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



Gene: glmZ Accession Numbers: G0-8873 (EcoCyc), b4456, ECK3795

Synonyms: psrA20, sraJ, k19, ryiA

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

Summary:
GlmZ is a small RNA involved in posttranscriptional regulation of glmS accumulation and translation in response to the intracellular concentration of glucosamine 6-phosphate [Kalamorz07]. The full-length form of GlmZ is thought to interact directly with the 5' UTR of the glmS mRNA, unmasking the ribosome binding site and thus activating translation [Urban08].

An efficient interaction between GlmZ RNA and Hfq protein has been detected [Wassarman01], and Hfq is required for the GlmZ-mediated increase in GlmS synthesis [Kalamorz07, Urban08].

GlmZ was detected as a small RNA that appears in two forms, a full-length species of approximately 210 nt and a processed species of approximately 172 nt in length [Wassarman01, Argaman01]. Posttranscriptional processing of GlmZ is dependent on RNase III [Argaman01] and on RapZ [Kalamorz07]. RapZ acts as an adaptor protein that guides processing of GlmZ by RNase E [Gopel13]. The GlmY small RNA antagonizes processing of GlmZ [Urban08, Reichenbach08] by binding and sequestering RapZ, thereby inhibiting RapZ-enabled processing of GlmZ [Gopel13].

Using a network biology approach, both GlmZ and McaS (IsrA) were predicted to be involved in the DNA damage response. A glmZ mcaS double mutant is less sensitive to DNA damaging agents and has a lower basal mutation rate than wild type [Modi11].

GlmZ is expressed in the early logarithmic growth phase and is slightly induced by cold shock [Argaman01]. The unprocessed form is prevalent in LB medium, while the shorter, processed form predominates in minimal medium [Wassarman01]. The half life of GlmZ in exponentially growing cells is 2 minutes [Vogel03].

SraJ: "small RNA" [Argaman01]

PsrA20: "predicted small RNA" [Argaman01]

Ryx: "RNA of unknown function at X position (10 minute) in the genome" [Wassarman01]

Reviews: [Gottesman01, Gottesman04, Gorke08a, Frohlich09, Gopel14]

Citations: [Salim12]

Map Position: [3,984,455 -> 3,984,626] (85.88 centisomes)
Length: 172 bp

Unification Links: ASAP:ABE-0047274 , EchoBASE:EB4539 , EcoGene:EG31165 , PortEco:glmZ , RegulonDB:G0-8873

GO Terms:

Biological Process: GO:0045948 - positive regulation of translational initiation Inferred from experiment [Urban08]
GO:0045975 - positive regulation of translation, ncRNA-mediated Inferred from experiment [Urban08]
GO:0070928 - regulation of mRNA stability, ncRNA-mediated Inferred from experiment [Kalamorz07]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Gopel13]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [Urban08]

MultiFun Terms: information transfer RNA related antisense RNA
regulation type of regulation posttranscriptional antisense RNA
regulation type of regulation posttranscriptional translation attenuation and efficiency

Regulated Transcription Units (2 total): ?

Notes:


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Argaman01: 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. PMID: 11448770

Frohlich09: Frohlich KS, Vogel J (2009). "Activation of gene expression by small RNA." Curr Opin Microbiol 12(6);674-82. PMID: 19880344

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

Gottesman01: Gottesman S, Storz G, Rosenow C, Majdalani N, Repoila F, Wassarman KM (2001). "Small RNA regulators of translation: mechanisms of action and approaches for identifying new small RNAs." Cold Spring Harb Symp Quant Biol 66;353-62. PMID: 12762038

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

Kalamorz07: Kalamorz F, Reichenbach B, Marz W, Rak B, Gorke B (2007). "Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli." Mol Microbiol 65(6);1518-33. PMID: 17824929

Modi11: Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ (2011). "Functional characterization of bacterial sRNAs using a network biology approach." Proc Natl Acad Sci U S A 108(37);15522-7. PMID: 21876160

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

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

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

Wassarman01: Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays." Genes Dev 15(13);1637-51. PMID: 11445539

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

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


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 21, 2014, biocyc14.