|Gene:||rnr||Accession Numbers: EG11259 (EcoCyc), b4179, ECK4175|
Synonyms: vacB, yjeC
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 [Chen05b, 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 [Liang11a]. 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].
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].
|Map Position: [4,404,677 -> 4,407,118] (94.94 centisomes, 342°)||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: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:PF08206 , Pfam:IN-FAMILY:PF08461 , Prosite:IN-FAMILY:PS01175 , Prosite:IN-FAMILY:PS50126 , Smart:IN-FAMILY:SM00316 , Smart:IN-FAMILY:SM00357
|Biological Process:||GO:0006402 - mRNA catabolic process
GO:0006950 - response to stress [Chen05b]
GO:0009409 - response to cold [Cairrao03]
GO:0034470 - ncRNA processing [Cairrao03]
GO:0090501 - RNA phosphodiester bond hydrolysis [GOA01, Cheng98, Cheng02]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic [GOA06, GOA01a, Kasai77, Cheng02]
GO:0009405 - pathogenesis [UniProtGOA11]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11, GOA01]
|Molecular Function:||GO:0000175 - 3'-5'-exoribonuclease activity
GO:0004540 - ribonuclease activity [GOA01, Cheng98]
GO:0005515 - protein binding [Liang10]
GO:0008997 - ribonuclease R activity [Cheng02]
GO:0016896 - exoribonuclease activity, producing 5'-phosphomonoesters [Cheng02]
GO:0034458 - 3'-5' RNA helicase activity [Awano10]
GO:0003676 - nucleic acid binding [GOA01]
GO:0003723 - RNA binding [UniProtGOA11, GOA06, GOA01]
GO:0004518 - nuclease activity [UniProtGOA11, GOA01]
GO:0004527 - exonuclease activity [UniProtGOA11]
GO:0008859 - exoribonuclease II activity [GOA06, GOA01a]
GO:0016787 - hydrolase activity [UniProtGOA11]
|Cellular Component:||GO:0005829 - cytosol
GO:0005737 - cytoplasm [UniProtGOA11a, UniProtGOA11, GOA06]
|MultiFun Terms:||information transfer → RNA related → RNA degradation|
|metabolism → degradation of macromolecules → RNA|
|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]|
Enzymatic reaction of: RNase R
Synonyms: ribonuclease R, exoribonuclease R
EC Number: 3.1.13.-
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].
pH(opt) (forward direction): 7.5-9.5 [Cheng02]
|Chain||2 -> 813|
|Conserved-Region||644 -> 725|
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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