Escherichia coli K-12 substr. MG1655 Enzyme: ribonuclease II

Gene: rnb Accession Numbers: EG11620 (EcoCyc), b1286, ECK1281

Synonyms: RNase II

Regulation Summary Diagram: ?

Regulation summary diagram for rnb

Ribonuclease II (RNase II) is an exonuclease that cleaves RNA from the 3' end to produce ribonucleoside 5'-monophosphates. RNase II is one of five exonucleases (RNase II, Rnase D, RNase BN, RNase T, RNase PH) that can process tRNA and is responsible for the first step in the conversion of tyrosine tRNA to its final form [Reuven93, Kitamura77]. It has been shown in vitro to cleave long 3' tRNA sequences to yield 2-4 nucleotide intermediates for subsequent processing [Li94a]. It also degrades the polycistronic tryptophan operon mRNA from its primary transcription termination site (trp t') to a secondary termination hairpin (trp t) to yield the mature tryptophan mRNA [Mott85]. RNase II is responsible for a signficant portion of the degradation of artificial hammerhead ribozymes in vivo [Wang96]. RNase II also contributes to the degradation of smaller RNA during carbon starvation, though it has no role in 23 S or 16 S RNA breakdown [Kaplan74, Kaplan75]. In concert with PNPase, RNase II degrades the major 3' cleavage product of the antisense RNA CopA, though it can also protect the 3' end from PNPase degradation [Soderbom98]. Temperature-sensitive double mutants in RNase II and PNPase are inviable at the nonpermissive temperature and accumulate mRNA fragments of 100 to 1,500 nucleotides in length [Donovan86]. Triple mutants in RNase II, PNPase and ams show a three- to four-fold increase in the half life of pulse-labeled RNA [Arraiano88]. RNase II degrades rpsO mRNA following removal of the transcript's 3' stem-loop structure by RNase E, but protects it from degradation by other factors if the 3' stem-loop is present [Hajnsdorf94]. RNase II also plays a role in bacteriophage T4 ribonucleic acid metabolism [Birenbaum80].

RNase II degrades the poly(A) tails of mRNA. In triple mutants lacking RNase II, PNPase and RNase E, the length and abundance of mRNA poly(A) tails increases dramatically [OHara95]. Double mutants in RNase II and PNPase show a twenty- to sixty-fold increase in appearance of poly(A) RNA and a three- to four-fold increase in the length of poly(A) tails relative to wild type, but less than a two-fold change in non-poly(A) RNA levels. Poly(A) synthesis is also higher in mutant cells, indicating that the exonucleases tested both degrade polyadenylated mRNA and reduce its rate of synthesis [Cao97]. RNase II removes poly(A) tails from rpsO mRNA. The resulting deadenylated rpsO mRNA is more stable than oligoadenylated rpsO mRNA [Marujo00]. RNase II is responsible for most degradation of of poly(A) tails associated with 23 S RNA and can be overexpressed to prevent toxicity due to excessive polyadenylation, which decreases the half-life of mRNA [Mohanty00, Mohanty99]. Hfq blocks the degradation of poly(A) tails by RNase II [Folichon03]. Polyadenylation of the mRNA for the ribosomal protein S20 allows RNase II and PNPase to degrade it [Coburn96].

RNase II catalyzes the direct removal of ribonucleoside 5'-monophosphates from the 3' end of oligoribonucleotides [Wade61, Wade61a, Sekiguchi63, Spahr63, Spahr64]. It degrades substrates with 3'-hydroxyl or 2',3'-cyclic phosphate ends somewhat more readily than those with 3'-phosphate or 2'-phosphate ends, and degrades substrate at a rate of seventy nucleotides per second at 37 degrees C. Its enzymatic activity has been extensively characterized with regards to substrate and reaction conditions [Cannistraro94]. RNase II preferentially degrades longer ribonucleotides and does so processively, leaving a short oligonucleotide and little evidence of intermediates [Nossal68]. It has been shown that the RNase II catalytic site binds the 3' end of substrate RNA and its anchor site binds 15-25 nucleotides from the 3' end, with both bindings needed to maintain the enzyme-RNA complex. The enzyme remains fixed at the anchor point on the RNA, processively cleaving twelve nucleotides from the 3' end and then dissociating [Cannistraro99]. An Asp-209-Asn mutant of RNase II binds but does not hydrolyze substrate [Amblar05].

