, 17512403, 18713320, 19850915,21893285, 21893286, 20025672, 22720735, 23504012,24187087; Product type e: enzyme
Functions	16.3: Control
	16.6: Maintain
Locus Tag	BSU_14530
Name	rnjA
Title	ribonuclease J1
Type	CDS

BsubCyc

Description	Information
Alternative Name	ykqC
Citation	Bechhofer DH Bacillus subtilis mRNA decay: new parts in the toolkit. Wiley Interdiscip Rev RNA 2(3);387-94 (2011) PUBMED: 21957024
	Cascante-Estepa N;Gunka K;Stulke J Localization of Components of the RNA-Degrading Machine in Bacillus subtilis. Front Microbiol 7;1492 (2016) PUBMED: 27708634
	Condon C;Bechhofer DH Regulated RNA stability in the Gram positives. Curr Opin Microbiol 14(2);148-54 (2011) PUBMED: 21334965
	Condon C What is the role of RNase J in mRNA turnover? RNA Biol 7(3);316-21 (2010) PUBMED: 20458164
	Deikus G;Bechhofer DH 5' End-independent RNase J1 Endonuclease Cleavage of Bacillus subtilis Model RNA. J Biol Chem 286(40);34932-34940 (2011) PUBMED: 21862575
	DiChiara JM;Liu B;Figaro S;Condon C;Bechhofer DH Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains. Nucleic Acids Res 44(7);3373-89 (2016) PUBMED: 26883633
	Dominski Z;Carpousis AJ;Clouet-d'Orval B Emergence of the β-CASP ribonucleases: highly conserved and ubiquitous metallo-enzymes involved in messenger RNA maturation and degradation. Biochim Biophys Acta 1829(6-7);532-51 (2013) PUBMED: 23403287
	Dorleans A;Li de la Sierra-Gallay I;Piton J;Zig L;Gilet L;Putzer H;Condon C Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J. Structure 19(9);1252-61 (2011) PUBMED: 21893286
	Durand S;Gilet L;Bessieres P;Nicolas P;Condon C Three Essential Ribonucleases-RNase Y, J1, and III-Control the Abundance of a Majority of Bacillus subtilis mRNAs. PLoS Genet 8(3);e1002520 (2012) PUBMED: 22412379
	Figaro S;Durand S;Gilet L;Cayet N;Sachse M;Condon C Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J Bacteriol 195(10);2340-8 (2013) PUBMED: 23504012
	Jamalli A;Hebert A;Zig L;Putzer H Control of expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol 196(2);318-24 (2014) PUBMED: 24187087
	Laalami S;Zig L;Putzer H Initiation of mRNA decay in bacteria. Cell Mol Life Sci 71(10);1799-828 (2014) PUBMED: 24064983
	Lehnik-Habrink M;Lewis RJ;Mader U;Stulke J RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 84(6);1005-17 (2012) PUBMED: 22568516
	Mathy N;Hebert A;Mervelet P;Benard L;Dorleans A;de la Sierra-Gallay IL;Noirot P;Putzer H;Condon C Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol 75(2);489-98 (2010) PUBMED: 20025672
	Newman JA;Hewitt L;Rodrigues C;Solovyova A;Harwood CR;Lewis RJ Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of RNase J1. Structure 19(9);1241-51 (2011) PUBMED: 21893285
	Yao S;Richards J;Belasco JG;Bechhofer DH Decay of a model mRNA in Bacillus subtilis by a combination of RNase J1 5' exonuclease and RNase Y endonuclease activities. J Bacteriol 193(22);6384-6 (2011) PUBMED: 21908660
Comment	16.3: Control 16.6: Maintain
Description	ribonuclease J1
Gene Ontology	GO:0003723 RNA binding
	GO:0004518 nuclease activity
	GO:0004519 endonuclease activity
	GO:0005515 protein binding
	GO:0005737 cytoplasm
	GO:0006364 rRNA processing
	GO:0006397 mRNA processing
	GO:0016787 hydrolase activity
	GO:0016788 hydrolase activity, acting on ester bonds
	GO:0046872 metal ion binding
	GO:0090305 nucleic acid phosphodiester bond hydrolysis
Locus Tag	BSU14530
Molecular weight	61.517
Name	rnjA

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU13190, BSU24280, BSU14660, new_1537029_1537112, new_2678724_2678943, new_3265241_3265327_c, BSU40280, new_1385938_1386023_c, BSU08590, new_1386984_1387035_c, BSU26910
Expression pos. correlated with	BSU00690, BSU06000, BSU11600, BSU11610, BSU22750, BSU16560, BSU22740, BSU11620, BSU06010, BSU16780
Highly expressed condition	(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].
	(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.
	(C90) 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.
	(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].
	(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.
	(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 .
	(LBtran) 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 .
	(M0t45) 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].
	(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].
	(M40t45) 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].
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].
	(B60) 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].
	(Gly) 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.
	(M9stat) Cells were grown in M9 supplemented with glucose (0.3 %) at 37°C with vigorous shaking. The composition of the M9 minimal medium is (per liter): 8.5 g Na2HPO4.2H20, 3 g KH2PO4, 1 g NH4Cl and 0.5 g NaCl. The following solutions were individually sterilized and added (volumes per liter of medium): 1 ml 0.1 M CaCl2.2H2O, 1 ml 1 M MgSO4.7H2O, 1 ml 50 mM Fe-Citrate. Also added was 10 ml of a trace salts solution containing (per liter): 170 mg ZnCl2, 100 mg MnCl2.4H2O, 60 mg CoCl2.6H2O, 60 mg Na2MoO4.2H2O and 43 mg CuCl2.2H2O. Overnight cultures were diluted 2000-fold in pre-warmed M9 medium and samples were harvested during exponential growth [M9exp], at the transition phase [M9tran] and during stationary phase [M9stat].
	(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.
	(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].
	(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].
Name	rnjA

KEGG Pathways

Description	Information
Pathway	RNA degradation (ko03018)

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