RegulonDB RegulonDB 10.8: Operon Form
   

metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: pnp
Gene(s): pnp   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Regnier P., et al., 1986
Promoter
Name: pnpp
+1: 3311326
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 158
Sequence: gagtggccccttttttcaagctgacggcagcaattcactggaaactaatgtattgttgctAtgaatgatcttccgttgcag
                             -35                   -10      +1                   
Note(s): The initiation efficiency at the pnp promoter is poor due to its poor homology to the consensus sequence in the -35 region. Regnier P,1986.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Regnier P., et al., 1986
Terminator(s)
Type: rho-independent
Sequence: cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s): [2] Regnier P., et al., 1987


Transcription unit       
Name: rpsO
Gene(s): rpsO   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Regnier P., et al., 1986
Promoter
Name: rpsOp
+1: 3311786
Distance from start of the gene: 102
Sequence: aatacccggcgtaatgttaaccgtcttgcgataacaggtcgctacgagtagaatactgccGcttaacgtcgcgtaaattgt
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Regnier P., et al., 1986
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gtcagcttgaAAAAAGGGGCCACTCAGGCCCCCTTTTctgaaactcg
Reference(s): [1] Regnier P., et al., 1986
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition rpsOp   [GEA] [4]
Evidence: [GEA] Gene expression analysis
Reference(s): [4] Traxler MF., et al., 2008


Transcription unit       
Name: rpsO-pnp
Gene(s): pnp, rpsO   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Regnier P., et al., 1986
Promoter
Name: rpsOp
+1: 3311786
Distance from start of the gene: 102
Sequence: aatacccggcgtaatgttaaccgtcttgcgataacaggtcgctacgagtagaatactgccGcttaacgtcgcgtaaattgt
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Regnier P., et al., 1986
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s): [2] Regnier P., et al., 1987
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition rpsOp   [GEA] [4]
Evidence: [GEA] Gene expression analysis
Reference(s): [4] Traxler MF., et al., 2008


Transcription unit       
Name: infB
Gene(s): infB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [5] Brandi A., et al., 2019
Promoter
Name: infBp
+1: 3316027
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 13
Sequence: actgattatggctgcccgtaatatttgctggttcggtgacgaagcgtaataaactgtagcAggaaggaacagcatgacaga
                         -35                      -10       +1                   
Note(s): The activity of the infBp promoter is increased under cold shock Brandi A,2019.
This transcription initiation of this promoter was mapped in the strain MRE600; however, the full size of the transcript unit of infB was determined in strains derived from K-12. On the other hand, the other promoters transcribing infBp mapped in the same nucleotide in a strain derived from K-12 as in MRE600 Brandi A,2019.
Evidence: [HIPP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
Terminator(s)
Type: rho-independent
Sequence: ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001


Transcription unit       
Name: nusA-infB
Gene(s): infB, nusA   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit was mapped in the strain MRE600; however, the full size of the transcript of the other transcription unit containing the infB gene was determined in a strain derived from K-12, suggesting that the transcription is similar in both strains Brandi A,2019.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [5] Brandi A., et al., 2019
Promoter
Name: nusAp
+1: 3317602
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 76
Sequence: cgttatcaaagcggtagacggtgaaatgatcacagttaccgtcgaaggtaaagatgaagtGttcgcgctgagtaatatcca
                             -35                  -10       +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
Terminator(s)
Type: rho-independent
Sequence: ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001


Transcription unit       
Name: rimP-nusA-infB
Synonym(s): yhbC-nusA-infB
Gene(s): infB, nusA, rimP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [8] Regnier P., et al., 1990
[9] Regnier P., et al., 1989
Promoter
Name: rimPp
+1: 3318175
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 169
Sequence: ttcaaatccggcccccgcaaccactttcccttagagtcctttttcaaatatactgtgaagActtcggccttcgtagtggga
                          -35                    -10        +1                   
Note(s): The activity of the rimPp promoter is increased under cold shock Brandi A,2019.
Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006.
Evidence: [CV(TIM)]
[HIPP]
[HTIM]
[IEP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[10] Maciag A., et al., 2011
[9] Regnier P., et al., 1989
[11] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001


Transcription unit          
Name: metY
Gene(s): metY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [12] Ishii S., et al., 1984
[13] Nagase T., et al., 1988
Promoter
Name: metYp1
+1: 3318297
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 8
Sequence: cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc
                         -35                    -10         +1                   
Note(s): Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence: [HIPP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[12] Ishii S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: taacaaaaaaCCCCGATAAATCGGGGctttatataa
Reference(s): [12] Ishii S., et al., 1984
[14] Peters JM., et al., 2009
[15] Zuker M. 2003
Type: rho-independent
Sequence: cataaaaaaaGGGCCTAAAGCCCagttattctg
Reference(s): [12] Ishii S., et al., 1984
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator metYp1 3318365 3318379 -75.0 actataatgcCTGCAGATTTTACGTcccgtctcgg nd [BCE], [IHBCE] [16]


