RegulonDB RegulonDB 11.1: Operon Form
   

cmk-rpsA-ihfB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: cmk-rpsA-ihfB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: cmk-rpsA
Gene(s): cmk, rpsA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under anaerobiosis, FNR represses rpsA gene expression, but it is not known which promoter (cmk, rpsAp1, or rpsAp3) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Fricke J., et al., 1995
[2] Pedersen S., et al., 1984
Promoter
Name: cmkp
+1: 961165
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: aaactggtttttgcacacaacgttaacgatttgtggcgtcggcgcgtataatgcgcgcggTtatgttaacggtacgcctgt
                       -35                     -10          +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[2] Pedersen S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: cagctaaaggCGAGTAATTCTCTGACTCTTCGGGATTTTTATTCCGAAGTTTGTTGAGTTTACTTgacagattgc
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001


Transcription unit       
Name: rpsA-ihfB
Synonym(s): rpsA-himD
Gene(s): rpsA, ihfB   Genome Browser M3D Gene expression COLOMBOS
Note(s): During exponential growth himD expression is mainly directed by the rpsAp1 or rpsAp3 promoter, while in the stationary phase the himD promoter is primarily responsible for himD activity.
Under anaerobiosis, FNR represses rpsA gene expression, but it is not known which promoter (cmk, rpsAp1, or rpsAp3) is affected, or even if this regulation is direct or indirect Salmon K,2003.
A possible role in the rpsA-ihfB, adhP, fecIR, and fecABCDE operons was described for functional abortive RNAs (faRNAs), based on computational prediction and described by Nair et al. 2017 Marcus JI, Hassoun S, Nair NU,2017
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [6] Weglenska A., et al., 1996
Promoter
Name: rpsAp1
+1: 961717
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 278
Sequence: gaacgtgcgcatcgccgcatgctacagttgcaggagaagggctttagtgttaactttgagCgccttttggccgagatcaaa
                            -35                    -10      +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Pedersen S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: ttaagtttttTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAatctggaact
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsAp1 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[7]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [7] Lemke JJ., et al., 2011


Transcription unit       
Name: rpsA-ihfB
Synonym(s): rpsA-himD
Gene(s): rpsA, ihfB   Genome Browser M3D Gene expression COLOMBOS
Note(s): During exponential growth himD expression is mainly directed by the rpsAp1 or rpsAp3 promoter, while in the stationary phase the himD promoter is primarily responsible for himD activity.
Under anaerobiosis, FNR represses rpsA gene expression, but it is not known which promoter (cmk, rpsAp1, or rpsAp3) is affected, or even if this regulation is direct or indirect Salmon K,2003.
A possible role in the rpsA-ihfB, adhP, fecIR, and fecABCDE operons was described for functional abortive RNAs (faRNAs), based on computational prediction and described by Nair et al. 2017 Marcus JI, Hassoun S, Nair NU,2017
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [6] Weglenska A., et al., 1996
Promoter
Name: rpsAp3
+1: 961859
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 136
Sequence: tagtgttggattccaccaccttaagcattgagcaagtgattgaaaaagcgctacaatacgCgcgccagaaattggctctcg
                            -35                     -10     +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Pedersen S., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: ttaagtttttTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAatctggaact
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsAp3 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[7]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [7] Lemke JJ., et al., 2011


Transcription unit          
Name: ihfB
Synonym(s): OP00241, himD
Gene(s): ihfB   Genome Browser M3D Gene expression COLOMBOS
Note(s): During exponential growth himD expression is mainly directed by rpsAp1 and rpsAp3 promoters, while in the stationary phase the himD promoter is primarily responsible for himD activity Weglenska A,1996.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [8] Aviv M., et al., 1994
[6] Weglenska A., et al., 1996
Promoter
Name: ihfBp
+1: 963749
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 79
Sequence: tttattccgaagtttgttgagtttacttgacagattgcaggtttcgtcctgtaatcaagcActaagggcggctacggccgc
                           -35               -10            +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Aviv M., et al., 1994
[6] Weglenska A., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: ttaagtttttTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAatctggaact
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[IHF,-] 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 IHF repressor ihfBp 963423 963435 -320.0 cgttgaaggtTACCTGCGTGCTTctgaagcatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp 963439 963451 -304.0 cgtgcttctgAAGCATCCCGTGAccgcgttgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp 963536 963548 -207.0 aaaaccgcgcAATCAGCCTGTCTgttcgtgcga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp 963586 963598 -157.0 aaagatgcaaTCGCAACTGTTAAcaaacaggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
proximal IHF repressor ihfBp 963666 963678 -77.0 taaaggcgagTAATTCTCTGACTcttcgggatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
proximal IHF repressor ihfBp 963741 963753 -2.0 ttcgtcctgtAATCAAGCACTAAgggcggctac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]


