Escherichia coli K-12 substr. MG1655 Protein: ribonuclease E inhibitor protein A

Gene: rraA Accession Numbers: EG11879 (EcoCyc), b3929, ECK3921

Synonyms: menG, yiiV

Regulation Summary Diagram: ?

Regulation summary diagram for rraA

Subunit composition of ribonuclease E inhibitor protein A = [RraA]3
         ribonuclease E inhibitor protein = RraA

RraA inhibits ribonuclease E (RNase E, Rne) activity by binding to and masking the C-terminal RNA binding domain of RNase E. The interaction of RraA with the degradosome is facilitated by protein-RNA remodeling via the ATPase activity of RhlB [Gorna10].

RraA physically interacts with RNase E, but does not interact with the RNA substrates [Lee03c]. High-affinity binding of RraA to RNase E requires the C-terminal domain (CTD) of RNase E [Lee03c, Gao06]. RraA interacts with both RNA-binding sites of RNase E and interferes with their interaction with RNA [Gorna10]. RraA also interacts with the RhlB helicase component of the degradosome, and a ternary complex of RraA, RNase E and RhlB can be observed [Gorna10]. Binding of RraA or RraB, a second modulator of RNase E activity, differently affect the composition of the degradosome [Gao06].

A crystal structure of RraA is presented at 2.0 Å resolution. RraA forms a homotrimer; the complex is shaped like a ring with a hole of 12 Å across. RraA is structurally related to a family of aldolases [Monzingo03].

The regulatory interaction between RraA and RNase E and their orthologs appears to be evolutionarily conserved [Yeom08, Yeom08a, Lee09f].

Transcription of rraA is σS-dependent and increased upon entry into stationary phase. The stability of rraA mRNA itself is dependent on the activity of RNase E [Zhao06c]. Overproduction of RraA causes pleiotropic phenotypes due to increased abundance of RNAs that are usually substrates of RNase E [Lee03c]. Overexpression of RraA rescues cells overexpressing RNase E from growth arrest [Yeom06].

RraA was originally mis-annotated as a SAM-dependent methyltransferase predicted to act in menaquinone biosynthesis, and given the name MenG (Hudspeth et al., unpublished; GenBank record U56082); however, the protein was found to lack both structural or functional indications of methyltransferase activity [Lee03c, Monzingo03].

RraA: "regulator of ribonuclease activity A" [Lee03c]

Reviews: [Regnier09, Kaberdin09]

Locations: cytosol

Map Position: [4,116,868 <- 4,117,353] (88.73 centisomes, 319°)
Length: 486 bp / 161 aa

Molecular Weight of Polypeptide: 17.36 kD (from nucleotide sequence), 17.4 kD (experimental)

Unification Links: ASAP:ABE-0012837 , DIP:DIP-35864N , EchoBASE:EB1825 , EcoGene:EG11879 , EcoliWiki:b3929 , ModBase:P0A8R0 , OU-Microarray:b3929 , PortEco:rraA , PR:PRO_000023875 , Pride:P0A8R0 , Protein Model Portal:P0A8R0 , RefSeq:NP_418364 , RegulonDB:EG11879 , SMR:P0A8R0 , String:511145.b3929 , UniProt:P0A8R0

Relationship Links: InterPro:IN-FAMILY:IPR005493 , InterPro:IN-FAMILY:IPR010203 , InterPro:IN-FAMILY:IPR014339 , PDB:Structure:1Q5X , PDB:Structure:2YJT , PDB:Structure:2YJV , Pfam:IN-FAMILY:PF03737

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006401 - RNA catabolic process Inferred from experiment [Lee03c]
GO:0060702 - negative regulation of endoribonuclease activity Inferred from experiment [Lee03c]
GO:0051252 - regulation of RNA metabolic process Inferred by computational analysis [GOA01a]
GO:0060699 - regulation of endoribonuclease activity Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Lee03c, Gorna10]
GO:0008428 - ribonuclease inhibitor activity Inferred from experiment Inferred by computational analysis [GOA01a, Lee03c]
GO:0019899 - enzyme binding Inferred by computational analysis [GOA06]
GO:0060698 - endoribonuclease inhibitor activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

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

Essentiality data for rraA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 02-Feb-2010 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3929 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11879; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gao06: Gao J, Lee K, Zhao M, Qiu J, Zhan X, Saxena A, Moore CJ, Cohen SN, Georgiou G (2006). "Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome." Mol Microbiol 61(2);394-406. PMID: 16771842

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gorna10: Gorna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernandez H, Robinson CV, Luisi BF (2010). "The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome." RNA 16(3):553-62. PMID: 20106955

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kaberdin09: Kaberdin VR, Lin-Chao S (2009). "Unraveling new roles for minor components of the E. coli RNA degradosome." RNA Biol 6(4);402-5. PMID: 19667755

Lee03c: Lee K, Zhan X, Gao J, Qiu J, Feng Y, Meganathan R, Cohen SN, Georgiou G (2003). "RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli." Cell 114(5);623-34. PMID: 13678585

Lee09f: Lee M, Yeom JH, Sim SH, Ahn S, Lee K (2009). "Effects of Escherichia coli RraA orthologs of Vibrio vulnificus on the ribonucleolytic activity of RNase E in vivo." Curr Microbiol 58(4);349-53. PMID: 19194749

Monzingo03: Monzingo AF, Gao J, Qiu J, Georgiou G, Robertus JD (2003). "The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing." J Mol Biol 332(5);1015-24. PMID: 14499605

Regnier09: Regnier P, Hajnsdorf E (2009). "Poly(A)-assisted RNA decay and modulators of RNA stability." Prog Mol Biol Transl Sci 85;137-85. PMID: 19215772

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Yeom06: Yeom JH, Lee K (2006). "RraA rescues Escherichia coli cells over-producing RNase E from growth arrest by modulating the ribonucleolytic activity." Biochem Biophys Res Commun 345(4);1372-6. PMID: 16725107

Yeom08: Yeom JH, Go H, Shin E, Kim HL, Han SH, Moore CJ, Bae J, Lee K (2008). "Inhibitory effects of RraA and RraB on RNAse E-related enzymes imply conserved functions in the regulated enzymatic cleavage of RNA." FEMS Microbiol Lett 285(1);10-5. PMID: 18510556

Yeom08a: Yeom JH, Shin E, Go H, Sim SH, Seong MJ, Lee K (2008). "Functional implications of the conserved action of regulators of ribonuclease activity." J Microbiol Biotechnol 18(8);1353-6. PMID: 18756093

Zhao06c: Zhao M, Zhou L, Kawarasaki Y, Georgiou G (2006). "Regulation of RraA, a protein inhibitor of RNase E-mediated RNA decay." J Bacteriol 188(9);3257-63. PMID: 16621818

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Suvarna98: Suvarna K, Stevenson D, Meganathan R, Hudspeth ME (1998). "Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli." J Bacteriol 180(10);2782-7. PMID: 9573170

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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