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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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Escherichia coli K-12 substr. MG1655 RNA: MicA small regulatory RNA



Gene: micA Accession Numbers: G0-8866 (EcoCyc), b4442, ECK2682

Synonyms: sraD, psrA10

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

Summary:
MicA is a small RNA that negatively regulates expression of a number of genes. The first identified target of MicA was OmpA, whose expression is regulated during stationary phase [Udekwu05, Rasmussen05, Urban07]. MicA acts as an antisense RNA, binding to the translation initiation region of ompA mRNA and blocking ribosome binding, thereby downregulating OmpA expression. This downregulation requires the RNA-binding protein Hfq [Udekwu05, Rasmussen05]. Hfq acts as an RNA chaperone, bringing MicA and ompA into close proximity and restructuring MicA to expose the ompA-binding site for pairing [Henderson13].

In addition, MicA downregulates expression of a number of other genes. The list includes phoPQ, linking the PhoPQ regulon to the envelope stress response [Coornaert10, Coornaert13], and a number of other genes [Gogol11]. MicA can also downregulate expression of OmpX -- likely under conditions where its primary regulator, CyaR, is poorly expressed [Johansen08]. MicA positively regulates motility, but not by regulating the expression of flhDC [De12].

MicA is able to form dimers; self-association is dependent on Mg2+ concentration and obstructs the ompA binding site [Henderson13].

A micA deletion mutant is sensitive to cell envelope stress [Hobbs10] and appears unable to establish long-term stationary phase [Nagamitsu13]. Overexpression of either MicA or RybB rescues the growth and viability phenotypes of σE depletion [Gogol11] and also leads to increased cell lysis in stationary phase [Murata12].

Expression of micA is controlled by the alternative sigma factor σE [Johansen06, Udekwu07] and is increased upon entry into stationary phase [Argaman01, Udekwu05]. MicA levels in stationary phase are increased in a pnp mutant [Andrade08]. The half life of micA in stationary phase is 4 minutes [Vogel03].

SraD: "small RNA D" [Argaman01]

Review: [Vogel06]

Citations: [Udekwu10]

Map Position: [2,812,824 -> 2,812,895] (60.63 centisomes)
Length: 72 bp

Unification Links: ASAP:ABE-0047262 , EchoBASE:EB4528 , EcoGene:EG31156 , EcoliWiki:b4442 , PortEco:micA , RegulonDB:G0-8866

GO Terms:

Biological Process: GO:0006950 - response to stress Inferred from experiment [Udekwu07, Hobbs10]
GO:0040033 - negative regulation of translation, ncRNA-mediated Inferred from experiment [Rasmussen05, Udekwu05]
Molecular Function: GO:0003729 - mRNA binding Inferred from experiment [Udekwu05, Rasmussen05]
GO:0005515 - protein binding Inferred from experiment [Rasmussen05, Udekwu05]

MultiFun Terms: information transfer RNA related antisense RNA
regulation type of regulation posttranscriptional antisense RNA

Regulated Transcription Units (21 total): ?

Notes:


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Ingrid Keseler on Thu May 31, 2007:
Gene position corrected based on Udekwu et al. [Udekwu05 ].
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome

Credits:
Last-Curated ? 25-Apr-2013 by Keseler I , SRI International


References

Andrade08: Andrade JM, Arraiano CM (2008). "PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins." RNA 14(3);543-51. PMID: 18203924

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

Coornaert10: Coornaert A, Lu A, Mandin P, Springer M, Gottesman S, Guillier M (2010). "MicA sRNA links the PhoP regulon to cell envelope stress." Mol Microbiol 76(2):467-79. PMID: 20345657

Coornaert13: Coornaert A, Chiaruttini C, Springer M, Guillier M (2013). "Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB." PLoS Genet 9(1);e1003156. PMID: 23300478

De12: De Lay N, Gottesman S (2012). "A complex network of small non-coding RNAs regulate motility in Escherichia coli." Mol Microbiol 86(3);524-38. PMID: 22925049

Gogol11: Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA (2011). "Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon." Proc Natl Acad Sci U S A 108(31);12875-80. PMID: 21768388

Henderson13: Henderson CA, Vincent HA, Stone CM, Phillips JO, Cary PD, Gowers DM, Callaghan AJ (2013). "Characterization of MicA interactions suggests a potential novel means of gene regulation by small non-coding RNAs." Nucleic Acids Res 41(5);3386-97. PMID: 23361466

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

Johansen06: Johansen J, Rasmussen AA, Overgaard M, Valentin-Hansen P (2006). "Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins." J Mol Biol 364(1);1-8. PMID: 17007876

Johansen08: Johansen J, Eriksen M, Kallipolitis B, Valentin-Hansen P (2008). "Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP-CRP- and sigma(E)-Dependent CyaR-ompX Regulatory Case." J Mol Biol 383(1):1-9. PMID: 18619465

Murata12: Murata M, Noor R, Nagamitsu H, Tanaka S, Yamada M (2012). "Novel pathway directed by σ E to cause cell lysis in Escherichia coli." Genes Cells 17(3);234-47. PMID: 22251246

Nagamitsu13: Nagamitsu H, Murata M, Kosaka T, Kawaguchi J, Mori H, Yamada M (2013). "Crucial Roles of MicA and RybB as Vital Factors for σ-Dependent Cell Lysis in Escherichia coli Long-Term Stationary Phase." J Mol Microbiol Biotechnol 23(3);227-232. PMID: 23594456

Rasmussen05: Rasmussen AA, Eriksen M, Gilany K, Udesen C, Franch T, Petersen C, Valentin-Hansen P (2005). "Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control." Mol Microbiol 58(5);1421-9. PMID: 16313626

Udekwu05: Udekwu KI, Darfeuille F, Vogel J, Reimegard J, Holmqvist E, Wagner EG (2005). "Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA." Genes Dev 19(19);2355-66. PMID: 16204185

Udekwu07: Udekwu KI, Wagner EG (2007). "Sigma E controls biogenesis of the antisense RNA MicA." Nucleic Acids Res 35(4);1279-88. PMID: 17267407

Udekwu10: Udekwu KI (2010). "Transcriptional and post-transcriptional regulation of the Escherichia coli luxS mRNA; involvement of the sRNA MicA." PLoS One 5(10);e13449. PMID: 20976191

Urban07: Urban JH, Vogel J (2007). "Translational control and target recognition by Escherichia coli small RNAs in vivo." Nucleic Acids Res 35(3);1018-37. PMID: 17264113

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

Vogel06: Vogel J, Papenfort K (2006). "Small non-coding RNAs and the bacterial outer membrane." Curr Opin Microbiol 9(6);605-11. PMID: 17055775


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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 Dec 19, 2014, BIOCYC14A.