RegulonDB RegulonDB 11.1: Operon Form
   

osmB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: osmB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: osmB
Gene(s): osmB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene osmB is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Jung JU., et al., 1989
Promoter
Name: osmBp
+1: 1343369
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 41
Sequence: gcgcgagcagatttcacggaataatttcaccagacttattcttagctattatagttatagAgagcttacttccgtgaatca
                              -35                   -10     +1                   
Note(s): The osmBp2 promoter is activated by potassium glutamate but only when σS is used. σ70 recognizes osmBp2 at low osmolarity. Only osmBp2 is induced by stationary phase at low osmolarity. The two promoters are active when both high osmolarity and stationary-phase signals are present simultaneously, but the osmBp2 activity is much greater than the osmBp1 activity.
osmBp2 was unambiguously characterized by Jung JU,1989 Boulanger A,2005.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Boulanger A., et al., 2005
[3] Ding Q., et al., 1995
[4] Huerta AM., et al., 2003
[5] Jung JU., et al., 1990
[1] Jung JU., et al., 1989
[6] Maciag A., et al., 2011


Transcription unit       
Name: osmB
Gene(s): osmB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene osmB is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Jung JU., et al., 1989
Promoter
Name: osmBp2
+1: 1343369
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: gcgcgagcagatttcacggaataatttcaccagacttattcttagctattatagttatagAgagcttacttccgtgaatca
                               -35                  -10     +1                   
Note(s): The osmBp2 promoter is activated by potassium glutamate but only when σS is used. σ70 recognizes osmBp2 at low osmolarity. Only osmBp2 is induced by stationary phase at low osmolarity. The two promoters are active when both high osmolarity and stationary-phase signals are present simultaneously, but the osmBp2 activity is much greater than the osmBp1 activity.
osmBp2 was unambiguously characterized by Jung JU,1989 Boulanger A,2005.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Boulanger A., et al., 2005
[3] Ding Q., et al., 1995
[4] Huerta AM., et al., 2003
[5] Jung JU., et al., 1990
[1] Jung JU., et al., 1989
[6] Maciag A., et al., 2011


Transcription unit          
Name: osmB
Gene(s): osmB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene osmB is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Jung JU., et al., 1989
Promoter
Name: osmBp1
+1: 1343476
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 148
Sequence: ctggttgataattaagactatttacctgttattaacactctcaagatataaaattattatCagcgatataacaggaagtca
                                     -35                    +10                  
Note(s): Only osmBp2 is induced during stationary phase at low osmolarity. The two promoters are active when both high osmolarity and stationary phase signals are present simultaneously, but the osmBp2 activity is much greater than the osmBp1 activity.
The transcriptional start site of the osmBp1 promoter determined by Jung JU,1989 is different by 1 bp from the one characterized by Boulanger A,2005
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Boulanger A., et al., 2005
[4] Huerta AM., et al., 2003
[5] Jung JU., et al., 1990
TF binding sites (TFBSs)
[RcsB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-phosphorylated activator osmBp1 1343511 1343524 -41.5 ggttgataatTAAGACTATTTACCtgttattaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Jung JU., Gutierrez C., Villarejo MR., 1989, Sequence of an osmotically inducible lipoprotein gene., J Bacteriol 171(1):511-20

 [2] Boulanger A., Francez-Charlot A., Conter A., Castanie-Cornet MP., Cam K., Gutierrez C., 2005, Multistress regulation in Escherichia coli: expression of osmB involves two independent promoters responding either to sigmaS or to the RcsCDB His-Asp phosphorelay., J Bacteriol 187(9):3282-6

 [3] Ding Q., Kusano S., Villarejo M., Ishihama A., 1995, Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by E sigma D and E sigma S holoenzymes., Mol Microbiol 16(4):649-56

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] Jung JU., Gutierrez C., Martin F., Ardourel M., Villarejo M., 1990, Transcription of osmB, a gene encoding an Escherichia coli lipoprotein, is regulated by dual signals. Osmotic stress and stationary phase., J Biol Chem 265(18):10574-81

 [6] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

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