RegulonDB RegulonDB 10.9: Gene Form

rprA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

ydiK ydiL rprA RcsB terminator anti-terminator anti-anti-terminator ydiMp1 ydiMp1 ydiMp5 ydiMp5 rprAp rprAp

Name: rprA    Texpresso search in the literature
Synonym(s): ECK1686, G0-8863, IS083, b4431, psrA5
Genome position(nucleotides): 1770372 --> 1770477 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
Reference(s): [1] Argaman L., et al., 2001
External database links:  

Name: small regulatory RNA RprA
Synonym(s): IS083, PsrA5, RprA
Type: small RNA
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> - antisense RNA
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
GO:0001072 - transcription antitermination factor activity, RNA binding
biological_process GO:0040033 - negative regulation of translation, ncRNA-mediated
GO:0045975 - positive regulation of translation, ncRNA-mediated
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
GO:0097532 - stress response to acid chemical
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
Reference(s): [2] Andreassen PR., et al., 2018
[3] Hu LI., et al., 2018
[4] Kim W., et al., 2020
[5] Lalaouna D., et al., 2018
[6] Majdalani N., et al., 2001
[7] Majdalani N., et al., 2002
[8] Mihailovic MK., et al., 2018
[9] Sahni A., et al., 2017
[10] Sahni A., et al., 2019
[11] Schilling B., et al., 2015
[12] Uchiyama J., et al., 2010
[13] Updegrove T., et al., 2008
[14] Urban JH., et al., 2007
[15] Webb J., et al., 2019
External database links:  

Name: rprA         
Operon arrangement:
Transcription unit        Promoter

Transcriptional Regulation      
Display Regulation             
Activated by: CpxR, RcsB

Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ydiMp5 1770926 forward Similarity to the consensus
Read more >
[ICWHO] [16]
  promoter ydiMp1 1770930 forward Similarity to the consensus
Read more >
[ICWHO] [16]


 [ICWHO] Inferred computationally without human oversight


 [1] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50

 [2] Andreassen PR., Pettersen JS., Szczerba M., Valentin-Hansen P., Moller-Jensen J., Jorgensen MG., 2018, sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA., Nucleic Acids Res 46(13):6746-6760

 [3] Hu LI., Filippova EV., Dang J., Pshenychnyi S., Ruan J., Kiryukhina O., Anderson WF., Kuhn ML., Wolfe AJ., 2018, The spermidine acetyltransferase SpeG regulates transcription of the small RNA rprA., PLoS One 13(12):e0207563

 [4] Kim W., Lee Y., 2020, Mechanism for coordinate regulation of rpoS by sRNA-sRNA interaction in Escherichia coli., RNA Biol 17(2):176-187

 [5] Lalaouna D., Prevost K., Laliberte G., Houe V., Masse E., 2018, Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli., Nucleic Acids Res 46(5):2600-2612

 [6] Majdalani N., Chen S., Murrow J., St John K., Gottesman S., 2001, Regulation of RpoS by a novel small RNA: the characterization of RprA., Mol Microbiol 39(5):1382-94

 [7] Majdalani N., Hernandez D., Gottesman S., 2002, Regulation and mode of action of the second small RNA activator of RpoS translation, RprA., Mol Microbiol 46(3):813-26

 [8] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [9] Sahni A., Hajjari M., Raheb J., Foroughmand AM., Asgari M., 2017, Cloning and over expression of non-coding RNA rprA in E.coli and its resistance to Kanamycin without osmotic shock., Bioinformation 13(1):21-24

 [10] Sahni A., Hajjari M., Raheb J., Foroughmand AM., Asgari M., 2019, The non-coding RNA rprA can increase the resistance to ampicillin in Escherichia coli., Microb Pathog 129:266-270

 [11] Schilling B., Christensen D., Davis R., Sahu AK., Hu LI., Walker-Peddakotla A., Sorensen DJ., Zemaitaitis B., Gibson BW., Wolfe AJ., 2015, Protein acetylation dynamics in response to carbon overflow in Escherichia coli., Mol Microbiol 98(5):847-63

 [12] Uchiyama J., Sasaki Y., Nagahama H., Itou A., Matsuoka S., Matsumoto K., Hara H., 2010, Accumulation of sigmaS due to enhanced synthesis and decreased degradation in acidic phospholipid-deficient Escherichia coli cells., FEMS Microbiol Lett 307(2):120-7

 [13] Updegrove T., Wilf N., Sun X., Wartell RM., 2008, Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5' rpoS mRNA leader region., Biochemistry 47(43):11184-95

 [14] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37

 [15] Webb J., Springthorpe V., Rossoni L., Minde DP., Langer S., Walker H., Alstrom-Moore A., Larson T., Lilley K., Eastham G., Stephens G., Thomas GH., Kelly DJ., Green J., 2019, Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate., mSystems 4(4)

 [16] 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