RegulonDB RegulonDB 11.1: Operon Form
   

argX-hisR-leuT-proM operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: argX-hisR-leuT-proM
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: argX-hisR-leuT-proM
Synonym(s): argX
Gene(s): argX, hisR, leuT, proM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Ow MC., et al., 2002
Promoter
Name: argXp
+1: 3982364
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 11
Sequence: gcaatttatttaaaaagggactagacagaggggtgggaagtccgtattatccacccccgcAacggcgctaagcgcccgtag
                      -35                    -10            +1                   
Note(s): argXp promoter activity is inhibited by the stringent response in vivo Rowley KB,1993.
The transcription of the argXp promoter, also called the argTp promoter, is reduced by guanosine tetraphosphate (ppGpp), which modifies the RNA polymerase that forms an inactive promoter complex Maitra A,2005. Toulokhonov II,2001.
Individually, DksA and ppGpp activate and inhibit, respectively, the transcription started from the argX promoter (argXp). On the other hand, argXp also is regulated negatively by DksA, and this response occurs in the absence of ppGpp Lyzen R,2016
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Maitra A., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: cgccgaccaaTTTTGAACCCCGCTTCGGCGGGGTTTTTTgttttctgtg
Reference(s): [3] Hsu LM., et al., 1984
[4] Peters JM., et al., 2009
[5] Zuker M. 2003
TF binding sites (TFBSs)
[Fis,+] 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
proximal Fis activator argXp 3982282 3982296 -75.0 agcagcaaaaCGCACAAACCGTAACcaaacgcgca nd [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA activation argXp nd   [EXP-IDA] [6]
  DksA-ppGpp inhibition argXp nd   [EXP-IDA] [6]
  ppGpp inhibition argXp nd   [EXP-IDA] [6]
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [6] Lyzen R., et al., 2016


Evidence    

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

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

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Ow MC., Kushner SR., 2002, Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli., Genes Dev 16(9):1102-15

 [2] Maitra A., Shulgina I., Hernandez VJ., 2005, Conversion of active promoter-RNA polymerase complexes into inactive promoter bound complexes in E. coli by the transcription effector, ppGpp., Mol Cell 17(6):817-29

 [3] Hsu LM., Klee HJ., Zagorski J., Fournier MJ., 1984, Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs., J Bacteriol 158(3):934-42

 [4] Peters JM., Mooney RA., Kuan PF., Rowland JL., Keles S., Landick R., 2009, Rho directs widespread termination of intragenic and stable RNA transcription., Proc Natl Acad Sci U S A 106(36):15406-11

 [5] Zuker M., 2003, Mfold web server for nucleic acid folding and hybridization prediction., Nucleic Acids Res 31(13):3406-15

 [6] Lyzen R., Maitra A., Milewska K., Kochanowska-Lyzen M., Hernandez VJ., Szalewska-Palasz A., 2016, The dual role of DksA protein in the regulation of Escherichia coli pArgX promoter., Nucleic Acids Res 44(21):10316-10325

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