RegulonDB RegulonDB 10.10: Operon Form
   

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


Transcription unit       
Name: rnd
Gene(s): rnd   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rnd upstream region shows some unusual features, which include a stable hairpin structure between the transcription and translation start sites. This structure could be a ρ-independent transcription terminator, and its location only 18 nucleotides after the transcription start site of rnd mRNA is particularly puzzling Zhang JR,1989 In addition, the rnd upstream region utilizes an infrequently used UUG initiator codon Zhang JR,1989 Based on the primer extension analysis, the hairpin structure does not represent an rnd terminator or an RNA processing site Zhang JR,1989
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Zhang JR., et al., 1989
Promoter
Name: rndp
+1: 1888061
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 70
Sequence: aaaaattttgcgacgagaattacgtgacgaagcgcgcggcaaagtggacaataaagcctgAgcgttaagtcagtcgtcaga
                    -35                        -10          +1                   
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Zhang JR., et al., 1989


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [3] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.3 1888015 1888043 gtcagtcgtcAGACGCCGGTTAATCCGGCGTTTTTTTTgacgcccact
  anti-terminator -6.22 1888033 1888067 tggacaataaAGCCTGAGCGTTAAGTCAGTCGTCAGACGCCGGTtaatccggcg
  anti-anti-terminator -9.66 1888052 1888095 gaattacgtgACGAAGCGCGCGGCAAAGTGGACAATAAAGCCTGAGCGTTAAGtcagtcgtca
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"


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Zhang JR., Deutscher MP., 1989, Analysis of the upstream region of the Escherichia coli rnd gene encoding RNase D. Evidence for translational regulation of a putative tRNA processing enzyme., J Biol Chem 264(30):18228-33

 [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] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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