Transcription unit          
Name: metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
Gene(s): pnp, rpsO, truB, rbfA, infB, nusA, rimP, metY   Genome Browser M3D Gene expression COLOMBOS
Note(s): Sometimes the transcription initiated upstream of the metY gene reads through into the rpsO-pnp genes Sands JF,1988.
Evidence: [PM] Polar mutation
Reference(s): [17] Nakamura Y., et al., 1985
[18] Sands JF., et al., 1988
Promoter
Name: metYp1
+1: 3318297
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 8
Sequence: cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc
                         -35                    -10         +1                   
Note(s): Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence: [HIPP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[12] Ishii S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s): [2] Regnier P., et al., 1987
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator metYp1 3318365 3318379 -75.0 actataatgcCTGCAGATTTTACGTcccgtctcgg nd [BCE], [IHBCE] [16]


Transcription unit          
Name: metY-yhbC-nusA-infB
Synonym(s): metY
Gene(s): infB, nusA, rimP, metY   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is processed by RNase III in a hairpin structure downstream of the metY gene Regnier P,1989.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [9] Regnier P., et al., 1989
Promoter
Name: metYp1
+1: 3318297
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 8
Sequence: cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc
                         -35                    -10         +1                   
Note(s): Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence: [HIPP]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[12] Ishii S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator metYp1 3318365 3318379 -75.0 actataatgcCTGCAGATTTTACGTcccgtctcgg nd [BCE], [IHBCE] [16]


Transcription unit          
Name: metY
Gene(s): metY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [12] Ishii S., et al., 1984
Promoter
Name: metYp2
+1: 3318375
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: cattcacatgattagcaataaacgttgacaaaatgtggcgtggatcactataatgcctgcAgattttacgtcccgtctcgg
                         -35                     -10        +1                   
Note(s): The activity of the metYp2 promoter is increased under cold shock Brandi A,2019.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[19] Granston AE., et al., 1990
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: taacaaaaaaCCCCGATAAATCGGGGctttatataa
Reference(s): [12] Ishii S., et al., 1984
[14] Peters JM., et al., 2009
[15] Zuker M. 2003
Type: rho-independent
Sequence: cataaaaaaaGGGCCTAAAGCCCagttattctg
Reference(s): [12] Ishii S., et al., 1984
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine repressor metYp2 3318428 3318445 -61.5 atgaaagtgaACTGGATATTCATTCACAtgattagcaa nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
remote ArgR-L-arginine repressor metYp2 3318547 3318564 -180.5 atgcaaaataAATGAGTTTTCATTTAATcatcttttat nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
remote ArgR-L-arginine repressor metYp2 3318568 3318585 -201.5 ttccgctctcACTGAATTTTTATGCAAAataaatgagt nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 repressor metYp2 3318384 3318405 -19.5 aacgttgacaAAATGTGGCGTGGATCACTATAatgcctgcag nd [BPP], [CV(SM)], [GEA], [SM] [22]
Note(s): 1CRP binds in just one site and activates argG gene expresion and represses the expression of the divergent operon, metY-yhbC-nusA-infB.4CRP binds in just one site and activates argG gene expresion and represses the expression of the divergent operon, metY-yhbC-nusA-infB.


