rny
BSGatlas-gene-1989
BSGatlas
Description | Information |
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Coordinates | 1767310..1768872 |
Genomic Size | 1563 bp |
Name | rny |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | + |
Type | CDS |
SubtiWiki
Description | Information |
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Alternative Name | rny |
rny | |
ymdA | |
Category | SW 3 Information processing |
SW 3.2 RNA synthesis and degradation | |
SW 3.2.4 RNases | |
SW 3.2.4.2 Endoribonucleases | |
SW 4 Lifestyles | |
SW 4.1 Exponential and early post-exponential lifestyles | |
SW 4.1.2 Biofilm formation | |
SW 4.1.2.5 Other proteins required for biofilm formation | |
SW 6 Groups of genes | |
SW 6.13 Quasi-essential genes | |
SW 6.2 Membrane proteins | |
Description | RNase Y, 5 end sensitive endoribonuclease, involved in the degradation/ processing of mRNA, part of the putative [SW|RNA degradosome] |
Enzyme Classifications | EC 3.1.4.16: 2',3'-cyclic-nucleotide 2'-phosphodiesterase |
Function | RNA processing and degradation |
Is essential? | no |
Isoelectric point | 5.39 |
Locus Tag | BSU_16960 |
Molecular weight | 58.748 |
Name | rny |
Product | RNase Y |
RefSeq
Description | Information |
---|---|
Alternative Locus Tag | BSU16960 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 12682299, 17005971,19779461, 21803996, 21815947, 21862575, 22720735,25402410, 26797123; Product type e: enzyme |
Functions | 16.2: Construct biomass (Anabolism) |
16.6: Maintain | |
Locus Tag | BSU_16960 |
Name | rny |
Title | endoribonuclease Y |
Type | CDS |
BsubCyc
Description | Information |
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Alternative Name | ymdA |
Citation | Bechhofer DH Bacillus subtilis mRNA decay: new parts in the toolkit. Wiley Interdiscip Rev RNA 2(3);387-94 (2011) PUBMED: 21957024 |
Bruscella P;Shahbabian K;Laalami S;Putzer H RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis. Mol Microbiol 81(6);1526-41 (2011) PUBMED: 21843271 | |
Burmann F;Sawant P;Bramkamp M Identification of interaction partners of the dynamin-like protein DynA from Bacillus subtilis. Commun Integr Biol 5(4);362-9 (2012) PUBMED: 23060960 | |
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 | |
Commichau FM;Rothe FM;Herzberg C;Wagner E;Hellwig D;Lehnik-Habrink M;Hammer E;Volker U;Stulke J Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8(6);1350-60 (2009) PUBMED: 19193632 | |
DeLoughery A;Dengler V;Chai Y;Losick R Biofilm formation by Bacillus subtilis requires an endoribonuclease-containing multisubunit complex that controls mRNA levels for the matrix gene repressor SinR. Mol Microbiol 99(2);425-37 (2016) PUBMED: 26434553 | |
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 | |
Gilet L;DiChiara JM;Figaro S;Bechhofer DH;Condon C Small stable RNA maturation and turnover in Bacillus subtilis. Mol Microbiol 95(2);270-82 (2015) PUBMED: 25402410 | |
Korza G;Setlow B;Rao L;Li Q;Setlow P Changes in Bacillus Spore Small Molecules, rRNA, Germination, and Outgrowth after Extended Sublethal Exposure to Various Temperatures: Evidence that Protein Synthesis Is Not Essential for Spore Germination. J Bacteriol 198(24);3254-3264 (2016) PUBMED: 27645383 | |
Laalami S;Bessieres P;Rocca A;Zig L;Nicolas P;Putzer H Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays. PLoS One 8(1);e54062 (2013) PUBMED: 23326572 | |
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 | |
Lehnik-Habrink M;Newman J;Rothe FM;Solovyova AS;Rodrigues C;Herzberg C;Commichau FM;Lewis RJ;Stulke J RNase Y in Bacillus subtilis: a Natively Disordered Protein That Is the Functional Equivalent of RNase E from Escherichia coli. J Bacteriol 193(19);5431-41 (2011) PUBMED: 21803996 | |
Lehnik-Habrink M;Schaffer M;Mader U;Diethmaier C;Herzberg C;Stulke J RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol 81(6);1459-73 (2011) PUBMED: 21815947 | |
Salvo E;Alabi S;Liu B;Schlessinger A;Bechhofer DH Interaction of Bacillus subtilis Polynucleotide Phosphorylase and RNase Y: STRUCTURAL MAPPING AND EFFECT ON mRNA TURNOVER. J Biol Chem 291(13);6655-63 (2016) PUBMED: 26797123 | |
Shahbabian K;Jamalli A;Zig L;Putzer H RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28(22);3523-33 (2009) PUBMED: 19779461 | |
Yao S;Bechhofer DH Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. J Bacteriol 192(13);3279-86 (2010) PUBMED: 20418391 | |
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 | |CITS: [12682299][17005971]| |
Description | ribonuclease Y |
Gene Ontology | GO:0003723 RNA binding |
GO:0003824 catalytic activity | |
GO:0004518 nuclease activity | |
GO:0004519 endonuclease activity | |
GO:0004521 endoribonuclease activity | |
GO:0005515 protein binding | |
GO:0005886 plasma membrane | |
GO:0006402 mRNA catabolic process | |
GO:0008081 phosphoric diester hydrolase activity | |
GO:0016020 membrane | |
GO:0016021 integral component of membrane | |
GO:0016787 hydrolase activity | |
GO:0042802 identical protein binding | |
GO:0046872 metal ion binding | |
GO:0090305 nucleic acid phosphodiester bond hydrolysis | |
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic | |
Locus Tag | BSU16960 |
Molecular weight | 58.919 |
Name | rny |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | BSU27420, new_2701783_2703117, BSU03690, new_3153832_3153982_c, BSU22040, BSU18760, BSU22250, new_1253669_1254769, BSU37200, BSU22050 |
Expression pos. correlated with | BSU13660, BSU21830, BSU08010, BSU30390, new_1767136_1767309, BSU21840, BSU31490, BSU38860, BSU23890, BSU31500 |
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]. | |
(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. | |
(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 . | |
(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]. | |
(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]. | |
(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]. | |
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. | |
(Heat) 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]. | |
(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. | |
(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. | |
Name | rny |
KEGG Pathways
Description | Information |
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Pathway | RNA degradation (ko03018) |