RegulonDB RegulonDB 10.9: Operon Form
   

yrbG-kdsDC-lptCAB-rpoN-hpf-ptsN-rapZ-npr operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yrbG-kdsDC-lptCAB-rpoN-hpf-ptsN-rapZ-npr
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: yrbG-kdsD
Gene(s): yrbG, kdsD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Martorana AM., et al., 2011
[2] Sperandeo P., et al., 2006
Promoter
Name: yrbGp
+1: 3340211
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 64
Sequence: cgtggttagcgaaagctggcatttgttttactttttagccgcataaagtcaaaattaagcAtccgttacggctttctgaaa
                       -35                  -10             +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[2] Sperandeo P., et al., 2006


Transcription unit       
Name: yrbG-kdsDC-lptCAB
Gene(s): yrbG, kdsD, kdsC, lptC, lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The yrbG-kdsDC-lptCAB operon encodes genes for LPS synthesis and transport. This operon is expressed differentially because it contains several internal promoters Martorana AM,2011 Even so, the transcription of this operon may be extended to the downstream operon, which contains the rpoN geneMartorana AM,2011
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Martorana AM., et al., 2011
Promoter
Name: yrbGp
+1: 3340211
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 64
Sequence: cgtggttagcgaaagctggcatttgttttactttttagccgcataaagtcaaaattaagcAtccgttacggctttctgaaa
                       -35                  -10             +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[2] Sperandeo P., et al., 2006


Transcription unit       
Name: kdsC-lptCAB
Gene(s): kdsC, lptC, lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Martorana AM., et al., 2011
Promoter
Name: kdsCp3
+1: 3341719
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 554
Sequence: cgcccggagagcagcatggcgcgcgccgcagatgtgcatctgtgtgttaaagtagcgaaaGaagcctgtccgttagggctg
                           -35                  -10         +1                   
Note(s): The kdsCp3 promoter contains an extended -10 box Martorana AM,2011
Evidence: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Martorana AM., et al., 2011


Transcription unit       
Name: kdsC-lptCAB
Gene(s): kdsC, lptC, lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Martorana AM., et al., 2011
Promoter
Name: kdsCp2
+1: 3342010
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 263
Sequence: ttgctggaagttacccgcaaaaatcttggtatgactgtcatttgcgatgacaatatgatgAttgaaggcatctttaccgac
                               -35                    -10   +1                   
Evidence: [HIPP]
[ICWHO]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Martorana AM., et al., 2011
[4] Salgado H, et al., 2012


Transcription unit       
Name: kdsC-lptCAB
Synonym(s): kdsC-yrbK
Gene(s): kdsC, lptC, lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Martorana AM., et al., 2011
[2] Sperandeo P., et al., 2006
Promoter
Name: kdsCp1
+1: 3342226
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 47
Sequence: catatcacctccgtgatggttgccgatggcgaccatttactcggtgtgttacatatgcatGatttactgcgtgcaggcgta
                           -35                        -10   +1                   
Note(s): The kdsCp1 promoter has an extended -10 box , and this property may compensate for the poor -35 box that it contains Martorana AM,2011
Evidence: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Martorana AM., et al., 2011


Transcription unit       
Name: lptAB
Gene(s): lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Martorana AM., et al., 2011
[2] Sperandeo P., et al., 2006
Promoter
Name: lptAp2
+1: 3343299
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 81
Sequence: agatcaatctggtgacgcaggatgttacctctgaagacctcgtcacgttatacggaacaaCatttaactccagcggtctga
                      -35                   -10             +1                   
Note(s): lptAp2 is a promoter that shows very weak activity, and its -10 and -35 boxes are poorly conserved, compared to consensus sequences of σ70 promoters Martorana AM,2011
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Martorana AM., et al., 2011


