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small RNA | ![]() ![]() |
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Gene name: | spf ![]() |
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Synonym(s): | IS197, Spf, Spf RNA | |
Genome position: | 4049899 --> 4050009 | |
Strand: | forward | |
Sequence: | Get ribonucleotide sequence FastaFormat | |
GC content %: |
41.44 | |
Note(s): | The small regulatory RNA Spot 42 (Spf) was first identified as an abundant, non-translated RNA in E. coli 4577761. 4577762. 390161. Sahagan BG, Dahlberg JE,1979. 2440852. Its first regulatory target, galK, was identified much later Moller T,2002. Urban JH,2007. Wang X,2015, and additional regulatory targets were identified by Beisel CL,2011. Beisel CL,2012. Wright PR,2013. Chen J,2017. Three conserved unstructured regions of Spot 42 are able to basepair with different mRNA targets Beisel CL,2012. Spot 42 was initially thought to be responsible for selective inhibition of translation of galK within the gal operon mRNA by occluding interaction of the ribosome with the galK Shine-Dalgarno sequence Moller T,2002. Later, it was shown that Spot 42 regulation of galK expression by Spot 42 at this site occurs after RNase cleavage of mRNAs transcribed from the galE promoter, which generates the so-called mK2 mRNA with a new 5' end Wang X,2014. Binding of Spot 42 leads to degradation of mK2 Wang X,2015. Spot 42 also affects polarity of gene expression; its binding site overlaps with a putative |FRAME: CPLX0-2441 Rho|-binding site and may enhance Rho-mediated transcription termination Wang X,2015. Spot 42 does not inhibit translation of the sdhCDAB operon directly. Instead, Spot 42 binds upstream of the translation initiation site and recruits Hfq to its binding site, which occludes the site for binding of the 30S subunit of the ribosome Desnoyers G,2012. Spot 42 downregulates expression of the high-affinity arabinose transporter at low inducer (arabinose) concentration, and thereby indirectly regulates expression from the pBAD promoter Chen J,2017. A candidate Spot 42 regulon was inferred by integrating information on experimentally supported targets and sRNA-mRNA interactions with transcription datasets; new targets with experimental support are fabA, fadL, lpd, lysS, mdh, mglB, rbsB, tktA, yjiA, and yjjK 32487739. An spf deletion mutant exhibits a mild growth defect in some, but not all, strain backgrounds 2940230. Overexpression of Spf RNA results in slow growth, particularly on succinate 6183252 as well as other carbon sources Beisel CL,2011, and a pronounced growth defect upon transfer from minimal to rich media, compared to wild type 6183252. Overexpression also leads to a two-fold increase in 6S RNA abundance 6183252 and increased DNA polymerase I activity 2452153. Transcription of spf is negatively regulated by cAMP-CRP Polayes DA,1988 and is highest during early exponential phase Wang X,2015. Spot 42 and CRP form a multi-output feedforward loop during catabolite repression. Both the steady-state level and dynamics of gene regulation are affected Beisel CL,2011. 21788732. Spot 42 RNA accumulates to 150-200 copies per cell in glucose-grown cells Sahagan BG, Dahlberg JE,1979. The Hfq protein stabilizes Spot 42 and stimulates pairing of Spf regions with complementary RNA sequences Moller T,2002. Spot 42 appears to be unable to compete effectively for Hfq binding Moon K,2011. The small RNA PspH is able to base-pair with Spot 42; overexpression of PspH leads to an almost 5-fold reduction in the level of Spot 42 Melamed S,2016. Spf: spot fourty-two Reviews: 2450678. 10068996. 12732300. 15063850. 15487940. 17381274. 18981470. 19239884. 21292156. 21843668. 26327359. 32213244 |
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Evidence: | [IMP] Inferred from mutant phenotype [IPI] Inferred from physical interaction |
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Reference(s): | [1] Chen S., et al., 2002 [2] Joyce CM., et al., 1982 [3] Komine Y., et al., 1991 [4] Mihailovic MK., et al., 2018 [5] Moller T., et al., 2002 [6] Wang X., et al., 2015 [7] Windbichler N., et al., 2008 [8] Wright PR., et al., 2013 |
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External database links: | ||
ECOCYC: |
SPF-RNA | |
ECOLIWIKI: |
b3864 | |
M3D: | small regulatory RNA Spot 42 |
Regulation exerted by the small RNA | ![]() |
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Target | Mechanism | Function | Target Type | Binding Site | Evidence Code |
Reference(s) | |||
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LeftPos | RightPos | Sequence | |||||||
MRNA-DEGRADATION
|
repressor
|
Gene
|
789924
|
789999
|
GCAGGGUAGCCAAAUGCGUUGGCAAACAGAGAUUGUGUUUUUUCUUUCAGACUCAUUUCUUACACUCCGGAUUCGC
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TRANSLATION-BLOCKING
|
repressor
|
Gene
|
755122
|
755133
|
ACCUCUGUGCCC
|
||||
repressor
|
Gene
|
1986158
|
1986165
|
GUAGGGCA
|
|||||
repressor
|
Gene
|
2839496
|
2839503
|
UACCCUAC
|
|||||
repressor
|
Gene
|
2323411
|
2323418
|
CUGUACCC
|
|||||
repressor
|
Gene
|
40382
|
40396
|
UCCAUCUUUCAACCU
|
|||||
activator
|
Gene
|
||||||||
repressor
|
Gene
|
||||||||
repressor
|
Gene
|
2934212
|
2934268
|
GCUUCUGAACCUAAGAGGAUGCUAUGGGAAACACAUCAAUACAAACGCAGAGUUACC
|
|||||
repressor
|
Gene
|
||||||||
repressor
|
Gene
|
2934196
|
2934206
|
CCGAUUACGUG
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|||||
repressor
|
Gene
|
1842450
|
1842464
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CCGUUCGUGAAGUAA
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|||||
repressor
|
Gene
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4118088
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4118098
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CAUAAUCGGAU
|
|||||
repressor
|
Gene
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754590
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754599
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GGGUACAGAG
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|||||
activator
|
Gene
|
||||||||
repressor
|
Gene
|
||||||||
repressor
|
Gene
|
||||||||
repressor
|
Gene
|
4539517
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4539534
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GUAGGAUACAGAAAGCAA
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|||||
repressor
|
Gene
|
3372624
|
3372634
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GUAGGGUACAG
|
|||||
repressor
|
Gene
|
1462115
|
1462123
|
GUACCCUAC
|
|||||
repressor
|
Gene
|
1365515
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1365548
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UCCGAUUAACCGUGAAGAGUCAAAAGGUGUGAAA
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|||||
repressor
|
Gene
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2825817
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2825831
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CUGAAGGAGAGAACA
|
|||||
repressor
|
Gene
|
4160769
|
4160776
|
CGUAAUCG
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|||||
repressor
|
Gene
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762994
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763005
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CUGAAGGAUGGA
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|||||
repressor
|
Gene
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3731132
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3731170
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UGAAAAUAAAGAACAUUCUACUCACCCUUUGCACCUCAC
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|||||
repressor
|
Gene
|
||||||||
repressor
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Gene
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Evidence: |
[IDA] Inferred from direct assay [IEP] Inferred from expression pattern [IMP] Inferred from mutant phenotype [SM] Site mutation |
Reference(s) |
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