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Escherichia coli K-12 substr. MG1655 Enzyme: RNase R

Gene: rnr Accession Numbers: EG11259 (EcoCyc), b4179, ECK4175

Synonyms: vacB, yjeC

Regulation Summary Diagram: ?

RNase R is a ribonuclease that has been implicated in rRNA maturation, mRNA degradation during stationary phase, degradation of polyadenylated mRNAs, and tmRNA-mediated degradation of non-stop mRNAs.

RNase R is a processive 3' to 5' exoribonuclease that releases 5'-nucleoside monophosphates, producing limit end products of di- and trinucleotides. Although it can cleave several RNA substrates, it shows greatest activity toward rRNA [Cheng02]. Unlike RNase II, RNase R is able to digest double-stranded RNA as long as a single-stranded region at the 3' end is available; it was shown that RNase R is involved in the decay of structured mRNAs [Cheng05]. The C-terminal S1 domain does not appear to be responsible for this ability [Amblar07], while the nuclease domain is sufficient for degradation of double-stranded RNA [Vincent09]. A 3' overhang of at least 7 nucleotides is required for RNase R binding and activity; the structure of the 3' sugar residue only plays a small role in substrate recognition [Vincent06]. The enzyme does not bind or degrade single-stranded DNA [Vincent06].

RNase R contains two N-terminal cold shock domains (CSDs) which appear to play a role in substrate recruitment, a central nuclease (RNB) domain, followed by an S1 domain that may position substrates for efficient catalysis, and a C-terminal basic domain [Vincent09]. The CSDs, especially CSD2, is responsible for an RNA helicase activity that is independent of the RNase activity of the protein and that is required for complementation of the cold-shock function of CsdA [Awano10]. The Asp280 residue in the RNB domain is required for RNase activity, but is not involved in substrate binding [Matos09], while Arg572 is required for degradation of structured RNA [Vincent09a]. Tyr324 [Matos09] and Arg572 [Vincent09a] influences the length of the final degradation product. Both CSDs and the S1 domain function as RNA-binding domains and are responsible for the selective degradation of double-stranded RNA substrates containing a single-stranded 3' overhang of five or more nucleotides [Matos09]. Swapping the S1 and RNB domains from RNase R into an RNase II context enables the degradation of ds RNA substrates and the appearance of the 2 nt final degradation product [Matos11].

RNase R appears to be specifically involved in the maturation of tmRNA, a small RNA involved in rescue of stalled ribosomes, at low growth temperatures [Cairrao03], and in the tmRNA-mediated degradation of non-stop mRNAs [Richards06]. Targeted non-stop mRNA decay requires interaction with SmpB/tmRNA and engagement with the stalled ribosome and involves the C-terminal basic domain of RNase R [Ge10]. RNase R also decreases ompA mRNA stability at stationary phase [Andrade06] and degrades oligoadenylated rpsO mRNA [Andrade09].

RNase R is involved in the degradation of ribosomal RNA both during starvation and for ribosomal quality control [Basturea11].

RNase R levels are induced 7- to 8-fold by cold shock, mainly as a result of increased mRNA stability. PNPase is involved in regulating RNase R levels [Cairrao03]. RNase R is also induced during entry into stationary phase and starvation [Chen05c, Andrade06]. Maturation of the operon mRNA containing rnr and RNase R levels are dependent on RNase E [Cairrao06]. RNase R levels are slightly increased at high temperatures and ~5-fold increased at high temperatures in an RNase E mutant [Andrade09]. The RNase R protein is highly unstable during exponential growth; the protein is stabilized in stationary phase and under cold shock and minimal media growth conditions, accounting for increased RNase R levels despite decreased levels of rnr mRNA [Chen10]. The trans-translation system (tmRNA and SmpB) is responsible for the short half life of RNase R during exponential growth via its interactions with the C-terminal domains of RNase R [Liang10]. During exponential phase, Lys544 is acetylated by Pka, resulting in tighter binding of tmRNA-SmpB to RNase R followed by proteolytic degradation [Liang11]. tmRNA-SmpB stimulates binding of the proteases HslUV and Lon to the N terminus of RNase R [Liang12]. Pka is not present in late exponential and stationary phase, resulting in increased stability of newly synthesized RNase R [Liang12a].

VacB (later shown to be identical to RNase R [Cheng98]) of enteroinvasive E. coli, Shigella flexneri, and other Shigella is important for the virulence of these organisms [Tobe92].