Stable stem-loops block RNase II, forcing it to dissociate from the substrate RNA [Spickler00, Coburn96a]. Stable stem-loops and other secondary structure elements have been shown to block RNase II degradation of the Tn10/IS10 antisense RNA RNA-OUT, rpsO mRNA and glyA mRNA, though stem-loop structures alone do not appear to stall RNase II long enough in vitro to account for their effectiveness in stabilizing mRNA in vivo [Pepe94, Hajnsdorf94, Plamann90, McLaren91]. RNase II degrades the tryptophan operon mRNA from its primary transcription termination site (trp t') down to a secondary termination hairpin (trp t), resulting in the final, mature 3' end of tryptophan operon mRNA [Mott85].

In addition to its exonuclease activity, one study claims a significant endonuclease function for RNase II [Spahr64]. A study based on a thermolabile RNase II appears to show that RNase II is not responsible for the majority of ribonucleoside 5'-monophosphate formation [Cohen77].

ATP has been reported to be a competitive inhibitor of RNase II [Venkov71]. This was subsequently demonstrated to be an experimental artifact caused by the presence of adenylate kinase, which works in concert with nucleoside monophosphate kinases to convert 5'-mononucleosides to insoluble nucleoside diposphates, thus resulting in an apparent diminishing of enzymatic output [Ko73, Holmes73].

Crystal structures of RNase II in the bound and unbound states have been determined to 2.74 and 2.44 Å resolution, respectively [Frazao06, McVey06, Zuo06]. Based on these structures, Rnase II appears to bind RNAs at two locations, and to constrain catalytic access to single-stranded RNA via a narrow, basic channel. Based on subsequent truncation mutants, the RNase II S1 domain is important for stable protein-RNA complexes, the amino-terminal domain prevents overbinding to poly(A) RNA, and there is a third RNA-binding domain in the amino-terminal portion of the catalytic domain [Amblar06].

PNPase degrades rnb mRNA, limiting RNase II expression. PNP expression is increased in an RNase II null strain, suggesting that this mRNA-based regulation is reciprocal [Zilhao96]. RNaseE and RNase III also affect RNase II expression, the latter indirectly and the former directly by cleaving rnb mRNA [Zilhao95]. Gmr regulates RNase II by modulating its degradation. In a gmr deletion mutant, RNase II is three times more abundant than in a wild type background [Cairrao01].

Strains deleted in five exoribonucleases (RNase II, RNase D, RNase BN, RNase T, RNase PH) are inviable, but any one of them can support growth with no accumulation of precursor RNA or disruption of RNA synthesis [Kelly92, Zaniewski84]. Mutants in RNase II do show reduced DNA degradation, possibly due to competitive inhibition of endonuclease I by RNA [Wright71].

Citations: [Cannistraro01]

Gene Citations: [Zilhao96a]

Locations: cytosol

Map Position: [1,345,002 <- 1,346,936] (28.99 centisomes, 104°)
Length: 1935 bp / 644 aa

Molecular Weight of Polypeptide: 72.491 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004320 , CGSC:272 , DIP:DIP-10724N , EchoBASE:EB1577 , EcoGene:EG11620 , EcoliWiki:b1286 , Mint:MINT-1248196 , ModBase:P30850 , OU-Microarray:b1286 , PortEco:rnb , PR:PRO_000023787 , Pride:P30850 , Protein Model Portal:P30850 , RefSeq:NP_415802 , RegulonDB:EG11620 , SMR:P30850 , String:511145.b1286 , UniProt:P30850

Relationship Links: InterPro:IN-FAMILY:IPR003029 , InterPro:IN-FAMILY:IPR004476 , InterPro:IN-FAMILY:IPR011129 , InterPro:IN-FAMILY:IPR011804 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013223 , InterPro:IN-FAMILY:IPR022966 , InterPro:IN-FAMILY:IPR022967 , Panther:IN-FAMILY:PTHR23355:SF6 , PDB:Structure:2ID0 , PDB:Structure:2IX0 , PDB:Structure:2IX1 , Pfam:IN-FAMILY:PF00575 , Pfam:IN-FAMILY:PF08206 , Prosite:IN-FAMILY:PS01175 , Smart:IN-FAMILY:SM00316 , Smart:IN-FAMILY:SM00357

