RegulonDB RegulonDB 11.2: 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
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[2] Paterson ES., et al., 2002
TF binding sites (TFBSs)
[MarA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator ybjCp 890842 890862 -40.5 ttaattgctaAAAGCTATAACTGTTAAACACaatacagtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [9]
[OxyR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor ybjCp 890812 890828 -72.0 attcgctgaaAGTAGGTTTAACCTGTTgcattaattg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [5]
proximal OxyR repressor ybjCp 890834 890850 -50.0 ctgttgcattAATTGCTAAAAGCTATAactgttaaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [5], [8]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator ybjCp 890842 890861 -40.5 ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [9]
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator ybjCp 890826 890845 -56.5 ggtttaacctGTTGCATTAATTGCTAAAAGctataactgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [6], [7], [8]
proximal SoxS activator ybjCp 890842 890862 -40.5 ttaattgctaAAAGCTATAACTGTTAAACACaatacagtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-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: [EXP-IEP]
Reference(s): [10] Zaslaver A., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-IEP] Inferred from expression pattern


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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