An rnr mutant has a growth defect during growth at low temperatures [Cairrao03]. An rnr pnp double mutant is not viable [Cheng98] and accumulates high levels of mRNAs containing REP sequences [Cheng05]. Overexpression of RNase R complements the cold-sensitive phenotype of a deaD mutant [Awano07], but not that of a pnp mutant [Awano08]. Overexpression of RNase R rescues the growth defect of a Δrph Δpnp mutant [Jain09].

Reviews: [Deutscher93, Andrade09a, Kaberdin11]

Citations: [Nikolaev76, Karzai01, Polissi03, Sundermeier08, Barbas08, Phadtare11, Tamura12, Jain12, Phadtare12]

Locations: cytosol

Map Position: [4,404,677 -> 4,407,118] (94.94 centisomes)
Length: 2442 bp / 813 aa

Molecular Weight of Polypeptide: 92.109 kD (from nucleotide sequence), 95 kD (experimental) [Cheng02 ]

Unification Links: ASAP:ABE-0013678 , DIP:DIP-10733N , EchoBASE:EB1239 , EcoGene:EG11259 , EcoliWiki:b4179 , ModBase:P21499 , OU-Microarray:b4179 , PortEco:rnr , PR:PRO_000023799 , Pride:P21499 , Protein Model Portal:P21499 , RefSeq:NP_418600 , RegulonDB:EG11259 , SMR:P21499 , String:511145.b4179 , UniProt:P21499

Relationship Links: InterPro:IN-FAMILY:IPR001900 , InterPro:IN-FAMILY:IPR003029 , InterPro:IN-FAMILY:IPR004476 , InterPro:IN-FAMILY:IPR011129 , InterPro:IN-FAMILY:IPR011805 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013223 , InterPro:IN-FAMILY:IPR013668 , InterPro:IN-FAMILY:IPR022966 , InterPro:IN-FAMILY:IPR022967 , Pfam:IN-FAMILY:PF00575 , Pfam:IN-FAMILY:PF00773 , Pfam:IN-FAMILY:PF08206 , Pfam:IN-FAMILY:PF08461 , Prosite:IN-FAMILY:PS01175 , Prosite:IN-FAMILY:PS50126 , Smart:IN-FAMILY:SM00316 , Smart:IN-FAMILY:SM00357 , Smart:IN-FAMILY:SM00955

In Paralogous Gene Group: 285 (5 members) , 526 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006402 - mRNA catabolic process Inferred from experiment [Cheng05]
GO:0006950 - response to stress Inferred from experiment Inferred by computational analysis [UniProtGOA11, Chen05c]
GO:0009409 - response to cold Inferred from experiment [Cairrao03]
GO:0034470 - ncRNA processing Inferred from experiment [Cairrao03]
GO:0090501 - RNA phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Cheng98, Cheng02, GOA01]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred by computational analysis Inferred from experiment [Kasai77, Cheng02, GOA06, GOA01a]
GO:0009405 - pathogenesis Inferred by computational analysis [UniProtGOA11]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0000175 - 3'-5'-exoribonuclease activity Inferred from experiment [Kasai77, Cheng02]
GO:0004540 - ribonuclease activity Inferred from experiment Inferred by computational analysis [GOA01, Cheng98]
GO:0005515 - protein binding Inferred from experiment [Liang10]
GO:0008997 - ribonuclease R activity Inferred from experiment [Cheng02]
GO:0016896 - exoribonuclease activity, producing 5'-phosphomonoesters Inferred from experiment [Cheng02]
GO:0034458 - 3'-5' RNA helicase activity Inferred from experiment [Awano10]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0008859 - exoribonuclease II activity Inferred by computational analysis [GOA06, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer RNA related RNA degradation
metabolism degradation of macromolecules RNA

Essentiality data for rnr 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-Jan-2013 by Keseler I , SRI International

Enzymatic reaction of: RNase R

Synonyms: ribonuclease R, exoribonuclease R

EC Number: 3.1.13.-

RNase R degradation substrate RNA + n-1 H2O <=> n-2 a nucleoside 5'-monophosphate + a diribonucleotide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

The Km for a poly(A) substrate is about 30 nM [Cheng02].

