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Escherichia coli K-12 substr. MG1655 RNA: GlmY small regulatory RNA



Gene: glmY Accession Numbers: G0-8910 (EcoCyc), b4441, ECK2554

Synonyms: tke1, sroF

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

Summary:
GlmY is a small RNA that specifically increases synthesis of GlmS, encoded by the second open reading frame in the glmUS operon, without affecting GlmU synthesis [Urban07a]. GlmY acts indirectly by antagonizing processing of a second small RNA, GlmZ. Only full-length GlmZ can stabilize glmS mRNA and enhance its translation [Urban08, Reichenbach08]. Unlike many other small RNAs, GlmY does not act by Hfq-facilitated base pairing. Instead, GlmY binds and sequesters RapZ, thereby inhibiting RapZ-enabled processing of GlmZ [Gopel13].

The GlmY small RNA was first reported to be present as two RNA species of approximately 150 and 180 nt in length [Rivas01]. Later, it was shown that the two GlmY RNAs have the same 5' end; thus, the shorter species may be generated by processing at the 3' end. The abundance and ratio of the two species changes with the growth phase [Vogel03].

The processed form of GlmY is polyadenylated by PcnB, and mutation of pcnB leads to stabilization of the processed form of the GlmY RNA [Urban08, Reichenbach08]. PNPase and RNase II are major factors controlling the steady-state level of GlmY RNA [Andrade12].

In growth competition experiments, a glmY deletion mutant is more sensitive to cell envelope stress than the wild type [Hobbs10].

glmY is expressed from overlapping σ70 and σ54 promoters [Reichenbach09]. Expression of glmY is lower in a phoP mutant than in wild type [Raghavan11a].

SroF: "small RNomics RNA" [Vogel03]

GlmY: "glmS activator RNA Y" [Urban07a]

Reviews: [Hershberg03, Gottesman04, Gorke08a, Gopel14]

Citations: [Salim12]

Map Position: [2,689,179 <- 2,689,362] (57.96 centisomes)
Length: 184 bp

Genetic Regulation Schematic: ?

Unification Links: ASAP:ABE-0047261 , EchoBASE:EB4527 , EcoGene:EG31155 , EcoliWiki:b4441 , PortEco:glmY , RegulonDB:G0-8910

GO Terms:

Biological Process: GO:0036460 - cellular response to cell envelope stress Inferred from experiment [Hobbs10]
GO:0048519 - negative regulation of biological process Inferred from experiment [Urban08]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Gopel13]

MultiFun Terms: regulation type of regulation posttranscriptional


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Ingrid Keseler on Fri Sep 28, 2007:
Gene end position corrected based on [Urban07a ].
Ingrid Keseler on Mon Oct 16, 2006:
Gene direction reversed according to Riley et al. (2006).
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome

Credits:
Last-Curated ? 19-Mar-2013 by Keseler I , SRI International


References

Andrade12: Andrade JM, Pobre V, Matos AM, Arraiano CM (2012). "The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq." RNA 18(4);844-55. PMID: 22355164

Gopel13: Gopel Y, Papenfort K, Reichenbach B, Vogel J, Gorke B (2013). "Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA." Genes Dev 27(5);552-64. PMID: 23475961

Gopel14: Gopel Y, Khan MA, Gorke B (2014). "Menage a trois: Post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic." RNA Biol 11(5). PMID: 24667238

Gorke08a: Gorke B, Vogel J (2008). "Noncoding RNA control of the making and breaking of sugars." Genes Dev 22(21);2914-25. PMID: 18981470

Gottesman04: Gottesman S (2004). "The Small RNA Regulators of Escherichia coli: Roles and Mechanisms*." Annu Rev Microbiol 58;303-28. PMID: 15487940

Hershberg03: Hershberg R, Altuvia S, Margalit H (2003). "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31(7);1813-20. PMID: 12654996

Hobbs10: Hobbs EC, Astarita JL, Storz G (2010). "Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli: Analysis of a Bar-coded Mutant Collection." J Bacteriol 192(1):59-62. PMID: 19734312

Raghavan11a: Raghavan R, Groisman EA, Ochman H (2011). "Genome-wide detection of novel regulatory RNAs in E. coli." Genome Res 21(9);1487-97. PMID: 21665928

Reichenbach08: Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Gorke B (2008). "The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli." Nucleic Acids Res 36(8);2570-80. PMID: 18334534

Reichenbach09: Reichenbach B, Gopel Y, Gorke B (2009). "Dual control by perfectly overlapping sigma(54)- and sigma(70)-promoters adjusts small RNA GlmY expression to different environmental signals." Mol Microbiol 74(5):1054-70. PMID: 19843219

Rivas01: Rivas E, Klein RJ, Jones TA, Eddy SR (2001). "Computational identification of noncoding RNAs in E. coli by comparative genomics." Curr Biol 11(17);1369-73. PMID: 11553332

Salim12: Salim NN, Faner MA, Philip JA, Feig AL (2012). "Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY." Nucleic Acids Res 40(16);8021-32. PMID: 22661574

Urban07a: Urban JH, Papenfort K, Thomsen J, Schmitz RA, Vogel J (2007). "A Conserved Small RNA Promotes Discoordinate Expression of the glmUS Operon mRNA to Activate GlmS Synthesis." J Mol Biol 373(3);521-8. PMID: 17854828

Urban08: Urban JH, Vogel J (2008). "Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation." PLoS Biol 6(3);e64. PMID: 18351803

Vogel03: Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A, Wagner EG (2003). "RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria." Nucleic Acids Res 31(22);6435-43. PMID: 14602901

Other References Related to Gene Regulation

Gopel11: Gopel Y, Luttmann D, Heroven AK, Reichenbach B, Dersch P, Gorke B (2011). "Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae." Nucleic Acids Res 39(4);1294-309. PMID: 20965974


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, BIOCYC13B.