RegulonDB RegulonDB 11.1: Operon Form
   

rpsP-rimM-trmD-rplS operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rpsP-rimM-trmD-rplS
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: rpsP-rimM-trmD-rplS
Gene(s): rplS, trmD, rimM, rpsP   Genome Browser M3D Gene expression COLOMBOS
Note(s): In an in vitro transcription experiment, at least two-thirds of the transcripts terminated at the attenuator-like structure located upstream of rpsP Bystrom AS,1989.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Bystrom AS., et al., 1989
[2] Persson BC., et al., 1995
Promoter
Name: rpsPp
+1: 2746254
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: tttacagcagagttagcaactgttgattgcaattcccgcaaaaatgagtaaaattttcggGcttttaatatgacaccggac
                                -35                   -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Bystrom AS., et al., 1989
[3] Huerta AM., et al., 2003
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: taaaacaccaGCAAACAGATAAAAAAGGGCCAGCCAATTGGCCAGCCCTTCTTAACAGGATGTCGcttaagcgaa
Reference(s): [5] Feng CQ., et al., 2019
[6] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[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 repressor rpsPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsPp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[8]
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): [8] 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 -21.3 2746202 2746242 ttttaatatgACACCGGACTCCGTTCCTCGATGGGGTCCGGTTGTTTTATtcacacaaga
  anti-terminator -5.06 2746224 2746269 ccgcaaaaatGAGTAAAATTTTCGGGCTTTTAATATGACACCGGACTCCGTTCCTcgatggggtc
  anti-anti-terminator -5.0 2746254 2746280 gattgcaattCCCGCAAAAATGAGTAAAATTTTCGGgcttttaata
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

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

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

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


Reference(s)    

 [1] Bystrom AS., von Gabain A., Bjork GR., 1989, Differentially expressed trmD ribosomal protein operon of Escherichia coli is transcribed as a single polycistronic mRNA species., J Mol Biol 208(4):575-86

 [2] Persson BC., Bylund GO., Berg DE., Wikstrom PM., 1995, Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics., J Bacteriol 177(19):5554-60

 [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] 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.

 [5] 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

 [6] 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

 [7] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [8] 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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