RegulonDB RegulonDB 10.8: smallRNA Form
   

Ffs small RNA in Escherichia coli K-12 genome


Gene local context to scale (view description)

atl ybaA ffs terminator terminator TSS_610 TSS_610 ffsp7 ffsp7 ffsp5 ffsp5 ffsp6 ffsp6
small RNA      
Gene name: ffs    Texpresso search in the literature
Synonym(s): 4.5S, signal recognition particle 4.5S RNA
Genome position: 476448 --> 476561
Strand: forward
Sequence: Get ribonucleotide sequence FastaFormat
GC content %:  
64.04
Note(s): The 4.5S RNA and Ffh together form the signal recognition particle (SRP) 2171778. 1701272. 1279430 which binds to the signal sequence 1279430 and targets the nascent protein to the SRP receptor, FtsY Miller JD,1994. The SRP is involved in integration of nascent proteins into the membrane 8521840. 8985168. 9843943. 10397756. 10781078.
The interaction between 4.5S RNA and Ffh 1281314. 7518399. 8608448. 9659905. 10556722, the GTP-dependent Miller JD,1994 interaction between the SRP and the SRP receptor Miller JD,1994. 10834842. 11233986, and the GTP hydrolysis cycle Miller JD,1994. 7660124. Moser C,1997. 9799502. 11735405 have been examined in detail. The 4.5S RNA catalyses the interaction of Ffh and the SRP receptor only when signal sequence is bound 19119234.
Independently of Ffh, 4.5S RNA binds to elongation factor G (FusA) and to ribosomes 2438050. 9914538. 10556722. 10780448. Rinke-Appel J,2002, and 4.5S RNA is proposed to modulate (specifically to release 10780448) the interaction of elongation factor G with the ribosome 9914538. 10780448.
RNase P processing of the precursor of 4.5S RNA has been examined 778851. Guerrier-Takada C,1983. 6199841. 8020097. 10525416. Processing by other RNases has been observed 9501180. The 4.5S RNA structure has been studied in detail 6366742. 1689715. 8608448. 10801497. 10944346. 12777762. 4.5S RNA folds into a single hairpin structure containing an apical GGAA tetraloop that caps one end plus five symmetric or asymmetic internal loops (reviews: 1707519. 7518075. The two ends of the 4.5S RNA hairpin have distinct functions in the targeting cycle 23235881. 4.5S RNA acts as a molecular scaffold for movement of the Ffh?-FtsY GTPase complex from the tetraloop region to the distal region. This movement facilitates docking of the ribosome to the translocon and hydrolysis of GTP which in turn stimulates SRP recycling 23235881. 23235870.
Any mutant lacking 4.5S RNA is inviable 6208371. Depletion of 4.5S RNA leads to induction of the heat shock response 1688840. 1701272, lambda phage induction 1688840, defects in translation 6208371. 2433587. 7513325, buildup of pre-beta-lactamase 2171778, decreased abundance of maltose binding protein 2171778, and cell inviability 6208371. Mutants exhibit defects in membrane protein assembly 10781078. 11741850. The 4.5S RNAdl1 allele is a dominant mutation that causes induction of the heat shock response, defects in translocation of a subset of proteins, aberrant cell envelope morphology, and eventual translation defects and cell inviability 1701272. Overexpression of 4.5S RNA suppresses the heat sensitivity of a ffh-10(Ts) mutant Park SK,2002. The inviability of a 4.5S RNA mutant is suppressed by fusA mutations 2438050. The phenotypes of a 4.5S RNA mutant are partially suppressed by mutations in 16S or 23S rRNA 11904179.
The inviability of a 4.5S RNA mutant is functionally complemented by expression of RNAs from various bacterial species 2512280. 1689715, including Haemophilus influenzae 9522453, by archaebacterial 1999396 or human SRP7S RNA 2171778. 1999396, and by a Mycoplasma pneumoniae RNA 1370291. The viability of a Bacillus subtilis scRNA mutant is functionally complemented by expression of E. coli 4.5S RNA 1372600, but the B. subtilis sporulation defect is not 8535524. Exogenous SRP54 protein exhibits binding to E. coli 4.5S RNA 1699948. 1702385.
Regulation has been described 8780771.
Reviews: 1715753. 8145649. 10068996. Muller M,2001. 11123669
Evidence: [IDA] Inferred from direct assay
Reference(s): [1] Avdeeva ON., et al., 2002
[2] Bailey SC., et al., 1979
[3] Gu SQ., et al., 2003
[4] Huang Y., et al., 1994
[5] Jensen CG., et al., 1994
[6] Malygin A., et al., 1996
[7] Phillips GJ., et al., 1992
[8] Zwieb C., et al., 2005
External database links:  
ECOCYC:
FFS-RNA
ECOLIWIKI:
b0455
M3D: Ffs


Regulation exerted by the small RNA    
  Target Regulation Type Mechanism Function Binding Site Evidence
Code
Reference(s)
LeftPos RightPos Distance
to the gene
Sequence
 
translocation
post-transcriptional regulation
activator
 
 
 
 
 
 


Reference(s)    

 [1] Avdeeva ON., Myasnikov AG., Sergiev PV., Bogdanov AA., Brimacombe R., Dontsova OA., 2002, Construction of the 'minimal' SRP that interacts with the translating ribosome but not with specific membrane receptors in Escherichia coli., FEBS Lett 514(1):70-3

 [2] Bailey SC., Apirion D., 1979, Repetitive DNA in Escherichia coli: multiple sequences complementary to small stable RNAs., Mol Gen Genet 172(3):339-43

 [3] Gu SQ., Peske F., Wieden HJ., Rodnina MV., Wintermeyer W., 2003, The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome., RNA 9(5):566-73

 [4] Huang Y., Gong L., Zhang L., Li S., Zhu S., 1994, [Comparative study of single strand conformation polymorphism of 4.5S RNA gene in enterobacteria], Wei Sheng Wu Xue Bao 34(2):100-5

 [5] Jensen CG., Pedersen S., 1994, Concentrations of 4.5S RNA and Ffh protein in Escherichia coli: the stability of Ffh protein is dependent on the concentration of 4.5S RNA., J Bacteriol 176(23):7148-54

 [6] Malygin A., Karpova G., Westermann P., 1996, Hybridization of two oligodeoxynucleotides to both strands of an RNA hairpin structure increases the efficiency of RNA-DNA duplex formation., FEBS Lett 392(2):114-6

 [7] Phillips GJ., Silhavy TJ., 1992, The E. coli ffh gene is necessary for viability and efficient protein export., Nature 359(6397):744-6

 [8] Zwieb C., van Nues RW., Rosenblad MA., Brown JD., Samuelsson T., 2005, A nomenclature for all signal recognition particle RNAs., RNA 11(1):7-13


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