Transcription unit          
Name: metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
Gene(s): pnp, rpsO, truB, rbfA, infB, nusA, rimP, metY   Genome Browser M3D Gene expression COLOMBOS
Note(s): Sometimes the transcription initiated upstream of the metY gene reads through into the rpsO-pnp genes Sands JF,1988.
It has been sugested that a DNA loop is formed when ArgR binds to the three Arg boxes. The binding of each of two regulators (CRP and ArgR) to the regulatory region of metY interferes with the binding of the other, but ArgR binding overrides CRP binding. ArgR repress the metY operon only when CRP is present.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [17] Nakamura Y., et al., 1985
[18] Sands JF., et al., 1988
Promoter
Name: metYp2
+1: 3318375
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: cattcacatgattagcaataaacgttgacaaaatgtggcgtggatcactataatgcctgcAgattttacgtcccgtctcgg
                         -35                     -10        +1                   
Note(s): The activity of the metYp2 promoter is increased under cold shock Brandi A,2019.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [5] Brandi A., et al., 2019
[19] Granston AE., et al., 1990
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s): [2] Regnier P., et al., 1987
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine repressor metYp2 3318428 3318445 -61.5 atgaaagtgaACTGGATATTCATTCACAtgattagcaa nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
remote ArgR-L-arginine repressor metYp2 3318547 3318564 -180.5 atgcaaaataAATGAGTTTTCATTTAATcatcttttat nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
remote ArgR-L-arginine repressor metYp2 3318568 3318585 -201.5 ttccgctctcACTGAATTTTTATGCAAAataaatgagt nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [20], [21], [22], [23]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 repressor metYp2 3318384 3318405 -19.5 aacgttgacaAAATGTGGCGTGGATCACTATAatgcctgcag nd [BPP], [CV(SM)], [GEA], [SM] [22]
Note(s): 1CRP binds in just one site and activates argG gene expresion and represses the expression of the divergent operon, metY-yhbC-nusA-infB.4CRP binds in just one site and activates argG gene expresion and represses the expression of the divergent operon, metY-yhbC-nusA-infB.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.9 3313193 3313217 taattttaaaAAGGGGCTAACAGCCCCTTTTTTGtcaggagaat
  terminator -14.6 3311370 3311394 tttcagaaaaGGGGGCCTGAGTGGCCCCTTTTTTcaagctgacg
  terminator -12.9 3318063 3318090 cagttatataAAGCCCCGATTTATCGGGGTTTTTTGTtatctgacta
  anti-terminator -8.4 3313210 3313245 caacgtgaacAGCCCTTCCACCTGAAATTAATTTTAAAAAGGGGCtaacagcccc
  anti-terminator -11.7 3311392 3311433 tcatcgagcgCCTGGGTCTGCGTCGCTAATTCTTGCGAGTTTCAGAAAAGGgggcctgagt
  anti-terminator -3.3 3318085 3318105 tgcggttataGGGTTCAGTTATATAAAGCCccgatttatc
  anti-anti-terminator -23.2 3313243 3313303 cgtttacgctGCATCCGGCATGGATTGCCTGATGTGACGCTGGCGCGTCTTATCAGGTCAACGTGAACAGcccttccacc
  anti-anti-terminator -16.8 3311417 3311460 gtaaagacgtAGCACGTTACACCCAGCTCATCGAGCGCCTGGGTCTGCGTCGCtaattcttgc
  anti-anti-terminator -12.6 3318098 3318139 aaaaatccttCTGGAAAGTGCTCCAGACCGCAGTTGCGGTTATAGGGTTCAgttatataaa
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: reverse
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  Ribosomal S15 leader 115.6 3311628 3311742 uaacguacacUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCAaacgacaccg
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"




Reference(s)    

 [1] Regnier P., Portier C., 1986, Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase., J Mol Biol 187(1):23-32

 [2] Regnier P., Grunberg-Manago M., Portier C., 1987, Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1., J Biol Chem 262(1):63-8

 [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] 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

 [5] Brandi A., Giangrossi M., Paoloni S., Spurio R., Giuliodori AM., Pon CL., Gualerzi CO., 2019, Transcriptional and post-transcriptional events trigger de novo infB expression in cold stressed Escherichia coli., Nucleic Acids Res 47(9):4638-4651

 [6] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [7] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [8] Regnier P., Grunberg-Manago M., 1990, RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression., Biochimie 72(11):825-34

 [9] Regnier P., Grunberg-Manago M., 1989, Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA., J Mol Biol 210(2):293-302

 [10] 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

 [11] 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

 [12] Ishii S., Kuroki K., Imamoto F., 1984, tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli., Proc Natl Acad Sci U S A 81(2):409-13

 [13] Nagase T., Ishii S., Imamoto F., 1988, Differential transcriptional control of the two tRNA(fMet) genes of Escherichia coli K-12., Gene 67(1):49-57

 [14] 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

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

 [16] Verbeek H., Nilsson L., Baliko G., Bosch L., 1990, Potential binding sites of the trans-activator FIS are present upstream of all rRNA operons and of many but not all tRNA operons., Biochim Biophys Acta 1050(1-3):302-6

 [17] Nakamura Y., Mizusawa S., 1985, In vivo evidence that the nusA and infB genes of E. coli are part of the same multi-gene operon which encodes at least four proteins., EMBO J 4(2):527-32

 [18] Sands JF., Regnier P., Cummings HS., Grunberg-Manago M., Hershey JW., 1988, The existence of two genes between infB and rpsO in the Escherichia coli genome: DNA sequencing and S1 nuclease mapping., Nucleic Acids Res 16(22):10803-16

 [19] Granston AE., Thompson DL., Friedman DI., 1990, Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli., J Bacteriol 172(5):2336-42

 [20] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

 [21] Charlier D., Roovers M., Van Vliet F., Boyen A., Cunin R., Nakamura Y., Glansdorff N., Pierard A., 1992, Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression., J Mol Biol 226(2):367-86

 [22] Krin E., Laurent-Winter C., Bertin PN., Danchin A., Kolb A., 2003, Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12., J Bacteriol 185(10):3139-46

 [23] Makarova KS., Mironov AA., Gelfand MS., 2001, Conservation of the binding site for the arginine repressor in all bacterial lineages., Genome Biol 2(4):RESEARCH0013


RegulonDB