RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: rnlAB
Synonym(s): rnlA-yfjO
Gene(s): rnlA, rnlB   Genome Browser M3D Gene expression COLOMBOS
Note(s): That the rnlA and rnlB genes are located together in the genome, such that the terminal region of the first gene overlaps the start region of the second one, that there is not a terminator sequence of transcription at the end of rnlA, and that both genes encode a toxin-antitoxin system, suggest that they are transcribed as an operon Koga M,2011
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Koga M., et al., 2011
Promoter
Name: rnlAp2
+1: 2765894
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: caggtggctaaatttagcaaatcaatacacttcaggggggtattattgtagagtttccccAtatgtttctatgggatccag
                     -35                    -10             +1                   
Note(s): Base on primer extension analysis, four 52'-termini specific to rnlA transcripts were identified 65, 46, 32, and 24 bp upstream of the initiation codon; however, only a strong signal for the last site was detected Otsuka Y,2010 rnlA promoter activity is much weaker than from the rnlB promoter Otsuka Y,2010
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Otsuka Y., et al., 2010
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR repressor rnlAp2 2765852 2765876 -29.5 taaatttagcAAATCAATACACTTCAGGGGGGTATtattgtagag nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [2]


Transcription unit       
Name: rnlA
Gene(s): rnlA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Nonaka G., et al., 2006
Promoter
Name: rnlAp
+1: 2765906
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 12
Sequence: tttagcaaatcaatacacttcaggggggtattattgtagagtttccccatatgtttctatGggatccaggaaatgacaatc
                          -35                -10            +1                   
Evidence: [AIPP]
[IDA]
Reference(s): [4] Nonaka G., et al., 2006


Transcription unit       
Name: rnlB
Synonym(s): yfjO
Gene(s): rnlB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Otsuka et al. in 2010 reported that there is a terminator sequence of transcription just downstream of the rnlB gene Otsuka Y,2010 but the sequence was not reported. Therefore, we have not added this terminator to the database.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Rhodius VA., et al., 2005
Promoter
Name: rnlBp
+1: 2766707
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 277
Sequence: cctgactactgtatgttactttatcctgaactacgcaccattgaaggtgtcttaaaaagtAagatgagtgggttaggcatg
                            -35                   -10       +1                   
Note(s): This promoter appears to be induced in two phases after σE induction. It is induced in a delayed way during the first 10 minutes following σE induction, decreased from 10 to 15 minutes, and induced from 15 to 20 minutes Lacoux C,2020.
Evidence: [AIPP]
[CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [5] Rhodius VA., et al., 2005
[3] Salgado H, et al., 2012


Transcription unit       
Name: rnlB
Synonym(s): yfjO
Gene(s): rnlB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Otsuka et al. in 2010 reported that there is a terminator sequence of transcription just downstream of the rnlB gene Otsuka Y,2010 but the sequence was not reported. Therefore, we have not added this terminator to the database.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [2] Otsuka Y., et al., 2010
Promoter
Name: rnlBp2
+1: 2766860
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 124
Sequence: tttgcagctactcttagaccggaacagattaacatcatcagcacagcctatactttttttAatgtggaacgtcattctctg
                            -35                  -10        +1                   
Note(s): Two transcriptional start site (TSS) rnlB transcripts were also detected 123 and 124 bp upstream of the initiation codon Otsuka Y,2010 Expression of the rnlB promoter was much higher than from the rnlA promoter, indicating that high rnlB activity is important for cell viability, because RnlA in the absence of RnlB induces cell death Otsuka Y,2010 rnlB can be transcribed from rnlA promoters as polycistronic mRNA (there is not a transcription terminator-like sequence upstream of the rnlB promoter) and from its own promoter as monocistronic mRNA Otsuka Y,2010
Evidence: [TIM]
Reference(s): [2] Otsuka Y., et al., 2010





RegulonDB