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0016078 - tRNA catabolic process Inferred from experiment [Reuven93]
GO:0006364 - rRNA processing Inferred by computational analysis [Gaudet10]
GO:0006401 - RNA catabolic process Inferred by computational analysis [GOA01a]
GO:0006402 - mRNA catabolic process Inferred by computational analysis [GOA06]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0008408 - 3'-5' exonuclease activity Inferred from experiment [Reuven93]
GO:0000175 - 3'-5'-exoribonuclease activity Inferred by computational analysis [Gaudet10]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004540 - ribonuclease activity Inferred by computational analysis [GOA01a]
GO:0008859 - exoribonuclease II activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0000178 - exosome (RNase complex) Inferred by computational analysis [Gaudet10]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

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

Essentiality data for rnb 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]

Enzymatic reaction of: ribonuclease

EC Number:

RNase II poly-A substrate mRNA + n H2O <=> RNase II substrate with no poly-A tail + n AMP

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.

Enzymatic reaction of: ribonuclease

EC Number:

a tRNA precursor with a 5' extension and a long 3' trailer + n H2O <=> a tRNA precursor with a 5' extension and a short 3' extension + n a nucleoside 5'-monophosphate

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 irreversible in the direction shown.

In Pathways: tRNA processing

Enzymatic reaction of: ribonuclease

EC Number:

RNase II degradation substrate mRNA + n H2O <=> n a nucleoside 5'-monophosphate

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 irreversible in the direction shown.

Cofactors or Prosthetic Groups: K+ [Spahr64], ammonium [Spahr64], Mg2+ [Spahr64], Mn2+ [Spahr64]

Inhibitors (Noncompetitive): Na+ [Venkov71]

Sequence Features

Protein sequence of ribonuclease II with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 384
[Zilhao93, UniProt10a]
UniProt: (in Ref. 1; CAA48112);
Sequence-Conflict 399
[Zilhao93, UniProt10a]
UniProt: (in Ref. 1; CAA48112);
Sequence-Conflict 513
[Zilhao93, UniProt10a]
UniProt: (in Ref. 1; CAA48112);
Conserved-Region 561 -> 643
UniProt: S1 motif;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1286 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11620; confirmed by SwissProt match.


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Cairrao01: Cairrao F, Chora A, Zilhao R, Carpousis AJ, Arraiano CM (2001). "RNase II levels change according to the growth conditions: characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II." Mol Microbiol 39(6);1550-61. PMID: 11260472

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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

Donovan86: Donovan WP, Kushner SR (1986). "Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12." Proc Natl Acad Sci U S A 83(1);120-4. PMID: 2417233

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Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

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."

Hajnsdorf94: Hajnsdorf E, Steier O, Coscoy L, Teysset L, Regnier P (1994). "Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant." EMBO J 13(14);3368-77. PMID: 7519147

Holmes73: Holmes RK, Singer MF (1973). "Purification and characterization of adenylate kinase as an apparent adenosine triphosphate-dependent inhibitor of ribonuclease II in Escherichia coli." J Biol Chem 1973;248(6);2014-21. PMID: 4570468

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

Kaplan74: Kaplan R, Apirion D (1974). "The involvement of ribonuclease I, ribonuclease II, and polynucleotide phosphorylase in the degradation of stable ribonucleic acid during carbon starvation in Escherichia coli." J Biol Chem 249(1);149-51. PMID: 4358625

Kaplan75: Kaplan R, Apirion D (1975). "Decay of ribosomal ribonucleic acid in Escherichia coli cells starved for various nutrients." J Biol Chem 250(8);3174-8. PMID: 1091648

Kelly92: Kelly KO, Deutscher MP (1992). "The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli." J Bacteriol 174(20);6682-4. PMID: 1400219

Kitamura77: Kitamura N, Ikeda H, Yamada Y, Ishikura H (1977). "Processing by ribonuclease II of the tRNATyr precursor of Escherichia coli synthesized in vitro." Eur J Biochem 73(1);297-306. PMID: 320007

Ko73: Ko TS, Gorelic L, Apirion D (1973). "Ribonuclease II of Escherichia coli is not inhibited by adenosine triphosphate." J Biol Chem 248(10);3748-9. PMID: 4573984

Li94a: Li Z, Deutscher MP (1994). "The role of individual exoribonucleases in processing at the 3' end of Escherichia coli tRNA precursors." J Biol Chem 269(8);6064-71. PMID: 7509797

Marujo00: Marujo PE, Hajnsdorf E, Le Derout J, Andrade R, Arraiano CM, Regnier P (2000). "RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli." RNA 6(8);1185-93. PMID: 10943897

