RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit       
Name: bssS
Gene(s): bssS   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: bssSp
+1: 1121020
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 65
Sequence: ttatctgtttccccctttaaaaattcggtgaatacccttacttattggtatactgaagttGcttcagataaaaacgcattg
                                                      -10   +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Maciag A., et al., 2011
[2] Mendoza-Vargas A., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit       
Name: bssS
Synonym(s): yceP
Gene(s): bssS   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: bssSp2
+1: 1121032
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 77
Sequence: aaaagcagaaatttatctgtttccccctttaaaaattcggtgaatacccttacttattggTatactgaagttgcttcagat
                                 -35               -10      +1                   
Note(s): The sigma factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[5] Nonaka G., et al., 2006
[6] Wade JT., et al., 2006
[7] Zhao K., et al., 2005


Transcription unit          
Name: bssS
Synonym(s): yceP
Gene(s): bssS   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: bssSp1
+1: 1121058
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 103
Sequence: gctgttttattgttcatataaatcttaaaagcagaaatttatctgtttccccctttaaaaAttcggtgaatacccttactt
                                     -35               -10  +1                   
Note(s): The sigma factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005. We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[6] Wade JT., et al., 2006
[7] Zhao K., et al., 2005
TF binding sites (TFBSs)
[YhaJ,+] 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
nd YhaJ activator bssSp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]


Evidence    

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [3] 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.

 [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] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [6] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [7] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68

 [8] Palevsky N., Shemer B., Connolly JP., Belkin S., 2016, The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation., Front Microbiol 7:1490

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