RegulonDB RegulonDB 10.9: Operon Form
   

rpsLG-fusA-tufA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rpsLG-fusA-tufA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: tufA
Gene(s): tufA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Zengel JM., et al., 1990
Promoter
Name: tufAp2
+1: 3471583
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 254
Sequence: ggaagagaacaccggtgacgttatcggtgacttgagccgtcgtcgtggtatgctcaaaggTcaggaatctgaagttactgg
                           -35                   -10        +1                   
Note(s): T1 nuclease mapping was used to identified the tufAp2 promoter; however, the exact position was not determined Zengel JM,1990
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
[4] Zengel JM., et al., 1984
[1] Zengel JM., et al., 1990


Transcription unit       
Name: tufA
Gene(s): tufA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Zengel JM., et al., 1990
Promoter
Name: tufAp1
+1: 3471724
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 395
Sequence: tctgcacttcggttcttaccatgacgttgactcctctgaactggcgtttaaactggctgcTtctatcgcctttaaagaagg
                           -35                   -10        +1                   
Note(s): T1 nuclease mapping was used to identified the tufAp1 promoter; however, the exact position was not determined Zengel JM,1990
Evidence: [HIPP]
[ICWHO]
[IEP]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[5] Zaslaver A., et al., 2006
[4] Zengel JM., et al., 1984
[1] Zengel JM., et al., 1990


Transcription unit       
Name: fusA-tufA
Gene(s): tufA, fusA   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses tufA gene expression under anaerobiosis, but it is not known which transcription unit is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [IC] Inferred by curator
Promoter
Name: fusAp
+1: 3473685
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 171
Sequence: gataaatccatggctctgcgcctggcgaacgaactttctgatgctgcagaaaacaaaggtActgcagttaagaaacgtgaa
                               -35                   -10    +1                   
Note(s):

Evidence: [AIPP]
[ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[6] Rezuchova B., et al., 2003
[7] Rhodius VA., et al., 2005


Transcription unit       
Name: rpsLG-fusA-tufA
Gene(s): tufA, fusA, rpsG, rpsL   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses tufA gene expression under anaerobiosis, but it is not known which transcription unit is affected, or even if this regulation is direct or indirect Salmon K,2003.
Reference(s): [8] Johanson U., et al., 1992
[9] Post LE., et al., 1978
[10] Saito K., et al., 1994
Promoter
Name: rpsLp
+1: 3474621
Distance from start of the gene: 69
Sequence: gtgatggcgggatcgttgtatatttcttgacaccttttcggcatcgccctaaaattcggcGtcctcatattgtgtgaggac
Evidence: [RPF]
Reference(s): [11] Post LE., et al., 1978
[9] Post LE., et al., 1978
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsLp nd Together ppGpp and DksA can inhibit more strongly the transcription initiation from the ribosomal protein promoter in vitro and in vivo Lemke JJ,2011 [APPH]
[GEA]
[IMP]
[12]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [12] Lemke JJ., et al., 2011


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.2 3474593 3474623 ctaaaattcgGCGTCCTCATATTGTGTGAGGACGTTTTATtacgtgttta
  terminator -19.7 3471349 3471374 ccaaagtcccGTGCTCTCTCCTGAAGGGGAGAGCActatagtaag
  anti-terminator -5.6 3474619 3474653 tatatttcttGACACCTTTTCGGCATCGCCCTAAAATTCGGCGTcctcatattg
  anti-anti-terminator -9.1 3474637 3474679 atggcctggtGATGGCGGGATCGTTGTATATTTCTTGACACCTTTTCGGCATcgccctaaaa
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"




Reference(s)    

 [1] Zengel JM., Lindahl L., 1990, Mapping of two promoters for elongation factor Tu within the structural gene for elongation factor G., Biochim Biophys Acta 1050(1-3):317-22

 [2] 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

 [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] Zengel JM., Archer RH., Lindahl L., 1984, The nucleotide sequence of the Escherichia coli fus gene, coding for elongation factor G., Nucleic Acids Res 12(4):2181-92

 [5] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [6] Rezuchova B., Miticka H., Homerova D., Roberts M., Kormanec J., 2003, New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system., FEMS Microbiol Lett 225(1):1-7

 [7] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [8] Johanson U., Hughes D., 1992, Comparison of the complete sequence of the str operon in Salmonella typhimurium and Escherichia coli., Gene 120(1):93-8

 [9] Post LE., Arfsten AE., Reusser F., Nomura M., 1978, DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli., Cell 15(1):215-29

 [10] Saito K., Mattheakis LC., Nomura M., 1994, Post-transcriptional regulation of the str operon in Escherichia coli. Ribosomal protein S7 inhibits coupled translation of S7 but not its independent translation., J Mol Biol 235(1):111-24

 [11] Post LE., Arfsten AE., Nomura M., Jaskunas SR., 1978, Isolation and characterization of a promoter mutant in the str ribosomal protein operon in E. coli., Cell 15(1):231-6

 [12] Lemke JJ., Sanchez-Vazquez P., Burgos HL., Hedberg G., Ross W., Gourse RL., 2011, Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA., Proc Natl Acad Sci U S A 108(14):5712-7


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