RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: otsA
Gene(s): otsA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kaasen I., et al., 1992
Promoter
Name: otsAp
+1: 1981651
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 39
Sequence: catcatggcgactggcgggtgtgccggatgtctggagctggcttgaaatgataaccaccgCattacaacaaaaaagagaaa
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Hengge-Aronis R., et al., 1991
[3] Huerta AM., et al., 2003
[1] Kaasen I., et al., 1992
[4] Kaasen I., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: aatcacagttTCTTTTCGCGAGCATCCTGCTCGGCGAAAAGagttattgcc
Reference(s): [4] Kaasen I., et al., 1994


Transcription unit       
Name: otsBA
Gene(s): otsA, otsB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kaasen I., et al., 1992
Promoter
Name: otsBp2
+1: 1982442
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 55
Sequence: taacggttggctgttcttcgttgcaaatggcgacccccgtcacactgtctatacttacatGtctgtaaagcgcgttctgcg
                                -35                    -10  +1                   
Note(s): The operon otsAB is positively regulated by RpoS in stationary phase and is mainly controlled at the transcription level Hengge-Aronis R,1991. Strøm AR, Kaasen I,1993 It is also osmotically regulated. Region 4 of the σ38 protein and the elements near the -35 DNA region are involved in triggering the response to high salt concentrations, which ensures the transcriptional activation of the otsBp2 promoter to counteract this physiological challenge Rosenthal AZ,2006.
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [5] Becker G., et al., 2001
[3] Huerta AM., et al., 2003
[4] Kaasen I., et al., 1994
[6] Maciag A., et al., 2011
[7] Rosenthal AZ., et al., 2006
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aatcacagttTCTTTTCGCGAGCATCCTGCTCGGCGAAAAGagttattgcc
Reference(s): [4] Kaasen I., et al., 1994


Transcription unit       
Name: otsBA
Gene(s): otsA, otsB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kaasen I., et al., 1992
Promoter
Name: otsBp1
+1: 1982465
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 78
Sequence: tttcccaccatagccaaccgccataacggttggctgttcttcgttgcaaatggcgaccccCgtcacactgtctatacttac
                                   -35                      +10                  
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Hengge-Aronis R., et al., 1991
[3] Huerta AM., et al., 2003
[1] Kaasen I., et al., 1992
[4] Kaasen I., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: aatcacagttTCTTTTCGCGAGCATCCTGCTCGGCGAAAAGagttattgcc
Reference(s): [4] Kaasen I., et al., 1994


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

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

 [EXP-IEP] Inferred from expression pattern

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Kaasen I., Falkenberg P., Styrvold OB., Strom AR., 1992, Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by katF (AppR), J Bacteriol 174(3):889-98

 [2] Hengge-Aronis R., Klein W., Lange R., Rimmele M., Boos W., 1991, Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli., J Bacteriol 173(24):7918-24

 [3] 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

 [4] Kaasen I., McDougall J., Strom AR., 1994, Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phosphate synthase/phosphatase complex., Gene 145(1):9-15

 [5] Becker G., Hengge-Aronis R., 2001, What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S)., Mol Microbiol 39(5):1153-65

 [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

 [7] Rosenthal AZ., Hu M., Gralla JD., 2006, Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS)., Mol Microbiol 59(3):1052-61

 [8] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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