RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: rfbBDACX
Gene(s): rfbX, rfbC, rfbA, rfbD, rfbB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Bastin DA., et al., 1995
[2] Stevenson G., et al., 1994
[3] Yao Z., et al., 1994


Transcription unit       
Name: rfbACX
Gene(s): rfbX, rfbC, rfbA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Promoter
Name: rfbAp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [IEP]
Reference(s): [4] Zaslaver A., et al., 2006


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown activator       [IMP] [5]
  gcvB unknown unknown activator       [IMP] [5]
[2]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.8 2111040 2111066 tagtttttgcATCTTGTTCGTGATGGTGGAGCAAGAtgaattaaaa
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg
Strand: reverse
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  JUMPstart RNA 60.0 2113137 2113175 ggcaugcaugCAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUGcauuaauacc
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Bastin DA., Reeves PR., 1995, Sequence and analysis of the O antigen gene (rfb) cluster of Escherichia coli O111., Gene 164(1):17-23

 [2] Stevenson G., Neal B., Liu D., Hobbs M., Packer NH., Batley M., Redmond JW., Lindquist L., Reeves P., 1994, Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster., J Bacteriol 176(13):4144-56

 [3] Yao Z., Valvano MA., 1994, Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a., J Bacteriol 176(13):4133-43

 [4] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [5] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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