RegulonDB RegulonDB 11.1: Operon Form
   

umpG-pcm operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: umpG-pcm
Synonym(s): surE-pcm
Gene(s): pcm, umpG   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on fusions with lacZ, a promoter (designated P3) was identified upstream of the pcm gene. It was induced both in growing cells and in cells approaching stationary phase, both independent of σS. However, any good promoter could be identified in this region by sequence comparison. Primer extension analysis was not done for identifying the +1 site of the transcriptional start site Li C, Wu PY, Hsieh M,1997
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Li C., et al., 1994
[2] Visick JE., et al., 1998
Promoter
Name: surEp2
+1: 2870686
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 412
Sequence: gatcgcaataaacggagtttttggttgtcggcagcccgcagtgcgttgtttaatcagattGttgctgagcgcctcaaaaaa
                              -35                        -10+1                   
Note(s): Although surEp2 is expressed in the stationary phase, it is not controlled by the rpoS sigma factor. surEp2 presents a typical σ70 promoter with homologous -10 and 35 regions Li C, Wu PY, Hsieh M,1997
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[1] Li C., et al., 1994
[4] Salgado H, et al., 2012


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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


Reference(s)    

 [1] Li C., Ichikawa JK., Ravetto JJ., Kuo HC., Fu JC., Clarke S., 1994, A new gene involved in stationary-phase survival located at 59 minutes on the Escherichia coli chromosome., J Bacteriol 176(19):6015-22

 [2] Visick JE., Ichikawa JK., Clarke S., 1998, Mutations in the Escherichia coli surE gene increase isoaspartyl accumulation in a strain lacking the pcm repair methyltransferase but suppress stress-survival phenotypes., FEMS Microbiol Lett 167(1):19-25

 [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.

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