RegulonDB RegulonDB 10.9: Operon Form
   

ybjC-nfsA-rimK-ybjN operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ybjC-nfsA-rimK-ybjN
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ybjC-nfsA-rimK-ybjN
Gene(s): ybjC, nfsA, rimK, ybjN   Genome Browser M3D Gene expression COLOMBOS
Note(s): nfsA is induced by glycolaldehyde in a way that is oxygen and SoxS dependent. This gene is expressed in a transcription unit together with other genes (ybjC-nfsA-rimK-ybjN). Therefore, it is probable that glycolaldehyde affects the expression of the complete transcription unit.
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kang WK., et al., 1989
[2] Paterson ES., et al., 2002
Promoter
Name: ybjCp
+1: 890892
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 21
Sequence: ttaattgctaaaagctataactgttaaacacaatacagtgaaaagttttagactgaaggcTcactttgcagagggaagcgt
                        -35                      -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[2] Paterson ES., et al., 2002
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 MarA activator ybjCp 890842 890861 -40.5 ttaattgctaAAAGCTATAACTGTTAAACACaatacagtga nd [AIBSCS], [APIORCISFBSCS], [CEEUMA], [GEA], [RSE] [7], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor ybjCp 890812 890828 -72.0 attcgctgaaAGTAGGTTTAACCTGTTGcattaattgc nd [APIORCISFBSCS], [BPP], [GEA] [4], [5]
proximal OxyR repressor ybjCp 890834 890850 -50.0 ctgttgcattAATTGCTAAAAGCTATAActgttaaaca nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [4], [5], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator ybjCp 890842 890861 -40.5 ttaattgctaAAAGCTATAACTGTTAAACACaatacagtga nd [AIBSCS], [APIORCISFBSCS], [CEEUMA], [GEA], [RSE] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator ybjCp 890826 890845 -56.5 ggtttaacctGTTGCATTAATTGCTAAAAGCtataactgtt nd [APIORCISFBSCS], [BPP], [CEEUMA], [GEA], [IHBCE], [RSE] [2], [6], [7], [8]
proximal SoxS activator ybjCp 890842 890861 -40.5 ttaattgctaAAAGCTATAACTGTTAAACACaatacagtga nd [AIBSCS], [APIORCISFBSCS], [CEEUMA], [GEA], [RSE] [7], [9]


Transcription unit       
Name: rimK-ybjN
Gene(s): rimK, ybjN   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rimK . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Kang WK., et al., 1989
Promoter
Name: rimKp
+1: 891876
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 91
Sequence: ctggagcgatcatatccgccgaacaatcattaaagaaagccgcccatttattctggattaTttgcacaaacagggttgggc
                          -35                    -10        +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
[ICWHO]
[IMP]
Reference(s): [3] Huerta AM., et al., 2003
[1] Kang WK., et al., 1989


Transcription unit       
Name: ybjN
Gene(s): ybjN   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: ybjNp
+1: Unknown
Evidence: [IEP]
Reference(s): [10] Zaslaver A., et al., 2006




Reference(s)    

 [1] Kang WK., Icho T., Isono S., Kitakawa M., Isono K., 1989, Characterization of the gene rimK responsible for the addition of glutamic acid residues to the C-terminus of ribosomal protein S6 in Escherichia coli K12., Mol Gen Genet 217(2-3):281-8

 [2] Paterson ES., Boucher SE., Lambert IB., 2002, Regulation of the nfsA Gene in Escherichia coli by SoxS., J Bacteriol 184(1):51-8

 [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] Tao K., 1997, oxyR-dependent induction of Escherichia coli grx gene expression by peroxide stress., J Bacteriol 179(18):5967-70

 [5] Zheng M., Wang X., Templeton LJ., Smulski DR., LaRossa RA., Storz G., 2001, DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide., J Bacteriol 183(15):4562-70

 [6] Benov L., Fridovich I., 2002, Induction of the soxRS regulon of Escherichia coli by glycolaldehyde., Arch Biochem Biophys 407(1):45-8

 [7] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15

 [8] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [9] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24

 [10] 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

 [11] Hao Y., Updegrove TB., Livingston NN., Storz G., 2016, Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA., Nucleic Acids Res 44(14):6935-48


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