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0  structures 13  species 0  interactions 13  sequences 1  architecture

Family: SgrT (PF15894)

Summary: Inhibitor of glucose uptake transporter SgrT

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This is the Wikipedia entry entitled "SgrS RNA". More...

SgrS RNA Edit Wikipedia article

SgrS RNA
RF00534.jpg
Identifiers
SymbolSgrS
RfamRF00534
Other data
RNA typeGene; antisense
Domain(s)Bacteria
GO0032057 0043488 0030371
SO0000655
PDB structuresPDBe

SgrS (sugar transport-related sRNA, previously named ryaA)[1] is a 227 nucleotide small RNA that is activated by SgrR in Escherichia coli during glucose-phosphate stress. The nature of glucose-phosphate stress is not fully understood, but is correlated with intracellular accumulation of glucose-6-phosphate.[2] SgrS helps cells recover from glucose-phosphate stress by base pairing with ptsG mRNA (encoding the glucose transporter) and causing its degradation in an RNase E dependent manner.[3][4] Base pairing between SgrS and ptsG mRNA also requires Hfq, an RNA chaperone frequently required by small RNAs that affect their targets through base pairing.[5] The inability of cells expressing sgrS to create new glucose transporters leads to less glucose uptake and reduced levels of glucose-6-phosphate. SgrS is an unusual small RNA in that it also encodes a 43 amino acid functional polypeptide, SgrT, which helps cells recover from glucose-phosphate stress by preventing glucose uptake. The activity of SgrT does not affect the levels of ptsG mRNA of PtsG protein. It has been proposed that SgrT exerts its effects through regulation of the glucose transporter, PtsG.[6][7]

SgrS was originally discovered in E. coli but homologues have since been identified in other Gammaproteobacteria such as Salmonella enterica and members of the genus Citrobacter.[8] A comparative genomics based target prediction approach that employs these homologs, has been developed and was used to predict the SgrS target, ptsI (b2416), which was subsequently verified experimentally.[9]

References

  1. ^ Vanderpool CK, Gottesman S (November 2004). "Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system". Molecular Microbiology. 54 (4): 1076–89. doi:10.1111/j.1365-2958.2004.04348.x. PMID 15522088.
  2. ^ Wadler CS, Vanderpool CK (December 2007). "A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide". Proceedings of the National Academy of Sciences of the United States of America. 104 (51): 20454–9. doi:10.1073/pnas.0708102104. PMC 2154452. PMID 18042713.
  3. ^ Vanderpool CK, Gottesman S (March 2007). "The novel transcription factor SgrR coordinates the response to glucose-phosphate stress". Journal of Bacteriology. 189 (6): 2238–48. doi:10.1128/JB.01689-06. PMC 1899371. PMID 17209026.
  4. ^ Rice JB, Vanderpool CK (May 2011). "The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes". Nucleic Acids Research. 39 (9): 3806–19. doi:10.1093/nar/gkq1219. PMC 3089445. PMID 21245045.
  5. ^ Kawamoto H, Koide Y, Morita T, Aiba H (August 2006). "Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq". Molecular Microbiology. 61 (4): 1013–22. doi:10.1111/j.1365-2958.2006.05288.x. PMID 16859494.
  6. ^ Maki K, Morita T, Otaka H, Aiba H (May 2010). "A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA". Molecular Microbiology. 76 (3): 782–92. doi:10.1111/j.1365-2958.2010.07141.x. PMID 20345651.
  7. ^ Kawamoto H, Morita T, Shimizu A, Inada T, Aiba H (February 2005). "Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli". Genes & Development. 19 (3): 328–38. doi:10.1101/gad.1270605. PMC 546511. PMID 15650111.
  8. ^ Horler RS, Vanderpool CK (September 2009). "Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence". Nucleic Acids Research. 37 (16): 5465–76. doi:10.1093/nar/gkp501. PMC 2760817. PMID 19531735.
  9. ^ Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (September 2013). "Comparative genomics boosts target prediction for bacterial small RNAs". Proceedings of the National Academy of Sciences of the United States of America. 110 (37): E3487–96. doi:10.1073/pnas.1303248110. PMC 3773804. PMID 23980183.

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Literature references

  1. Wadler CS, Vanderpool CK;, Proc Natl Acad Sci U S A. 2007;104:20454-20459.: A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. PUBMED:18042713 EPMC:18042713


This tab holds annotation information from the InterPro database.

InterPro entry IPR031767

SgrT is a small regulatory polypeptide that inhibits glucose transport activity by a yet unknown mechanism. It is part of a posttranscriptional regulation system in E. coli which consists of a small regulatory RNA (SgrS) and SgrT. During accumulation of glucose-6-phosphate or fructose-6-phosphate, SgrS is involved in downregulation of ptsG mRNA stability, whereas SgrT inhibits glucose transport [ PUBMED:24957761 ].

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(73)
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(0)
RP35
(5)
RP55
(13)
RP75
(25)
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Seed source: Jackhmmer:C1P5Z7
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 1
Number in full: 13
Average length of the domain: 48.50 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 84.47 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 31.2 28.1
Noise cut-off 25.7 23.2
Model length: 53
Family (HMM) version: 7
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