McLaren91: McLaren RS, Newbury SF, Dance GS, Causton HC, Higgins CF (1991). "mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo." J Mol Biol 221(1);81-95. PMID: 1920421

McVey06: McVey CE, Amblar M, Barbas A, Cairrao F, Coelho R, Romao C, Arraiano CM, Carrondo MA, Frazao C (2006). "Expression, purification, crystallization and preliminary diffraction data characterization of Escherichia coli ribonuclease II (RNase II)." Acta Crystallograph Sect F Struct Biol Cryst Commun 62(Pt 7);684-7. PMID: 16820694

Mohanty00: Mohanty BK, Kushner SR (2000). "Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli." Mol Microbiol 36(4);982-94. PMID: 10844684

Mohanty99: Mohanty BK, Kushner SR (1999). "Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism." Mol Microbiol 34(5);1094-108. PMID: 10594833

Mott85: Mott JE, Galloway JL, Platt T (1985). "Maturation of Escherichia coli tryptophan operon mRNA: evidence for 3' exonucleolytic processing after rho-dependent termination." EMBO J 4(7);1887-91. PMID: 2992951

Nossal68: Nossal NG, Singer MF (1968). "The processive degradation of individual polyribonucleotide chains. I. Escherichia coli ribonuclease II." J Biol Chem 243(5);913-22. PMID: 4867942

OHara95: O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR (1995). "Polyadenylylation helps regulate mRNA decay in Escherichia coli." Proc Natl Acad Sci U S A 92(6);1807-11. PMID: 7534403

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Plamann90: Plamann MD, Stauffer GV (1990). "Escherichia coli glyA mRNA decay: the role of 3' secondary structure and the effects of the pnp and rnb mutations." Mol Gen Genet 220(2);301-6. PMID: 1691434

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Reuven93: Reuven NB, Deutscher MP (1993). "Multiple exoribonucleases are required for the 3' processing of Escherichia coli tRNA precursors in vivo." FASEB J 7(1);143-8. PMID: 8422961

Sekiguchi63: Sekiguchi M, Cohen SS (1963). "The selective degradation of phage-induced ribonucleic acid by polynucleotide phosphorylase." J Biol Chem 238;349-56. PMID: 13992679

Soderbom98: Soderbom F, Wagner EG (1998). "Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1." Microbiology 144 ( Pt 7);1907-17. PMID: 9695924

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Spickler00: Spickler C, Mackie GA (2000). "Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure." J Bacteriol 182(9);2422-7. PMID: 10762241

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UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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."

Venkov71: Venkov P, Schlessinger D, Longo D (1971). "Inhibition of ribonuclease II of Escherichia coli by sodium ions, adenosine-5'-triphosphate, and transfer ribonucleic acid." J Bacteriol 108(1);601-3. PMID: 4941574

Wade61: Wade HE (1961). "The autodegradation of ribonucleoprotein in Escherichia coli." Biochem J 78;457-72. PMID: 13782415

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Zaniewski84: Zaniewski R, Petkaitis E, Deutscher MP (1984). "A multiple mutant of Escherichia coli lacking the exoribonucleases RNase II, RNase D, and RNase BN." J Biol Chem 259(19);11651-3. PMID: 6207170

Zilhao93: Zilhao R, Camelo L, Arraiano CM (1993). "DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II." Mol Microbiol 8(1);43-51. PMID: 8497196

Zilhao95: Zilhao R, Regnier P, Arraiano CM (1995). "The role of endonucleases in the expression of ribonuclease II in Escherichia coli." FEMS Microbiol Lett 130(2-3);237-44. PMID: 7649446

Zilhao96: Zilhao R, Cairrao F, Regnier P, Arraiano CM (1996). "PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism." Mol Microbiol 20(5);1033-42. PMID: 8809756

Zilhao96a: Zilhao R, Plumbridge J, Hajnsdorf E, Regnier P, Arraiano CM (1996). "Escherichia coli RNase II: characterization of the promoters involved in the transcription of rnb." Microbiology 1996;142 ( Pt 2);367-75. PMID: 8932710

Zuo06: Zuo Y, Vincent HA, Zhang J, Wang Y, Deutscher MP, Malhotra A (2006). "Structural basis for processivity and single-strand specificity of RNase II." Mol Cell 24(1);149-56. PMID: 16996291

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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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