RegulonDB RegulonDB 11.1: Operon Form
   

nrdR-ribDE-nusB-thiL-pgpA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: nrdR-ribDE-nusB-thiL-pgpA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: nrdR-ribDE-nusB-thiL-pgpA
Gene(s): nrdR, ribD, ribE, nusB, thiL, pgpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IMP-POLAR-MUTATION] Polar mutation
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Torrents E., et al., 2007
Promoter
Name: nrdRp
+1: 432977
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: ctttatctcaaaagcgttgcgcctttgttgtatcgtcagttcagggtaaaatagatttccGttaaccacctggtcaggacg
                         -35                   -10          +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
[1] Torrents E., et al., 2007


Transcription unit       
Name: ribE-nusB-thiL-pgpA
Gene(s): ribE, nusB, thiL, pgpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [4] Nonaka G., et al., 2006
Promoter
Name: ribEp
+1: 434504
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 143
Sequence: ccgcggattatgcacgctgccagggcttgagaaattagccgacgccccccaatttaaattCaaagagatacgtcatgtagg
                           -35                 -10          +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[4] Nonaka G., et al., 2006
[3] Salgado H, et al., 2012


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] Torrents E., Grinberg I., Gorovitz-Harris B., Lundstrom H., Borovok I., Aharonowitz Y., Sjoberg BM., Cohen G., 2007, NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes., J Bacteriol 189(14):5012-21

 [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] 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.

 [4] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

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