RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit       
Name: hisLGDCBHAFI
Gene(s): hisL, hisG, hisD, hisC, hisB, hisH, hisA, hisF, hisI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hisLGDCBHAFI operon codes for the enzymes of the histidine
biosynthesis pathway. It is controlled by attenuation in response to
histidine availability. When histidine is abundant, the ribosome quickly
translates through a stretch of seven histidine codons in the hisL
leader region, allowing formation of the transcriptional terminator between hisL
and hisG. In contrast, when histidine is not available, the
ribosome stalls within the leader region and the terminator will not form,
allowing transcription to continue Di Nocera PP,1978. Verde P,1981. Frunzio R, Bruni CB, Blasi F,1981.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
Reference(s): [1] Alifano P., et al., 1992
[2] Goldschmidt EP., et al., 1970
Promoter
Name: hisLp
+1: 2089965
Distance from start of the gene: 31
Sequence: ccataaaatatataaaaaagcccttgctttctaacgtgaaagtggtttaggttaaaagacAtcagttgaataaacattcac
Evidence: [CV(RPF/RS-EPT-CBR)]
[HIPP]
[RPF]
[RS-EPT-CBR]
Reference(s): [3] Salgado H, et al., 2012
[4] Verde P., et al., 1981
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp activation hisLp nd   [IDA] [5]
Evidence: [IDA] Inferred from direct assay
Reference(s): [5] Lee JH., et al., 2012


Transcription unit       
Name: hisL
Gene(s): hisL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [6] Di Nocera PP., et al., 1978
[4] Verde P., et al., 1981
Promoter
Name: hisLp
+1: 2089965
Distance from start of the gene: 31
Sequence: ccataaaatatataaaaaagcccttgctttctaacgtgaaagtggtttaggttaaaagacAtcagttgaataaacattcac
Evidence: [CV(RPF/RS-EPT-CBR)]
[HIPP]
[RPF]
[RS-EPT-CBR]
Reference(s): [3] Salgado H, et al., 2012
[4] Verde P., et al., 1981
Terminator(s)
Type: rho-independent
Sequence: aacgcatgagAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTtttattgcgc
Reference(s): [6] Di Nocera PP., et al., 1978
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp activation hisLp nd   [IDA] [5]
Evidence: [IDA] Inferred from direct assay
Reference(s): [5] Lee JH., et al., 2012


Transcription unit       
Name: hisBHAFI
Gene(s): hisB, hisH, hisA, hisF, hisI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hisA gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [7] Grisolia V., et al., 1983
Promoter
Name: hisBp
+1: 2093360
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 108
Sequence: ggcgcgctttaaagcctccagtgcggtgtttaaatctttgtgggatcagggcattatcttAcgtgatcagaataaacaacc
                             -35                       -10  +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [7] Grisolia V., et al., 1983
[8] Huerta AM., et al., 2003


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [9] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -27.0 2090108 2090146 acgcatgagaAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTgcgcggttga
  anti-terminator -16.9 2090079 2090124 agacattcagATCTTCCAGTGGTGCATGAACGCATGAGAAAGCCCCCGGAAGATCaccttccggg
  anti-anti-terminator -16.3 2090050 2090099 gactagtcttTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAAcgcatgagaa
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg; leader
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [10] null null
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  Histidine operon leader 131.6 2090022 2090145 uuaaacaccaCCAUCAUCACCAUCAUCCUGACUAGUCUUUCAGGCGAUGUGUGCUGGAAGACAUUCAGAUCUUCCAGUGGUGCAUGAACGCAUGAGAAAGCCCCCGGAAGAUCACCUUCCGGGGGCUUUUUUAUugcgcgguug
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

 [CV(RPF/RS-EPT-CBR)] cross validation(RPF/RS-EPT-CBR)

 [HIPP] Human inference of promoter position

 [RPF] RNA polymerase footprinting

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

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Alifano P., Carlomagno MS., Bruni CB., 1992, Location of the hisGDCBHAFI operon on the physical map of Escherichia coli., J Bacteriol 174(11):3830-1

 [2] Goldschmidt EP., Cater MS., Matney TS., Butler MA., Greene A., 1970, Genetic analysis of the histidine operon in Escherichia coli K12., Genetics 66(2):219-29

 [3] 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.

 [4] Verde P., Frunzio R., di Nocera PP., Blasi F., Bruni CB., 1981, Identification, nucleotide sequence and expression of the regulatory region of the histidine operon of Escherichia coli K-12., Nucleic Acids Res 9(9):2075-86

 [5] Lee JH., Lennon CW., Ross W., Gourse RL., 2012, Role of the coiled-coil tip of Escherichia coli DksA in promoter control., J Mol Biol 416(4):503-17

 [6] Di Nocera PP., Blasi F., Di Lauro R., Frunzio R., Bruni CB., 1978, Nucleotide sequence of the attenuator region of the histidine operon of Escherichia coli K-12., Proc Natl Acad Sci U S A 75(9):4276-80

 [7] Grisolia V., Riccio A., Bruni CB., 1983, Structure and function of the internal promoter (hisBp) of the Escherichia coli K-12 histidine operon., J Bacteriol 155(3):1288-96

 [8] 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

 [9] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

 [10] null, null, null, null


RegulonDB