Transcription unit          
Name: ihfB
Synonym(s): OP00241, himD
Gene(s): ihfB   Genome Browser M3D Gene expression COLOMBOS
Note(s): During exponential growth himD expression is mainly directed by rpsAp1 and rpsAp3 promoters, while in the stationary phase the himD promoter is primarily responsible for himD activity Weglenska A,1996.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [8] Aviv M., et al., 1994
[6] Weglenska A., et al., 1996
Promoter
Name: ihfBp2
+1: 963749
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 79
Sequence: tttattccgaagtttgttgagtttacttgacagattgcaggtttcgtcctgtaatcaagcActaagggcggctacggccgc
                           -35               -10            +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Aviv M., et al., 1994
[3] Huerta AM., et al., 2003
[6] Weglenska A., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: ttaagtttttTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAatctggaact
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[IHF,-] 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 IHF repressor ihfBp2 963423 963435 -320.0 cgttgaaggtTACCTGCGTGCTTctgaagcatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp2 963439 963451 -304.0 cgtgcttctgAAGCATCCCGTGAccgcgttgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp2 963536 963548 -207.0 aaaaccgcgcAATCAGCCTGTCTgttcgtgcga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
remote IHF repressor ihfBp2 963586 963598 -157.0 aaagatgcaaTCGCAACTGTTAAcaaacaggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
proximal IHF repressor ihfBp2 963666 963678 -77.0 taaaggcgagTAATTCTCTGACTcttcgggatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
proximal IHF repressor ihfBp2 963741 963753 -2.0 ttcgtcctgtAATCAAGCACTAAgggcggctac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.2 963679 963706 tctctgactcTTCGGGATTTTTATTCCGAAGTTTGTTgagtttactt
  anti-terminator -3.0 963644 963686 ggctgaagctTTCAAAGCAGCTAAAGGCGAGTAATTCTCTGACTCTTCGGGAtttttattcc
  anti-anti-terminator -9.2 963629 963663 ctccaacaacGCAATGGCTGAAGCTTTCAAAGCAGCTAAAGGCGagtaattctc
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [COMP-HINF] Inferred by a human based on computational evidence

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

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


Reference(s)    

 [1] Fricke J., Neuhard J., Kelln RA., Pedersen S., 1995, The cmk gene encoding cytidine monophosphate kinase is located in the rpsA operon and is required for normal replication rate in Escherichia coli., J Bacteriol 177(3):517-23

 [2] Pedersen S., Skouv J., Kajitani M., Ishihama A., 1984, Transcriptional organization of the rpsA operon of Escherichia coli., Mol Gen Genet 196(1):135-40

 [3] 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

 [4] 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

 [5] 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

 [6] Weglenska A., Jacob B., Sirko A., 1996, Transcriptional pattern of Escherichia coli ihfB (himD) gene expression., Gene 181(1-2):85-8

 [7] 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

 [8] Aviv M., Giladi H., Schreiber G., Oppenheim AB., Glaser G., 1994, Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation., Mol Microbiol 14(5):1021-31

 [9] Bykowski T., Sirko A., 1998, Selected phenotypes of ihf mutants of Escherichia coli., Biochimie 80(12):987-1001

 [10] Mihailovic MK., Ekdahl AM., Chen A., Leistra AN., Li B., Gonzalez Martinez J., Law M., Ejindu C., Masse E., Freddolino PL., Contreras LM., 2021, Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study., Front Cell Infect Microbiol 11:696533

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