ylbF
BSGatlas-gene-1773
BSGatlas
Description | Information |
---|---|
Coordinates | 1568420..1568869 |
Genomic Size | 450 bp |
Name | ylbF |
Outside Links | SubtiWiki |
BsubCyc | |
Strand | + |
Type | CDS |
SubtiWiki
Description | Information |
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Alternative Name | ricF |
ylbF | |
ylbF | |
Category | SW 3 Information processing |
SW 3.2 RNA synthesis and degradation | |
SW 3.2.4 RNases | |
SW 3.2.4.5 Effectors of RNA degradation | |
SW 3.4 Regulation of gene expression | |
SW 3.4.2 Transcription factors and their control | |
SW 3.4.2.7 Control of transcription factor (other than two-component system) | |
SW 3.4.7 phosphorelay | |
SW 3.4.7.6 Other protein controlling the activity of the phosphorelay | |
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 4.2 Sporulation | |
SW 4.2.2 phosphorelay | |
SW 4.2.2.6 Other protein controlling the activity of the phosphorelay | |
Description | subunit of the regulatory iron-sulfur containing [[protein|EE52DFA35B935E551871D079A9BE877DB2001A3B]]-[[protein|6C9A092F38739A3759793EF8B496569CD02C2E3F]]-[[protein|EBD15C174A03B7FCDFFE4C5DB5D86E93F1B9CAC4]] complex, required for [[protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y]] dependent maturation of polycistronic mRNAs, antagonist of biofilm repression by [[protein|5A6FBAE6553343092862CB79E150F934978C32A9]], control of the [SW|phosphorelay] |
Function | control of [[protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y]] activity, see [SW|Targets of the Y complex] |
Is essential? | no |
Isoelectric point | 5.01 |
Locus Tag | BSU_14990 |
Molecular weight | 16.7712 |
Name | ylbF |
Product | subunit of the regulatory iron-sulfur containing [[protein|EE52DFA35B935E551871D079A9BE877DB2001A3B]]-[[protein|6C9A092F38739A3759793EF8B496569CD02C2E3F]]-[[protein|EBD15C174A03B7FCDFFE4C5DB5D86E93F1B9CAC4]] complex |
RefSeq
Description | Information |
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Alternative Locus Tag | BSU14990 |
Description | Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 10712692, 15175311,15661000, 23490197, 26434553, 27501195, 28295778; Producttype r: regulator |
Functions | 16.3: Control |
Locus Tag | BSU_14990 |
Name | ricF |
Title | subunit of a sporulation, competence and biofilmformation regulatory complex controlling RNase Y (RicAFTcomplex / FAD / two [4Fe-4S]2+) |
Type | CDS |
BsubCyc
Description | Information |
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Citation | Bridier A;Le Coq D;Dubois-Brissonnet F;Thomas V;Aymerich S;Briandet R The Spatial Architecture of Bacillus subtilis Biofilms Deciphered Using a Surface-Associated Model and In Situ Imaging. PLoS One 6(1);e16177 (2011) PUBMED: 21267464 |
Carabetta VJ;Tanner AW;Greco TM;Defrancesco M;Cristea IM;Dubnau D A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Mol Microbiol 88(2);283-300 (2013) PUBMED: 23490197 | |
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 | |
Dubnau EJ;Carabetta VJ;Tanner AW;Miras M;Diethmaier C;Dubnau D A protein complex supports the production of Spo0A-P and plays additional roles for biofilms and the K-state in Bacillus subtilis. Mol Microbiol 101(4);606-24 (2016) PUBMED: 27501195 | |
Comment | YmcA, YlbF and YaaT interact to form a tripartite complex; all three proteins are required for proper establishment of sporulation, competence and biofilm formation by regulating the activity of Spo0A |CITS: [23490197]|. |
Description | regulator of Spo0A activity |
Gene Ontology | GO:0005515 protein binding |
GO:0005737 cytoplasm | |
GO:0030420 establishment of competence for transformation | |
GO:0030435 sporulation resulting in formation of a cellular spore | |
GO:0042173 regulation of sporulation resulting in formation of a cellular spore | |
GO:0045304 regulation of establishment of competence for transformation | |
GO:1900190 regulation of single-species biofilm formation | |
Locus Tag | BSU14990 |
Molecular weight | 16.914 |
Name | ylbF |
Nicolas et al. predictions
Description | Information |
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Expression neg. correlated with | BSU03780, BSU33640, BSU14900, BSU13340, BSU39330, BSU09889, BSU11040, BSU01680, new_1560362_1560465, new_1211286_1211370 |
Expression pos. correlated with | BSU15660, new_2925027_2925099_c, BSU28610, BSU27520, BSU27510, BSU29590, BSU24520, BSU36980, BSU28600, BSU33680, BSU31430 |
Highly expressed condition | (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]. |
(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. | |
(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]. | |
(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 | |
(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 | |
(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 . | |
(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 . | |
(LPhT) Cells were harvested (i) during exponential growth in high phosphate defined medium [HPh]; (ii) during exponential growth in low phosphate defined medium [LPh] (J. P. Muller, Z. An, T. Merad, I. C. Hancock, C. R. Harwood, Microbiology 143, 947, Mar, 1997);and (iii) at three hours after the outset of the phosphate-limitation induced stationary phase [LPhT]. | |
(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 | |
Lowely expressed condition | (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]. |
(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. | |
(S3) 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. | |
(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. | |
(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. | |
(SMMPr) 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]. | |
Name | ylbF |