BSGatlas

rnjB

BSGatlas-gene-1972

BSGatlas

Description	Information
Coordinates	1749418..1751085
Genomic Size	1668 bp
Name	rnjB
Outside Links	SubtiWiki
	BsubCyc
Strand	+
Type	CDS

SubtiWiki

Description	Information
Alternative Name	rnjB
	rnjB
	ymfA
Category	SW 3 Information processing
	SW 3.2 RNA synthesis and degradation
	SW 3.2.4 RNases
	SW 3.2.4.2 Endoribonucleases
Description	RNase J2
Function	RNA processing and degradation
Is essential?	no
Isoelectric point	9.18
Locus Tag	BSU_16780
Molecular weight	56.673
Name	rnjB
Product	RNase J2

RefSeq

Description	Information
Alternative Locus Tag	BSU16780
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 15831787, 18713320,20025672, 20729365, 24187087, 26296725, 28384222; Producttype e: enzyme
Functions	16.11: Scavenge (Catabolism)
	16.3: Control
	16.6: Maintain
Locus Tag	BSU_16780
Name	rnjB
Title	dual activity 5' exo-and endoribonuclease J2
Type	CDS

BsubCyc

Description	Information
Alternative Name	ymfA
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 What is the role of RNase J in mRNA turnover? RNA Biol 7(3);316-21 (2010) PUBMED: 20458164
	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
	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
	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
	Waters SM;Zeigler DR;Nicholson WL Experimental Evolution of Enhanced Growth by Bacillus subtilis at Low Atmospheric Pressure: Genomic Changes Revealed by Whole-Genome Sequencing. Appl Environ Microbiol 81(21);7525-32 (2015) PUBMED: 26296725
Comment	16.6: Maintain 16.3: Control 16.11: Scavenge (Catabolism)
Description	ribonuclease J2
Gene Ontology	GO:0003723 RNA binding
	GO:0004518 nuclease activity
	GO:0004519 endonuclease activity
	GO:0005737 cytoplasm
	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	BSU16780
Molecular weight	61.175
Name	rnjB

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU18700, BSU27450, BSU40270, BSU27460, BSU40280, new_1603592_1604734_c, BSU13360, new_3715928_3716008_c, new_1121267_1121506, BSU36060
Expression pos. correlated with	BSU27590, new_2467979_2468158_c, BSU23750, BSU27600, BSU31500, BSU06330, BSU31490, BSU34060, BSU06340, BSU24270
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].
	(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.
	(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 .
	(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 .
	(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].
	(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	(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].
	(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	rnjB

KEGG Pathways

Description	Information
Pathway	RNA degradation (ko03018)

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