Cofactors or Prosthetic Groups: Mg2+ [Cheng02]

Activators (Unknown Mechanism): K+ [Cheng02]

pH(opt) (forward direction): 7.5-9.5 [Cheng02]

pH(opt): 7 [BRENDA14, Spahr64], 8 [BRENDA14, Arraiano08]

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Cheng02, UniProt11, Cheng02]
UniProt: Removed.
Chain 2 -> 813
UniProt: Ribonuclease R.
Mutagenesis-Variant 272
[Awano10, UniProt11]
Alternate sequence: D → N; UniProt: Loss of RNase activity, but exhibits helicase activity.
Mutagenesis-Variant 280
[Awano10, UniProt11]
Alternate sequence: D → N; UniProt: Loss of RNase activity, but exhibits helicase activity.
Acetylation-Modification 544
[Zhang09a, UniProt11a]
UniProt: N6-acetyllysine.
Conserved-Region 644 -> 725
UniProt: S1 motif;

Gene Local Context (not to scale): ?

Transcription Units:


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b4179 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11259; confirmed by SwissProt match.


Amblar07: Amblar M, Barbas A, Gomez-Puertas P, Arraiano CM (2007). "The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization." RNA 13(3);317-27. PMID: 17242308

Andrade06: Andrade JM, Cairrao F, Arraiano CM (2006). "RNase R affects gene expression in stationary phase: regulation of ompA." Mol Microbiol 60(1);219-28. PMID: 16556233

Andrade09: Andrade JM, Hajnsdorf E, Regnier P, Arraiano CM (2009). "The poly(A)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R." RNA 15(2);316-26. PMID: 19103951

Andrade09a: Andrade JM, Pobre V, Silva IJ, Domingues S, Arraiano CM (2009). "The role of 3'-5' exoribonucleases in RNA degradation." Prog Mol Biol Transl Sci 85;187-229. PMID: 19215773

Arraiano08: Arraiano CM, Barbas A, Amblar M (2008). "Characterizing ribonucleases in vitro examples of synergies between biochemical and structural analysis." Methods Enzymol 447;131-60. PMID: 19161842

Awano07: Awano N, Xu C, Ke H, Inoue K, Inouye M, Phadtare S (2007). "Complementation analysis of the cold-sensitive phenotype of the Escherichia coli csdA deletion strain." J Bacteriol 189(16);5808-15. PMID: 17557820

Awano08: Awano N, Inouye M, Phadtare S (2008). "RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II." J Bacteriol 190(17);5924-33. PMID: 18606734

Awano10: Awano N, Rajagopal V, Arbing M, Patel S, Hunt J, Inouye M, Phadtare S (2010). "Escherichia coli RNase R has dual activities, helicase and RNase." J Bacteriol 192(5);1344-52. PMID: 20023028

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

Barbas08: Barbas A, Matos RG, Amblar M, Lopez-Vinas E, Gomez-Puertas P, Arraiano CM (2008). "New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product." J Biol Chem 283(19);13070-6. PMID: 18337246

Basturea11: Basturea GN, Zundel MA, Deutscher MP (2011). "Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH." RNA 17(2);338-45. PMID: 21135037

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Cairrao03: Cairrao F, Cruz A, Mori H, Arraiano CM (2003). "Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA." Mol Microbiol 50(4);1349-60. PMID: 14622421

Cairrao06: Cairrao F, Arraiano CM (2006). "The role of endoribonucleases in the regulation of RNase R." Biochem Biophys Res Commun 343(3);731-7. PMID: 16563345

Chen05c: Chen C, Deutscher MP (2005). "Elevation of RNase R in response to multiple stress conditions." J Biol Chem 280(41);34393-6. PMID: 16135521

Chen10: Chen C, Deutscher MP (2010). "RNase R is a highly unstable protein regulated by growth phase and stress." RNA 16(4);667-72. PMID: 20185542

Cheng02: Cheng ZF, Deutscher MP (2002). "Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II." J Biol Chem 277(24);21624-9. PMID: 11948193

Cheng05: Cheng ZF, Deutscher MP (2005). "An important role for RNase R in mRNA decay." Mol Cell 17(2);313-8. PMID: 15664199

Cheng98: Cheng ZF, Zuo Y, Li Z, Rudd KE, Deutscher MP (1998). "The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R." J Biol Chem 273(23);14077-80. PMID: 9603904

Deutscher93: Deutscher MP (1993). "Promiscuous exoribonucleases of Escherichia coli." J Bacteriol 175(15);4577-83. PMID: 8335617

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

Ge10: Ge Z, Mehta P, Richards J, Karzai AW (2010). "Non-stop mRNA decay initiates at the ribosome." Mol Microbiol 78(5);1159-70. PMID: 21091502

