RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: rpmE
Gene(s): rpmE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: rpmEp1
+1: 4126854
Distance from start of the gene: 159
Sequence: acgtgggcaacgggcatagcatcatcctgacttgaaattcggtgggttagtatacacattGccgtagaagagtgcggatca
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Aseev LV., et al., 2020
[2] Thomason MK., et al., 2015
Terminator(s)
Type: rho-independent
Sequence: gatttccgaaAAAAGCGCCGCACGGCGCTTTTtttgtgcctg
Reference(s): [1] Aseev LV., et al., 2020


Transcription unit       
Name: rpmE
Gene(s): rpmE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: rpmEp2
+1: 4126908
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 105
Sequence: cacattgccgtagaagagtgcggatcagtttgcatacgctggttaatttctgtatgatttCgcgccttcgtacgaaatgat
Evidence: [EXP-IDA]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IEP]
Reference(s): [1] Aseev LV., et al., 2020
[3] Mendoza-Vargas A., et al., 2009
[4] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: gatttccgaaAAAAGCGCCGCACGGCGCTTTTtttgtgcctg
Reference(s): [1] Aseev LV., et al., 2020
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition rpmEp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [5] Traxler MF., et al., 2008


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.8 4126966 4127001 gtggtgtctgGCGTTAGGGCTGGAAGAGCGACGCGGCCTTAAACCgaggttttcc
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

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

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-IDA] Inferred from direct assay

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Aseev LV., Koledinskaya LS., Boni IV., 2020, Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b., RNA 26(7):814-826

 [2] Thomason MK., Bischler T., Eisenbart SK., Forstner KU., Zhang A., Herbig A., Nieselt K., Sharma CM., Storz G., 2015, Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli., J Bacteriol 197(1):18-28

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [5] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48

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