RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: rutABCDEFG
Gene(s): rutG, rutF, rutE, rutD, rutC, rutB, rutA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Loh KD., et al., 2006
[2] Zimmer DP., et al., 2000
Promoter
Name: rutAp
+1: 1074026
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 15
Sequence: aacagattaataacattaactttttaaaaactggcatccgctttgcaaacaagccaatacGcggctgaaaaggatatgcag
                                     -24        -12         +1                   
Note(s): This promoter was identified by microarray and ChIP assays with a mutant
σ54 strain and a σ54-overexpressing strain,
and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [3] Huerta AM., et al., 2003
[4] Reitzer L., et al., 2001
[5] Zhao K., et al., 2010
TF binding sites (TFBSs)
[ArcA,+] 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
remote ArcA-phosphorylated activator rutAp 1074116 1074130 -97.0 ctgttttgacCGTTTAGTCCACTTTttaccagata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
[NtrC,+] 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
remote NtrC-phosphorylated activator rutAp 1074142 1074158 -124.0 cgcgcacagaTGCATGTTTTATGTGCAactgttttga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
remote NtrC-phosphorylated activator rutAp 1074163 1074179 -145.0 ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
[PhoP,+] 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
remote PhoP-phosphorylated activator rutAp 1074125 1074140 -106.0 ttatgtgcaaCTGTTTTGACCGTTTAgtccactttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[RutR,-] 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
remote RutR repressor rutAp 1074120 1074138 -102.5 atgtgcaactGTTTTGACCGTTTAGTCCActttttacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

 [EXP-IEP] Inferred from expression pattern

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Loh KD., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim KS., Parales R., Zhou Z., Inwood W., Kustu S., 2006, A previously undescribed pathway for pyrimidine catabolism., Proc Natl Acad Sci U S A 103(13):5114-9

 [2] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

 [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] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [5] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [6] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [7] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57

 [8] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5

 [9] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

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