RegulonDB RegulonDB 10.10: Operon Form
   

rfaD-waaFCL operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: rfaDFCL
Gene(s): rfaD, waaF, waaC, waaL   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was experimentally demonstrated that the Rho protein negatively regulates expression of the genes waaF and waaL Hafeezunnisa M, Sen R,2020. Rho loading sites (rut sites) were identified upstream of these two genes Hafeezunnisa M, Sen R,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Klena JD., et al., 1992
Promoter
Name: rfaDp3
+1: 3793865
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 122
Sequence: gcactattcacatgcaaaaccaacatccgccatgaaggactagctaaaacccaaactagtTtgttgcaattagcatccttg
                                -35              -10        +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Raina S., et al., 1991


Transcription unit       
Name: rfaDFCL
Gene(s): rfaD, waaF, waaC, waaL   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was experimentally demonstrated that the Rho protein negatively regulates expression of the genes waaF and waaL Hafeezunnisa M, Sen R,2020. Rho loading sites (rut sites) were identified upstream of these two genes Hafeezunnisa M, Sen R,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Klena JD., et al., 1992
[4] Sirisena DM., et al., 1994
Promoter
Name: rfaDp2
+1: 3793896
Distance from start of the gene: 91
Sequence: atgaaggactagctaaaacccaaactagtttgttgcaattagcatccttgcacctctatgTaaagggctgaagggattcgg
Evidence: [HIPP]
[TIM]
Reference(s): [3] Raina S., et al., 1991


Transcription unit       
Name: rfaDFCL
Gene(s): rfaD, waaF, waaC, waaL   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was experimentally demonstrated that the Rho protein negatively regulates expression of the genes waaF and waaL Hafeezunnisa M, Sen R,2020. Rho loading sites (rut sites) were identified upstream of these two genes Hafeezunnisa M, Sen R,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Klena JD., et al., 1992
[4] Sirisena DM., et al., 1994
Promoter
Name: rfaDp1
+1: 3793939
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 48
Sequence: atccttgcacctctatgtaaagggctgaagggattcggatgtgatggtatgattacagacAttcgtgtctgagattgtctc
                         -35                    -10         +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[5] Pegues JC., et al., 1990
[3] Raina S., et al., 1991
[6] Salgado H, et al., 2012


Transcription unit       
Name: rfaDFCL
Gene(s): rfaD, waaF, waaC, waaL   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was experimentally demonstrated that the Rho protein negatively regulates expression of the genes waaF and waaL Hafeezunnisa M, Sen R,2020. Rho loading sites (rut sites) were identified upstream of these two genes Hafeezunnisa M, Sen R,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Klena JD., et al., 1992
[4] Sirisena DM., et al., 1994
Promoter
Name: rfaDp4
+1: 3793970
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 17
Sequence: gattcggatgtgatggtatgattacagacattcgtgtctgagattgtctctgactccataAttcgaaggttacagttatga
                           -35                   -10        +1                   
Evidence: [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM]
Reference(s): [7] Dartigalongue C., et al., 2001
[2] Huerta AM., et al., 2003


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

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

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Klena JD., Pradel E., Schnaitman CA., 1992, Comparison of lipopolysaccharide biosynthesis genes rfaK, rfaL, rfaY, and rfaZ of Escherichia coli K-12 and Salmonella typhimurium., J Bacteriol 174(14):4746-52

 [2] 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

 [3] Raina S., Georgopoulos C., 1991, The htrM gene, whose product is essential for Escherichia coli viability only at elevated temperatures, is identical to the rfaD gene., Nucleic Acids Res 19(14):3811-9

 [4] Sirisena DM., MacLachlan PR., Liu SL., Hessel A., Sanderson KE., 1994, Molecular analysis of the rfaD gene, for heptose synthesis, and the rfaF gene, for heptose transfer, in lipopolysaccharide synthesis in Salmonella typhimurium., J Bacteriol 176(8):2379-85

 [5] Pegues JC., Chen LS., Gordon AW., Ding L., Coleman WG., 1990, Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene., J Bacteriol 172(8):4652-60

 [6] 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.

 [7] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

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