RegulonDB

Gene
Name:	rprA
Synonym(s):	ECK1686, G0-8863, IS083, b4431, psrA5
Genome position(nucleotides):	1770372 --> 1770477
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	38.68
Reference(s):	[1] Argaman L., et al., 2001
External database links:

ASAP:	ABE-0047251
ECHOBASE:	EB4292
ECOLIHUB:	rprA
COLOMBOS:	rprA

Product

Name:

small regulatory RNA RprA

Synonym(s):

IS083, PsrA5, RprA

Type:

small RNA

Classification:

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 --> 3.1.3.1 - translation attenuation and efficiency
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - 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 - RNA-mediated gene silencing by inhibition of translation 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:

[EXP-IDA] Inferred from direct assay
[EXP-IEP] Inferred from expression pattern
[EXP-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:

ECOCYC:

RPRA-RNA

ECOLIWIKI:

b4431

Operon

Name:

rprA

Operon arrangement:

Transcription unit	Promoter
rprA	rprAp

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	nd	[COMP-AINF]	[16]
	promoter	ydiMp1	1770930		forward	nd	[COMP-AINF]	[16]

Evidence
[COMP-AINF] Inferred computationally without human oversight

Reference(s)
[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