RegulonDB RegulonDB 11.1: Operon Form
   

garPLRK-rnpB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: rnpB
Gene(s): rnpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Fis activates rnpB transcription most effectively at moderate salt concentrations Choi HS,2005.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rnpB. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Lundberg U., et al., 1995
Promoter
Name: rnpBp
+1: 3270592
Distance from start of the gene: 0
Sequence: ggcgattggaatgcgcaacgcggggtgacaagggcgcgcaaaccctctatactgcgcgccGaagctgaccagacagtcgcc
Note(s): Based on mutational analysis, a short sequence, up to 7 bp downstream of the -10 region, is involved in the stringent response of the rnpB promoter Choi HS,2008
Primer extension analysis shows that rnpBp initiates not only at the +1 G position (70% efficiency) Lundberg U,1995. Lee Y,1989but also at the -1 C position (30% efficiency) Choi HS,2008
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Choi HS., et al., 2008
[3] Lee Y., et al., 1989
[1] Lundberg U., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: aaagtaaaaaCCCGCCGAAGCGGGtttttacgta
Reference(s): [4] Kim S., et al., 1997
Type: rho-independent
Sequence: aaagcaaaaaCCCGCCGAAGCGGGtttttacgta
Reference(s): [4] Kim S., et al., 1997
Type: rho-independent
Sequence: aaagcaaaaaCCCGCCGAAGCGGGtttttacgta
Reference(s): [4] Kim S., et al., 1997
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 rnpBp 3270635 3270649 -50.0 cgacactggcGATTGGAATGCGCAAcgcggggtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote Fis activator rnpBp 3270703 3270717 -118.0 aggtacgttgGACGAAGCATTCCGCggggcttatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote Fis activator rnpBp 3270741 3270755 -156.0 catggcattgATGCGGTCTTCAGCGtattgaccag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[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 repressor rnpBp 3270575 3270589 11.0 gcgcgccgaaGCTGACCAGACAGTCgccgcttcgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Transcription unit       
Name: garR
Gene(s): garR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [6] Li Z., et al., 2019
Promoter
Name: garRp
+1: 3272820
Distance from start of the gene: 69
Sequence: tctggaatggggcgcgacgtttgtggctgtcggcagcgatctcggcgtcttccgctctgcCactcagaaactggctgatac
Evidence: [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Li Z., et al., 2019


Transcription unit          
Name: garPLRK-rnpB
Synonym(s): yhaUFED-rnpB
Gene(s): rnpB, garK, garR, garL, garP   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] Lundberg U., et al., 1995
[7] Monterrubio R., et al., 2000
Promoter
Name: garPp
+1: 3274934
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: tcattgtcgttacggcataaatgaaactcataaataacaccttccccataataataaaaaTcagcataagtacccgaggta
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[IC]
Reference(s): [8] Huerta AM., et al., 2003
[7] Monterrubio R., et al., 2000
Terminator(s)
Type: rho-independent
Sequence: ccaaaagtaaAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGtgaaactgac
Reference(s): [1] Lundberg U., et al., 1995
TF binding sites (TFBSs)
[CdaR,+] 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
nd CdaR activator garPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7], [10]
[FNR,+] 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
nd FNR activator garPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]
[Fur,-] 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
remote Fur-Fe2+ repressor garPp 3274836 3274854 90.0 cccgctatttAATATTACTGATTATTTTTattgttaccg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [9]
[H-NS,-] 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
nd H-NS repressor garPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [12]


Evidence    

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [IC] Inferred by curator

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Lundberg U., Altman S., 1995, Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli., RNA 1(3):327-34

 [2] Choi HS., Park JW., Hong SK., Lee K., Lee Y., 2008, Effects of base changes at the transcription start site on stringent control of rnpB in Escherichia coli., Mol Cells 26(2):212-5

 [3] Lee Y., Ramamoorthy R., Park CU., Schmidt FJ., 1989, Sites of initiation and pausing in the Escherichia coli rnpB (M1 RNA) transcript., J Biol Chem 264(9):5098-103

 [4] Kim S., Lee Y., 1997, Function of the repeated sequence in the 3' flanking region of the Escherichia coli rnpB gene on transcription termination and RNA processing., FEBS Lett 407(3):353-6

 [5] Choi HS., Kim KS., Park JW., Jung YH., Lee Y., 2005, Effects of FIS protein on rnpB transcription in Escherichia coli., Mol Cells 19(2):239-45

 [6] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [7] Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J., 2000, A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli., J Bacteriol 182(9):2672-4

 [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] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [10] Sampaio MM., Chevance F., Dippel R., Eppler T., Schlegel A., Boos W., Lu YJ., Rock CO., 2004, Phosphotransferase-mediated transport of the osmolyte 2-O-alpha-mannosyl-D-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor., J Biol Chem 279(7):5537-48

 [11] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [12] White-Ziegler CA., Malhowski AJ., Young S., 2007, Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12., J Bacteriol 189(15):5429-40

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