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

Jain09: Jain C (2009). "Identification and characterization of growth suppressors of Escherichia coli strains lacking phosphorolytic ribonucleases." J Bacteriol 191(18);5622-7. PMID: 19617368

Jain12: Jain C (2012). "Novel role for RNase PH in the degradation of structured RNA." J Bacteriol 194(15);3883-90. PMID: 22609921

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

Kaberdin11: Kaberdin VR, Singh D, Lin-Chao S (2011). "Composition and conservation of the mRNA-degrading machinery in bacteria." J Biomed Sci 18;23. PMID: 21418661

Karzai01: Karzai AW, Sauer RT (2001). "Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex." Proc Natl Acad Sci U S A 98(6);3040-4. PMID: 11248028

Kasai77: Kasai T, Gupta RS, Schlessinger D (1977). "Exoribonucleases in wild type Escherichia coli and RNase II-deficient mutants." J Biol Chem 252(24);8950-6. PMID: 336626

Liang10: Liang W, Deutscher MP (2010). "A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R." J Biol Chem 285(38);29054-8. PMID: 20688916

Liang11: Liang W, Malhotra A, Deutscher MP (2011). "Acetylation Regulates the Stability of a Bacterial Protein: Growth Stage-Dependent Modification of RNase R." Mol Cell 44(1);160-6. PMID: 21981926

Liang12: Liang W, Deutscher MP (2012). "Transfer-messenger RNA-SmpB protein regulates ribonuclease R turnover by promoting binding of HslUV and Lon proteases." J Biol Chem 287(40);33472-9. PMID: 22879590

Liang12a: Liang W, Deutscher MP (2012). "Post-translational modification of RNase R is regulated by stress-dependent reduction in the acetylating enzyme Pka (YfiQ)." RNA 18(1);37-41. PMID: 22124017

Matos09: Matos RG, Barbas A, Arraiano CM (2009). "RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation." Biochem J 423(2);291-301. PMID: 19630750

Matos11: Matos RG, Barbas A, Gomez-Puertas P, Arraiano CM (2011). "Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade ds RNA." Proteins 79(6);1853-67. PMID: 21465561

Nikolaev76: Nikolaev N, Folsom V, Schlessinger D (1976). "Escherichia coli mutants deficient in exoribonucleases." Biochem Biophys Res Commun 70(3);920-4. PMID: 779788

Phadtare11: Phadtare S (2011). "Unwinding activity of cold shock proteins and RNA metabolism." RNA Biol 8(3);394-7. PMID: 21445001

Phadtare12: Phadtare S (2012). "Escherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism." Genes Cells 17(10);850-74. PMID: 22957931

Polissi03: Polissi A, De Laurentis W, Zangrossi S, Briani F, Longhi V, Pesole G, Deho G (2003). "Changes in Escherichia coli transcriptome during acclimatization at low temperature." Res Microbiol 154(8);573-80. PMID: 14527658

Richards06: Richards J, Mehta P, Karzai AW (2006). "RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner." Mol Microbiol 62(6);1700-12. PMID: 17087776

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Spahr64: Spahr PF (1964). "Purification and properties of ribonuclease II from Escherichia coli." J Biol Chem 239;3716-26. PMID: 14257598

Sundermeier08: Sundermeier T, Ge Z, Richards J, Dulebohn D, Karzai AW (2008). "Studying tmRNA-mediated surveillance and nonstop mRNA decay." Methods Enzymol 447;329-58. PMID: 19161851

Tamura12: Tamura M, Kers JA, Cohen SN (2012). "Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli." J Bacteriol 194(8);1919-26. PMID: 22328678

Tobe92: Tobe T, Sasakawa C, Okada N, Honma Y, Yoshikawa M (1992). "vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri." J Bacteriol 174(20);6359-67. PMID: 1400189

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

Vincent06: Vincent HA, Deutscher MP (2006). "Substrate recognition and catalysis by the exoribonuclease RNase R." J Biol Chem 281(40);29769-75. PMID: 16893880

Vincent09: Vincent HA, Deutscher MP (2009). "The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA." J Biol Chem 284(1);486-94. PMID: 19004832

Vincent09a: Vincent HA, Deutscher MP (2009). "Insights into how RNase R degrades structured RNA: analysis of the nuclease domain." J Mol Biol 387(3);570-83. PMID: 19361424

Zhang09a: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

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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 Mon Nov 24, 2014, BIOCYC13B.