RegulonDB RegulonDB 10.8: Operon Form
   

yicR-rpmBG-mutM operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yicR-rpmBG-mutM
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: mutM
Gene(s): mutM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutMp
+1: 3811175
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 23
Sequence: taacaaaaaacctcgctccggcggggttttttgttatctgcttgcccccatattgactgcAtctgttcattcctggagatg
                           -35                -10           +1                   
Note(s): The sigma factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005.
Evidence: [AIPP]
[TIM]
Reference(s): [1] Gifford CM., et al., 1999
[2] Nonaka G., et al., 2006
[3] Zhao K., et al., 2005


Transcription unit       
Name: rpmBG-mutM
Gene(s): mutM, rpmG, rpmB   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a strong attenuator downstream of the rpmG gene.
FNR represses rpmB gene expression under anaerobiosis, but it is still not known which of the two promoters (rpmBp or radCp) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: rpmBp
+1: 3811995
Distance from start of the gene: 321
Sequence:
Evidence: [CV(TA/TIM)]
[HTIM]
[TIM]
Reference(s): [1] Gifford CM., et al., 1999
[4] Maciag A., et al., 2011
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpmBp The rpmB-rpmG operon is regulated by ppGpp-DksA-dependent negative stringent control under amino acid starvation, most likely due to the features of the discriminator region (G/C rich) separating the -10 promoter element from the transcription start site (TSS) Aseev LV,2016 [GEA] [5]
Evidence: [GEA] Gene expression analysis
Reference(s): [5] Aseev LV., et al., 2016


Transcription unit       
Name: rpmBG
Gene(s): rpmG, rpmB   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a strong attenuator downstream of rpmG gene.
FNR represses rpmB gene expression under anaerobiosis, but it is still not know which of the two promoters (rpmBp, radCp) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Reference(s): [6] Maguire BA., et al., 1997
Promoter
Name: rpmBp
+1: 3811995
Distance from start of the gene: 321
Sequence:
Evidence: [CV(TA/TIM)]
[HTIM]
[TIM]
Reference(s): [1] Gifford CM., et al., 1999
[4] Maciag A., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: ataacaaaaaACCCCGCCGGAGCGAGGttttttgtta
Reference(s): [7] Lee JS., et al., 1981
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpmBp The rpmB-rpmG operon is regulated by ppGpp-DksA-dependent negative stringent control under amino acid starvation, most likely due to the features of the discriminator region (G/C rich) separating the -10 promoter element from the transcription start site (TSS) Aseev LV,2016 [GEA] [5]
Evidence: [GEA] Gene expression analysis
Reference(s): [5] Aseev LV., et al., 2016


Transcription unit       
Name: yicR-rpmBG
Gene(s): rpmG, rpmB, yicR   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a strong attenuator downstream of the rpmG gene.
FNR represses rpmB gene expression under anaerobiosis, but it is still not known which of the two promoters (rpmBp or radCp) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: yicRp
+1: 3812577
Distance from start of the gene: 18
Sequence: gctttccaggattgaaaactggccgtcgatttaacgaaacggctatgacaggatgcgagcAccacaaaggaggtgaaggtg
Note(s): This promoter appears to be a weak promoter.
Evidence: [TIM]
Reference(s): [1] Gifford CM., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: ataacaaaaaACCCCGCCGGAGCGAGGttttttgtta
Reference(s): [7] Lee JS., et al., 1981


Transcription unit       
Name: yicR-rpmBG-mutM
Gene(s): mutM, rpmG, rpmB, yicR   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a strong attenuator downstream of the rpmG gene.
FNR represses rpmB gene expression under anaerobiosis, but it is still not known which of the two promoters (rpmBp or radCp) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: yicRp
+1: 3812577
Distance from start of the gene: 18
Sequence: gctttccaggattgaaaactggccgtcgatttaacgaaacggctatgacaggatgcgagcAccacaaaggaggtgaaggtg
Note(s): This promoter appears to be a weak promoter.
Evidence: [TIM]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: mutM
Gene(s): mutM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999




Reference(s)    

 [1] Gifford CM., Wallace SS., 1999, The genes encoding formamidopyrimidine and MutY DNA glycosylases in Escherichia coli are transcribed as part of complex operons., J Bacteriol 181(14):4223-36

 [2] 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

 [3] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [5] Aseev LV., Koledinskaya LS., Boni IV., 2016, Regulation of Ribosomal Protein Operons rplM-rpsI, rpmB-rpmG, and rplU-rpmA at the Transcriptional and Translational Levels., J Bacteriol 198(18):2494-502

 [6] Maguire BA., Wild DG., 1997, Mutations in the rpmBG operon of Escherichia coli that affect ribosome assembly., J Bacteriol 179(8):2486-93

 [7] Lee JS., An G., Friesen JD., Isono K., 1981, Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB) and L33 (rpmG)., Mol Gen Genet 184(2):218-23


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