Transcription unit       
Name: lptAB
Gene(s): lptA, lptB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Martorana AM., et al., 2011
[2] Sperandeo P., et al., 2006
Promoter
Name: lptAp1
+1: 3343326
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 54
Sequence: cctctgaagacctcgtcacgttatacggaacaacatttaactccagcggtctgaaaatgcGcggcaacttacgcagcaaga
                            -35                   -10       +1                   
Note(s): The lptAp1 promoter depends on σE for its activity; however, this promoter is not activated under all stress conditions that activate σE, although the promoter is activated by a very specific stress condition that induces modifications in lipopolysaccharide (LPS) composition and biogenesis Martorana AM,2011 For that, it is possible that at least an additional transcription factor, whose activity is affected by LPS stress, is also involved in the regulation of the lptAp1 promoter Martorana AM,2011
Evidence: [HIPP]
[ICWHO]
[IDA]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Martorana AM., et al., 2011
[5] Sperandeo P., et al., 2007
[2] Sperandeo P., et al., 2006


Transcription unit       
Name: lptB-rpoN-hpf-ptsN-yhbJ
Synonym(s): lptB-rpoN-yhbH-ptsN-yhbJ, yhbG-rpoN-yhbH-ptsN-yhbJ
Gene(s): lptB, rpoN, hpf, ptsN, rapZ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the rpoN gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants of two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [6] Rhodius VA., et al., 2005
Promoter
Name: lptBp
+1: 3343396
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 548
Sequence: acgcagcaagaacgccgagctgattgaaaaggttagaacatcctatgaaattcaaaacaaAcaaactcagccttaatcttg
                            -35                     -10     +1                   
Evidence: [AIPP]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[6] Rhodius VA., et al., 2005


Transcription unit       
Name: rpoN-hpf-ptsN-yhbJ-npr
Synonym(s): rpoN-ORFII-ORF-III-ORF-IV-ORFV, rpoN-yhbH-ptsN-yhbJ-npr, rpoN-yhbH-ptsN-yhbJ-ptsO
Gene(s): rpoN, hpf, ptsN, rapZ, npr   Genome Browser M3D Gene expression COLOMBOS
Note(s): To test whether the ORFs downstream of the rpoN gene are cotranscribed and encode proteins, this region was subjected to Maxicell and T7 promoter analysis. The results show they are coexpressed with the rpoN gene.
The ORFV is the last ORF of the rpoN operon, consistent with our identification of a likely rho-dependent terminator after ORFV.
The expression of the rpoN gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants of two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [7] Jones DH., et al., 1994
Promoter
Name: rpoNp
+1: 3344662
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 55
Sequence: cgcctacagaaatcttacaagacgaacacgttaagcgtgtataccttggggaagacttcaGactctgatagggtagaagtt
                               -35                  -10     +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [3] Huerta AM., et al., 2003
[7] Jones DH., et al., 1994
Terminator(s)
Type: rho-dependent
Sequence: tgacatacaaCTCCCTTCAAACTCCCCCCGACAATAAGAaaatcacgta
Reference(s): [7] Jones DH., et al., 1994


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.1 3340155 3340179 cccgccgtggTTAGCGAAAGCTGGCATTTGTTTTactttttagc
  terminator -18.1 3346532 3346570 gttaatgctcCGAGCCTGTTCCACTGTTTGAGTGGGCAGGTTCTTAGGtgaaattatg
  anti-terminator -4.6 3340104 3340161 taagcatggcGCTCAATTTAACCTTGAACCCAACATATTTACAGAATATTACCCGCCGTGGTTAGCGaaagctggca
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"




Reference(s)    

 [1] Martorana AM., Sperandeo P., Polissi A., Deho G., 2011, Complex transcriptional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis., Res Microbiol 162(5):470-82

 [2] Sperandeo P., Pozzi C., Deho G., Polissi A., 2006, Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus., Res Microbiol 157(6):547-58

 [3] 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

 [4] 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.

 [5] Sperandeo P., Cescutti R., Villa R., Di Benedetto C., Candia D., Deho G., Polissi A., 2007, Characterization of lptA and lptB, two essential genes implicated in lipopolysaccharide transport to the outer membrane of Escherichia coli., J Bacteriol 189(1):244-53

 [6] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [7] Jones DH., Franklin FC., Thomas CM., 1994, Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli., Microbiology 140 ( Pt 5):1035-43


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